Starting phenix.real_space_refine on Thu Mar 14 15:48:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ajq_11806/03_2024/7ajq_11806.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ajq_11806/03_2024/7ajq_11806.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ajq_11806/03_2024/7ajq_11806.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ajq_11806/03_2024/7ajq_11806.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ajq_11806/03_2024/7ajq_11806.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ajq_11806/03_2024/7ajq_11806.pdb" } resolution = 4.0 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= 0.001 sd= 0.074 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: 4 Type Number sf(0) Gaussians S 29 5.16 5 C 5817 2.51 5 N 1675 2.21 5 O 1689 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 153": "OE1" <-> "OE2" Residue "A ARG 154": "NH1" <-> "NH2" Residue "A ARG 155": "NH1" <-> "NH2" Residue "A PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 237": "NH1" <-> "NH2" Residue "A ARG 243": "NH1" <-> "NH2" Residue "A ASP 248": "OD1" <-> "OD2" Residue "A GLU 268": "OE1" <-> "OE2" Residue "B PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 154": "NH1" <-> "NH2" Residue "B ARG 155": "NH1" <-> "NH2" Residue "B PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 237": "NH1" <-> "NH2" Residue "B ARG 243": "NH1" <-> "NH2" Residue "C PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 154": "NH1" <-> "NH2" Residue "C ARG 155": "NH1" <-> "NH2" Residue "C TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 237": "NH1" <-> "NH2" Residue "C ARG 243": "NH1" <-> "NH2" Residue "C GLU 268": "OE1" <-> "OE2" Residue "D TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 110": "OE1" <-> "OE2" Residue "D GLU 131": "OE1" <-> "OE2" Residue "D PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 154": "NH1" <-> "NH2" Residue "D ARG 155": "NH1" <-> "NH2" Residue "D PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 237": "NH1" <-> "NH2" Residue "D ARG 243": "NH1" <-> "NH2" Residue "D ASP 248": "OD1" <-> "OD2" Residue "D GLU 268": "OE1" <-> "OE2" Residue "E TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 151": "NH1" <-> "NH2" Residue "E ARG 154": "NH1" <-> "NH2" Residue "E ARG 155": "NH1" <-> "NH2" Residue "E TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 237": "NH1" <-> "NH2" Residue "E ARG 243": "NH1" <-> "NH2" Residue "F PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 25": "OD1" <-> "OD2" Residue "F PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 25": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9210 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1729 Classifications: {'peptide': 230} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 4, 'TRANS': 225} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1777 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 4, 'TRANS': 231} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1777 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 4, 'TRANS': 231} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1777 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 4, 'TRANS': 231} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1777 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 4, 'TRANS': 231} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 177 Classifications: {'peptide': 23} Link IDs: {'PTRANS': 2, 'TRANS': 20} Chain: "G" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 196 Classifications: {'peptide': 25} Link IDs: {'PTRANS': 2, 'TRANS': 22} Time building chain proxies: 4.98, per 1000 atoms: 0.54 Number of scatterers: 9210 At special positions: 0 Unit cell: (84.293, 87.494, 133.375, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 29 16.00 O 1689 8.00 N 1675 7.00 C 5817 6.00 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: 3.81 Conformation dependent library (CDL) restraints added in 1.9 seconds 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2246 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 0 sheets defined 87.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 57 through 100 Processing helix chain 'A' and resid 104 through 113 removed outlier: 3.530A pdb=" N ALA A 108 " --> pdb=" O SER A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 136 Processing helix chain 'A' and resid 140 through 164 Processing helix chain 'A' and resid 166 through 199 Proline residue: A 178 - end of helix Processing helix chain 'A' and resid 206 through 272 removed outlier: 4.633A pdb=" N GLY A 210 " --> pdb=" O VAL A 206 " (cutoff:3.500A) Proline residue: A 227 - end of helix removed outlier: 4.246A pdb=" N ALA A 267 " --> pdb=" O LEU A 263 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU A 268 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER A 272 " --> pdb=" O GLU A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 280 removed outlier: 3.509A pdb=" N HIS A 276 " --> pdb=" O SER A 272 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN A 277 " --> pdb=" O GLN A 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 100 Processing helix chain 'B' and resid 104 through 114 removed outlier: 4.395A pdb=" N ASN B 114 " --> pdb=" O GLU B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 136 Processing helix chain 'B' and resid 140 through 164 Processing helix chain 'B' and resid 165 through 199 removed outlier: 4.107A pdb=" N PHE B 169 " --> pdb=" O ARG B 165 " (cutoff:3.500A) Proline residue: B 178 - end of helix Processing helix chain 'B' and resid 206 through 280 removed outlier: 4.098A pdb=" N GLY B 210 " --> pdb=" O VAL B 206 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE B 211 " --> pdb=" O VAL B 207 " (cutoff:3.500A) Proline residue: B 227 - end of helix removed outlier: 4.524A pdb=" N ALA B 267 " --> pdb=" O LEU B 263 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N GLU B 268 " --> pdb=" O ALA B 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 53 removed outlier: 4.207A pdb=" N TYR C 53 " --> pdb=" O ILE C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 100 Processing helix chain 'C' and resid 105 through 113 Processing helix chain 'C' and resid 119 through 135 Processing helix chain 'C' and resid 140 through 164 removed outlier: 3.608A pdb=" N ILE C 144 " --> pdb=" O ASP