Starting phenix.real_space_refine on Sun Apr 14 14:33:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j02_35881/04_2024/8j02_35881_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j02_35881/04_2024/8j02_35881.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j02_35881/04_2024/8j02_35881_neut_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j02_35881/04_2024/8j02_35881_neut_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j02_35881/04_2024/8j02_35881_neut_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j02_35881/04_2024/8j02_35881.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j02_35881/04_2024/8j02_35881.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j02_35881/04_2024/8j02_35881_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j02_35881/04_2024/8j02_35881_neut_trim_updated.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 12 5.49 5 S 88 5.16 5 C 10440 2.51 5 N 2684 2.21 5 O 2892 1.98 5 H 15244 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C GLU 120": "OE1" <-> "OE2" Residue "E GLU 120": "OE1" <-> "OE2" Residue "H GLU 120": "OE1" <-> "OE2" Residue "F GLU 120": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 31360 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 5641 Classifications: {'peptide': 354} Link IDs: {'PTRANS': 7, 'TRANS': 346} Chain breaks: 2 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'ARG:plan': 5} Unresolved non-hydrogen planarities: 27 Chain: "B" Number of atoms: 5641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 5641 Classifications: {'peptide': 354} Link IDs: {'PTRANS': 7, 'TRANS': 346} Chain breaks: 2 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'ARG:plan': 5} Unresolved non-hydrogen planarities: 27 Chain: "C" Number of atoms: 2129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2129 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "D" Number of atoms: 5641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 5641 Classifications: {'peptide': 354} Link IDs: {'PTRANS': 7, 'TRANS': 346} Chain breaks: 2 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'ARG:plan': 5} Unresolved non-hydrogen planarities: 27 Chain: "E" Number of atoms: 2129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2129 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "G" Number of atoms: 5641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 5641 Classifications: {'peptide': 354} Link IDs: {'PTRANS': 7, 'TRANS': 346} Chain breaks: 2 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'ARG:plan': 5} Unresolved non-hydrogen planarities: 27 Chain: "H" Number of atoms: 2129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2129 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "F" Number of atoms: 2129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2129 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 70 Unusual residues: {'P0T': 1, 'PIO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 70 Unusual residues: {'P0T': 1, 'PIO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 70 Unusual residues: {'P0T': 1, 'PIO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 70 Unusual residues: {'P0T': 1, 'PIO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 13.67, per 1000 atoms: 0.44 Number of scatterers: 31360 At special positions: 0 Unit cell: (119.97, 119.97, 124.62, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 88 16.00 P 12 15.00 O 2892 8.00 N 2684 7.00 C 10440 6.00 H 15244 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 26.39 Conformation dependent library (CDL) restraints added in 3.2 seconds 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3696 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 88 helices and 0 sheets defined 76.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.34 Creating SS restraints... Processing helix chain 'A' and resid 71 through 85 Processing helix chain 'A' and resid 92 through 114 Processing helix chain 'A' and resid 119 through 149 removed outlier: 4.027A pdb=" N ILE A 128 " --> pdb=" O GLY A 124 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLY A 149 " --> pdb=" O ILE A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 165 removed outlier: 3.699A pdb=" N ARG A 160 " --> pdb=" O GLY A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 183 Processing helix chain 'A' and resid 196 through 212 removed outlier: 4.743A pdb=" N ASP A 212 " --> pdb=" O MET A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 227 Processing helix chain 'A' and resid 229 through 254 Processing helix chain 'A' and resid 259 through 261 No H-bonds generated for 'chain 'A' and resid 259 through 261' Processing helix chain 'A' and resid 264 through 275 Processing helix chain 'A' and resid 288 through 349 removed outlier: 4.388A pdb=" N ILE A 300 " --> pdb=" O THR A 296 " (cutoff:3.500A) Proline residue: A 308 - end of helix Proline residue: A 335 - end of helix Processing helix chain 'A' and resid 358 through 366 Processing helix chain 'A' and resid 536 through 558 Processing helix chain 'A' and resid 564 through 599 Proline residue: A 597 - end of helix Processing helix chain 'B' and resid 71 through 85 Processing helix chain 'B' and resid 92 through 114 Processing helix chain 'B' and resid 119 through 149 removed outlier: 4.027A pdb=" N ILE B 128 " --> pdb=" O GLY B 124 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLY B 149 " --> pdb=" O ILE B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 165 removed outlier: 3.699A pdb=" N ARG B 160 " --> pdb=" O GLY B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 183 Processing helix chain 'B' and resid 196 through 212 removed outlier: 4.743A pdb=" N ASP B 212 " --> pdb=" O MET B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 227 Processing helix chain 'B' and resid 229 through 254 Processing helix chain 'B' and resid 259 through 261 No H-bonds generated for 'chain 'B' and resid 259 through 261' Processing helix chain 'B' and resid 264 through 275 Processing helix chain 'B' and resid 288 through 349 removed outlier: 4.388A pdb=" N ILE B 300 " --> pdb=" O THR B 296 " (cutoff:3.500A) Proline residue: B 308 - end of helix Proline residue: B 335 - end of helix Processing helix chain 'B' and resid 358 through 366 Processing helix chain 'B' and resid 536 through 558 Processing helix chain 'B' and resid 564 through 599 Proline residue: B 597 - end of helix Processing helix chain 'C' and resid 7 through 20 Processing helix chain 'C' and resid 30 through 40 Processing helix chain 'C' and resid 46 through 56 Processing helix chain 'C' and resid 66 through 74 Processing helix chain 'C' and resid 84 through 93 Processing helix chain 'C' and resid 103 through 110 Processing helix chain 'C' and resid 119 through 129 Processing helix chain 'C' and resid 139 through 147 Processing helix chain 'D' and resid 71 through 85 Processing helix chain 'D' and resid 92 through 114 Processing helix chain 'D' and resid 119 through 149 removed outlier: 4.027A pdb=" N ILE D 128 " --> pdb=" O GLY D 124 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLY D 149 " --> pdb=" O ILE D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 165 removed outlier: 3.699A pdb=" N ARG D 160 " --> pdb=" O GLY D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 183 Processing helix chain 'D' and resid 196 through 212 removed outlier: 4.743A pdb=" N ASP D 212 " --> pdb=" O MET D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 227 Processing helix chain 'D' and resid 229 through 254 Processing helix chain 'D' and resid 259 through 261 No H-bonds generated for 'chain 'D' and resid 259 through 261' Processing helix chain 'D' and resid 264 through 275 Processing helix chain 'D' and resid 288 through 349 removed outlier: 4.388A pdb=" N ILE D 300 " --> pdb=" O THR D 296 " (cutoff:3.500A) Proline residue: D 308 - end of helix Proline residue: D 335 - end of helix Processing helix chain 