Starting phenix.real_space_refine on Fri Feb 16 08:57:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g5c_29739/02_2024/8g5c_29739_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g5c_29739/02_2024/8g5c_29739.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g5c_29739/02_2024/8g5c_29739_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g5c_29739/02_2024/8g5c_29739_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g5c_29739/02_2024/8g5c_29739_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g5c_29739/02_2024/8g5c_29739.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g5c_29739/02_2024/8g5c_29739.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g5c_29739/02_2024/8g5c_29739_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g5c_29739/02_2024/8g5c_29739_neut_updated.pdb" } resolution = 2.2 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= -0.004 sd= 0.182 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 P 18 5.49 5 S 106 5.16 5 C 9426 2.51 5 N 2504 2.21 5 O 2819 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 163": "OE1" <-> "OE2" Residue "A GLU 1046": "OE1" <-> "OE2" Residue "B GLU 866": "OE1" <-> "OE2" Residue "B GLU 1009": "OE1" <-> "OE2" Residue "C GLU 1009": "OE1" <-> "OE2" Residue "C GLU 1046": "OE1" <-> "OE2" Residue "D GLU 1097": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 14873 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 7989 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1032, 7981 Classifications: {'peptide': 1032} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 982} Chain breaks: 2 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Conformer: "B" Number of residues, atoms: 1032, 7981 Classifications: {'peptide': 1032} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 982} Chain breaks: 2 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 bond proxies already assigned to first conformer: 8143 Chain: "B" Number of atoms: 2163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2163 Classifications: {'peptide': 279} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 12, 'TRANS': 266} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 2163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2163 Classifications: {'peptide': 279} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 12, 'TRANS': 266} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 2163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2163 Classifications: {'peptide': 279} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 12, 'TRANS': 266} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 153 Unusual residues: {'ADP': 1, 'COA': 1, 'FLC': 1, 'PO4': 1, 'Q5B': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 61 Unusual residues: {'COA': 1, 'FLC': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 61 Unusual residues: {'COA': 1, 'FLC': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 61 Unusual residues: {'COA': 1, 'FLC': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "C" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Time building chain proxies: 12.27, per 1000 atoms: 0.82 Number of scatterers: 14873 At special positions: 0 Unit cell: (132.8, 113.71, 131.97, 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) S 106 16.00 P 18 15.00 O 2819 8.00 N 2504 7.00 C 9426 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: 6.30 Conformation dependent library (CDL) restraints added in 4.5 seconds 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3382 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 80 helices and 7 sheets defined 48.1% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.24 Creating SS restraints... Processing helix chain 'A' and resid 8 through 18 Processing helix chain 'A' and resid 40 through 46 Processing helix chain 'A' and resid 66 through 68 No H-bonds generated for 'chain 'A' and resid 66 through 68' Processing helix chain 'A' and resid 78 through 86 removed outlier: 3.591A pdb=" N LYS A 86 " --> pdb=" O LYS A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 167 Processing helix chain 'A' and resid 175 through 194 removed outlier: 3.579A pdb=" N SER A 183 " --> pdb=" O GLU A 179 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N SER A 186 " --> pdb=" O ALA A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 233 removed outlier: 4.423A pdb=" N TYR A 227 " --> pdb=" O THR A 224 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N LYS A 230 " --> pdb=" O TYR A 227 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N VAL A 231 " --> pdb=" O ILE A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 257 Processing helix chain 'A' and resid 282 through 294 Processing helix chain 'A' and resid 313 through 329 removed outlier: 3.642A pdb=" N ARG A 329 " --> pdb=" O SER A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 362 removed outlier: 4.065A pdb=" N GLY A 356 " --> pdb=" O ALA A 352 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ILE A 357 " --> pdb=" O THR A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 368 No H-bonds generated for 'chain 'A' and resid 366 through 368' Processing helix chain 'A' and resid 384 through 398 Processing helix chain 'A' and resid 413 through 419 Processing helix chain 'A' and resid 506 through 518 Processing helix chain 'A' and resid 556 through 562 Processing helix chain 'A' and resid 578 through 587 Processing helix chain 'A' and resid 603 through 616 Processing helix chain 'A' and resid 643 through 648 Processing helix chain 'A' and resid 664 through 677 Processing helix chain 'A' and resid 697 through 706 Processing helix chain 'A' and resid 723 through 732 Processing helix chain 'A' and resid 747 through 749 No H-bonds generated for 'chain 'A' and resid 747 through 749' Processing helix chain 'A' and resid 772 through 782 Processing helix chain 'A' and resid 793 through 807 Processing helix chain 'A' and resid 825 through 830 Processing helix chain 'A' and resid 859 through 864 Processing helix chain 'A' and resid 869 through 878 Processing helix chain 'A' and resid 884 through 896 Processing helix chain 'A' and resid 905 through 915 Processing helix chain 'A' and resid 920 through 930 removed outlier: 4.149A pdb=" N THR A 930 " --> pdb=" O SER A 926 " (cutoff:3.500A) Processing helix chain 'A' and resid 938 through 951 Processing helix chain 'A' and resid 956 through 965 Processing helix chain 'A' and resid 985 through 997 Processing helix chain 'A' and resid 1002 through 1017 Processing helix chain 'A' and resid 1025 through 1039 Processing helix chain 'A' and resid 1045 through 1054 Processing helix chain 'A' and resid 1056 through 1079 removed outlier: 3.857A pdb=" N MET A1067 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLY A1068 " --> pdb=" O GLY A1064 " (cutoff:3.500A) Processing helix chain 'A' and resid 1088 through 1090 No H-bonds generated for 'chain 'A' and resid 1088 through 1090' Processing helix chain 'B' and resid 825 through 830 Processing helix chain 'B' and resid 859 through 864 Processing helix chain 'B' and resid 868 through 878 Processing helix chain 'B' and resid 884 through 896 Processing helix chain 'B' and resid 905 through 915 Processing helix chain 'B' and resid 920 through 930 removed outlier: 4.052A pdb=" N THR B 930 " --> pdb=" O SER B 926 " (cutoff:3.500A) Processing helix chain 'B' and resid 938 through 951 Processing helix chain 'B' and resid 956 through 966 Processing helix chain 'B' and resid 985 through 997 Processing helix chain 'B' and resid 1002 through 1015 Processing helix chain 'B' and resid 1025 through 1039 Processing helix chain 'B' and resid 1045 through 1054 Processing helix chain 'B' and resid 1056 through 1079 removed outlier: 3.809A pdb=" N MET B1067 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLY B1068 " --> pdb=" O GLY B1064 " (cutoff:3.500A) Processing helix chain 'C' and resid 825 through 831 Processing helix chain 'C' and resid 859 through 864 Processing helix chain 'C' and resid 869 through 878 Processing helix chain 'C' and resid 884 through 896 Processing helix chain 'C' and resid 905 through 915 Processing helix chain 'C' and resid 920 through 930 removed outlier: 4.124A pdb=" N THR C 930 " --> pdb=" O SER C 926 " (cutoff:3.500A) Processing helix chain 'C' and resid 938 through 951 Processing helix chain 