C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 199 Proline residue: C 178 - end of helix Processing helix chain 'C' and resid 207 through 280 Proline residue: C 227 - end of helix removed outlier: 4.447A pdb=" N ALA C 267 " --> pdb=" O LEU C 263 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N GLU C 268 " --> pdb=" O ALA C 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 52 Processing helix chain 'D' and resid 57 through 99 Processing helix chain 'D' and resid 100 through 102 No H-bonds generated for 'chain 'D' and resid 100 through 102' Processing helix chain 'D' and resid 104 through 114 removed outlier: 3.515A pdb=" N ASN D 114 " --> pdb=" O GLU D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 135 Processing helix chain 'D' and resid 140 through 164 Processing helix chain 'D' and resid 165 through 199 removed outlier: 4.232A pdb=" N PHE D 169 " --> pdb=" O ARG D 165 " (cutoff:3.500A) Proline residue: D 178 - end of helix Processing helix chain 'D' and resid 204 through 206 No H-bonds generated for 'chain 'D' and resid 204 through 206' Processing helix chain 'D' and resid 207 through 272 removed outlier: 3.506A pdb=" N ILE D 211 " --> pdb=" O VAL D 207 " (cutoff:3.500A) Proline residue: D 227 - end of helix removed outlier: 3.908A pdb=" N ALA D 267 " --> pdb=" O LEU D 263 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLU D 268 " --> pdb=" O ALA D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 277 removed outlier: 4.551A pdb=" N GLN D 277 " --> pdb=" O GLN D 273 " (cutoff:3.500A) Processing helix chain 'E' and resid 59 through 100 Processing helix chain 'E' and resid 104 through 113 Processing helix chain 'E' and resid 119 through 135 Processing helix chain 'E' and resid 140 through 164 Processing helix chain 'E' and resid 166 through 199 Proline residue: E 178 - end of helix Processing helix chain 'E' and resid 207 through 277 removed outlier: 3.945A pdb=" N ILE E 211 " --> pdb=" O VAL E 207 " (cutoff:3.500A) Proline residue: E 227 - end of helix Processing helix chain 'F' and resid 22 through 38 removed outlier: 4.068A pdb=" N VAL F 26 " --> pdb=" O PRO F 22 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 38 removed outlier: 4.168A pdb=" N ASP G 25 " --> pdb=" O THR G 21 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N VAL G 26 " --> pdb=" O PRO G 22 " (cutoff:3.500A) 865 hydrogen bonds defined for protein. 2589 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: 2.45 Time building geometry restraints manager: 4.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3175 1.34 - 1.46: 1464 1.46 - 1.57: 4643 1.57 - 1.69: 0 1.69 - 1.81: 58 Bond restraints: 9340 Sorted by residual: bond pdb=" C THR F 21 " pdb=" N PRO F 22 " ideal model delta sigma weight residual 1.337 1.369 -0.033 9.80e-03 1.04e+04 1.11e+01 bond pdb=" C HIS E 276 " pdb=" O HIS E 276 " ideal model delta sigma weight residual 1.235 1.249 -0.014 1.43e-02 4.89e+03 1.00e+00 bond pdb=" CA ALA A 136 " pdb=" C ALA A 136 " ideal model delta sigma weight residual 1.532 1.523 0.009 9.60e-03 1.09e+04 9.64e-01 bond pdb=" CA THR F 21 " pdb=" C THR F 21 " ideal model delta sigma weight residual 1.524 1.534 -0.010 1.26e-02 6.30e+03 6.14e-01 bond pdb=" C ALA F 38 " pdb=" N PRO F 39 " ideal model delta sigma weight residual 1.334 1.351 -0.017 2.34e-02 1.83e+03 5.33e-01 ... (remaining 9335 not shown) Histogram of bond angle deviations from ideal: 100.52 - 107.23: 200 107.23 - 113.94: 5490 113.94 - 120.64: 4086 120.64 - 127.35: 2804 127.35 - 134.06: 77 Bond angle restraints: 12657 Sorted by residual: angle pdb=" N THR G 21 " pdb=" CA THR G 21 " pdb=" C THR G 21 " ideal model delta sigma weight residual 109.81 116.15 -6.34 2.21e+00 2.05e-01 8.23e+00 angle pdb=" N THR F 21 " pdb=" CA THR F 21 " pdb=" C THR F 21 " ideal model delta sigma weight residual 109.81 116.10 -6.29 2.21e+00 2.05e-01 8.10e+00 angle pdb=" CA LEU B 278 " pdb=" CB LEU B 278 " pdb=" CG LEU B 278 " ideal model delta sigma weight residual 116.30 108.10 8.20 3.50e+00 8.16e-02 5.49e+00 angle pdb=" N SER A 135 " pdb=" CA SER A 135 " pdb=" C SER A 135 " ideal model delta sigma weight residual 111.11 108.33 2.78 1.20e+00 6.94e-01 5.37e+00 angle pdb=" C ALA D 136 " pdb=" N GLU D 137 " pdb=" CA GLU D 137 " ideal model delta sigma weight residual 121.54 125.90 -4.36 1.91e+00 2.74e-01 5.20e+00 ... (remaining 12652 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.43: 5113 17.43 - 34.86: 395 34.86 - 52.29: 69 52.29 - 69.72: 9 69.72 - 87.14: 8 Dihedral angle restraints: 5594 sinusoidal: 2118 harmonic: 3476 Sorted by residual: dihedral pdb=" CA LEU B 278 " pdb=" C LEU B 278 " pdb=" N ARG B 279 " pdb=" CA ARG B 279 " ideal model delta harmonic sigma weight residual 180.00 156.98 23.02 0 5.00e+00 4.00e-02 2.12e+01 dihedral pdb=" CA HIS E 276 " pdb=" C HIS E 276 " pdb=" N GLN E 277 " pdb=" CA GLN E 277 " ideal model delta harmonic sigma weight residual -180.00 -157.27 -22.73 0 5.00e+00 4.00e-02 2.07e+01 dihedral pdb=" CA THR G 21 " pdb=" C THR G 21 " pdb=" N PRO G 22 " pdb=" CA PRO G 22 " ideal model delta harmonic sigma weight residual -180.00 -158.70 -21.30 0 5.00e+00 4.00e-02 1.82e+01 ... (remaining 5591 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 935 0.025 - 0.051: 339 0.051 - 0.076: 164 0.076 - 0.102: 46 0.102 - 0.127: 18 Chirality restraints: 1502 Sorted by residual: chirality pdb=" CA THR F 21 " pdb=" N THR F 21 " pdb=" C THR F 21 " pdb=" CB THR F 21 " both_signs ideal model delta sigma weight residual False 2.53 2.40 0.13 2.00e-01 2.50e+01 4.03e-01 chirality pdb=" CB VAL A 223 " pdb=" CA VAL A 223 " pdb=" CG1 VAL A 223 " pdb=" CG2 VAL A 223 " both_signs ideal model delta sigma weight residual False -2.63 -2.51 -0.12 2.00e-01 2.50e+01 3.79e-01 chirality pdb=" CB VAL G 29 " pdb=" CA VAL G 29 " pdb=" CG1 VAL G 29 " pdb=" CG2 VAL G 29 " both_signs ideal model delta sigma weight residual False -2.63 -2.51 -0.12 2.00e-01 2.50e+01 3.73e-01 ... (remaining 1499 not shown) Planarity restraints: 1642 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS C 274 " 0.008 2.00e-02 2.50e+03 1.66e-02 2.75e+00 pdb=" C HIS C 274 " -0.029 2.00e-02 2.50e+03 pdb=" O HIS C 274 " 0.011 2.00e-02 2.50e+03 pdb=" N ALA C 275 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE G 33 " 0.006 2.00e-02 2.50e+03 1.18e-02 1.38e+00 pdb=" C