'D' and resid 358 through 366 Processing helix chain 'D' and resid 536 through 558 Processing helix chain 'D' and resid 564 through 599 Proline residue: D 597 - end of helix Processing helix chain 'E' and resid 7 through 20 Processing helix chain 'E' and resid 30 through 40 Processing helix chain 'E' and resid 46 through 56 Processing helix chain 'E' and resid 66 through 74 Processing helix chain 'E' and resid 84 through 93 Processing helix chain 'E' and resid 103 through 110 Processing helix chain 'E' and resid 119 through 129 Processing helix chain 'E' and resid 139 through 147 Processing helix chain 'G' and resid 71 through 85 Processing helix chain 'G' and resid 92 through 114 Processing helix chain 'G' and resid 119 through 149 removed outlier: 4.027A pdb=" N ILE G 128 " --> pdb=" O GLY G 124 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLY G 149 " --> pdb=" O ILE G 145 " (cutoff:3.500A) Processing helix chain 'G' and resid 156 through 165 removed outlier: 3.699A pdb=" N ARG G 160 " --> pdb=" O GLY G 156 " (cutoff:3.500A) Processing helix chain 'G' and resid 167 through 183 Processing helix chain 'G' and resid 196 through 212 removed outlier: 4.743A pdb=" N ASP G 212 " --> pdb=" O MET G 208 " (cutoff:3.500A) Processing helix chain 'G' and resid 216 through 227 Processing helix chain 'G' and resid 229 through 254 Processing helix chain 'G' and resid 259 through 261 No H-bonds generated for 'chain 'G' and resid 259 through 261' Processing helix chain 'G' and resid 264 through 275 Processing helix chain 'G' and resid 288 through 349 removed outlier: 4.388A pdb=" N ILE G 300 " --> pdb=" O THR G 296 " (cutoff:3.500A) Proline residue: G 308 - end of helix Proline residue: G 335 - end of helix Processing helix chain 'G' and resid 358 through 366 Processing helix chain 'G' and resid 536 through 558 Processing helix chain 'G' and resid 564 through 599 Proline residue: G 597 - end of helix Processing helix chain 'H' and resid 7 through 20 Processing helix chain 'H' and resid 30 through 40 Processing helix chain 'H' and resid 46 through 56 Processing helix chain 'H' and resid 66 through 74 Processing helix chain 'H' and resid 84 through 93 Processing helix chain 'H' and resid 103 through 110 Processing helix chain 'H' and resid 119 through 129 Processing helix chain 'H' and resid 139 through 147 Processing helix chain 'F' and resid 7 through 20 Processing helix chain 'F' and resid 30 through 40 Processing helix chain 'F' and resid 46 through 56 Processing helix chain 'F' and resid 66 through 74 Processing helix chain 'F' and resid 84 through 93 Processing helix chain 'F' and resid 103 through 110 Processing helix chain 'F' and resid 119 through 129 Processing helix chain 'F' and resid 139 through 147 1112 hydrogen bonds defined for protein. 3336 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.70 Time building geometry restraints manager: 27.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 15216 1.03 - 1.23: 40 1.23 - 1.42: 6956 1.42 - 1.62: 9308 1.62 - 1.81: 172 Bond restraints: 31692 Sorted by residual: bond pdb=" C07 P0T A 801 " pdb=" C09 P0T A 801 " ideal model delta sigma weight residual 1.336 1.594 -0.258 2.00e-02 2.50e+03 1.66e+02 bond pdb=" C07 P0T B 802 " pdb=" C09 P0T B 802 " ideal model delta sigma weight residual 1.336 1.593 -0.257 2.00e-02 2.50e+03 1.66e+02 bond pdb=" C07 P0T G 802 " pdb=" C09 P0T G 802 " ideal model delta sigma weight residual 1.336 1.593 -0.257 2.00e-02 2.50e+03 1.65e+02 bond pdb=" C07 P0T D 802 " pdb=" C09 P0T D 802 " ideal model delta sigma weight residual 1.336 1.593 -0.257 2.00e-02 2.50e+03 1.65e+02 bond pdb=" C10 P0T A 801 " pdb=" C19 P0T A 801 " ideal model delta sigma weight residual 1.331 1.552 -0.221 2.00e-02 2.50e+03 1.22e+02 ... (remaining 31687 not shown) Histogram of bond angle deviations from ideal: 81.38 - 91.94: 4 91.94 - 102.50: 56 102.50 - 113.06: 36104 113.06 - 123.62: 18044 123.62 - 134.18: 2620 Bond angle restraints: 56828 Sorted by residual: angle pdb=" C07 P0T A 801 " pdb=" C04 P0T A 801 " pdb=" C08 P0T A 801 " ideal model delta sigma weight residual 112.03 81.38 30.65 3.00e+00 1.11e-01 1.04e+02 angle pdb=" C07 P0T G 802 " pdb=" C04 P0T G 802 " pdb=" C08 P0T G 802 " ideal model delta sigma weight residual 112.03 81.38 30.65 3.00e+00 1.11e-01 1.04e+02 angle pdb=" C07 P0T B 802 " pdb=" C04 P0T B 802 " pdb=" C08 P0T B 802 " ideal model delta sigma weight residual 112.03 81.43 30.60 3.00e+00 1.11e-01 1.04e+02 angle pdb=" C07 P0T D 802 " pdb=" C04 P0T D 802 " pdb=" C08 P0T D 802 " ideal model delta sigma weight residual 112.03 81.44 30.59 3.00e+00 1.11e-01 1.04e+02 angle pdb=" C03 P0T G 802 " pdb=" C04 P0T G 802 " pdb=" C08 P0T G 802 " ideal model delta sigma weight residual 111.12 130.51 -19.39 3.00e+00 1.11e-01 4.18e+01 ... (remaining 56823 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.88: 13272 21.88 - 43.76: 1168 43.76 - 65.64: 332 65.64 - 87.52: 52 87.52 - 109.40: 20 Dihedral angle restraints: 14844 sinusoidal: 7968 harmonic: 6876 Sorted by residual: dihedral pdb=" C03 P0T G 802 " pdb=" C05 P0T G 802 " pdb=" C06 P0T G 802 " pdb=" C09 P0T G 802 " ideal model delta sinusoidal sigma weight residual 49.00 -60.40 109.40 1 3.00e+01 1.11e-03 1.42e+01 dihedral pdb=" C03 P0T B 802 " pdb=" C05 P0T B 802 " pdb=" C06 P0T B 802 " pdb=" C09 P0T B 802 " ideal model delta sinusoidal sigma weight residual 49.00 -60.40 109.40 1 3.00e+01 1.11e-03 1.42e+01 dihedral pdb=" C03 P0T D 802 " pdb=" C05 P0T D 802 " pdb=" C06 P0T D 802 " pdb=" C09 P0T D 802 " ideal model delta sinusoidal sigma weight residual 49.00 -60.39 109.39 1 3.00e+01 1.11e-03 1.42e+01 ... (remaining 14841 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.023: 1524 0.023 - 0.045: 572 0.045 - 0.068: 208 0.068 - 0.090: 108 0.090 - 0.113: 52 Chirality restraints: 2464 Sorted by residual: chirality pdb=" CA PRO B 167 " pdb=" N PRO B 167 " pdb=" C PRO B 167 " pdb=" CB PRO B 167 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 3.18e-01 chirality pdb=" CA PRO D 167 " pdb=" N PRO D 167 " pdb=" C PRO D 167 " pdb=" CB PRO D 167 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 3.18e-01 chirality pdb=" CA PRO A 167 " pdb=" N PRO A 167 " pdb=" C PRO A 167 " pdb=" CB PRO A 167 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 3.18e-01 ... (remaining 2461 not shown) Planarity restraints: 4700 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE H 66 " 0.031 5.00e-02 4.00e+02 4.78e-02 3.65e+00 pdb=" N PRO H 67 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO H 67 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO H 67 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE E 66 " 0.031 5.00e-02 4.00e+02 4.78e-02 3.65e+00 pdb=" N PRO E 67 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO E 67 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO E 67 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE C 66 " 0.031 5.00e-02 4.00e+02 4.78e-02 3.65e+00 pdb=" N PRO C 67 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO C 67 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 67 " 0.027 5.00e-02 4.00e+02 ... (remaining 4697 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.21: 2976 2.21 - 2.81: 65928 2.81 - 3.41: 90560 3.41 - 4.00: 109817 4.00 - 4.60: 171083 Nonbonded interactions: 440364 Sorted by model distance: nonbonded pdb=" O VAL C 36 " pdb=" HG SER C 39 " model vdw 1.615 1.850 nonbonded pdb=" O VAL F 36 " pdb=" HG SER F 39 " model vdw 1.615 1.850 nonbonded pdb=" O VAL E 36 " pdb=" HG SER E 39 " model vdw 1.615 1.850 nonbonded pdb=" O VAL H 36 " pdb=" HG SER H 39 " model vdw 1.615 1.850 nonbonded pdb=" OE1 GLU E 120 " pdb=" H GLU E 120 " model vdw 1.633 1.850 ... (remaining 440359 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 70 through 600) selection = (chain 'B' and resid 70 through 600) selection = (chain 'D' and resid 70 through 600) selection = (chain 'G' and resid 70 through 600) } ncs_group { reference = chain 'C' selection = chain 'E' selection = chain 'F' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.430 Extract box with map and model: 4.630 Check model and map are aligned: 0.480 Set scattering table: 0.270 Process input model: 99.520 Find NCS groups from input model: 2.330 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 111.