Starting phenix.real_space_refine on Fri Feb 16 14:19:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vnq_32045/02_2024/7vnq_32045_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vnq_32045/02_2024/7vnq_32045.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vnq_32045/02_2024/7vnq_32045.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vnq_32045/02_2024/7vnq_32045.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vnq_32045/02_2024/7vnq_32045_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vnq_32045/02_2024/7vnq_32045_trim_updated.pdb" } resolution = 2.96 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= 0.012 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: 5 Type Number sf(0) Gaussians K 3 8.98 5 S 88 5.16 5 C 9984 2.51 5 N 2656 2.21 5 O 2776 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 81": "NH1" <-> "NH2" Residue "A ARG 82": "NH1" <-> "NH2" Residue "A ARG 159": "NH1" <-> "NH2" Residue "A ARG 161": "NH1" <-> "NH2" Residue "A ARG 213": "NH1" <-> "NH2" Residue "A ARG 339": "NH1" <-> "NH2" Residue "A GLU 551": "OE1" <-> "OE2" Residue "A ARG 554": "NH1" <-> "NH2" Residue "A GLU 563": "OE1" <-> "OE2" Residue "A ARG 575": "NH1" <-> "NH2" Residue "B GLU 139": "OE1" <-> "OE2" Residue "C ARG 81": "NH1" <-> "NH2" Residue "C ARG 82": "NH1" <-> "NH2" Residue "C ARG 159": "NH1" <-> "NH2" Residue "C ARG 161": "NH1" <-> "NH2" Residue "C ARG 213": "NH1" <-> "NH2" Residue "C ARG 339": "NH1" <-> "NH2" Residue "C GLU 551": "OE1" <-> "OE2" Residue "C ARG 554": "NH1" <-> "NH2" Residue "C GLU 563": "OE1" <-> "OE2" Residue "D GLU 139": "OE1" <-> "OE2" Residue "E ARG 81": "NH1" <-> "NH2" Residue "E ARG 82": "NH1" <-> "NH2" Residue "E ARG 159": "NH1" <-> "NH2" Residue "E ARG 161": "NH1" <-> "NH2" Residue "E ARG 213": "NH1" <-> "NH2" Residue "E ARG 339": "NH1" <-> "NH2" Residue "E GLU 551": "OE1" <-> "OE2" Residue "E ARG 554": "NH1" <-> "NH2" Residue "E GLU 563": "OE1" <-> "OE2" Residue "F GLU 139": "OE1" <-> "OE2" Residue "G ARG 81": "NH1" <-> "NH2" Residue "G ARG 82": "NH1" <-> "NH2" Residue "G ARG 159": "NH1" <-> "NH2" Residue "G ARG 161": "NH1" <-> "NH2" Residue "G ARG 213": "NH1" <-> "NH2" Residue "G ARG 339": "NH1" <-> "NH2" Residue "G GLU 551": "OE1" <-> "OE2" Residue "G ARG 554": "NH1" <-> "NH2" Residue "G GLU 563": "OE1" <-> "OE2" Residue "H GLU 139": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 15507 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2747 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 6, 'TRANS': 332} Chain breaks: 2 Chain: "B" Number of atoms: 1110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1110 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 2, 'TRANS': 138} Chain: "C" Number of atoms: 2747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2747 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 6, 'TRANS': 332} Chain breaks: 2 Chain: "D" Number of atoms: 1110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1110 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 2, 'TRANS': 138} Chain: "E" Number of atoms: 2747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2747 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 6, 'TRANS': 332} Chain breaks: 2 Chain: "F" Number of atoms: 1110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1110 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 2, 'TRANS': 138} Chain: "G" Number of atoms: 2747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2747 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 6, 'TRANS': 332} Chain breaks: 2 Chain: "H" Number of atoms: 1110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1110 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 2, 'TRANS': 138} Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 22 Unusual residues: {' K': 3, '7YV': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 19 Unusual residues: {'7YV': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 19 Unusual residues: {'7YV': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 19 Unusual residues: {'7YV': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.73, per 1000 atoms: 0.50 Number of scatterers: 15507 At special positions: 0 Unit cell: (120.54, 120.54, 121.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) K 3 19.00 S 88 16.00 O 2776 8.00 N 2656 7.00 C 9984 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: 6.23 Conformation dependent library (CDL) restraints added in 2.7 seconds 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3576 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 88 helices and 4 sheets defined 72.9% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.72 Creating SS restraints... Processing helix chain 'A' and resid 75 through 95 removed outlier: 3.828A pdb=" N ARG A 93 " --> pdb=" O ASN A 89 " (cutoff:3.500A) Proline residue: A 94 - end of helix Processing helix chain 'A' and resid 98 through 120 Processing helix chain 'A' and resid 126 through 153 removed outlier: 3.627A pdb=" N ILE A 148 " --> pdb=" O GLY A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 168 Processing helix chain 'A' and resid 171 through 190 Processing helix chain 'A' and resid 200 through 216 Processing helix chain 'A' and resid 223 through 233 Processing helix chain 'A' and resid 235 through 260 Processing helix chain 'A' and resid 270 through 281 Processing helix chain 'A' and resid 294 through 307 removed outlier: 3.614A pdb=" N VAL A 298 " --> pdb=" O TRP A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 334 Proline residue: A 314 - end of helix Processing helix chain 'A' and resid 339 through 356 removed outlier: 4.330A pdb=" N ASP A 356 " --> pdb=" O LEU A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 550 Processing helix chain 'A' and resid 560 through 586 Processing helix chain 'B' and resid 8 through 19 removed outlier: 3.604A pdb=" N PHE B 19 " --> pdb=" O ALA B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 38 Processing helix chain 'B' and resid 45 through 54 Processing helix chain 'B' and resid 65 through 74 Processing helix chain 'B' and resid 79 through 92 removed outlier: 4.072A pdb=" N PHE B 92 " --> pdb=" O ALA B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 111 Processing helix chain 'B' and resid 118 through 127 Processing helix chain 'B' and resid 138 through 145 Processing helix chain 'C' and resid 75 through 95 removed outlier: 3.828A pdb=" N ARG C 93 " --> pdb=" O ASN C 89 " (cutoff:3.500A) Proline residue: C 94 - end of helix Processing helix chain 'C' and resid 98 through 120 Processing helix chain 'C' and resid 126 through 153 removed outlier: 3.627A pdb=" N ILE C 148 " --> pdb=" O GLY C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 168 Processing helix chain 'C' and resid 171 through 190 Processing helix chain 'C' and resid 200 through 216 Processing helix chain 'C' and resid 223 through 233 Processing helix chain 'C' and resid 235 through 260 Processing helix chain 'C' and resid 270 through 281 Processing helix chain 'C' and resid 294 through 307 removed outlier: 3.613A pdb=" N VAL C 298 " --> pdb=" O TRP C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 334 Proline residue: C 314 - end of helix Processing helix chain 'C' and resid 339 through 356 removed outlier: 4.329A pdb=" N ASP C 356 " --> pdb=" O LEU C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 533 through 550 Processing helix chain 'C' and resid 560 through 586 Processing helix chain 'D' and resid 8 through 19 removed outlier: 3.605A pdb=" N PHE D 19 " --> pdb=" O ALA D 15 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 38 Processing helix chain 'D' and resid 45 through 54 Processing helix chain 'D' and resid 65 through 74 Processing helix chain 'D' and resid 79 through 92 removed outlier: 4.072A pdb=" N PHE D 92 " --> pdb=" O ALA D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 111 Processing helix chain 'D' and resid 118 through 127 Processing helix chain 'D' and resid 138 through 145 Processing helix chain 'E' and resid 75 through 95 removed outlier: 3.828A pdb=" N ARG E 93 " --> pdb=" O ASN E 89 " (cutoff:3.500A) Proline