ILE G 33 " -0.020 2.00e-02 2.50e+03 pdb=" O ILE G 33 " 0.008 2.00e-02 2.50e+03 pdb=" N PHE G 34 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP C 248 " -0.006 2.00e-02 2.50e+03 1.15e-02 1.32e+00 pdb=" CG ASP C 248 " 0.020 2.00e-02 2.50e+03 pdb=" OD1 ASP C 248 " -0.007 2.00e-02 2.50e+03 pdb=" OD2 ASP C 248 " -0.007 2.00e-02 2.50e+03 ... (remaining 1639 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1227 2.75 - 3.28: 10405 3.28 - 3.82: 16218 3.82 - 4.36: 17160 4.36 - 4.90: 28997 Nonbonded interactions: 74007 Sorted by model distance: nonbonded pdb=" OG1 THR E 185 " pdb=" OG1 THR E 218 " model vdw 2.208 2.440 nonbonded pdb=" O GLU D 268 " pdb=" OG SER D 272 " model vdw 2.226 2.440 nonbonded pdb=" OG SER B 104 " pdb=" OD1 ASP B 106 " model vdw 2.239 2.440 nonbonded pdb=" O ASP C 262 " pdb=" OG1 THR C 266 " model vdw 2.253 2.440 nonbonded pdb=" O ASN D 162 " pdb=" NH1 ARG D 165 " model vdw 2.263 2.520 ... (remaining 74002 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' selection = (chain 'B' and resid 52 through 281) selection = (chain 'C' and resid 52 through 281) selection = (chain 'D' and resid 52 through 281) selection = (chain 'E' and resid 52 through 281) } ncs_group { reference = chain 'F' selection = (chain 'G' and resid 18 through 40) } 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.680 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: 0.010 Extract box with map and model: 3.920 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 27.010 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.040 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: 0.000 Load rotamer database and sin/cos tables:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 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 : 0.002 0.033 9340 Z= 0.146 Angle : 0.553 8.204 12657 Z= 0.315 Chirality : 0.035 0.127 1502 Planarity : 0.003 0.029 1642 Dihedral : 13.098 87.144 3348 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % 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: -0.98 (0.22), residues: 1208 helix: -0.03 (0.15), residues: 1015 sheet: None (None), residues: 0 loop : -3.52 (0.36), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 187 HIS 0.003 0.001 HIS C 274 PHE 0.006 0.001 PHE C 193 TYR 0.007 0.001 TYR A 232 ARG 0.002 0.000 ARG E 271 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 304 time to evaluate : 1.036 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: A 79 PHE cc_start: 0.8721 (m-10) cc_final: 0.8438 (m-10) REVERT: A 81 LYS cc_start: 0.8074 (mmmm) cc_final: 0.7861 (mmmm) REVERT: A 126 ASN cc_start: 0.8808 (t0) cc_final: 0.8240 (p0) REVERT: A 193 PHE cc_start: 0.8916 (m-10) cc_final: 0.8473 (m-10) REVERT: A 252 GLN cc_start: 0.8769 (tt0) cc_final: 0.8555 (tm-30) REVERT: B 61 LYS cc_start: 0.3876 (tttt) cc_final: 0.2932 (mmmt) REVERT: B 81 LYS cc_start: 0.9321 (tppt) cc_final: 0.8717 (mmmt) REVERT: B 187 TRP cc_start: 0.8553 (t60) cc_final: 0.8306 (t-100) REVERT: B 270 LYS cc_start: 0.7512 (pttt) cc_final: 0.7073 (tptp) REVERT: C 169 PHE cc_start: 0.8946 (t80) cc_final: 0.8730 (t80) REVERT: C 232 TYR cc_start: 0.7957 (t80) cc_final: 0.7752 (t80) REVERT: C 245 GLN cc_start: 0.8276 (mm-40) cc_final: 0.8013 (mm-40) REVERT: C 248 ASP cc_start: 0.8370 (m-30) cc_final: 0.7993 (t70) REVERT: C 252 GLN cc_start: 0.8417 (mt0) cc_final: 0.7883 (mt0) REVERT: D 169 PHE cc_start: 0.9004 (t80) cc_final: 0.8730 (t80) REVERT: D 190 MET cc_start: 0.9085 (ppp) cc_final: 0.8739 (tmm) REVERT: D 216 LEU cc_start: 0.8898 (pp) cc_final: 0.8664 (pp) REVERT: D 220 MET cc_start: 0.9033 (mmt) cc_final: 0.8724 (mpp) REVERT: E 231 ILE cc_start: 0.9236 (mm) cc_final: 0.8990 (tp) REVERT: F 27 MET cc_start: 0.7647 (mmt) cc_final: 0.7387 (mmp) REVERT: F 34 PHE cc_start: 0.3922 (m-10) cc_final: 0.3163 (m-80) outliers start: 0 outliers final: 0 residues processed: 304 average time/residue: 0.2258 time to fit residues: 91.5186 Evaluate side-chains 224 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 224 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 100 optimal weight: 0.6980 chunk 90 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 30 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 93 optimal weight: 8.9990 chunk 36 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 69 optimal weight: 0.6980 chunk 108 optimal weight: 7.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 ASN A 245 GLN C 96 GLN C 129 GLN ** C 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 242 HIS ** D 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 191 ASN E 273 GLN ** E 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 19 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9340 Z= 0.192 Angle : 0.677 11.429 12657 Z= 0.339 Chirality : 0.041 0.208 1502 Planarity : 0.004 0.039 1642 Dihedral : 4.100 23.166 1320 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 18.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.14 % Allowed : 16.70 % Favored : 81.16 % 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: 0.59 (0.24), residues: 1208 helix: 1.06 (0.16), residues: 1021 sheet: None (None), residues: 0 loop : -3.26 (0.40), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 75 HIS 0.012 0.001 HIS C 242 PHE 0.026 0.002 PHE B 179 TYR 0.016 0.002 TYR A 232 ARG 0.005 0.000 ARG C 271 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 251 time to evaluate : 1.033 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: A 79 PHE cc_start: 0.8682 (m-10) cc_final: 0.8447 (m-10) REVERT: A 126 ASN cc_start: 0.8782 (t0) cc_final: 0.8220 (p0) REVERT: A 140 ASP cc_start: 0.6655 (m-30) cc_final: 0.6355 (m-30) REVERT: A 193 PHE cc_start: 0.8901 (m-10) cc_final: 0.8480 (m-10) REVERT: A 232 TYR cc_start: 0.8700 (t80) cc_final: 0.8432 (t80) REVERT: A 235 PHE cc_start: 0.9126 (m-80) cc_final: 0.8751 (m-80) REVERT: B 61 LYS cc_start: 0.3774 (tttt) cc_final: 0.3071 (mmmt) REVERT: B 81 LYS cc_start: 0.9178 (tppt) cc_final: 0.8786 (mmmt) REVERT: B 130 ASN cc_start: 0.9029 (p0) cc_final: 0.8799 (p0) REVERT: B 179 PHE cc_start: 0.8865 (m-80) cc_final: 0.8625 (m-80) REVERT: B 187 TRP cc_start: 0.8547 (t60) cc_final: 0.8285 (t-100) REVERT: B 270 LYS cc_start: 0.7564 (pttt) cc_final: 0.7121 (tptp) REVERT: C 169 PHE cc_start: 0.8982 (t80) cc_final: 0.8747 (t80) REVERT: C 220 