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.258 16448 Z= 0.535 Angle : 0.823 30.650 22156 Z= 0.374 Chirality : 0.033 0.113 2464 Planarity : 0.003 0.048 2768 Dihedral : 18.837 109.399 6020 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 15.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 0.72 % Allowed : 24.16 % Favored : 75.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.29 (0.19), residues: 1956 helix: 1.97 (0.13), residues: 1596 sheet: None (None), residues: 0 loop : -0.53 (0.35), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 344 HIS 0.001 0.000 HIS A 96 PHE 0.028 0.001 PHE H 20 TYR 0.012 0.001 TYR A 362 ARG 0.003 0.000 ARG H 87 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue THR 354 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue SER 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue TYR 362 is missing expected H atoms. Skipping. Residue TYR 363 is missing expected H atoms. Skipping. Residue THR 366 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue THR 354 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue SER 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue TYR 362 is missing expected H atoms. Skipping. Residue TYR 363 is missing expected H atoms. Skipping. Residue THR 366 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue THR 354 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue SER 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue TYR 362 is missing expected H atoms. Skipping. Residue TYR 363 is missing expected H atoms. Skipping. Residue THR 366 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue THR 354 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue SER 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue TYR 362 is missing expected H atoms. Skipping. Residue TYR 363 is missing expected H atoms. Skipping. Residue THR 366 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Evaluate side-chains 284 residues out of total 1688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 272 time to evaluate : 2.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 8 residues processed: 276 average time/residue: 0.5810 time to fit residues: 242.7637 Evaluate side-chains 248 residues out of total 1688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 240 time to evaluate : 2.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 TYR Chi-restraints excluded: chain B residue 74 TYR Chi-restraints excluded: chain C residue 139 TYR Chi-restraints excluded: chain D residue 74 TYR Chi-restraints excluded: chain E residue 139 TYR Chi-restraints excluded: chain G residue 74 TYR Chi-restraints excluded: chain H residue 139 TYR Chi-restraints excluded: chain F residue 139 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 165 optimal weight: 4.9990 chunk 148 optimal weight: 0.9990 chunk 82 optimal weight: 20.0000 chunk 50 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 79 optimal weight: 9.9990 chunk 153 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 93 optimal weight: 0.0570 chunk 114 optimal weight: 10.0000 chunk 177 optimal weight: 0.6980 overall best weight: 0.9504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.0692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 16448 Z= 0.161 Angle : 0.513 5.026 22156 Z= 0.276 Chirality : 0.032 0.119 2464 Planarity : 0.003 0.044 2768 Dihedral : 9.868 92.703 2320 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.91 % Allowed : 22.73 % Favored : 75.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.60 (0.19), residues: 1956 helix: 2.16 (0.13), residues: 1612 sheet: None (None), residues: 0 loop : -0.37 (0.36), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 344 HIS 0.001 0.000 HIS D 96 PHE 0.022 0.001 PHE C 20 TYR 0.010 0.001 TYR G 571 ARG 0.002 0.000 ARG A 581 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue THR 354 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue SER 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue TYR 362 is missing expected H atoms. Skipping. Residue TYR 363 is missing expected H atoms. Skipping. Residue THR 366 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue THR 354 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue SER 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue TYR 362 is missing expected H atoms. Skipping. Residue TYR 363 is missing expected H atoms. Skipping. Residue THR 366 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue THR 354 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue SER 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue TYR 362 is missing expected H atoms. Skipping. Residue TYR 363 is missing expected H atoms. Skipping. Residue THR 366 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue THR 354 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue SER 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue TYR 362 is missing expected H atoms. Skipping. Residue TYR 363 is missing expected H atoms. Skipping. Residue THR 366 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Evaluate side-chains 284 residues out of total 1688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 252 time to evaluate : 2.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 24 residues processed: 272 average time/residue: 0.6321 time to fit residues: 255.4449 Evaluate side-chains 248 residues out of total 1688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 224 time to evaluate : 2.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 TYR Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain B residue 74 TYR Chi-restraints excluded: chain B residue 93 PHE Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 589 VAL Chi-restraints excluded: chain C residue 139 TYR Chi-restraints excluded: chain D residue 74 TYR Chi-restraints excluded: chain D residue 93 PHE Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 229 SER Chi-restraints excluded: chain D residue 589 VAL Chi-restraints excluded: chain E residue 139 TYR Chi-restraints excluded: chain G residue 74 TYR Chi-restraints excluded: chain G residue 93 PHE Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 229 SER Chi-restraints excluded: chain G residue 589 VAL Chi-restraints excluded: chain H residue 139 TYR Chi-restraints excluded: chain F residue 139 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 chunk 148 optimal weight: 2.9990 chunk 121 optimal weight: 7.9990 chunk 49 optimal weight: 3.9990 chunk 178 optimal weight: 2.9990 chunk 192 optimal weight: 4.9990 chunk 158 optimal weight: 4.9990 chunk 176 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 143 optimal weight: 7.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.1232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 16448 Z= 0.273 Angle : 0.545 5.443 22156 Z= 0.304 Chirality : 0.034 0.134 2464 Planarity : 0.003 0.042 2768 Dihedral : 8.861 82.140 2320 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 16.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 3.11 % Allowed : 22.25 % Favored : 74.