residue: E 94 - end of helix Processing helix chain 'E' and resid 98 through 120 Processing helix chain 'E' and resid 126 through 153 removed outlier: 3.626A pdb=" N ILE E 148 " --> pdb=" O GLY E 144 " (cutoff:3.500A) Processing helix chain 'E' and resid 163 through 168 Processing helix chain 'E' and resid 171 through 190 Processing helix chain 'E' and resid 200 through 216 Processing helix chain 'E' and resid 223 through 233 Processing helix chain 'E' and resid 235 through 260 Processing helix chain 'E' and resid 270 through 281 Processing helix chain 'E' and resid 294 through 307 removed outlier: 3.613A pdb=" N VAL E 298 " --> pdb=" O TRP E 294 " (cutoff:3.500A) Processing helix chain 'E' and resid 310 through 334 Proline residue: E 314 - end of helix Processing helix chain 'E' and resid 339 through 356 removed outlier: 4.329A pdb=" N ASP E 356 " --> pdb=" O LEU E 352 " (cutoff:3.500A) Processing helix chain 'E' and resid 533 through 550 Processing helix chain 'E' and resid 560 through 586 Processing helix chain 'F' and resid 8 through 19 removed outlier: 3.604A pdb=" N PHE F 19 " --> pdb=" O ALA F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 38 Processing helix chain 'F' and resid 45 through 54 Processing helix chain 'F' and resid 65 through 74 Processing helix chain 'F' and resid 79 through 92 removed outlier: 4.073A pdb=" N PHE F 92 " --> pdb=" O ALA F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 111 Processing helix chain 'F' and resid 118 through 127 Processing helix chain 'F' and resid 138 through 145 Processing helix chain 'G' and resid 75 through 95 removed outlier: 3.829A pdb=" N ARG G 93 " --> pdb=" O ASN G 89 " (cutoff:3.500A) Proline residue: G 94 - end of helix Processing helix chain 'G' and resid 98 through 120 Processing helix chain 'G' and resid 126 through 153 removed outlier: 3.627A pdb=" N ILE G 148 " --> pdb=" O GLY G 144 " (cutoff:3.500A) Processing helix chain 'G' and resid 163 through 168 Processing helix chain 'G' and resid 171 through 190 Processing helix chain 'G' and resid 200 through 216 Processing helix chain 'G' and resid 223 through 233 Processing helix chain 'G' and resid 235 through 260 Processing helix chain 'G' and resid 270 through 281 Processing helix chain 'G' and resid 294 through 307 removed outlier: 3.612A pdb=" N VAL G 298 " --> pdb=" O TRP G 294 " (cutoff:3.500A) Processing helix chain 'G' and resid 310 through 334 Proline residue: G 314 - end of helix Processing helix chain 'G' and resid 339 through 356 removed outlier: 4.330A pdb=" N ASP G 356 " --> pdb=" O LEU G 352 " (cutoff:3.500A) Processing helix chain 'G' and resid 533 through 550 Processing helix chain 'G' and resid 560 through 586 Processing helix chain 'H' and resid 8 through 19 removed outlier: 3.605A pdb=" N PHE H 19 " --> pdb=" O ALA H 15 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 38 Processing helix chain 'H' and resid 45 through 54 Processing helix chain 'H' and resid 65 through 74 Processing helix chain 'H' and resid 79 through 92 removed outlier: 4.072A pdb=" N PHE H 92 " --> pdb=" O ALA H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 102 through 111 Processing helix chain 'H' and resid 118 through 127 Processing helix chain 'H' and resid 138 through 145 Processing sheet with id= A, first strand: chain 'B' and resid 99 through 101 Processing sheet with id= B, first strand: chain 'D' and resid 99 through 101 Processing sheet with id= C, first strand: chain 'F' and resid 99 through 101 Processing sheet with id= D, first strand: chain 'H' and resid 99 through 101 1016 hydrogen bonds defined for protein. 2844 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: 4.25 Time building geometry restraints manager: 6.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 2512 1.31 - 1.44: 4436 1.44 - 1.57: 8708 1.57 - 1.70: 20 1.70 - 1.82: 152 Bond restraints: 15828 Sorted by residual: bond pdb=" C04 7YV C1101 " pdb=" C05 7YV C1101 " ideal model delta sigma weight residual 1.531 1.336 0.195 2.00e-02 2.50e+03 9.53e+01 bond pdb=" C04 7YV A1101 " pdb=" C05 7YV A1101 " ideal model delta sigma weight residual 1.531 1.336 0.195 2.00e-02 2.50e+03 9.51e+01 bond pdb=" C04 7YV E1101 " pdb=" C05 7YV E1101 " ideal model delta sigma weight residual 1.531 1.336 0.195 2.00e-02 2.50e+03 9.50e+01 bond pdb=" C04 7YV G1101 " pdb=" C05 7YV G1101 " ideal model delta sigma weight residual 1.531 1.336 0.195 2.00e-02 2.50e+03 9.46e+01 bond pdb=" C03 7YV E1101 " pdb=" C05 7YV E1101 " ideal model delta sigma weight residual 1.531 1.347 0.184 2.00e-02 2.50e+03 8.46e+01 ... (remaining 15823 not shown) Histogram of bond angle deviations from ideal: 93.66 - 101.75: 50 101.75 - 109.83: 2150 109.83 - 117.92: 9542 117.92 - 126.00: 9386 126.00 - 134.09: 232 Bond angle restraints: 21360 Sorted by residual: angle pdb=" N LEU A 553 " pdb=" CA LEU A 553 " pdb=" C LEU A 553 " ideal model delta sigma weight residual 113.72 104.62 9.10 1.30e+00 5.92e-01 4.90e+01 angle pdb=" N LEU C 553 " pdb=" CA LEU C 553 " pdb=" C LEU C 553 " ideal model delta sigma weight residual 113.72 104.65 9.07 1.30e+00 5.92e-01 4.87e+01 angle pdb=" N LEU G 553 " pdb=" CA LEU G 553 " pdb=" C LEU G 553 " ideal model delta sigma weight residual 113.72 104.66 9.06 1.30e+00 5.92e-01 4.86e+01 angle pdb=" N LEU E 553 " pdb=" CA LEU E 553 " pdb=" C LEU E 553 " ideal model delta sigma weight residual 113.72 104.66 9.06 1.30e+00 5.92e-01 4.85e+01 angle pdb=" N CYS A 175 " pdb=" CA CYS A 175 " pdb=" C CYS A 175 " ideal model delta sigma weight residual 111.36 104.74 6.62 1.09e+00 8.42e-01 3.69e+01 ... (remaining 21355 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.62: 8285 17.62 - 35.23: 766 35.23 - 52.85: 255 52.85 - 70.47: 66 70.47 - 88.08: 8 Dihedral angle restraints: 9380 sinusoidal: 3840 harmonic: 5540 Sorted by residual: dihedral pdb=" CA LEU G 553 " pdb=" C LEU G 553 " pdb=" N ARG G 554 " pdb=" CA ARG G 554 " ideal model delta harmonic sigma weight residual 180.00 152.72 27.28 0 5.00e+00 4.00e-02 2.98e+01 dihedral pdb=" CA LEU C 553 " pdb=" C LEU C 553 " pdb=" N ARG C 554 " pdb=" CA ARG C 554 " ideal model delta harmonic sigma weight residual 180.00 152.74 27.26 0 5.00e+00 4.00e-02 2.97e+01 dihedral pdb=" CA LEU E 553 " pdb=" C LEU E 553 " pdb=" N ARG E 554 " pdb=" CA ARG E 554 " ideal model delta harmonic sigma weight residual 180.00 152.75 27.25 0 5.00e+00 4.00e-02 2.97e+01 ... (remaining 9377 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 2209 0.111 - 0.222: 143 0.222 - 0.334: 4 0.334 - 0.445: 0 0.445 - 0.556: 8 Chirality restraints: 2364 Sorted by residual: chirality pdb=" C03 7YV A1101 " pdb=" C05 7YV A1101 " pdb=" C06 7YV A1101 " pdb=" C08 7YV A1101 " both_signs ideal model delta sigma weight residual False -3.26 -2.71 -0.56 2.00e-01 2.50e+01 7.72e+00 chirality pdb=" C03 7YV G1101 " pdb=" C05 7YV G1101 " pdb=" C06 7YV G1101 " pdb=" C08 7YV G1101 " both_signs ideal model delta sigma weight residual False -3.26 -2.71 -0.55 2.00e-01 2.50e+01 7.66e+00 chirality pdb=" C03 7YV E1101 " pdb=" C05 7YV E1101 " pdb=" C06 7YV E1101 " pdb=" C08 7YV E1101 " both_signs ideal model delta sigma weight residual False -3.26 -2.71 -0.55 2.00e-01 2.50e+01 7.64e+00 ... (remaining 2361 not shown) Planarity restraints: 2692 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS E 172 " 0.069 5.00e-02 4.00e+02 1.04e-01 1.73e+01 pdb=" N PRO E 173 " -0.180 5.00e-02 4.00e+02 pdb=" CA PRO E 173 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO E 173 " 0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS G 172 " -0.069 5.00e-02 4.00e+02 1.04e-01 1.73e+01 pdb=" N PRO G 173 " 0.180 5.00e-02 4.00e+02 pdb=" CA PRO G 173 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO G 173 " -0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 172 " -0.069 5.00e-02 4.00e+02 1.04e-01 1.73e+01 pdb=" N PRO A 173 " 0.180 5.00e-02 4.00e+02 pdb=" CA PRO A 173 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO A 173 " -0.057 5.00e-02 4.00e+02 ... (remaining 2689 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.79: 4100 2.79 - 3.38: 18838 3.38 - 3.97: 30253 3.97 - 4.55: 42405 4.55 - 5.14: 59290 Nonbonded interactions: 154886 Sorted by model distance: nonbonded pdb=" O THR G 282 " pdb=" OG1 THR G 283 " model vdw 2.207 2.440 nonbonded pdb=" O THR E 282 " pdb=" OG1 THR E 283 " model vdw 2.208 2.440 nonbonded pdb=" O THR C 282 " pdb=" OG1 THR C 283 " model vdw 2.208 2.440 nonbonded pdb=" O THR A 282 " pdb=" OG1 THR A 283 " model vdw 2.208 2.440 nonbonded pdb=" OG1 THR H 28 " pdb=" OE1 GLU H 31 " model vdw 2.217 2.440 ... (remaining 154881 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 74 through 588 or resid 1101)) selection = chain 'C' selection = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 2.190 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: 7.810 Check model and map are aligned: 0.220 Set scattering table: 0.160 Process input model: 42.290 Find NCS groups from input model: 1.040 Set up NCS constraints: 0.100 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:10.