MET cc_start: 0.8606 (ptt) cc_final: 0.8385 (ptt) REVERT: C 235 PHE cc_start: 0.8665 (t80) cc_final: 0.8335 (m-80) REVERT: C 245 GLN cc_start: 0.8298 (mm-40) cc_final: 0.8034 (mm-40) REVERT: C 248 ASP cc_start: 0.8356 (m-30) cc_final: 0.8051 (t70) REVERT: C 252 GLN cc_start: 0.8398 (mt0) cc_final: 0.7871 (mt0) REVERT: D 169 PHE cc_start: 0.8945 (t80) cc_final: 0.8659 (t80) REVERT: D 189 ILE cc_start: 0.9360 (tp) cc_final: 0.9086 (pt) REVERT: D 190 MET cc_start: 0.9039 (ppp) cc_final: 0.8792 (tmm) REVERT: E 64 MET cc_start: 0.7894 (OUTLIER) cc_final: 0.7628 (ppp) REVERT: E 270 LYS cc_start: 0.7321 (tmmt) cc_final: 0.6864 (pttt) outliers start: 20 outliers final: 10 residues processed: 259 average time/residue: 0.1960 time to fit residues: 70.4052 Evaluate side-chains 232 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 221 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain A residue 167 ASN Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain E residue 64 MET Chi-restraints excluded: chain E residue 218 THR Chi-restraints excluded: chain E residue 248 ASP Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain G residue 21 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 60 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 116 optimal weight: 0.9990 chunk 96 optimal weight: 5.9990 chunk 107 optimal weight: 0.0050 chunk 36 optimal weight: 0.9990 chunk 86 optimal weight: 0.9990 overall best weight: 0.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 233 ASN B 257 GLN ** C 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 191 ASN ** D 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9340 Z= 0.176 Angle : 0.684 12.409 12657 Z= 0.337 Chirality : 0.041 0.290 1502 Planarity : 0.003 0.023 1642 Dihedral : 4.138 22.888 1320 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 17.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.25 % Allowed : 20.77 % Favored : 76.98 % 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: 1.02 (0.25), residues: 1208 helix: 1.33 (0.16), residues: 1027 sheet: None (None), residues: 0 loop : -3.12 (0.41), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 75 HIS 0.009 0.001 HIS C 242 PHE 0.038 0.002 PHE B 79 TYR 0.020 0.002 TYR B 53 ARG 0.004 0.000 ARG B 90 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 248 time to evaluate : 1.002 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: A 126 ASN cc_start: 0.8744 (t0) cc_final: 0.8175 (p0) REVERT: A 140 ASP cc_start: 0.6730 (m-30) cc_final: 0.6276 (m-30) REVERT: A 187 TRP cc_start: 0.8106 (t-100) cc_final: 0.7718 (t-100) REVERT: A 193 PHE cc_start: 0.8901 (m-10) cc_final: 0.8556 (m-10) REVERT: A 235 PHE cc_start: 0.9090 (m-80) cc_final: 0.8378 (m-80) REVERT: A 270 LYS cc_start: 0.6133 (mttt) cc_final: 0.5503 (tmtt) REVERT: B 61 LYS cc_start: 0.3723 (tttt) cc_final: 0.3083 (mmmt) REVERT: B 81 LYS cc_start: 0.9256 (tppt) cc_final: 0.8976 (mttt) REVERT: B 153 GLU cc_start: 0.9268 (pt0) cc_final: 0.9052 (pp20) REVERT: B 163 MET cc_start: 0.8440 (mmm) cc_final: 0.8074 (mmm) REVERT: B 179 PHE cc_start: 0.8733 (m-80) cc_final: 0.8490 (m-80) REVERT: B 270 LYS cc_start: 0.7615 (pttt) cc_final: 0.7192 (tptp) REVERT: C 113 GLN cc_start: 0.8010 (tm-30) cc_final: 0.7703 (tm-30) REVERT: C 169 PHE cc_start: 0.8967 (t80) cc_final: 0.8739 (t80) REVERT: C 235 PHE cc_start: 0.8659 (t80) cc_final: 0.8324 (m-80) REVERT: C 245 GLN cc_start: 0.8289 (mm-40) cc_final: 0.8011 (mm-40) REVERT: C 248 ASP cc_start: 0.8302 (m-30) cc_final: 0.8085 (t70) REVERT: C 252 GLN cc_start: 0.8381 (mt0) cc_final: 0.7879 (mt0) REVERT: D 67 LEU cc_start: 0.9352 (mt) cc_final: 0.9079 (pp) REVERT: E 64 MET cc_start: 0.7783 (OUTLIER) cc_final: 0.7565 (ppp) REVERT: E 270 LYS cc_start: 0.7489 (tmmt) cc_final: 0.7062 (pttt) REVERT: G 35 MET cc_start: 0.8125 (mtm) cc_final: 0.7830 (mtm) outliers start: 21 outliers final: 15 residues processed: 259 average time/residue: 0.2080 time to fit residues: 73.5768 Evaluate side-chains 236 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 220 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain A residue 150 PHE Chi-restraints excluded: chain A residue 167 ASN Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain E residue 64 MET Chi-restraints excluded: chain E residue 248 ASP Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain G residue 21 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 106 optimal weight: 0.8980 chunk 81 optimal weight: 6.9990 chunk 56 optimal weight: 6.9990 chunk 11 optimal weight: 4.9990 chunk 51 optimal weight: 7.9990 chunk 72 optimal weight: 5.9990 chunk 108 optimal weight: 0.0030 chunk 115 optimal weight: 5.9990 chunk 102 optimal weight: 0.8980 chunk 30 optimal weight: 5.9990 chunk 95 optimal weight: 7.9990 overall best weight: 2.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 GLN ** C 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 277 GLN ** D 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 54 GLN ** E 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.2895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9340 Z= 0.240 Angle : 0.709 10.447 12657 Z= 0.359 Chirality : 0.042 0.203 1502 Planarity : 0.004 0.026 1642 Dihedral : 4.335 24.197 1320 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 20.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 4.07 % Allowed : 21.31 % Favored : 74.63 % 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: 0.94 (0.24), residues: 1208 helix: 1.27 (0.16), residues: 1027 sheet: None (None), residues: 0 loop : -3.04 (0.41), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 75 HIS 0.007 0.001 HIS C 242 PHE 0.040 0.002 PHE B 79 TYR 0.024 0.002 TYR C 232 ARG 0.007 0.000 ARG D 151 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 228 time to evaluate : 1.024 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: A 61 LYS cc_start: 0.9260 (pttp) cc_final: 0.8913 (tppt) REVERT: A 126 ASN cc_start: 0.8797 (t0) cc_final: 0.8202 (p0) REVERT: A 140 ASP cc_start: 0.7011 (m-30) cc_final: 0.6700 (m-30) REVERT: A 187 TRP cc_start: 0.7970 (t-100) cc_final: 0.7543 (t-100) REVERT: A 190 MET cc_start: 0.8193 (ptp) cc_final: 0.7791 (ptp) REVERT: A 193 PHE cc_start: 0.9021 (m-10) cc_final: 0.8589 (m-10) REVERT: A 270 LYS cc_start: 0.6034 (mttt) cc_final: 0.5635 (tmtt) REVERT: B 61 LYS cc_start: 0.3785 (tttt) cc_final: 0.3370 (tttt) REVERT: B 81 LYS cc_start: 0.9267 (tppt) cc_final: 0.9002 (mttt) REVERT: B 163 MET cc_start: 0.8550 (mmm) cc_final: 0.8132 (mmm) REVERT: B 179 PHE cc_start: 0.8845 (m-10) cc_final: 0.8554 (m-80) REVERT: B 220 MET cc_start: 0.9104 (mtp) cc_final: 0.8810 (mtm) REVERT: B 270 LYS cc_start: 0.7552 (pttt) cc_final: 0.7126 (tptp) REVERT: C 169 PHE cc_start: 0.8988 (t80) cc_final: 0.8774 (t80) REVERT: C 235 PHE cc_start: 0.8713 (t80) cc_final: 0.8383 (m-80) REVERT: C 245 GLN cc_start: 0.8348 (mm-40) cc_final: 0.8105 (mm-40) REVERT: C 248 ASP cc_start: 0.8441 (m-30) cc_final: 0.8231 (t70) REVERT: C 252 GLN cc_start: 0.8482 (mt0) cc_final: 0.7967 (mt0) REVERT: D 145 LYS cc_start: 0.9438 (mmtp) cc_final: 0.9053 (mmtm) REVERT: F 35 MET cc_start: 0.3135 (mmm) cc_final: 0.2797 (mmm) REVERT: G 27 MET cc_start: 0.8665 (mmm) cc_final: 0.8382 (mpp) outliers start: 38 outliers final: 27 residues processed: 250 average time/residue: 0.1985 time to fit residues: 68.7212 Evaluate side-chains 242 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 215 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 150 PHE Chi-restraints excluded: chain A residue 167 ASN Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 75 TRP Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 150 PHE Chi-restraints excluded: chain E residue 153 GLU Chi-restraints excluded: chain E residue 218 THR Chi-restraints excluded: chain E residue 229 VAL Chi-restraints excluded: chain E residue 248 ASP Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain G residue 21 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 65 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 85 optimal weight: 0.7980 chunk 47 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 58 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 38 optimal weight: 0.2980 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 139 ASN ** C 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 277 GLN ** D 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 257 GLN ** E 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9340 Z= 0.201 Angle : 0.730 11.641 12657 Z= 0.360 Chirality : 0.042 0.210 1502 Planarity : 0.004 0.028 1642 Dihedral : 4.335 23.930 1320 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 19.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 4.07 % Allowed : 23.66 % Favored : 72.27 % 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: 1.08 (0.25), residues: 1208 helix: 1.34 (0.16), residues: 1028 sheet: None (None), residues: 0 loop : -2.88 (0.42), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 75 HIS 0.006 0.001 HIS C 242 PHE 0.041 0.002 PHE B 79 TYR 0.019 0.002 TYR D 159 ARG 0.003 0.000 ARG D 151 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 233 time to evaluate : 0.966 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: A 61 LYS cc_start: 0.9232 (pttp) cc_final: 0.8913 (tppt) REVERT: A 106 ASP cc_start: 0.8158 (OUTLIER) cc_final: 0.7773 (p0) REVERT: A 126 ASN cc_start: 0.8763 (t0) cc_final: 0.8189 (p0) REVERT: A 140 ASP cc_start: 0.6884 (m-30) cc_final: 0.6560 (m-30) REVERT: A 187 TRP cc_start: 0.7886 (t-100) cc_final: 0.7472 (t-100) REVERT: A 190 MET cc_start: 0.8297 (ptp) cc_final: 0.7746 (ptp) REVERT: A 193 PHE cc_start: 0.9053 (m-10) cc_final: 0.8560 (m-10) REVERT: A 235 PHE cc_start: 0.8896 (m-80) cc_final: 0.8600 (m-80) REVERT: A 270 LYS cc_start: 0.6212 (mttt) cc_final: 0.5829 (tmtt) REVERT: B 61 LYS cc_start: 0.4160 (tttt) cc_final: 0.3885 (tttt) REVERT: B 81 LYS cc_start: 0.9269 (tppt) cc_final: 0.9005 (mttt) REVERT: B 163 MET cc_start: 0.8539 (mmm) cc_final: 0.8170 (mmm) REVERT: B 187 TRP cc_start: 0.8757 (t-100) cc_final: 0.8532 (t-100) REVERT: B 270 LYS cc_start: 0.7556 (pttt) cc_final: 0.7156 (tptp) REVERT: C 154 ARG cc_start: 0.8320 (mmt-90) cc_final: 0.8042 (mmm-85) REVERT: C 169 PHE cc_start: 0.8986 (t80) cc_final: 0.8746 (t80) REVERT: C 235 PHE cc_start: 0.8674 (t80) cc_final: 0.8315 (m-80) REVERT: C 245 GLN cc_start: 0.8314 (mm-40) cc_final: 0.8042 (mm-40) REVERT: C 252 GLN cc_start: 0.8431 (mt0) cc_final: 0.7929 (mt0) REVERT: C 277 GLN cc_start: 0.6077 (OUTLIER) cc_final: 0.5772 (pm20) REVERT: D 145 LYS cc_start: 0.9446 (mmtp) cc_final: 0.9168 (mmtm) REVERT: D 190 MET cc_start: 0.9023 (tmm) cc_final: 0.8612 (ptt) REVERT: D 220 MET cc_start: 0.9349 (mmm) cc_final: 0.8747 (mpp) REVERT: E 190 MET cc_start: 0.9061 (ptp) cc_final: 0.8651 (ptp) REVERT: E 270 LYS cc_start: 0.7329 (pptt) cc_final: 0.6639 (pttt) REVERT: G 27 MET cc_start: 0.8756 (mmm) cc_final: 0.8483 (mpp) REVERT: G 35 MET cc_start: 0.7963 (mtm) cc_final: 0.7730 (mtt) outliers start: 38 outliers final: 27 residues processed: 255 average time/residue: 0.2024 time to fit residues: 70.9477 Evaluate side-chains 247 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 218 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain A residue 150 PHE Chi-restraints excluded: chain A residue 167 ASN Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 142 ASN Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 150 PHE Chi-restraints excluded: chain E residue 218 THR Chi-restraints excluded: chain E residue 229 VAL Chi-restraints excluded: chain E residue 248 ASP Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain G residue 21 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 103 optimal weight: 7.9990 chunk 22 optimal weight: 4.9990 chunk 67 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 115 optimal weight: 4.9990 chunk 95 optimal weight: 1.9990 chunk 53 optimal weight: 0.4980 chunk 9 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 60 optimal weight: 0.9980 chunk 111 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 277 GLN ** D 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.3153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9340 Z= 0.185 Angle : 0.729 12.465 12657 Z= 0.360 Chirality : 0.042 0.221 1502 Planarity : 0.003 0.024 1642 Dihedral : 4.310 23.259 1320 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 18.