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.30 (0.19), residues: 1956 helix: 1.99 (0.13), residues: 1600 sheet: None (None), residues: 0 loop : -0.59 (0.34), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 288 HIS 0.002 0.001 HIS A 328 PHE 0.018 0.001 PHE C 20 TYR 0.009 0.001 TYR G 571 ARG 0.002 0.000 ARG G 541 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue THR 354 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue SER 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue TYR 362 is missing expected H atoms. Skipping. Residue TYR 363 is missing expected H atoms. Skipping. Residue THR 366 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue THR 354 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue SER 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue TYR 362 is missing expected H atoms. Skipping. Residue TYR 363 is missing expected H atoms. Skipping. Residue THR 366 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue THR 354 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue SER 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue TYR 362 is missing expected H atoms. Skipping. Residue TYR 363 is missing expected H atoms. Skipping. Residue THR 366 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue THR 354 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue SER 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue TYR 362 is missing expected H atoms. Skipping. Residue TYR 363 is missing expected H atoms. Skipping. Residue THR 366 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Evaluate side-chains 248 residues out of total 1688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 196 time to evaluate : 2.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 52 outliers final: 48 residues processed: 228 average time/residue: 0.6616 time to fit residues: 222.5785 Evaluate side-chains 240 residues out of total 1688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 192 time to evaluate : 2.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 TYR Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 157 TRP Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 326 GLN Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain B residue 74 TYR Chi-restraints excluded: chain B residue 93 PHE Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 157 TRP Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 326 GLN Chi-restraints excluded: chain B residue 589 VAL Chi-restraints excluded: chain C residue 110 MET Chi-restraints excluded: chain C residue 139 TYR Chi-restraints excluded: chain C residue 141 GLU Chi-restraints excluded: chain D residue 74 TYR Chi-restraints excluded: chain D residue 93 PHE Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 157 TRP Chi-restraints excluded: chain D residue 229 SER Chi-restraints excluded: chain D residue 326 GLN Chi-restraints excluded: chain D residue 589 VAL Chi-restraints excluded: chain E residue 110 MET Chi-restraints excluded: chain E residue 139 TYR Chi-restraints excluded: chain E residue 141 GLU Chi-restraints excluded: chain G residue 74 TYR Chi-restraints excluded: chain G residue 93 PHE Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 157 TRP Chi-restraints excluded: chain G residue 229 SER Chi-restraints excluded: chain G residue 326 GLN Chi-restraints excluded: chain G residue 589 VAL Chi-restraints excluded: chain H residue 110 MET Chi-restraints excluded: chain H residue 139 TYR Chi-restraints excluded: chain H residue 141 GLU Chi-restraints excluded: chain F residue 110 MET Chi-restraints excluded: chain F residue 139 TYR Chi-restraints excluded: chain F residue 141 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 176 optimal weight: 8.9990 chunk 134 optimal weight: 7.9990 chunk 92 optimal weight: 10.0000 chunk 19 optimal weight: 0.9990 chunk 85 optimal weight: 7.9990 chunk 119 optimal weight: 3.9990 chunk 178 optimal weight: 5.9990 chunk 189 optimal weight: 9.9990 chunk 93 optimal weight: 1.9990 chunk 169 optimal weight: 20.0000 chunk 51 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.1368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 16448 Z= 0.234 Angle : 0.520 6.518 22156 Z= 0.288 Chirality : 0.033 0.150 2464 Planarity : 0.003 0.041 2768 Dihedral : 8.098 68.593 2320 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 15.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 3.11 % Allowed : 22.25 % Favored : 74.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.32 (0.19), residues: 1956 helix: 2.01 (0.13), residues: 1600 sheet: None (None), residues: 0 loop : -0.63 (0.34), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 218 HIS 0.002 0.000 HIS B 328 PHE 0.021 0.001 PHE C 20 TYR 0.010 0.001 TYR A 571 ARG 0.002 0.000 ARG G 581 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue THR 354 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue SER 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue TYR 362 is missing expected H atoms. Skipping. Residue TYR 363 is missing expected H atoms. Skipping. Residue THR 366 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue THR 354 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue SER 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue TYR 362 is missing expected H atoms. Skipping. Residue TYR 363 is missing expected H atoms. Skipping. Residue THR 366 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue THR 354 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue SER 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue TYR 362 is missing expected H atoms. Skipping. Residue TYR 363 is missing expected H atoms. Skipping. Residue THR 366 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue THR 354 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue SER 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue TYR 362 is missing expected H atoms. Skipping. Residue TYR 363 is missing expected H atoms. Skipping. Residue THR 366 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Evaluate side-chains 267 residues out of total 1688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 215 time to evaluate : 2.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 304 PHE cc_start: 0.8941 (m-80) cc_final: 0.8732 (m-80) REVERT: B 304 PHE cc_start: 0.8941 (m-80) cc_final: 0.8735 (m-80) REVERT: D 304 PHE cc_start: 0.8940 (m-80) cc_final: 0.8735 (m-80) REVERT: G 304 PHE cc_start: 0.8941 (m-80) cc_final: 0.8736 (m-80) outliers start: 52 outliers final: 44 residues processed: 247 average time/residue: 0.6757 time to fit residues: 254.8049 Evaluate side-chains 248 residues out of total 1688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 204 time to evaluate : 2.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 TYR Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 157 TRP Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 326 GLN Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain B residue 74 TYR Chi-restraints excluded: chain B residue 93 PHE Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 157 TRP Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 326 GLN Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 589 VAL Chi-restraints excluded: chain C residue 139 TYR Chi-restraints excluded: chain D residue 74 TYR Chi-restraints excluded: chain D residue 93 PHE Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 157 TRP Chi-restraints excluded: chain D residue 229 SER Chi-restraints excluded: chain D residue 326 GLN Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 589 VAL Chi-restraints excluded: chain E residue 139 TYR Chi-restraints excluded: chain G residue 74 TYR Chi-restraints excluded: chain G residue 93 PHE Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 157 TRP Chi-restraints excluded: chain G residue 229 SER Chi-restraints excluded: chain G residue 326 GLN Chi-restraints excluded: chain G residue 545 VAL Chi-restraints excluded: chain G residue 589 VAL Chi-restraints excluded: chain H residue 139 TYR Chi-restraints excluded: chain F residue 139 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 157 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 141 optimal weight: 9.9990 chunk 78 optimal weight: 7.9990 chunk 161 optimal weight: 7.9990 chunk 130 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 96 optimal weight: 10.0000 chunk 170 optimal weight: 10.0000 chunk 47 optimal weight: 9.