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4509 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 : 0.010 0.195 15828 Z= 0.628 Angle : 1.024 9.425 21360 Z= 0.645 Chirality : 0.064 0.556 2364 Planarity : 0.007 0.104 2692 Dihedral : 15.831 88.083 5804 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.72 % Favored : 93.86 % Rotamer: Outliers : 6.90 % Allowed : 7.27 % Favored : 85.84 % 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: -1.00 (0.18), residues: 1888 helix: -0.48 (0.12), residues: 1536 sheet: None (None), residues: 0 loop : -0.69 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP E 86 HIS 0.006 0.002 HIS G 292 PHE 0.030 0.003 PHE A 169 TYR 0.016 0.002 TYR G 101 ARG 0.008 0.001 ARG E 351 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 420 time to evaluate : 2.376 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: A 86 TRP cc_start: 0.8392 (m100) cc_final: 0.7999 (m-90) REVERT: A 104 PHE cc_start: 0.8742 (OUTLIER) cc_final: 0.8327 (t80) REVERT: A 146 GLU cc_start: 0.8812 (mm-30) cc_final: 0.8593 (mm-30) REVERT: C 104 PHE cc_start: 0.8715 (OUTLIER) cc_final: 0.8365 (t80) REVERT: C 329 GLN cc_start: 0.8811 (pt0) cc_final: 0.8364 (pp30) REVERT: C 330 HIS cc_start: 0.8497 (m90) cc_final: 0.8254 (m90) REVERT: C 333 LYS cc_start: 0.9606 (pptt) cc_final: 0.9327 (pptt) REVERT: E 104 PHE cc_start: 0.8731 (OUTLIER) cc_final: 0.8394 (t80) REVERT: E 333 LYS cc_start: 0.9629 (pptt) cc_final: 0.9424 (pptt) REVERT: G 86 TRP cc_start: 0.8449 (m100) cc_final: 0.7872 (m-90) REVERT: G 104 PHE cc_start: 0.8717 (OUTLIER) cc_final: 0.8259 (t80) REVERT: G 146 GLU cc_start: 0.8754 (mm-30) cc_final: 0.8544 (mm-30) outliers start: 112 outliers final: 16 residues processed: 483 average time/residue: 1.4506 time to fit residues: 760.1720 Evaluate side-chains 257 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 237 time to evaluate : 1.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 104 PHE Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 559 LYS Chi-restraints excluded: chain A residue 575 ARG Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 104 PHE Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 559 LYS Chi-restraints excluded: chain C residue 575 ARG Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 104 PHE Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 559 LYS Chi-restraints excluded: chain G residue 87 VAL Chi-restraints excluded: chain G residue 104 PHE Chi-restraints excluded: chain G residue 212 LEU Chi-restraints excluded: chain G residue 554 ARG Chi-restraints excluded: chain G residue 559 LYS Chi-restraints excluded: chain G residue 575 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 158 optimal weight: 0.9990 chunk 142 optimal weight: 20.0000 chunk 79 optimal weight: 10.0000 chunk 48 optimal weight: 7.9990 chunk 96 optimal weight: 5.9990 chunk 76 optimal weight: 10.0000 chunk 147 optimal weight: 6.9990 chunk 57 optimal weight: 5.9990 chunk 89 optimal weight: 40.0000 chunk 109 optimal weight: 0.9990 chunk 170 optimal weight: 1.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 344 ASN ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 107 HIS C 344 ASN ** D 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 344 ASN ** F 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4682 moved from start: 0.4036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 15828 Z= 0.331 Angle : 0.766 12.052 21360 Z= 0.391 Chirality : 0.042 0.157 2364 Planarity : 0.006 0.101 2692 Dihedral : 7.099 58.635 2240 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 19.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 6.59 % Allowed : 16.13 % Favored : 77.28 % 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: 0.81 (0.19), residues: 1888 helix: 0.75 (0.13), residues: 1508 sheet: None (None), residues: 0 loop : 0.13 (0.37), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 294 HIS 0.005 0.001 HIS E 102 PHE 0.020 0.002 PHE E 169 TYR 0.017 0.002 TYR E 147 ARG 0.010 0.001 ARG C 547 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 260 time to evaluate : 1.702 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: A 139 MET cc_start: 0.7695 (OUTLIER) cc_final: 0.7226 (tmm) REVERT: A 207 ARG cc_start: 0.8267 (mtt180) cc_final: 0.7983 (mtp180) REVERT: A 217 MET cc_start: 0.5517 (ppp) cc_final: 0.4168 (ppp) REVERT: A 220 ARG cc_start: 0.7759 (OUTLIER) cc_final: 0.7158 (ptp90) REVERT: B 18 LEU cc_start: -0.0018 (OUTLIER) cc_final: -0.0333 (tm) REVERT: C 104 PHE cc_start: 0.8788 (OUTLIER) cc_final: 0.8429 (t80) REVERT: C 139 MET cc_start: 0.7519 (OUTLIER) cc_final: 0.7112 (tmm) REVERT: C 182 PHE cc_start: 0.7586 (t80) cc_final: 0.7311 (t80) REVERT: C 207 ARG cc_start: 0.8234 (mtt180) cc_final: 0.7614 (mtp-110) REVERT: C 220 ARG cc_start: 0.7703 (OUTLIER) cc_final: 0.7141 (pmm150) REVERT: C 243 TYR cc_start: 0.8642 (t80) cc_final: 0.8423 (t80) REVERT: C 328 GLU cc_start: 0.8662 (tm-30) cc_final: 0.8455 (tm-30) REVERT: D 18 LEU cc_start: 0.0624 (OUTLIER) cc_final: 0.0353 (tm) REVERT: E 104 PHE cc_start: 0.8777 (OUTLIER) cc_final: 0.8449 (t80) REVERT: E 139 MET cc_start: 0.7686 (OUTLIER) cc_final: 0.7203 (tmm) REVERT: E 220 ARG cc_start: 0.7647 (OUTLIER) cc_final: 0.7090 (pmm150) REVERT: E 243 TYR cc_start: 0.8598 (t80) cc_final: 0.8393 (t80) REVERT: E 328 GLU cc_start: 0.8646 (tm-30) cc_final: 0.8409 (tm-30) REVERT: F 18 LEU cc_start: 0.0747 (OUTLIER) cc_final: 0.0210 (tm) REVERT: G 182 PHE cc_start: 0.7437 (t80) cc_final: 0.7224 (t80) REVERT: G 207 ARG cc_start: 0.8217 (mtt180) cc_final: 0.7791 (mtp-110) REVERT: G 220 ARG cc_start: 0.7830 (OUTLIER) cc_final: 0.7397 (pmm150) REVERT: G 243 TYR cc_start: 0.8603 (t80) cc_final: 0.8341 (t80) outliers start: 107 outliers final: 40 residues processed: 332 average time/residue: 1.3431 time to fit residues: 489.5020 Evaluate side-chains 260 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 208 time to evaluate : 1.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 104 PHE Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 220 ARG Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 550 LYS Chi-restraints excluded: chain A residue 569 HIS Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 95 ASP Chi-restraints excluded: chain B residue 107 HIS Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 104 PHE Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 139 MET Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 220 ARG Chi-restraints excluded: chain C residue 559 LYS Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 95 ASP Chi-restraints excluded: chain D residue 107 HIS Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 104 PHE Chi-restraints excluded: chain E residue 111 SER Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 139 MET Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 220 ARG Chi-restraints excluded: chain E residue 559 LYS Chi-restraints excluded: chain E residue 569 HIS Chi-restraints excluded: chain E residue 587 VAL Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain F residue 95 ASP Chi-restraints excluded: chain F residue 107 HIS Chi-restraints excluded: chain G residue 87 VAL Chi-restraints excluded: chain G residue 111 SER Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 212 LEU Chi-restraints excluded: chain G residue 220 ARG Chi-restraints excluded: chain G residue 559 LYS Chi-restraints excluded: chain G residue 575 ARG Chi-restraints excluded: chain G residue 587 VAL Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 95 ASP Chi-restraints excluded: chain H residue 107 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 94 optimal weight: 40.0000 chunk 52 optimal weight: 8.9990 chunk 142 optimal weight: 0.8980 chunk 116 optimal weight: 0.8980 chunk 47 optimal weight: 40.0000 chunk 171 optimal weight: 9.9990 chunk 184 optimal weight: 20.0000 chunk 152 optimal weight: 40.0000 chunk 169 optimal weight: 30.0000 chunk 58 optimal weight: 30.0000 chunk 137 optimal weight: 3.9990 overall best weight: 4.