'C' and resid 956 through 965 Processing helix chain 'C' and resid 985 through 997 Processing helix chain 'C' and resid 1002 through 1017 Processing helix chain 'C' and resid 1025 through 1039 Processing helix chain 'C' and resid 1045 through 1054 Processing helix chain 'C' and resid 1056 through 1078 removed outlier: 3.823A pdb=" N MET C1067 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLY C1068 " --> pdb=" O GLY C1064 " (cutoff:3.500A) Processing helix chain 'C' and resid 1088 through 1090 No H-bonds generated for 'chain 'C' and resid 1088 through 1090' Processing helix chain 'D' and resid 825 through 831 Processing helix chain 'D' and resid 859 through 864 Processing helix chain 'D' and resid 869 through 878 Processing helix chain 'D' and resid 884 through 896 Processing helix chain 'D' and resid 905 through 915 Processing helix chain 'D' and resid 920 through 930 removed outlier: 4.122A pdb=" N THR D 930 " --> pdb=" O SER D 926 " (cutoff:3.500A) Processing helix chain 'D' and resid 938 through 951 Processing helix chain 'D' and resid 956 through 965 Processing helix chain 'D' and resid 985 through 997 Processing helix chain 'D' and resid 1002 through 1016 Processing helix chain 'D' and resid 1025 through 1039 Processing helix chain 'D' and resid 1045 through 1054 Processing helix chain 'D' and resid 1056 through 1079 removed outlier: 3.844A pdb=" N MET D1067 " --> pdb=" O LEU D1063 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLY D1068 " --> pdb=" O GLY D1064 " (cutoff:3.500A) Processing helix chain 'D' and resid 1088 through 1090 No H-bonds generated for 'chain 'D' and resid 1088 through 1090' Processing sheet with id= A, first strand: chain 'A' and resid 3 through 6 removed outlier: 4.580A pdb=" N ALA A 219 " --> pdb=" O ILE A 6 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N ASP A 222 " --> pdb=" O PHE A 197 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N PHE A 197 " --> pdb=" O ASP A 222 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N THR A 198 " --> pdb=" O ALA A 125 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 32 through 34 Processing sheet with id= C, first strand: chain 'A' and resid 205 through 207 Processing sheet with id= D, first strand: chain 'A' and resid 263 through 268 Processing sheet with id= E, first strand: chain 'A' and resid 275 through 277 removed outlier: 6.388A pdb=" N ILE A 337 " --> pdb=" O TRP A 276 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 537 through 543 removed outlier: 8.278A pdb=" N ALA A 527 " --> pdb=" O LEU A 549 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N ALA A 499 " --> pdb=" O ALA A 527 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N MET A 529 " --> pdb=" O ALA A 499 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N VAL A 501 " --> pdb=" O MET A 529 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N ILE A 500 " --> pdb=" O ASP A 567 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N LEU A 569 " --> pdb=" O ILE A 500 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N TRP A 502 " --> pdb=" O LEU A 569 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N ASN A 571 " --> pdb=" O TRP A 502 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N THR A 593 " --> pdb=" O LEU A 569 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N ASN A 571 " --> pdb=" O THR A 593 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ALA A 595 " --> pdb=" O ASN A 571 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N THR A 619 " --> pdb=" O ILE A 594 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N ILE A 596 " --> pdb=" O THR A 619 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ILE A 621 " --> pdb=" O ILE A 596 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 739 through 745 removed outlier: 7.489A pdb=" N TYR A 659 " --> pdb=" O TYR A 682 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N GLY A 684 " --> pdb=" O TYR A 659 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N SER A 661 " --> pdb=" O GLY A 684 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ALA A 686 " --> pdb=" O SER A 661 " (cutoff:3.500A) 637 hydrogen bonds defined for protein. 