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 16448 Z= 0.294 Angle : 0.559 6.512 22156 Z= 0.311 Chirality : 0.034 0.167 2464 Planarity : 0.003 0.041 2768 Dihedral : 7.949 55.299 2320 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 16.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 4.55 % Allowed : 22.25 % Favored : 73.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.15 (0.19), residues: 1956 helix: 1.90 (0.13), residues: 1600 sheet: None (None), residues: 0 loop : -0.69 (0.34), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 218 HIS 0.002 0.001 HIS G 328 PHE 0.018 0.001 PHE E 20 TYR 0.011 0.001 TYR E 139 ARG 0.002 0.000 ARG A 581 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue THR 354 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue SER 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue TYR 362 is missing expected H atoms. Skipping. Residue TYR 363 is missing expected H atoms. Skipping. Residue THR 366 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue THR 354 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue SER 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue TYR 362 is missing expected H atoms. Skipping. Residue TYR 363 is missing expected H atoms. Skipping. Residue THR 366 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue THR 354 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue SER 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue TYR 362 is missing expected H atoms. Skipping. Residue TYR 363 is missing expected H atoms. Skipping. Residue THR 366 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue THR 354 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue SER 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue TYR 362 is missing expected H atoms. Skipping. Residue TYR 363 is missing expected H atoms. Skipping. Residue THR 366 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Evaluate side-chains 276 residues out of total 1688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 200 time to evaluate : 2.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 76 outliers final: 64 residues processed: 256 average time/residue: 0.5797 time to fit residues: 226.3457 Evaluate side-chains 260 residues out of total 1688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 196 time to evaluate : 2.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 TYR Chi-restraints excluded: chain A residue 91 TRP Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 157 TRP Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 326 GLN Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain B residue 74 TYR Chi-restraints excluded: chain B residue 91 TRP Chi-restraints excluded: chain B residue 93 PHE Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 157 TRP Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 326 GLN Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 584 SER Chi-restraints excluded: chain B residue 589 VAL Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 110 MET Chi-restraints excluded: chain C residue 139 TYR Chi-restraints excluded: chain C residue 141 GLU Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain D residue 74 TYR Chi-restraints excluded: chain D residue 91 TRP Chi-restraints excluded: chain D residue 93 PHE Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 157 TRP Chi-restraints excluded: chain D residue 229 SER Chi-restraints excluded: chain D residue 326 GLN Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 584 SER Chi-restraints excluded: chain D residue 589 VAL Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 110 MET Chi-restraints excluded: chain E residue 139 TYR Chi-restraints excluded: chain E residue 141 GLU Chi-restraints excluded: chain E residue 146 MET Chi-restraints excluded: chain G residue 74 TYR Chi-restraints excluded: chain G residue 91 TRP Chi-restraints excluded: chain G residue 93 PHE Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 157 TRP Chi-restraints excluded: chain G residue 229 SER Chi-restraints excluded: chain G residue 326 GLN Chi-restraints excluded: chain G residue 545 VAL Chi-restraints excluded: chain G residue 584 SER Chi-restraints excluded: chain G residue 589 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 110 MET Chi-restraints excluded: chain H residue 139 TYR Chi-restraints excluded: chain H residue 141 GLU Chi-restraints excluded: chain H residue 146 MET Chi-restraints excluded: chain F residue 27 THR Chi-restraints excluded: chain F residue 110 MET Chi-restraints excluded: chain F residue 139 TYR Chi-restraints excluded: chain F residue 141 GLU Chi-restraints excluded: chain F residue 146 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 63 optimal weight: 20.0000 chunk 170 optimal weight: 10.0000 chunk 37 optimal weight: 9.9990 chunk 111 optimal weight: 20.0000 chunk 46 optimal weight: 6.9990 chunk 189 optimal weight: 9.9990 chunk 157 optimal weight: 0.6980 chunk 87 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 62 optimal weight: 10.0000 chunk 99 optimal weight: 1.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 16448 Z= 0.242 Angle : 0.533 5.965 22156 Z= 0.295 Chirality : 0.033 0.135 2464 Planarity : 0.003 0.041 2768 Dihedral : 7.398 48.728 2320 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 15.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 3.29 % Allowed : 24.22 % Favored : 72.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.25 (0.19), residues: 1956 helix: 1.97 (0.13), residues: 1600 sheet: None (None), residues: 0 loop : -0.68 (0.34), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 218 HIS 0.002 0.000 HIS B 96 PHE 0.020 0.001 PHE E 20 TYR 0.011 0.001 TYR E 139 ARG 0.002 0.000 ARG A 144 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue THR 354 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue SER 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue TYR 362 is missing expected H atoms. Skipping. Residue TYR 363 is missing expected H atoms. Skipping. Residue THR 366 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue THR 354 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue SER 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue TYR 362 is missing expected H atoms. Skipping. Residue TYR 363 is missing expected H atoms. Skipping. Residue THR 366 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue THR 354 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue SER 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue TYR 362 is missing expected H atoms. Skipping. Residue TYR 363 is missing expected H atoms. Skipping. Residue THR 366 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue THR 354 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue SER 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue TYR 362 is missing expected H atoms. Skipping. Residue TYR 363 is missing expected H atoms. Skipping. Residue THR 366 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Evaluate side-chains 251 residues out of total 1688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 196 time to evaluate : 2.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 55 outliers final: 52 residues processed: 231 average time/residue: 0.6301 time to fit residues: 222.7758 Evaluate side-chains 251 residues out of total 1688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 199 time to evaluate : 2.