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 HIS ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 107 HIS C 569 HIS ** D 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 143 GLN G 124 HIS ** H 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4773 moved from start: 0.5143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 15828 Z= 0.453 Angle : 0.778 11.545 21360 Z= 0.398 Chirality : 0.043 0.147 2364 Planarity : 0.006 0.096 2692 Dihedral : 6.725 59.474 2222 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 24.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 5.97 % Allowed : 21.12 % Favored : 72.91 % 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: 0.72 (0.19), residues: 1888 helix: 0.73 (0.13), residues: 1544 sheet: None (None), residues: 0 loop : -0.23 (0.37), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 294 HIS 0.014 0.002 HIS B 107 PHE 0.032 0.002 PHE B 89 TYR 0.021 0.002 TYR C 147 ARG 0.008 0.001 ARG F 106 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 228 time to evaluate : 1.906 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: A 104 PHE cc_start: 0.8829 (t80) cc_final: 0.8535 (t80) REVERT: A 139 MET cc_start: 0.7626 (OUTLIER) cc_final: 0.7325 (tmm) REVERT: A 182 PHE cc_start: 0.7416 (t80) cc_final: 0.7148 (t80) REVERT: A 207 ARG cc_start: 0.8058 (mtt180) cc_final: 0.7498 (mtp-110) REVERT: A 219 ARG cc_start: 0.8892 (ttm110) cc_final: 0.8641 (tmm-80) REVERT: B 18 LEU cc_start: -0.0073 (OUTLIER) cc_final: -0.0546 (tm) REVERT: B 85 ILE cc_start: 0.1016 (mm) cc_final: 0.0622 (mt) REVERT: C 104 PHE cc_start: 0.8813 (t80) cc_final: 0.8540 (t80) REVERT: C 182 PHE cc_start: 0.7364 (OUTLIER) cc_final: 0.7130 (t80) REVERT: C 207 ARG cc_start: 0.8103 (mtt180) cc_final: 0.7511 (mtp-110) REVERT: C 219 ARG cc_start: 0.8008 (mpp-170) cc_final: 0.7632 (mtm-85) REVERT: C 220 ARG cc_start: 0.8277 (OUTLIER) cc_final: 0.7707 (pmm150) REVERT: C 328 GLU cc_start: 0.8778 (tm-30) cc_final: 0.8470 (tm-30) REVERT: D 18 LEU cc_start: 0.0528 (OUTLIER) cc_final: 0.0261 (tm) REVERT: D 144 MET cc_start: 0.4603 (pp-130) cc_final: 0.4178 (ptt) REVERT: E 104 PHE cc_start: 0.8793 (t80) cc_final: 0.8534 (t80) REVERT: E 217 MET cc_start: 0.5707 (ppp) cc_final: 0.4939 (ppp) REVERT: E 219 ARG cc_start: 0.7930 (mpp-170) cc_final: 0.7605 (ttm110) REVERT: E 220 ARG cc_start: 0.8292 (OUTLIER) cc_final: 0.7937 (pmm150) REVERT: E 243 TYR cc_start: 0.8654 (t80) cc_final: 0.8439 (t80) REVERT: E 328 GLU cc_start: 0.8767 (tm-30) cc_final: 0.8466 (tm-30) REVERT: F 18 LEU cc_start: 0.0695 (OUTLIER) cc_final: 0.0441 (tm) REVERT: F 76 MET cc_start: 0.0055 (ptt) cc_final: -0.0421 (pmt) REVERT: F 144 MET cc_start: 0.4588 (ppp) cc_final: 0.3878 (ptt) REVERT: F 145 MET cc_start: 0.1807 (ttp) cc_final: 0.1161 (tmm) REVERT: G 139 MET cc_start: 0.7685 (OUTLIER) cc_final: 0.6812 (tmm) REVERT: G 182 PHE cc_start: 0.7219 (OUTLIER) cc_final: 0.6955 (t80) REVERT: G 207 ARG cc_start: 0.7998 (mtt180) cc_final: 0.7488 (mtp-110) REVERT: G 220 ARG cc_start: 0.8298 (OUTLIER) cc_final: 0.7797 (pmm150) REVERT: H 72 MET cc_start: 0.2452 (tpt) cc_final: 0.2231 (pp-130) outliers start: 97 outliers final: 50 residues processed: 296 average time/residue: 1.3356 time to fit residues: 432.9715 Evaluate side-chains 253 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 193 time to evaluate : 1.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 559 LYS Chi-restraints excluded: chain A residue 564 GLN Chi-restraints excluded: chain A residue 569 HIS Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 95 ASP Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 182 PHE Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 220 ARG Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 95 ASP Chi-restraints excluded: chain D residue 107 HIS Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 111 SER Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 220 ARG Chi-restraints excluded: chain E residue 559 LYS Chi-restraints excluded: chain E residue 569 HIS Chi-restraints excluded: chain E residue 587 VAL Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain F residue 95 ASP Chi-restraints excluded: chain F residue 107 HIS Chi-restraints excluded: chain F residue 126 ARG Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain G residue 87 VAL Chi-restraints excluded: chain G residue 111 SER Chi-restraints excluded: chain G residue 120 THR Chi-restraints excluded: chain G residue 137 PHE Chi-restraints excluded: chain G residue 139 MET Chi-restraints excluded: chain G residue 182 PHE Chi-restraints excluded: chain G residue 212 LEU Chi-restraints excluded: chain G residue 220 ARG Chi-restraints excluded: chain G residue 239 ILE Chi-restraints excluded: chain G residue 359 ARG Chi-restraints excluded: chain G residue 569 HIS Chi-restraints excluded: chain G residue 571 ASP Chi-restraints excluded: chain G residue 587 VAL Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 95 ASP Chi-restraints excluded: chain H residue 107 HIS Chi-restraints excluded: chain H residue 136 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 168 optimal weight: 20.0000 chunk 128 optimal weight: 4.9990 chunk 88 optimal weight: 30.0000 chunk 18 optimal weight: 0.8980 chunk 81 optimal weight: 7.9990 chunk 114 optimal weight: 1.9990 chunk 171 optimal weight: 5.9990 chunk 181 optimal weight: 8.9990 chunk 89 optimal weight: 30.0000 chunk 162 optimal weight: 0.8980 chunk 48 optimal weight: 20.0000 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 GLN ** D 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 111 ASN D 143 GLN ** F 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 344 ASN ** H 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4739 moved from start: 0.5606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 15828 Z= 0.301 Angle : 0.713 11.836 21360 Z= 0.358 Chirality : 0.040 0.154 2364 Planarity : 0.005 0.087 2692 Dihedral : 6.008 57.947 2204 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 20.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 6.71 % Allowed : 20.94 % Favored : 72.35 % 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: 0.94 (0.19), residues: 1888 helix: 0.91 (0.13), residues: 1540 sheet: None (None), residues: 0 loop : -0.25 (0.37), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 350 HIS 0.004 0.001 HIS G 102 PHE 0.029 0.002 PHE B 89 TYR 0.020 0.002 TYR A 147 ARG 0.005 0.000 ARG C 575 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 249 time to evaluate : 1.689 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: A 104 PHE cc_start: 0.8805 (t80) cc_final: 0.8487 (t80) REVERT: A 139 MET cc_start: 0.7608 (OUTLIER) cc_final: 0.7300 (tmm) REVERT: A 182 PHE cc_start: 0.7422 (t80) cc_final: 0.7207 (t80) REVERT: A 207 ARG cc_start: 0.8073 (mtt180) cc_final: 0.7594 (mtp-110) REVERT: B 18 LEU cc_start: 0.0168 (OUTLIER) cc_final: -0.0526 (tm) REVERT: B 72 MET cc_start: 0.3479 (tmm) cc_final: 0.2868 (pp-130) REVERT: B 85 ILE cc_start: 0.1130 (mm) cc_final: 0.0918 (mt) REVERT: C 104 PHE cc_start: 0.8743 (t80) cc_final: 0.8472 (t80) REVERT: C 139 MET cc_start: 0.7706 (OUTLIER) cc_final: 0.6872 (tmm) REVERT: C 182 PHE cc_start: 0.7330 (OUTLIER) cc_final: 0.7105 (t80) REVERT: C 207 ARG cc_start: 