1869 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: 5.09 Time building geometry restraints manager: 6.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.73: 14949 1.73 - 2.29: 176 2.29 - 2.84: 0 2.84 - 3.40: 4 3.40 - 3.96: 4 Bond restraints: 15133 Sorted by residual: bond pdb=" AO6 COA C2101 " pdb=" AP2 COA C2101 " ideal model delta sigma weight residual 1.610 3.959 -2.349 2.00e-02 2.50e+03 1.38e+04 bond pdb=" AP1 COA D2101 " pdb="AO5* COA D2101 " ideal model delta sigma weight residual 1.610 3.958 -2.348 2.00e-02 2.50e+03 1.38e+04 bond pdb=" AP1 COA B1201 " pdb="AO5* COA B1201 " ideal model delta sigma weight residual 1.610 3.902 -2.292 2.00e-02 2.50e+03 1.31e+04 bond pdb=" AP1 COA A1202 " pdb="AO5* COA A1202 " ideal model delta sigma weight residual 1.610 3.861 -2.251 2.00e-02 2.50e+03 1.27e+04 bond pdb=" AP1 COA C2101 " pdb="AO5* COA C2101 " ideal model delta sigma weight residual 1.610 3.377 -1.767 2.00e-02 2.50e+03 7.81e+03 ... (remaining 15128 not shown) Histogram of bond angle deviations from ideal: 19.08 - 47.86: 5 47.86 - 76.65: 4 76.65 - 105.43: 384 105.43 - 134.22: 20095 134.22 - 163.01: 13 Bond angle restraints: 20501 Sorted by residual: angle pdb=" AO3 COA D2101 " pdb=" AP1 COA D2101 " pdb="AO5* COA D2101 " ideal model delta sigma weight residual 102.60 19.08 83.52 3.00e+00 1.11e-01 7.75e+02 angle pdb=" AO3 COA B1201 " pdb=" AP1 COA B1201 " pdb="AO5* COA B1201 " ideal model delta sigma weight residual 102.60 19.16 83.44 3.00e+00 1.11e-01 7.74e+02 angle pdb=" AO3 COA C2101 " pdb=" AP2 COA C2101 " pdb=" AO6 COA C2101 " ideal model delta sigma weight residual 102.60 19.77 82.83 3.00e+00 1.11e-01 7.62e+02 angle pdb=" AO3 COA A1202 " pdb=" AP1 COA A1202 " pdb="AO5* COA A1202 " ideal model delta sigma weight residual 102.60 22.19 80.41 3.00e+00 1.11e-01 7.18e+02 angle pdb=" AO3 COA C2101 " pdb=" AP1 COA C2101 " pdb="AO5* COA C2101 " ideal model delta sigma weight residual 102.60 45.02 57.58 3.00e+00 1.11e-01 3.68e+02 ... (remaining 20496 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.89: 8655 35.89 - 71.77: 304 71.77 - 107.66: 39 107.66 - 143.54: 1 143.54 - 179.43: 6 Dihedral angle restraints: 9005 sinusoidal: 3689 harmonic: 5316 Sorted by residual: dihedral pdb=" AO3 COA A1202 " pdb=" AP1 COA A1202 " pdb="AO5* COA A1202 " pdb="AC5* COA A1202 " ideal model delta sinusoidal sigma weight residual 291.94 112.51 179.43 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" AO3 COA B1201 " pdb=" AP1 COA B1201 " pdb="AO5* COA B1201 " pdb="AC5* COA B1201 " ideal model delta sinusoidal sigma weight residual 291.94 117.97 173.97 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb="AC4* COA C2101 " pdb="AC3* COA C2101 " pdb="AO3* COA C2101 " pdb="AP3* COA C2101 " ideal model delta sinusoidal sigma weight residual 190.95 23.69 167.26 1 2.00e+01 2.50e-03 4.74e+01 ... (remaining 9002 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 2145 0.094 - 0.187: 95 0.187 - 0.281: 1 0.281 - 0.375: 2 0.375 - 0.468: 1 Chirality restraints: 2244 Sorted by residual: chirality pdb=" C7 Q5B A1205 " pdb=" C6 Q5B A1205 " pdb=" C8 Q5B A1205 " pdb=" O8 Q5B A1205 " both_signs ideal model delta sigma weight residual False 2.37 2.84 -0.47 2.00e-01 2.50e+01 5.49e+00 chirality pdb="AC3* COA A1202 " pdb="AC2* COA A1202 " pdb="AC4* COA A1202 " pdb="AO3* COA A1202 " both_signs ideal model delta sigma weight residual False -2.47 -2.84 0.36 2.00e-01 2.50e+01 3.32e+00 chirality pdb="AC3* COA B1201 " pdb="AC2* COA B1201 " pdb="AC4* COA B1201 " pdb="AO3* COA B1201 " both_signs ideal model delta sigma weight residual False -2.47 -2.81 0.34 2.00e-01 2.50e+01 2.89e+00 ... (remaining 2241 not shown) Planarity restraints: 2590 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' ADP A1201 " 0.360 2.00e-02 2.50e+03 4.00e-01 3.60e+03 pdb=" C2' ADP A1201 " -0.428 2.00e-02 2.50e+03 pdb=" C3' ADP A1201 " -0.453 2.00e-02 2.50e+03 pdb=" C4' ADP A1201 " 0.381 2.00e-02 2.50e+03 pdb=" C5' ADP A1201 " -0.366 2.00e-02 2.50e+03 pdb=" N9 ADP A1201 " -0.462 2.00e-02 2.50e+03 pdb=" O2' ADP A1201 " 0.283 2.00e-02 2.50e+03 pdb=" O3' ADP A1201 " 0.104 2.00e-02 2.50e+03 pdb=" O4' ADP A1201 " 0.581 