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 157 TRP Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 326 GLN Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain B residue 93 PHE Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 157 TRP Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 326 GLN Chi-restraints excluded: chain B residue 584 SER Chi-restraints excluded: chain B residue 589 VAL Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 96 ASP Chi-restraints excluded: chain C residue 110 MET Chi-restraints excluded: chain C residue 139 TYR Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain D residue 93 PHE Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 157 TRP Chi-restraints excluded: chain D residue 229 SER Chi-restraints excluded: chain D residue 326 GLN Chi-restraints excluded: chain D residue 584 SER Chi-restraints excluded: chain D residue 589 VAL Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 96 ASP Chi-restraints excluded: chain E residue 110 MET Chi-restraints excluded: chain E residue 139 TYR Chi-restraints excluded: chain E residue 146 MET Chi-restraints excluded: chain G residue 93 PHE Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 157 TRP Chi-restraints excluded: chain G residue 229 SER Chi-restraints excluded: chain G residue 326 GLN Chi-restraints excluded: chain G residue 584 SER Chi-restraints excluded: chain G residue 589 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 96 ASP Chi-restraints excluded: chain H residue 110 MET Chi-restraints excluded: chain H residue 139 TYR Chi-restraints excluded: chain H residue 146 MET Chi-restraints excluded: chain F residue 27 THR Chi-restraints excluded: chain F residue 96 ASP Chi-restraints excluded: chain F residue 110 MET Chi-restraints excluded: chain F residue 139 TYR Chi-restraints excluded: chain F residue 146 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 182 optimal weight: 0.0020 chunk 21 optimal weight: 4.9990 chunk 108 optimal weight: 4.9990 chunk 138 optimal weight: 8.9990 chunk 107 optimal weight: 0.7980 chunk 159 optimal weight: 9.9990 chunk 105 optimal weight: 5.9990 chunk 188 optimal weight: 4.9990 chunk 118 optimal weight: 10.0000 chunk 115 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 overall best weight: 2.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16448 Z= 0.226 Angle : 0.523 4.870 22156 Z= 0.290 Chirality : 0.033 0.130 2464 Planarity : 0.003 0.041 2768 Dihedral : 6.993 49.346 2312 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 15.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 4.55 % Allowed : 24.10 % Favored : 71.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.31 (0.19), residues: 1956 helix: 2.01 (0.13), residues: 1600 sheet: None (None), residues: 0 loop : -0.64 (0.34), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 288 HIS 0.002 0.000 HIS G 96 PHE 0.021 0.001 PHE F 20 TYR 0.010 0.001 TYR E 139 ARG 0.002 0.000 ARG G 581 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue THR 354 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue SER 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue TYR 362 is missing expected H atoms. Skipping. Residue TYR 363 is missing expected H atoms. Skipping. Residue THR 366 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue THR 354 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue SER 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue TYR 362 is missing expected H atoms. Skipping. Residue TYR 363 is missing expected H atoms. Skipping. Residue THR 366 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue THR 354 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue SER 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue TYR 362 is missing expected H atoms. Skipping. Residue TYR 363 is missing expected H atoms. Skipping. Residue THR 366 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue THR 354 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue SER 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue TYR 362 is missing expected H atoms. Skipping. Residue TYR 363 is missing expected H atoms. Skipping. Residue THR 366 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Evaluate side-chains 279 residues out of total 1688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 203 time to evaluate : 2.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 76 outliers final: 63 residues processed: 256 average time/residue: 0.6066 time to fit residues: 232.2046 Evaluate side-chains 267 residues out of total 1688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 204 time to evaluate : 2.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 TRP Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 157 TRP Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 326 GLN Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain B residue 91 TRP Chi-restraints excluded: chain B residue 93 PHE Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 157 TRP Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 326 GLN Chi-restraints excluded: chain B residue 330 GLU Chi-restraints excluded: chain B residue 584 SER Chi-restraints excluded: chain B residue 589 VAL Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 96 ASP Chi-restraints excluded: chain C residue 110 MET Chi-restraints excluded: chain C residue 139 TYR Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain D residue 91 TRP Chi-restraints excluded: chain D residue 93 PHE Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 157 TRP Chi-restraints excluded: chain D residue 229 SER Chi-restraints excluded: chain D residue 326 GLN Chi-restraints excluded: chain D residue 330 GLU Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 584 SER Chi-restraints excluded: chain D residue 589 VAL Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 96 ASP Chi-restraints excluded: chain E residue 110 MET Chi-restraints excluded: chain E residue 139 TYR Chi-restraints excluded: chain E residue 146 MET Chi-restraints excluded: chain G residue 91 TRP Chi-restraints excluded: chain G residue 93 PHE Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 157 TRP Chi-restraints excluded: chain G residue 229 SER Chi-restraints excluded: chain G residue 326 GLN Chi-restraints excluded: chain G residue 330 GLU Chi-restraints excluded: chain G residue 579 LEU Chi-restraints excluded: chain G residue 584 SER Chi-restraints excluded: chain G residue 589 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 96 ASP Chi-restraints excluded: chain H residue 110 MET Chi-restraints excluded: chain H residue 139 TYR Chi-restraints excluded: chain H residue 146 MET Chi-restraints excluded: chain F residue 27 THR Chi-restraints excluded: chain F residue 96 ASP Chi-restraints excluded: chain F residue 110 MET Chi-restraints excluded: chain F residue 139 TYR Chi-restraints excluded: chain F residue 146 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 116 optimal weight: 7.9990 chunk 75 optimal weight: 9.9990 chunk 112 optimal weight: 20.0000 chunk 56 optimal weight: 4.9990 chunk 37 optimal weight: 10.0000 chunk 36 optimal weight: 0.9980 chunk 120 optimal weight: 20.0000 chunk 128 optimal weight: 0.1980 chunk 93 optimal weight: 10.0000 chunk 17 optimal weight: 4.9990 chunk 148 optimal weight: 3.9990 overall best weight: 3.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16448 Z= 0.243 Angle : 0.532 4.779 22156 Z= 0.295 Chirality : 0.033 0.131 2464 Planarity : 0.003 0.041 2768 Dihedral : 7.015 52.225 2312 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 15.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 3.71 % Allowed : 25.24 % Favored : 71.