0.8063 (mtt180) cc_final: 0.7585 (mtp-110) REVERT: C 220 ARG cc_start: 0.8153 (OUTLIER) cc_final: 0.7781 (pmm150) REVERT: C 328 GLU cc_start: 0.8771 (tm-30) cc_final: 0.8492 (tm-30) REVERT: D 18 LEU cc_start: 0.0482 (OUTLIER) cc_final: 0.0195 (tm) REVERT: D 144 MET cc_start: 0.3810 (OUTLIER) cc_final: 0.3553 (ptt) REVERT: E 104 PHE cc_start: 0.8731 (t80) cc_final: 0.8486 (t80) REVERT: E 139 MET cc_start: 0.7752 (OUTLIER) cc_final: 0.6907 (tmm) REVERT: E 328 GLU cc_start: 0.8785 (tm-30) cc_final: 0.8498 (tm-30) REVERT: F 18 LEU cc_start: 0.0740 (OUTLIER) cc_final: 0.0515 (tm) REVERT: F 76 MET cc_start: 0.0392 (ptt) cc_final: -0.0044 (pmt) REVERT: G 139 MET cc_start: 0.7731 (OUTLIER) cc_final: 0.6822 (tmm) REVERT: G 182 PHE cc_start: 0.7334 (OUTLIER) cc_final: 0.7103 (t80) REVERT: G 207 ARG cc_start: 0.7995 (mtt180) cc_final: 0.7574 (mtp-110) REVERT: G 219 ARG cc_start: 0.7667 (mtm-85) cc_final: 0.7411 (mtm-85) REVERT: G 328 GLU cc_start: 0.8860 (tm-30) cc_final: 0.8643 (tm-30) outliers start: 109 outliers final: 51 residues processed: 322 average time/residue: 1.3179 time to fit residues: 464.4482 Evaluate side-chains 270 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 208 time to evaluate : 1.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 137 PHE Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 559 LYS Chi-restraints excluded: chain A residue 564 GLN Chi-restraints excluded: chain A residue 569 HIS Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 95 ASP Chi-restraints excluded: chain B residue 99 TYR Chi-restraints excluded: chain B residue 107 HIS Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 137 PHE Chi-restraints excluded: chain C residue 139 MET Chi-restraints excluded: chain C residue 174 PHE Chi-restraints excluded: chain C residue 182 PHE Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 220 ARG Chi-restraints excluded: chain C residue 569 HIS Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 95 ASP Chi-restraints excluded: chain D residue 107 HIS Chi-restraints excluded: chain D residue 144 MET Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 111 SER Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 137 PHE Chi-restraints excluded: chain E residue 139 MET Chi-restraints excluded: chain E residue 174 PHE Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 569 HIS Chi-restraints excluded: chain E residue 587 VAL Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain F residue 95 ASP Chi-restraints excluded: chain F residue 107 HIS Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain G residue 87 VAL Chi-restraints excluded: chain G residue 111 SER Chi-restraints excluded: chain G residue 120 THR Chi-restraints excluded: chain G residue 137 PHE Chi-restraints excluded: chain G residue 139 MET Chi-restraints excluded: chain G residue 174 PHE Chi-restraints excluded: chain G residue 182 PHE Chi-restraints excluded: chain G residue 212 LEU Chi-restraints excluded: chain G residue 359 ARG Chi-restraints excluded: chain G residue 569 HIS Chi-restraints excluded: chain G residue 587 VAL Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 95 ASP Chi-restraints excluded: chain H residue 99 TYR Chi-restraints excluded: chain H residue 107 HIS Chi-restraints excluded: chain H residue 136 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 151 optimal weight: 9.9990 chunk 103 optimal weight: 7.9990 chunk 2 optimal weight: 4.9990 chunk 135 optimal weight: 6.9990 chunk 74 optimal weight: 20.0000 chunk 155 optimal weight: 3.9990 chunk 125 optimal weight: 4.9990 chunk 0 optimal weight: 50.0000 chunk 92 optimal weight: 3.9990 chunk 163 optimal weight: 0.9980 chunk 45 optimal weight: 4.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 124 HIS ** D 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 124 HIS ** F 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 143 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4782 moved from start: 0.6149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 15828 Z= 0.368 Angle : 0.763 14.738 21360 Z= 0.381 Chirality : 0.042 0.148 2364 Planarity : 0.005 0.073 2692 Dihedral : 6.019 59.174 2200 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 21.39 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.87 % Favored : 95.07 % Rotamer: Outliers : 6.59 % Allowed : 23.46 % Favored : 69.95 % 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: 0.77 (0.19), residues: 1888 helix: 0.88 (0.13), residues: 1528 sheet: None (None), residues: 0 loop : -0.76 (0.35), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 350 HIS 0.005 0.001 HIS G 102 PHE 0.022 0.002 PHE D 12 TYR 0.020 0.002 TYR G 147 ARG 0.011 0.001 ARG G 547 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 215 time to evaluate : 1.757 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 104 PHE cc_start: 0.8770 (t80) cc_final: 0.8478 (t80) REVERT: A 139 MET cc_start: 0.7675 (mtp) cc_final: 0.7394 (tmm) REVERT: A 207 ARG cc_start: 0.7953 (mtt180) cc_final: 0.7581 (mtp-110) REVERT: C 104 PHE cc_start: 0.8728 (t80) cc_final: 0.8467 (t80) REVERT: C 139 MET cc_start: 0.7794 (OUTLIER) cc_final: 0.6898 (tmm) REVERT: C 182 PHE cc_start: 0.7369 (OUTLIER) cc_final: 0.7150 (t80) REVERT: C 207 ARG cc_start: 0.7997 (mtt180) cc_final: 0.7591 (mtp-110) REVERT: C 218 ASP cc_start: 0.7563 (OUTLIER) cc_final: 0.7310 (t0) REVERT: D 18 LEU cc_start: 0.0422 (OUTLIER) cc_final: 0.0124 (tm) REVERT: E 104 PHE cc_start: 0.8734 (t80) cc_final: 0.8474 (t80) REVERT: E 139 MET cc_start: 0.7779 (OUTLIER) cc_final: 0.6916 (tmm) REVERT: E 214 MET cc_start: 0.8005 (tpt) cc_final: 0.7566 (tpt) REVERT: E 218 ASP cc_start: 0.7271 (OUTLIER) cc_final: 0.7029 (m-30) REVERT: F 76 MET cc_start: 0.0345 (ptt) cc_final: 0.0054 (pmt) REVERT: G 139 MET cc_start: 0.7808 (OUTLIER) cc_final: 0.6904 (tmm) REVERT: G 182 PHE cc_start: 0.7310 (OUTLIER) cc_final: 0.7109 (t80) REVERT: G 207 ARG cc_start: 0.7940 (mtt180) cc_final: 0.7576 (mtp-110) REVERT: G 217 MET cc_start: 0.8198 (tpp) cc_final: 0.7819 (tpp) REVERT: G 556 TYR cc_start: 0.4327 (OUTLIER) cc_final: 0.3786 (p90) REVERT: H 72 MET cc_start: 0.3520 (tpt) cc_final: 0.3194 (pp-130) outliers start: 107 outliers final: 53 residues processed: 292 average time/residue: 1.1872 time to fit residues: 383.9854 Evaluate side-chains 256 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 194 time to evaluate : 1.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 137 PHE Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 550 LYS Chi-restraints excluded: chain A residue 559 LYS Chi-restraints excluded: chain A residue 564 GLN Chi-restraints excluded: chain A residue 569 HIS Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 95 ASP Chi-restraints excluded: chain B residue 107 HIS Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 137 PHE Chi-restraints excluded: chain C residue 139 MET Chi-restraints excluded: chain C residue 174 PHE Chi-restraints excluded: chain C residue 182 PHE Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 569 HIS Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 95 ASP Chi-restraints excluded: chain D residue 107 HIS Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 111 SER Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 137 PHE Chi-restraints excluded: chain E residue 139 MET Chi-restraints excluded: chain E residue 174 PHE Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 218 ASP Chi-restraints excluded: chain E residue 239 ILE Chi-restraints excluded: chain E residue 569 HIS Chi-restraints excluded: chain E residue 587 VAL Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain F residue 95 ASP Chi-restraints excluded: chain F residue 107 HIS Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain G residue 87 VAL Chi-restraints excluded: chain G residue 111 SER Chi-restraints excluded: chain G residue 120 THR Chi-restraints excluded: chain G residue 137 PHE Chi-restraints excluded: chain G residue 139 MET Chi-restraints excluded: chain G residue 182 PHE Chi-restraints excluded: chain G residue 212 LEU Chi-restraints excluded: chain G residue 239 ILE Chi-restraints excluded: chain G residue 359 ARG Chi-restraints excluded: chain G residue 556 TYR Chi-restraints excluded: chain G residue 569 HIS Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 95 ASP Chi-restraints excluded: chain H residue 99 TYR Chi-restraints excluded: chain H residue 107 HIS Chi-restraints excluded: chain H residue 136 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 61 optimal weight: 6.9990 chunk 163 optimal weight: 0.9980 chunk 35 optimal weight: 5.9990 chunk 106 optimal weight: 8.9990 chunk 44 optimal weight: 6.9990 chunk 181 optimal weight: 9.9990 chunk 150 optimal weight: 7.9990 chunk 84 optimal weight: 7.9990 chunk 15 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 chunk 95 optimal weight: 8.9990 overall best weight: 3.