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 3.96 % Allowed : 25.80 % Favored : 70.24 % 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: 1.22 (0.25), residues: 1208 helix: 1.42 (0.16), residues: 1028 sheet: None (None), residues: 0 loop : -2.69 (0.44), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 75 HIS 0.006 0.001 HIS C 242 PHE 0.044 0.002 PHE B 79 TYR 0.027 0.002 TYR C 232 ARG 0.002 0.000 ARG C 279 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 227 time to evaluate : 1.040 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: A 61 LYS cc_start: 0.9206 (pttp) cc_final: 0.8863 (tppt) REVERT: A 106 ASP cc_start: 0.8183 (OUTLIER) cc_final: 0.7796 (p0) REVERT: A 126 ASN cc_start: 0.8753 (t0) cc_final: 0.8175 (p0) REVERT: A 140 ASP cc_start: 0.6790 (m-30) cc_final: 0.6436 (m-30) REVERT: A 187 TRP cc_start: 0.7944 (t-100) cc_final: 0.7525 (t-100) REVERT: A 190 MET cc_start: 0.8186 (ptp) cc_final: 0.7535 (ptp) REVERT: A 193 PHE cc_start: 0.9045 (m-10) cc_final: 0.8512 (m-10) REVERT: A 235 PHE cc_start: 0.8754 (m-80) cc_final: 0.8197 (m-80) REVERT: A 270 LYS cc_start: 0.6255 (mttt) cc_final: 0.5901 (tmtt) REVERT: B 81 LYS cc_start: 0.9265 (tppt) cc_final: 0.9039 (mttt) REVERT: B 163 MET cc_start: 0.8545 (mmm) cc_final: 0.8190 (mmm) REVERT: B 220 MET cc_start: 0.9036 (mtp) cc_final: 0.8712 (mtt) REVERT: B 270 LYS cc_start: 0.7556 (pttt) cc_final: 0.7096 (tptp) REVERT: C 92 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8280 (pp) REVERT: C 169 PHE cc_start: 0.8950 (t80) cc_final: 0.8732 (t80) REVERT: C 179 PHE cc_start: 0.8836 (m-10) cc_final: 0.8586 (m-80) REVERT: C 235 PHE cc_start: 0.8640 (t80) cc_final: 0.8269 (m-80) REVERT: C 252 GLN cc_start: 0.8207 (mt0) cc_final: 0.7999 (mt0) REVERT: C 277 GLN cc_start: 0.5949 (OUTLIER) cc_final: 0.5599 (pm20) REVERT: D 145 LYS cc_start: 0.9388 (mmtp) cc_final: 0.9123 (mmtm) REVERT: D 190 MET cc_start: 0.8966 (tmm) cc_final: 0.8673 (ptt) REVERT: D 220 MET cc_start: 0.9309 (mmm) cc_final: 0.8710 (mpp) REVERT: E 150 PHE cc_start: 0.8438 (OUTLIER) cc_final: 0.8177 (t80) REVERT: E 190 MET cc_start: 0.9067 (ptp) cc_final: 0.8701 (ptp) outliers start: 37 outliers final: 28 residues processed: 250 average time/residue: 0.2014 time to fit residues: 69.3621 Evaluate side-chains 246 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 214 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 150 PHE Chi-restraints excluded: chain A residue 167 ASN Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 142 ASN Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 248 ASP Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 150 PHE Chi-restraints excluded: chain E residue 218 THR Chi-restraints excluded: chain E residue 229 VAL Chi-restraints excluded: chain E residue 248 ASP Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain G residue 21 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 12 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 84 optimal weight: 6.9990 chunk 96 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 114 optimal weight: 10.0000 chunk 71 optimal weight: 0.7980 chunk 69 optimal weight: 0.1980 chunk 52 optimal weight: 0.0770 chunk 70 optimal weight: 6.9990 chunk 45 optimal weight: 10.0000 overall best weight: 0.8140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 245 GLN C 277 GLN ** D 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.3303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9340 Z= 0.185 Angle : 0.743 12.830 12657 Z= 0.367 Chirality : 0.042 0.226 1502 Planarity : 0.003 0.024 1642 Dihedral : 4.279 23.000 1320 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 17.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.85 % Allowed : 25.48 % Favored : 70.66 % 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: 1.28 (0.25), residues: 1208 helix: 1.45 (0.16), residues: 1028 sheet: None (None), residues: 0 loop : -2.66 (0.43), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 75 HIS 0.005 0.001 HIS C 276 PHE 0.046 0.002 PHE B 79 TYR 0.032 0.002 TYR C 232 ARG 0.004 0.000 ARG A 165 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 224 time to evaluate : 1.026 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: A 61 LYS cc_start: 0.9204 (pttp) cc_final: 0.8862 (tppt) REVERT: A 106 ASP cc_start: 0.8161 (OUTLIER) cc_final: 0.7764 (p0) REVERT: A 126 ASN cc_start: 0.8778 (t0) cc_final: 0.8201 (p0) REVERT: A 140 ASP cc_start: 0.6760 (m-30) cc_final: 0.6363 (m-30) REVERT: A 190 MET cc_start: 0.8178 (ptp) cc_final: 0.7615 (ptp) REVERT: A 193 PHE cc_start: 0.9053 (m-10) cc_final: 0.8657 (m-10) REVERT: A 235 PHE cc_start: 0.8774 (m-80) cc_final: 0.8455 (m-80) REVERT: A 270 LYS cc_start: 0.6256 (mttt) cc_final: 0.5929 (tmtt) REVERT: B 81 LYS cc_start: 0.9266 (tppt) cc_final: 0.8894 (mttt) REVERT: B 85 LEU cc_start: 0.8894 (mt) cc_final: 0.8647 (pp) REVERT: B 163 MET cc_start: 0.8543 (mmm) cc_final: 0.8132 (mmm) REVERT: B 220 MET cc_start: 0.9023 (mtp) cc_final: 0.8666 (mtt) REVERT: B 270 LYS cc_start: 0.7573 (pttt) cc_final: 0.7134 (tptp) REVERT: C 92 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8039 (pp) REVERT: C 169 PHE cc_start: 0.8944 (t80) cc_final: 0.8732 (t80) REVERT: C 179 PHE cc_start: 0.8800 (m-10) cc_final: 0.8536 (m-80) REVERT: C 235 PHE cc_start: 0.8630 (t80) cc_final: 0.8216 (m-80) REVERT: C 277 GLN cc_start: 0.5856 (OUTLIER) cc_final: 0.5499 (pm20) REVERT: D 145 LYS cc_start: 0.9386 (mmtp) cc_final: 0.9115 (mmtm) REVERT: D 190 MET cc_start: 0.8942 (tmm) cc_final: 0.8675 (ptp) REVERT: D 220 MET cc_start: 0.9277 (mmm) cc_final: 0.8712 (mpp) REVERT: D 237 ARG cc_start: 0.8895 (ttm170) cc_final: 0.8629 (ttm170) REVERT: E 52 MET cc_start: 0.5735 (mmp) cc_final: 0.5271 (mmp) REVERT: E 190 MET cc_start: 0.9098 (ptp) cc_final: 0.8739 (ptp) REVERT: E 270 LYS cc_start: 0.7329 (pptt) cc_final: 0.6505 (pttt) outliers start: 36 outliers final: 30 residues processed: 244 average time/residue: 0.1986 time to fit residues: 66.8436 Evaluate side-chains 248 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 215 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 150 PHE Chi-restraints excluded: chain A residue 167 ASN Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 142 ASN Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain C residue 75 TRP Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 248 ASP Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 218 THR Chi-restraints excluded: chain E residue 229 VAL Chi-restraints excluded: chain E residue 248 ASP Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain G residue 21 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 68 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 22 optimal weight: 0.0270 chunk 72 optimal weight: 3.9990 chunk 78 optimal weight: 0.0670 chunk 56 optimal weight: 0.9990 chunk 10 optimal weight: 6.9990 chunk 90 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 chunk 100 optimal weight: 4.