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.27 (0.19), residues: 1956 helix: 1.98 (0.13), residues: 1600 sheet: None (None), residues: 0 loop : -0.65 (0.34), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 218 HIS 0.002 0.000 HIS A 96 PHE 0.021 0.001 PHE C 20 TYR 0.010 0.001 TYR G 571 ARG 0.002 0.000 ARG B 581 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue THR 354 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue SER 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue TYR 362 is missing expected H atoms. Skipping. Residue TYR 363 is missing expected H atoms. Skipping. Residue THR 366 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue THR 354 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue SER 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue TYR 362 is missing expected H atoms. Skipping. Residue TYR 363 is missing expected H atoms. Skipping. Residue THR 366 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue THR 354 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue SER 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue TYR 362 is missing expected H atoms. Skipping. Residue TYR 363 is missing expected H atoms. Skipping. Residue THR 366 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue THR 354 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue SER 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue TYR 362 is missing expected H atoms. Skipping. Residue TYR 363 is missing expected H atoms. Skipping. Residue THR 366 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Evaluate side-chains 263 residues out of total 1688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 201 time to evaluate : 2.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 PHE cc_start: 0.6739 (OUTLIER) cc_final: 0.6418 (t80) REVERT: B 93 PHE cc_start: 0.6734 (OUTLIER) cc_final: 0.6416 (t80) REVERT: C 119 ASP cc_start: 0.8644 (t0) cc_final: 0.8384 (p0) REVERT: D 93 PHE cc_start: 0.6736 (OUTLIER) cc_final: 0.6417 (t80) REVERT: E 119 ASP cc_start: 0.8645 (t0) cc_final: 0.8385 (p0) REVERT: G 93 PHE cc_start: 0.6737 (OUTLIER) cc_final: 0.6416 (t80) REVERT: H 119 ASP cc_start: 0.8645 (t0) cc_final: 0.8385 (p0) REVERT: F 119 ASP cc_start: 0.8646 (t0) cc_final: 0.8385 (p0) outliers start: 62 outliers final: 54 residues processed: 241 average time/residue: 0.6229 time to fit residues: 230.9547 Evaluate side-chains 259 residues out of total 1688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 201 time to evaluate : 2.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 TRP Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 157 TRP Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 326 GLN Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain B residue 91 TRP Chi-restraints excluded: chain B residue 93 PHE Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 157 TRP Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 326 GLN Chi-restraints excluded: chain B residue 579 LEU Chi-restraints excluded: chain B residue 584 SER Chi-restraints excluded: chain B residue 589 VAL Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 96 ASP Chi-restraints excluded: chain C residue 110 MET Chi-restraints excluded: chain C residue 139 TYR Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain D residue 91 TRP Chi-restraints excluded: chain D residue 93 PHE Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 157 TRP Chi-restraints excluded: chain D residue 229 SER Chi-restraints excluded: chain D residue 326 GLN Chi-restraints excluded: chain D residue 584 SER Chi-restraints excluded: chain D residue 589 VAL Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 96 ASP Chi-restraints excluded: chain E residue 110 MET Chi-restraints excluded: chain E residue 139 TYR Chi-restraints excluded: chain E residue 146 MET Chi-restraints excluded: chain G residue 91 TRP Chi-restraints excluded: chain G residue 93 PHE Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 157 TRP Chi-restraints excluded: chain G residue 229 SER Chi-restraints excluded: chain G residue 326 GLN Chi-restraints excluded: chain G residue 584 SER Chi-restraints excluded: chain G residue 589 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 96 ASP Chi-restraints excluded: chain H residue 110 MET Chi-restraints excluded: chain H residue 139 TYR Chi-restraints excluded: chain H residue 146 MET Chi-restraints excluded: chain F residue 27 THR Chi-restraints excluded: chain F residue 96 ASP Chi-restraints excluded: chain F residue 110 MET Chi-restraints excluded: chain F residue 139 TYR Chi-restraints excluded: chain F residue 146 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 171 optimal weight: 20.0000 chunk 180 optimal weight: 10.0000 chunk 165 optimal weight: 5.9990 chunk 176 optimal weight: 8.9990 chunk 105 optimal weight: 4.9990 chunk 76 optimal weight: 5.9990 chunk 138 optimal weight: 9.9990 chunk 54 optimal weight: 2.9990 chunk 159 optimal weight: 8.9990 chunk 166 optimal weight: 10.0000 chunk 175 optimal weight: 6.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 16448 Z= 0.379 Angle : 0.610 5.670 22156 Z= 0.344 Chirality : 0.036 0.148 2464 Planarity : 0.004 0.041 2768 Dihedral : 7.574 54.359 2312 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 17.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 4.49 % Allowed : 25.48 % Favored : 70.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.19), residues: 1956 helix: 1.62 (0.13), residues: 1604 sheet: None (None), residues: 0 loop : -0.60 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 218 HIS 0.004 0.001 HIS D 328 PHE 0.018 0.002 PHE C 20 TYR 0.012 0.002 TYR B 562 ARG 0.003 0.000 ARG B 541 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue THR 354 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue SER 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue TYR 362 is missing expected H atoms. Skipping. Residue TYR 363 is missing expected H atoms. Skipping. Residue THR 366 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue THR 354 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue SER 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue TYR 362 is missing expected H atoms. Skipping. Residue TYR 363 is missing expected H atoms. Skipping. Residue THR 366 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue THR 354 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue SER 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue TYR 362 is missing expected H atoms. Skipping. Residue TYR 363 is missing expected H atoms. Skipping. Residue THR 366 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue THR 354 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue SER 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue TYR 362 is missing expected H atoms. Skipping. Residue TYR 363 is missing expected H atoms. Skipping. Residue THR 366 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Evaluate side-chains 271 residues out of total 1688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 196 time to evaluate : 2.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 119 ASP cc_start: 0.8753 (t0) cc_final: 0.8481 (p0) REVERT: E 119 ASP cc_start: 0.8751 (t0) cc_final: 0.8483 (p0) REVERT: H 119 ASP cc_start: 0.8754 (t0) cc_final: 0.8482 (p0) REVERT: F 119 ASP cc_start: 0.8753 (t0) cc_final: 0.8482 (p0) outliers start: 75 outliers final: 63 residues processed: 248 average time/residue: 0.6190 time to fit residues: 228.8325 Evaluate side-chains 255 residues out of total 1688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 192 time to evaluate : 2.