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 330 HIS ** D 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4776 moved from start: 0.6591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 15828 Z= 0.322 Angle : 0.765 11.763 21360 Z= 0.382 Chirality : 0.042 0.172 2364 Planarity : 0.005 0.076 2692 Dihedral : 5.915 59.669 2200 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 20.97 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.87 % Favored : 94.97 % Rotamer: Outliers : 5.36 % Allowed : 25.49 % Favored : 69.15 % 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: 0.73 (0.19), residues: 1888 helix: 0.87 (0.13), residues: 1524 sheet: None (None), residues: 0 loop : -0.84 (0.34), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 350 HIS 0.005 0.001 HIS G 102 PHE 0.021 0.002 PHE H 68 TYR 0.019 0.001 TYR B 99 ARG 0.008 0.001 ARG A 554 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 229 time to evaluate : 2.161 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: A 104 PHE cc_start: 0.8741 (t80) cc_final: 0.8446 (t80) REVERT: A 207 ARG cc_start: 0.7967 (mtt180) cc_final: 0.7663 (mtp-110) REVERT: A 218 ASP cc_start: 0.7516 (OUTLIER) cc_final: 0.7130 (m-30) REVERT: B 72 MET cc_start: 0.3325 (tpt) cc_final: 0.3071 (tpt) REVERT: C 104 PHE cc_start: 0.8710 (t80) cc_final: 0.8473 (t80) REVERT: C 139 MET cc_start: 0.7791 (OUTLIER) cc_final: 0.6934 (tmm) REVERT: C 207 ARG cc_start: 0.7960 (mtt180) cc_final: 0.7597 (mtp-110) REVERT: D 18 LEU cc_start: 0.0538 (OUTLIER) cc_final: 0.0210 (tm) REVERT: D 72 MET cc_start: 0.3627 (tpt) cc_final: 0.3372 (tpt) REVERT: E 104 PHE cc_start: 0.8736 (t80) cc_final: 0.8492 (t80) REVERT: E 139 MET cc_start: 0.7786 (OUTLIER) cc_final: 0.6932 (tmm) REVERT: E 212 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8769 (mm) REVERT: F 76 MET cc_start: 0.0544 (ptt) cc_final: 0.0149 (pmt) REVERT: F 124 MET cc_start: 0.5075 (ppp) cc_final: 0.4845 (ppp) REVERT: G 139 MET cc_start: 0.7809 (OUTLIER) cc_final: 0.6926 (tmm) REVERT: G 207 ARG cc_start: 0.7898 (mtt180) cc_final: 0.7573 (mtp-110) REVERT: G 556 TYR cc_start: 0.4316 (OUTLIER) cc_final: 0.3977 (p90) REVERT: H 72 MET cc_start: 0.3689 (tpt) cc_final: 0.3478 (pp-130) outliers start: 87 outliers final: 45 residues processed: 289 average time/residue: 1.3289 time to fit residues: 423.2645 Evaluate side-chains 248 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 196 time to evaluate : 1.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 137 PHE Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 550 LYS Chi-restraints excluded: chain A residue 559 LYS Chi-restraints excluded: chain A residue 564 GLN Chi-restraints excluded: chain A residue 569 HIS Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 95 ASP Chi-restraints excluded: chain B residue 99 TYR Chi-restraints excluded: chain B residue 107 HIS Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 137 PHE Chi-restraints excluded: chain C residue 139 MET Chi-restraints excluded: chain C residue 338 ARG Chi-restraints excluded: chain C residue 569 HIS Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 95 ASP Chi-restraints excluded: chain D residue 99 TYR Chi-restraints excluded: chain D residue 107 HIS Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 111 SER Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 137 PHE Chi-restraints excluded: chain E residue 139 MET Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 569 HIS Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain F residue 95 ASP Chi-restraints excluded: chain F residue 107 HIS Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain G residue 87 VAL Chi-restraints excluded: chain G residue 111 SER Chi-restraints excluded: chain G residue 120 THR Chi-restraints excluded: chain G residue 137 PHE Chi-restraints excluded: chain G residue 139 MET Chi-restraints excluded: chain G residue 212 LEU Chi-restraints excluded: chain G residue 359 ARG Chi-restraints excluded: chain G residue 556 TYR Chi-restraints excluded: chain G residue 569 HIS Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 95 ASP Chi-restraints excluded: chain H residue 107 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 175 optimal weight: 30.0000 chunk 20 optimal weight: 0.6980 chunk 103 optimal weight: 7.9990 chunk 132 optimal weight: 40.0000 chunk 102 optimal weight: 30.0000 chunk 153 optimal weight: 7.9990 chunk 101 optimal weight: 20.0000 chunk 181 optimal weight: 30.0000 chunk 113 optimal weight: 0.8980 chunk 110 optimal weight: 1.9990 chunk 83 optimal weight: 7.9990 overall best weight: 3.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 580 GLN ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 41 GLN ** F 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 580 GLN H 41 GLN ** H 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4811 moved from start: 0.7032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 15828 Z= 0.377 Angle : 0.829 14.510 21360 Z= 0.411 Chirality : 0.043 0.170 2364 Planarity : 0.005 0.073 2692 Dihedral : 5.897 58.480 2198 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 22.26 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.82 % Favored : 95.02 % Rotamer: Outliers : 4.99 % Allowed : 26.91 % Favored : 68.10 % 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: 0.47 (0.19), residues: 1888 helix: 0.68 (0.13), residues: 1520 sheet: None (None), residues: 0 loop : -0.88 (0.34), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 350 HIS 0.006 0.001 HIS G 102 PHE 0.027 0.002 PHE B 12 TYR 0.019 0.002 TYR B 99 ARG 0.015 0.001 ARG G 547 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 216 time to evaluate : 1.902 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 104 PHE cc_start: 0.8756 (t80) cc_final: 0.8431 (t80) REVERT: A 139 MET cc_start: 0.7867 (ttm) cc_final: 0.7019 (tmm) REVERT: A 212 LEU cc_start: 0.9174 (OUTLIER) cc_final: 0.8684 (mm) REVERT: A 217 MET cc_start: 0.8189 (tpp) cc_final: 0.7894 (tpp) REVERT: C 104 PHE cc_start: 0.8744 (t80) cc_final: 0.8399 (t80) REVERT: C 139 MET cc_start: 0.7819 (OUTLIER) cc_final: 0.6962 (tmm) REVERT: C 207 ARG cc_start: 0.8008 (mtt180) cc_final: 0.7697 (mtp-110) REVERT: D 18 LEU cc_start: 0.0611 (OUTLIER) cc_final: 0.0231 (tm) REVERT: E 104 PHE cc_start: 0.8740 (t80) cc_final: 0.8394 (t80) REVERT: E 139 MET cc_start: 0.7798 (OUTLIER) cc_final: 0.6927 (tmm) REVERT: F 76 MET cc_start: 0.0496 (ptt) cc_final: 0.0138 (pmm) REVERT: G 139 MET cc_start: 0.7851 (OUTLIER) cc_final: 0.6954 (tmm) REVERT: G 212 LEU cc_start: 0.9169 (OUTLIER) cc_final: 0.8830 (mm) REVERT: G 556 TYR cc_start: 0.4137 (OUTLIER) cc_final: 0.3801 (p90) outliers start: 81 outliers final: 40 residues processed: 275 average time/residue: 1.1686 time to fit residues: 357.3443 Evaluate side-chains 236 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 189 time to evaluate : 1.