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 252 GLN C 277 GLN ** D 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.3431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9340 Z= 0.194 Angle : 0.769 12.889 12657 Z= 0.378 Chirality : 0.043 0.227 1502 Planarity : 0.004 0.052 1642 Dihedral : 4.246 22.623 1320 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 17.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.43 % Allowed : 27.19 % Favored : 69.38 % 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: 1.34 (0.25), residues: 1208 helix: 1.49 (0.16), residues: 1027 sheet: None (None), residues: 0 loop : -2.57 (0.44), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 75 HIS 0.007 0.001 HIS C 242 PHE 0.044 0.002 PHE B 79 TYR 0.019 0.002 TYR C 232 ARG 0.006 0.000 ARG A 165 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 223 time to evaluate : 1.057 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: A 61 LYS cc_start: 0.9200 (pttp) cc_final: 0.8877 (tppt) REVERT: A 106 ASP cc_start: 0.8162 (OUTLIER) cc_final: 0.7745 (p0) REVERT: A 126 ASN cc_start: 0.8746 (t0) cc_final: 0.8185 (p0) REVERT: A 140 ASP cc_start: 0.6819 (m-30) cc_final: 0.6358 (m-30) REVERT: A 190 MET cc_start: 0.8243 (ptp) cc_final: 0.7624 (ptp) REVERT: A 193 PHE cc_start: 0.9055 (m-10) cc_final: 0.8646 (m-10) REVERT: A 235 PHE cc_start: 0.8886 (m-80) cc_final: 0.8543 (m-80) REVERT: A 270 LYS cc_start: 0.6344 (mttt) cc_final: 0.6011 (tmtt) REVERT: B 81 LYS cc_start: 0.9314 (tppt) cc_final: 0.8863 (mttt) REVERT: B 85 LEU cc_start: 0.8882 (mt) cc_final: 0.8666 (pp) REVERT: B 163 MET cc_start: 0.8552 (mmm) cc_final: 0.8110 (mmm) REVERT: B 220 MET cc_start: 0.9053 (mtp) cc_final: 0.8705 (mtt) REVERT: B 270 LYS cc_start: 0.7608 (pttt) cc_final: 0.7174 (tptp) REVERT: C 113 GLN cc_start: 0.8020 (tm-30) cc_final: 0.7702 (tm-30) REVERT: C 169 PHE cc_start: 0.8958 (t80) cc_final: 0.8706 (t80) REVERT: C 179 PHE cc_start: 0.8758 (m-10) cc_final: 0.8515 (m-80) REVERT: C 232 TYR cc_start: 0.8117 (t80) cc_final: 0.7736 (t80) REVERT: C 277 GLN cc_start: 0.5861 (OUTLIER) cc_final: 0.5495 (pm20) REVERT: D 145 LYS cc_start: 0.9382 (mmtp) cc_final: 0.9096 (mmtm) REVERT: D 220 MET cc_start: 0.9235 (mmm) cc_final: 0.8692 (mpp) REVERT: D 237 ARG cc_start: 0.8901 (ttm170) cc_final: 0.8617 (ttm170) REVERT: E 52 MET cc_start: 0.6107 (mmp) cc_final: 0.5772 (mmp) REVERT: E 190 MET cc_start: 0.9086 (ptp) cc_final: 0.8726 (ptp) REVERT: G 27 MET cc_start: 0.8708 (mmm) cc_final: 0.8484 (mpp) outliers start: 32 outliers final: 29 residues processed: 242 average time/residue: 0.1917 time to fit residues: 64.5458 Evaluate side-chains 241 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 210 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 150 PHE Chi-restraints excluded: chain A residue 167 ASN Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 142 ASN Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 75 TRP Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 191 ASN Chi-restraints excluded: chain C residue 248 ASP Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 218 THR Chi-restraints excluded: chain E residue 248 ASP Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain G residue 21 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 106 optimal weight: 0.8980 chunk 109 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 83 optimal weight: 2.9990 chunk 32 optimal weight: 0.0770 chunk 96 optimal weight: 2.9990 chunk 101 optimal weight: 7.9990 chunk 70 optimal weight: 5.9990 chunk 113 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 overall best weight: 1.1342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 257 GLN ** C 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 277 GLN ** D 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.3538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9340 Z= 0.196 Angle : 0.785 13.613 12657 Z= 0.385 Chirality : 0.044 0.237 1502 Planarity : 0.003 0.026 1642 Dihedral : 4.238 22.814 1320 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 17.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.75 % Allowed : 27.09 % Favored : 69.16 % 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: 1.31 (0.25), residues: 1208 helix: 1.45 (0.16), residues: 1028 sheet: None (None), residues: 0 loop : -2.51 (0.44), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 187 HIS 0.007 0.001 HIS C 242 PHE 0.046 0.002 PHE D 193 TYR 0.016 0.002 TYR A 232 ARG 0.006 0.000 ARG A 165 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 221 time to evaluate : 0.806 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: A 61 LYS cc_start: 0.9206 (pttp) cc_final: 0.8884 (tppt) REVERT: A 106 ASP cc_start: 0.8182 (m-30) cc_final: 0.7739 (p0) REVERT: A 126 ASN cc_start: 0.8773 (t0) cc_final: 0.8201 (p0) REVERT: A 140 ASP cc_start: 0.6804 (m-30) cc_final: 0.6327 (m-30) REVERT: A 190 MET cc_start: 0.8262 (ptp) cc_final: 0.7706 (ptp) REVERT: A 193 PHE cc_start: 0.9047 (m-10) cc_final: 0.8700 (m-10) REVERT: A 235 PHE cc_start: 0.8919 (m-80) cc_final: 0.8587 (m-80) REVERT: A 270 LYS cc_start: 0.6570 (mttt) cc_final: 0.6234 (tmtt) REVERT: B 81 LYS cc_start: 0.9319 (tppt) cc_final: 0.8828 (mttt) REVERT: B 85 LEU cc_start: 0.8877 (mt) cc_final: 0.8666 (pp) REVERT: B 163 MET cc_start: 0.8510 (mmm) cc_final: 0.8049 (mmm) REVERT: B 220 MET cc_start: 0.9058 (mtp) cc_final: 0.8838 (mtm) REVERT: B 270 LYS cc_start: 0.7609 (pttt) cc_final: 0.7184 (tptp) REVERT: C 113 GLN cc_start: 0.8060 (tm-30) cc_final: 0.7726 (tm-30) REVERT: C 169 PHE cc_start: 0.8940 (t80) cc_final: 0.8711 (t80) REVERT: C 232 TYR cc_start: 0.8115 (t80) cc_final: 0.7779 (t80) REVERT: C 233 ASN cc_start: 0.8385 (t0) cc_final: 0.7928 (t0) REVERT: C 277 GLN cc_start: 0.5850 (OUTLIER) cc_final: 0.5476 (pm20) REVERT: D 145 LYS cc_start: 0.9360 (mmtp) cc_final: 0.9091 (mmtm) REVERT: D 220 MET cc_start: 0.9233 (mmm) cc_final: 0.8701 (mpp) REVERT: D 237 ARG cc_start: 0.8918 (ttm170) cc_final: 0.8633 (ttm170) REVERT: E 89 LYS cc_start: 0.9247 (tppt) cc_final: 0.8831 (tptt) REVERT: E 190 MET cc_start: 0.9084 (ptp) cc_final: 0.8739 (ptp) REVERT: G 27 MET cc_start: 0.8734 (mmm) cc_final: 0.8504 (mpp) outliers start: 35 outliers final: 29 residues processed: 241 average time/residue: 0.1901 time to fit residues: 63.6458 Evaluate side-chains 250 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 220 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 150 PHE Chi-restraints excluded: chain A residue 167 ASN Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 142 ASN Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 75 TRP Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 248 ASP Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 150 PHE Chi-restraints excluded: chain E residue 218 THR Chi-restraints excluded: chain E residue 248 ASP Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain G residue 21 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 53 optimal weight: 2.9990 chunk 78 optimal weight: 0.0170 chunk 118 optimal weight: 6.9990 chunk 109 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 72 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 74 optimal weight: 0.0870 chunk 100 optimal weight: 5.9990 chunk 28 optimal weight: 10.0000 overall best weight: 0.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 277 GLN ** D 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.3645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9340 Z= 0.196 Angle : 0.854 20.252 12657 Z= 0.409 Chirality : 0.045 0.255 1502 Planarity : 0.003 0.031 1642 Dihedral : 4.264 23.140 1320 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 18.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.21 % Allowed : 27.62 % Favored : 69.16 % 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: 1.27 (0.25), residues: 1208 helix: 1.42 (0.16), residues: 1027 sheet: None (None), residues: 0 loop : -2.47 (0.44), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 187 HIS 0.007 0.001 HIS C 274 PHE 0.049 0.002 PHE D 193 TYR 0.017 0.002 TYR A 232 ARG 0.004 0.000 ARG A 165 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 221 time to evaluate : 1.031 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: A 61 LYS cc_start: 0.9204 (pttp) cc_final: 0.8878 (tppt) REVERT: A 106 ASP cc_start: 0.8178 (m-30) cc_final: 0.7752 (p0) REVERT: A 126 ASN cc_start: 0.8751 (t0) cc_final: 0.8209 (p0) REVERT: A 140 ASP cc_start: 0.6844 (m-30) cc_final: 0.6376 (m-30) REVERT: A 190 MET cc_start: 0.8173 (ptp) cc_final: 0.7638 (ptp) REVERT: A 193 PHE cc_start: 0.9030 (m-10) cc_final: 0.8676 (m-10) REVERT: A 235 PHE cc_start: 0.9149 (m-80) cc_final: 0.8599 (m-80) REVERT: A 270 LYS cc_start: 0.6621 (mttt) cc_final: 0.6289 (tmtt) REVERT: B 81 LYS cc_start: 0.9313 (tppt) cc_final: 0.8806 (mttt) REVERT: B 85 LEU cc_start: 0.8874 (mt) cc_final: 0.8658 (pp) REVERT: B 163 MET cc_start: 0.8521 (mmm) cc_final: 0.8018 (mmm) REVERT: B 220 MET cc_start: 0.9072 (mtp) cc_final: 0.8785 (mtt) REVERT: B 270 LYS cc_start: 0.7507 (pttt) cc_final: 0.7086 (tptp) REVERT: C 113 GLN cc_start: 0.8097 (tm-30) cc_final: 0.7729 (tm-30) REVERT: C 169 PHE cc_start: 0.8976 (t80) cc_final: 0.8709 (t80) REVERT: C 232 TYR cc_start: 0.8115 (t80) cc_final: 0.7836 (t80) REVERT: C 233 ASN cc_start: 0.8351 (t0) cc_final: 0.7910 (t0) REVERT: C 277 GLN cc_start: 0.5780 (OUTLIER) cc_final: 0.5424 (pm20) REVERT: D 145 LYS cc_start: 0.9366 (mmtp) cc_final: 0.9098 (mmtm) REVERT: D 220 MET cc_start: 0.9220 (mmm) cc_final: 0.8697 (mpp) REVERT: E 190 MET cc_start: 0.9056 (ptp) cc_final: 0.8698 (ptp) REVERT: E 270 LYS cc_start: 0.7274 (pptt) cc_final: 0.6731 (pttt) REVERT: G 27 MET cc_start: 0.8720 (mmm) cc_final: 0.8487 (mpp) outliers start: 30 outliers final: 26 residues processed: 238 average time/residue: 0.2038 time to fit residues: 66.6562 Evaluate side-chains 245 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 218 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 150 PHE Chi-restraints excluded: chain A residue 167 ASN Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 142 ASN Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 75 TRP Chi-restraints excluded: chain C residue 191 ASN Chi-restraints excluded: chain C residue 248 ASP Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 150 PHE Chi-restraints excluded: chain E residue 218 THR Chi-restraints excluded: chain E residue 248 ASP Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain G residue 21 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 87 optimal weight: 9.9990 chunk 13 optimal weight: 5.9990 chunk 26 optimal weight: 0.7980 chunk 94 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 97 optimal weight: 10.0000 chunk 11 optimal weight: 8.9990 chunk 17 optimal weight: 6.9990 chunk 83 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 242 HIS ** C 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 277 GLN ** D 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.076365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.062855 restraints weight = 48455.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.064119 restraints weight = 35343.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.064983 restraints weight = 27552.170| |-----------------------------------------------------------------------------| r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.3763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9340 Z= 0.266 Angle : 0.902 18.634 12657 Z= 0.442 Chirality : 0.046 0.320 1502 Planarity : 0.006 0.163 1642 Dihedral : 4.488 24.372 1320 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 21.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 3.64 % Allowed : 27.73 % Favored : 68.63 % 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: 0.96 (0.25), residues: 1208 helix: 1.20 (0.16), residues: 1025 sheet: None (None), residues: 0 loop : -2.50 (0.44), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 50 HIS 0.007 0.001 HIS C 242 PHE 0.050 0.003 PHE D 193 TYR 0.018 0.002 TYR D 232 ARG 0.010 0.001 ARG E 155 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2018.29 seconds wall clock time: 36 minutes 58.32 seconds (2218.32 seconds total)