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 TRP Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 326 GLN Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain B residue 91 TRP Chi-restraints excluded: chain B residue 93 PHE Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 326 GLN Chi-restraints excluded: chain B residue 330 GLU Chi-restraints excluded: chain B residue 584 SER Chi-restraints excluded: chain B residue 589 VAL Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 96 ASP Chi-restraints excluded: chain C residue 110 MET Chi-restraints excluded: chain C residue 139 TYR Chi-restraints excluded: chain C residue 141 GLU Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain D residue 91 TRP Chi-restraints excluded: chain D residue 93 PHE Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 229 SER Chi-restraints excluded: chain D residue 326 GLN Chi-restraints excluded: chain D residue 330 GLU Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 584 SER Chi-restraints excluded: chain D residue 589 VAL Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 96 ASP Chi-restraints excluded: chain E residue 110 MET Chi-restraints excluded: chain E residue 139 TYR Chi-restraints excluded: chain E residue 141 GLU Chi-restraints excluded: chain E residue 146 MET Chi-restraints excluded: chain G residue 91 TRP Chi-restraints excluded: chain G residue 93 PHE Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 229 SER Chi-restraints excluded: chain G residue 326 GLN Chi-restraints excluded: chain G residue 330 GLU Chi-restraints excluded: chain G residue 579 LEU Chi-restraints excluded: chain G residue 584 SER Chi-restraints excluded: chain G residue 589 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 96 ASP Chi-restraints excluded: chain H residue 110 MET Chi-restraints excluded: chain H residue 139 TYR Chi-restraints excluded: chain H residue 141 GLU Chi-restraints excluded: chain H residue 146 MET Chi-restraints excluded: chain F residue 27 THR Chi-restraints excluded: chain F residue 96 ASP Chi-restraints excluded: chain F residue 110 MET Chi-restraints excluded: chain F residue 139 TYR Chi-restraints excluded: chain F residue 141 GLU Chi-restraints excluded: chain F residue 146 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 115 optimal weight: 2.9990 chunk 186 optimal weight: 0.0870 chunk 113 optimal weight: 9.9990 chunk 88 optimal weight: 7.9990 chunk 129 optimal weight: 0.9990 chunk 195 optimal weight: 6.9990 chunk 179 optimal weight: 0.9990 chunk 155 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 120 optimal weight: 4.9990 chunk 95 optimal weight: 9.9990 overall best weight: 0.7762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16448 Z= 0.166 Angle : 0.530 6.437 22156 Z= 0.288 Chirality : 0.033 0.113 2464 Planarity : 0.003 0.041 2768 Dihedral : 6.761 58.999 2312 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 14.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.63 % Allowed : 26.61 % Favored : 70.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.42 (0.19), residues: 1956 helix: 2.09 (0.13), residues: 1600 sheet: None (None), residues: 0 loop : -0.65 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 344 HIS 0.002 0.001 HIS A 260 PHE 0.024 0.001 PHE E 20 TYR 0.010 0.001 TYR A 571 ARG 0.003 0.000 ARG G 207 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue THR 354 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue SER 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue TYR 362 is missing expected H atoms. Skipping. Residue TYR 363 is missing expected H atoms. Skipping. Residue THR 366 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue THR 354 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue SER 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue TYR 362 is missing expected H atoms. Skipping. Residue TYR 363 is missing expected H atoms. Skipping. Residue THR 366 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue THR 354 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue SER 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue TYR 362 is missing expected H atoms. Skipping. Residue TYR 363 is missing expected H atoms. Skipping. Residue THR 366 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue THR 354 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue SER 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue TYR 362 is missing expected H atoms. Skipping. Residue TYR 363 is missing expected H atoms. Skipping. Residue THR 366 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Evaluate side-chains 255 residues out of total 1688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 211 time to evaluate : 3.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 PHE cc_start: 0.6716 (OUTLIER) cc_final: 0.6438 (t80) REVERT: A 102 LEU cc_start: 0.7244 (mm) cc_final: 0.6880 (tt) REVERT: B 93 PHE cc_start: 0.6709 (OUTLIER) cc_final: 0.6435 (t80) REVERT: B 102 LEU cc_start: 0.7247 (mm) cc_final: 0.6883 (tt) REVERT: C 119 ASP cc_start: 0.8606 (t0) cc_final: 0.8379 (p0) REVERT: D 93 PHE cc_start: 0.6711 (OUTLIER) cc_final: 0.6438 (t80) REVERT: D 102 LEU cc_start: 0.7245 (mm) cc_final: 0.6881 (tt) REVERT: E 119 ASP cc_start: 0.8607 (t0) cc_final: 0.8381 (p0) REVERT: G 93 PHE cc_start: 0.6715 (OUTLIER) cc_final: 0.6438 (t80) REVERT: G 102 LEU cc_start: 0.7246 (mm) cc_final: 0.6881 (tt) REVERT: H 119 ASP cc_start: 0.8607 (t0) cc_final: 0.8378 (p0) REVERT: F 119 ASP cc_start: 0.8608 (t0) cc_final: 0.8379 (p0) outliers start: 44 outliers final: 40 residues processed: 231 average time/residue: 0.5921 time to fit residues: 209.7018 Evaluate side-chains 247 residues out of total 1688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 203 time to evaluate : 2.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 TYR Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 326 GLN Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain B residue 74 TYR Chi-restraints excluded: chain B residue 93 PHE Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 326 GLN Chi-restraints excluded: chain B residue 579 LEU Chi-restraints excluded: chain B residue 589 VAL Chi-restraints excluded: chain C residue 110 MET Chi-restraints excluded: chain C residue 139 TYR Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain D residue 74 TYR Chi-restraints excluded: chain D residue 93 PHE Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 229 SER Chi-restraints excluded: chain D residue 326 GLN Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 589 VAL Chi-restraints excluded: chain E residue 110 MET Chi-restraints excluded: chain E residue 139 TYR Chi-restraints excluded: chain E residue 146 MET Chi-restraints excluded: chain G residue 74 TYR Chi-restraints excluded: chain G residue 93 PHE Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 229 SER Chi-restraints excluded: chain G residue 326 GLN Chi-restraints excluded: chain G residue 579 LEU Chi-restraints excluded: chain G residue 589 VAL Chi-restraints excluded: chain H residue 110 MET Chi-restraints excluded: chain H residue 139 TYR Chi-restraints excluded: chain H residue 146 MET Chi-restraints excluded: chain F residue 110 MET Chi-restraints excluded: chain F residue 139 TYR Chi-restraints excluded: chain F residue 146 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 123 optimal weight: 5.9990 chunk 165 optimal weight: 6.9990 chunk 47 optimal weight: 9.9990 chunk 143 optimal weight: 2.9990 chunk 22 optimal weight: 0.3980 chunk 43 optimal weight: 20.0000 chunk 155 optimal weight: 1.9990 chunk 65 optimal weight: 7.9990 chunk 159 optimal weight: 10.0000 chunk 19 optimal weight: 0.6980 chunk 28 optimal weight: 20.0000 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 HIS B 357 HIS D 357 HIS G 357 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.155674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.111999 restraints weight = 98749.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.113320 restraints weight = 45879.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.113155 restraints weight = 32046.596| |-----------------------------------------------------------------------------| r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16448 Z= 0.220 Angle : 0.542 6.265 22156 Z= 0.302 Chirality : 0.033 0.126 2464 Planarity : 0.003 0.041 2768 Dihedral : 6.919 59.746 2312 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 15.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.87 % Allowed : 26.97 % Favored : 70.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.43 (0.19), residues: 1956 helix: 2.10 (0.13), residues: 1596 sheet: None (None), residues: 0 loop : -0.66 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 218 HIS 0.003 0.001 HIS D 228 PHE 0.021 0.001 PHE C 20 TYR 0.010 0.001 TYR A 571 ARG 0.002 0.000 ARG G 581 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5779.95 seconds wall clock time: 104 minutes 30.89 seconds (6270.89 seconds total)