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 137 PHE Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 550 LYS Chi-restraints excluded: chain A residue 559 LYS Chi-restraints excluded: chain A residue 564 GLN Chi-restraints excluded: chain A residue 569 HIS Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 95 ASP Chi-restraints excluded: chain B residue 107 HIS Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 137 PHE Chi-restraints excluded: chain C residue 139 MET Chi-restraints excluded: chain C residue 569 HIS Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 95 ASP Chi-restraints excluded: chain D residue 107 HIS Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 111 SER Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 137 PHE Chi-restraints excluded: chain E residue 139 MET Chi-restraints excluded: chain E residue 569 HIS Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 95 ASP Chi-restraints excluded: chain F residue 99 TYR Chi-restraints excluded: chain F residue 107 HIS Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain G residue 87 VAL Chi-restraints excluded: chain G residue 111 SER Chi-restraints excluded: chain G residue 120 THR Chi-restraints excluded: chain G residue 137 PHE Chi-restraints excluded: chain G residue 139 MET Chi-restraints excluded: chain G residue 212 LEU Chi-restraints excluded: chain G residue 359 ARG Chi-restraints excluded: chain G residue 556 TYR Chi-restraints excluded: chain G residue 569 HIS Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 95 ASP Chi-restraints excluded: chain H residue 107 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 112 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 chunk 35 optimal weight: 8.9990 chunk 115 optimal weight: 0.9990 chunk 123 optimal weight: 0.6980 chunk 89 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 142 optimal weight: 10.0000 chunk 164 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 HIS ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 ASN C 102 HIS ** D 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 102 HIS ** F 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 102 HIS ** H 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4716 moved from start: 0.7373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15828 Z= 0.208 Angle : 0.828 15.456 21360 Z= 0.403 Chirality : 0.043 0.283 2364 Planarity : 0.005 0.070 2692 Dihedral : 5.596 58.684 2196 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 18.93 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.56 % Favored : 95.29 % Rotamer: Outliers : 4.13 % Allowed : 28.69 % Favored : 67.18 % 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: 0.69 (0.19), residues: 1888 helix: 0.88 (0.13), residues: 1516 sheet: None (None), residues: 0 loop : -1.02 (0.34), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP G 350 HIS 0.006 0.001 HIS G 102 PHE 0.027 0.002 PHE D 12 TYR 0.018 0.001 TYR B 99 ARG 0.013 0.001 ARG C 538 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 261 time to evaluate : 1.857 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 139 MET cc_start: 0.7824 (ttm) cc_final: 0.7000 (tmm) REVERT: A 216 ARG cc_start: 0.4840 (OUTLIER) cc_final: 0.3989 (mmp-170) REVERT: A 218 ASP cc_start: 0.7161 (OUTLIER) cc_final: 0.6805 (m-30) REVERT: B 72 MET cc_start: 0.3384 (tpt) cc_final: 0.2789 (pp-130) REVERT: C 139 MET cc_start: 0.7775 (OUTLIER) cc_final: 0.6962 (tmm) REVERT: C 146 GLU cc_start: 0.8785 (mm-30) cc_final: 0.8573 (mm-30) REVERT: C 182 PHE cc_start: 0.7424 (t80) cc_final: 0.7170 (t80) REVERT: D 18 LEU cc_start: 0.0685 (OUTLIER) cc_final: 0.0303 (tm) REVERT: D 72 MET cc_start: 0.3903 (tpt) cc_final: 0.3550 (tpt) REVERT: E 139 MET cc_start: 0.7748 (OUTLIER) cc_final: 0.6903 (tmm) REVERT: E 146 GLU cc_start: 0.8832 (mm-30) cc_final: 0.8601 (mm-30) REVERT: E 217 MET cc_start: 0.8018 (tpp) cc_final: 0.7578 (tpp) REVERT: F 71 MET cc_start: 0.5050 (mtt) cc_final: 0.4849 (mtm) REVERT: F 76 MET cc_start: 0.0519 (ptt) cc_final: 0.0214 (pmm) REVERT: F 124 MET cc_start: 0.5367 (ppp) cc_final: 0.4763 (ppp) REVERT: G 139 MET cc_start: 0.7782 (OUTLIER) cc_final: 0.6908 (tmm) REVERT: G 219 ARG cc_start: 0.8491 (mtt90) cc_final: 0.8127 (mpt180) REVERT: G 335 PHE cc_start: 0.7354 (t80) cc_final: 0.6296 (t80) REVERT: G 556 TYR cc_start: 0.4172 (OUTLIER) cc_final: 0.3971 (p90) outliers start: 67 outliers final: 32 residues processed: 302 average time/residue: 1.2197 time to fit residues: 408.6667 Evaluate side-chains 258 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 219 time to evaluate : 1.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 137 PHE Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 216 ARG Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 559 LYS Chi-restraints excluded: chain A residue 564 GLN Chi-restraints excluded: chain A residue 569 HIS Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 95 ASP Chi-restraints excluded: chain B residue 107 HIS Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 137 PHE Chi-restraints excluded: chain C residue 139 MET Chi-restraints excluded: chain C residue 569 HIS Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 95 ASP Chi-restraints excluded: chain D residue 107 HIS Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 137 PHE Chi-restraints excluded: chain E residue 139 MET Chi-restraints excluded: chain E residue 569 HIS Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 95 ASP Chi-restraints excluded: chain F residue 99 TYR Chi-restraints excluded: chain F residue 107 HIS Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain G residue 87 VAL Chi-restraints excluded: chain G residue 120 THR Chi-restraints excluded: chain G residue 137 PHE Chi-restraints excluded: chain G residue 139 MET Chi-restraints excluded: chain G residue 212 LEU Chi-restraints excluded: chain G residue 359 ARG Chi-restraints excluded: chain G residue 556 TYR Chi-restraints excluded: chain G residue 569 HIS Chi-restraints excluded: chain H residue 95 ASP Chi-restraints excluded: chain H residue 107 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 173 optimal weight: 20.0000 chunk 158 optimal weight: 0.9990 chunk 168 optimal weight: 5.9990 chunk 101 optimal weight: 10.0000 chunk 73 optimal weight: 0.8980 chunk 132 optimal weight: 50.0000 chunk 51 optimal weight: 1.9990 chunk 152 optimal weight: 0.5980 chunk 159 optimal weight: 0.9990 chunk 110 optimal weight: 0.6980 chunk 178 optimal weight: 7.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 122 GLN ** H 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 143 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4713 moved from start: 0.7673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15828 Z= 0.206 Angle : 0.879 16.110 21360 Z= 0.421 Chirality : 0.044 0.266 2364 Planarity : 0.005 0.077 2692 Dihedral : 5.579 58.875 2196 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 18.96 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.93 % Favored : 94.92 % Rotamer: Outliers : 4.06 % Allowed : 29.43 % Favored : 66.50 % 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 (0.20), residues: 1888 helix: 1.06 (0.14), residues: 1492 sheet: None (None), residues: 0 loop : -0.68 (0.34), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 350 HIS 0.003 0.001 HIS G 569 PHE 0.032 0.002 PHE H 141 TYR 0.024 0.001 TYR D 99 ARG 0.019 0.001 ARG C 554 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 236 time to evaluate : 1.679 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: A 139 MET cc_start: 0.7801 (ttm) cc_final: 0.6975 (tmm) REVERT: A 146 GLU cc_start: 0.8862 (mm-30) cc_final: 0.8621 (mm-30) REVERT: A 216 ARG cc_start: 0.4524 (OUTLIER) cc_final: 0.3777 (mmp-170) REVERT: A 218 ASP cc_start: 0.7021 (OUTLIER) cc_final: 0.6782 (m-30) REVERT: B 72 MET cc_start: 0.3534 (tpt) cc_final: 0.3220 (tpt) REVERT: B 124 MET cc_start: 0.5254 (ppp) cc_final: 0.4892 (ppp) REVERT: C 139 MET cc_start: 0.7794 (ttm) cc_final: 0.6997 (tmm) REVERT: C 146 GLU cc_start: 0.8825 (mm-30) cc_final: 0.8607 (mm-30) REVERT: D 18 LEU cc_start: 0.0690 (OUTLIER) cc_final: 0.0284 (tm) REVERT: E 83 LEU cc_start: 0.8690 (tm) cc_final: 0.8479 (pp) REVERT: E 139 MET cc_start: 0.7802 (OUTLIER) cc_final: 0.7015 (tmm) REVERT: E 146 GLU cc_start: 0.8848 (mm-30) cc_final: 0.8617 (mm-30) REVERT: F 71 MET cc_start: 0.5127 (mtt) cc_final: 0.4919 (mtm) REVERT: F 124 MET cc_start: 0.5473 (ppp) cc_final: 0.5027 (ppp) REVERT: G 139 MET cc_start: 0.7781 (OUTLIER) cc_final: 0.6980 (tmm) REVERT: G 146 GLU cc_start: 0.8874 (mm-30) cc_final: 0.8620 (mm-30) REVERT: G 217 MET cc_start: 0.8037 (tpp) cc_final: 0.7789 (tpp) REVERT: G 556 TYR cc_start: 0.4150 (OUTLIER) cc_final: 0.3921 (p90) REVERT: H 72 MET cc_start: 0.3883 (tpt) cc_final: 0.3498 (tpt) REVERT: H 136 VAL cc_start: 0.4347 (OUTLIER) cc_final: 0.4045 (m) REVERT: H 144 MET cc_start: 0.4025 (pp-130) cc_final: 0.3287 (pp-130) outliers start: 66 outliers final: 34 residues processed: 280 average time/residue: 1.1868 time to fit residues: 368.4735 Evaluate side-chains 244 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 203 time to evaluate : 1.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 137 PHE Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 216 ARG Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 559 LYS Chi-restraints excluded: chain A residue 564 GLN Chi-restraints excluded: chain A residue 569 HIS Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 95 ASP Chi-restraints excluded: chain B residue 99 TYR Chi-restraints excluded: chain B residue 107 HIS Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 137 PHE Chi-restraints excluded: chain C residue 569 HIS Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 95 ASP Chi-restraints excluded: chain D residue 99 TYR Chi-restraints excluded: chain D residue 107 HIS Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 137 PHE Chi-restraints excluded: chain E residue 139 MET Chi-restraints excluded: chain E residue 569 HIS Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 95 ASP Chi-restraints excluded: chain F residue 99 TYR Chi-restraints excluded: chain F residue 107 HIS Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain G residue 87 VAL Chi-restraints excluded: chain G residue 137 PHE Chi-restraints excluded: chain G residue 139 MET Chi-restraints excluded: chain G residue 212 LEU Chi-restraints excluded: chain G residue 359 ARG Chi-restraints excluded: chain G residue 556 TYR Chi-restraints excluded: chain G residue 569 HIS Chi-restraints excluded: chain H residue 95 ASP Chi-restraints excluded: chain H residue 99 TYR Chi-restraints excluded: chain H residue 107 HIS Chi-restraints excluded: chain H residue 136 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 108 optimal weight: 4.9990 chunk 84 optimal weight: 0.9990 chunk 124 optimal weight: 6.9990 chunk 187 optimal weight: 3.9990 chunk 172 optimal weight: 0.8980 chunk 149 optimal weight: 0.0980 chunk 15 optimal weight: 3.9990 chunk 115 optimal weight: 0.7980 chunk 91 optimal weight: 20.0000 chunk 118 optimal weight: 0.7980 chunk 158 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4698 moved from start: 0.7947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15828 Z= 0.211 Angle : 0.909 15.661 21360 Z= 0.433 Chirality : 0.044 0.243 2364 Planarity : 0.005 0.070 2692 Dihedral : 5.441 57.705 2196 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 19.32 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.87 % Favored : 94.97 % Rotamer: Outliers : 2.52 % Allowed : 31.65 % Favored : 65.83 % 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: 0.79 (0.20), residues: 1888 helix: 0.93 (0.13), residues: 1496 sheet: None (None), residues: 0 loop : -0.77 (0.34), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 350 HIS 0.003 0.000 HIS G 569 PHE 0.031 0.002 PHE A 137 TYR 0.028 0.001 TYR B 99 ARG 0.019 0.001 ARG A 331 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 226 time to evaluate : 1.883 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: A 139 MET cc_start: 0.7790 (ttm) cc_final: 0.7003 (tmm) REVERT: A 146 GLU cc_start: 0.8889 (mm-30) cc_final: 0.8610 (mm-30) REVERT: A 217 MET cc_start: 0.8032 (tpp) cc_final: 0.7685 (tpp) REVERT: B 72 MET cc_start: 0.3624 (tpt) cc_final: 0.3367 (tpt) REVERT: B 145 MET cc_start: 0.2421 (mmp) cc_final: 0.1048 (tpt) REVERT: C 139 MET cc_start: 0.7792 (OUTLIER) cc_final: 0.7004 (tmm) REVERT: C 214 MET cc_start: 0.8037 (tpt) cc_final: 0.7405 (ttt) REVERT: D 18 LEU cc_start: 0.0667 (OUTLIER) cc_final: 0.0266 (tm) REVERT: E 83 LEU cc_start: 0.8722 (tm) cc_final: 0.8513 (pp) REVERT: E 139 MET cc_start: 0.7799 (ttm) cc_final: 0.7010 (tmm) REVERT: E 146 GLU cc_start: 0.8860 (mm-30) cc_final: 0.8611 (mm-30) REVERT: E 329 GLN cc_start: 0.8619 (pt0) cc_final: 0.8345 (pp30) REVERT: F 124 MET cc_start: 0.5354 (ppp) cc_final: 0.4970 (ppp) REVERT: G 139 MET cc_start: 0.7837 (OUTLIER) cc_final: 0.7075 (tmm) REVERT: G 146 GLU cc_start: 0.8903 (mm-30) cc_final: 0.8628 (mm-30) REVERT: G 329 GLN cc_start: 0.8703 (pt0) cc_final: 0.8339 (pp30) REVERT: H 109 MET cc_start: 0.2801 (ppp) cc_final: 0.2569 (ppp) outliers start: 41 outliers final: 31 residues processed: 256 average time/residue: 1.1515 time to fit residues: 327.6675 Evaluate side-chains 244 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 210 time to evaluate : 1.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 559 LYS Chi-restraints excluded: chain A residue 564 GLN Chi-restraints excluded: chain A residue 569 HIS Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 95 ASP Chi-restraints excluded: chain B residue 99 TYR Chi-restraints excluded: chain B residue 107 HIS Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 137 PHE Chi-restraints excluded: chain C residue 139 MET Chi-restraints excluded: chain C residue 569 HIS Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 95 ASP Chi-restraints excluded: chain D residue 99 TYR Chi-restraints excluded: chain D residue 107 HIS Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 137 PHE Chi-restraints excluded: chain E residue 569 HIS Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 95 ASP Chi-restraints excluded: chain F residue 99 TYR Chi-restraints excluded: chain F residue 107 HIS Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain G residue 87 VAL Chi-restraints excluded: chain G residue 137 PHE Chi-restraints excluded: chain G residue 139 MET Chi-restraints excluded: chain G residue 212 LEU Chi-restraints excluded: chain G residue 359 ARG Chi-restraints excluded: chain G residue 569 HIS Chi-restraints excluded: chain H residue 95 ASP Chi-restraints excluded: chain H residue 99 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 45 optimal weight: 20.0000 chunk 137 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 41 optimal weight: 8.9990 chunk 149 optimal weight: 8.9990 chunk 62 optimal weight: 4.9990 chunk 153 optimal weight: 8.9990 chunk 18 optimal weight: 2.9990 chunk 27 optimal weight: 6.9990 chunk 131 optimal weight: 9.9990 chunk 8 optimal weight: 40.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4745 r_free = 0.4745 target = 0.192126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.108217 restraints weight = 36278.573| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 3.60 r_work: 0.3073 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3062 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3062 r_free = 0.3062 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3061 r_free = 0.3061 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 37 | |-----------------------------------------------------------------------------| r_final: 0.3061 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.8061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 15828 Z= 0.419 Angle : 0.953 16.546 21360 Z= 0.467 Chirality : 0.048 0.281 2364 Planarity : 0.005 0.063 2692 Dihedral : 5.585 58.992 2194 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 24.41 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.46 % Favored : 94.39 % Rotamer: Outliers : 2.52 % Allowed : 32.08 % Favored : 65.39 % 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: 0.62 (0.20), residues: 1888 helix: 0.77 (0.13), residues: 1504 sheet: None (None), residues: 0 loop : -0.69 (0.34), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 350 HIS 0.003 0.001 HIS G 569 PHE 0.053 0.002 PHE B 89 TYR 0.030 0.002 TYR B 99 ARG 0.012 0.001 ARG C 554 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7214.98 seconds wall clock time: 128 minutes 16.97 seconds (7696.97 seconds total)