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A1018 " 0.075 5.00e-02 4.00e+02 1.11e-01 1.98e+01 pdb=" N PRO A1019 " -0.192 5.00e-02 4.00e+02 pdb=" CA PRO A1019 " 0.057 5.00e-02 4.00e+02 pdb=" CD PRO A1019 " 0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 270 " -0.061 5.00e-02 4.00e+02 9.14e-02 1.34e+01 pdb=" N PRO A 271 " 0.158 5.00e-02 4.00e+02 pdb=" CA PRO A 271 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO A 271 " -0.050 5.00e-02 4.00e+02 ... (remaining 2587 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.24: 8 2.24 - 2.91: 5940 2.91 - 3.57: 23006 3.57 - 4.24: 38621 4.24 - 4.90: 64049 Nonbonded interactions: 131624 Sorted by model distance: nonbonded pdb=" AP2 COA A1202 " pdb="AO5* COA A1202 " model vdw 1.577 2.720 nonbonded pdb=" AP2 COA B1201 " pdb="AO5* COA B1201 " model vdw 1.582 2.720 nonbonded pdb=" AP2 COA C2101 " pdb="AO5* COA C2101 " model vdw 1.600 2.720 nonbonded pdb=" AP2 COA D2101 " pdb="AO5* COA D2101 " model vdw 1.603 2.720 nonbonded pdb=" AO6 COA A1202 " pdb=" AP1 COA A1202 " model vdw 1.604 2.720 ... (remaining 131619 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 'B' selection = chain 'C' selection = chain 'D' } 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=0.40 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: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 3.330 Check model and map are aligned: 0.210 Set scattering table: 0.140 Process input model: 49.270 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.090 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:11.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 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 : 0.046 2.349 15133 Z= 3.026 Angle : 1.773 83.523 20501 Z= 0.629 Chirality : 0.044 0.468 2244 Planarity : 0.009 0.400 2590 Dihedral : 18.457 179.427 5623 Min Nonbonded Distance : 1.577 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.04 % Allowed : 22.61 % Favored : 76.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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: 1.38 (0.20), residues: 1859 helix: 1.69 (0.16), residues: 1000 sheet: 0.59 (0.47), residues: 133 loop : -0.04 (0.24), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 827 HIS 0.003 0.001 HIS A 997 PHE 0.011 0.001 PHE A 752 TYR 0.030 0.002 TYR A 304 ARG 0.008 0.001 ARG D1085 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 279 residues out of total 1551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 263 time to evaluate : 1.716 Fit side-chains REVERT: A 30 LYS cc_start: 0.6330 (mttm) cc_final: 0.5296 (tmtt) REVERT: A 61 GLN cc_start: 0.7085 (mt0) cc_final: 0.6696 (mt0) REVERT: A 158 GLU cc_start: 0.6472 (pt0) cc_final: 0.6142 (pt0) REVERT: A 199 TYR cc_start: 0.7787 (t80) cc_final: 0.7560 (t80) REVERT: A 204 PRO cc_start: 0.7104 (Cg_endo) cc_final: 0.6571 (Cg_exo) REVERT: A 205 LEU cc_start: 0.5181 (tp) cc_final: 0.4870 (tp) REVERT: A 256 LEU cc_start: 0.7168 (mt) cc_final: 0.6575 (mt) REVERT: A 294 ASP cc_start: 0.7071 (t70) cc_final: 0.6800 (t0) REVERT: A 385 GLN cc_start: 0.7204 (pm20) cc_final: 0.6827 (pm20) REVERT: A 751 MET cc_start: 0.5386 (ppp) cc_final: 0.5113 (pmm) REVERT: A 791 ASP cc_start: 0.7073 (m-30) cc_final: 0.6853 (m-30) REVERT: A 865 GLU cc_start: 0.7930 (mm-30) cc_final: 0.7640 (mm-30) REVERT: A 1024 ASN cc_start: 0.7482 (m110) cc_final: 0.7191 (m-40) REVERT: A 1089 ASP cc_start: 0.7690 (p0) cc_final: 0.7401 (p0) REVERT: B 826 SER cc_start: 0.8396 (OUTLIER) cc_final: 0.7979 (p) REVERT: B 988 GLN cc_start: 0.7594 (tp40) cc_final: 0.7096 (mm110) REVERT: B 1067 MET cc_start: 0.7773 (mtp) cc_final: 0.7469 (mtm) REVERT: C 857 MET cc_start: 0.8705 (ttm) cc_final: 0.8254 (mtp) REVERT: C 864 LYS cc_start: 0.8257 (ttmt) cc_final: 0.8048 (mttm) REVERT: C 940 ASP cc_start: 0.7920 (t70) cc_final: 0.7618 (t70) REVERT: C 992 ASP cc_start: 0.7877 (m-30) cc_final: 0.7607 (m-30) REVERT: C 1067 MET cc_start: 0.7518 (ttm) cc_final: 0.7254 (mtm) REVERT: C 1089 ASP cc_start: 0.7847 (p0) cc_final: 0.7555 (p0) REVERT: D 857 MET cc_start: 0.8775 (ttm) cc_final: 0.8541 (ttp) REVERT: D 881 ARG cc_start: 0.7624 (tpt-90) cc_final: 0.7384 (tpt-90) REVERT: D 940 ASP cc_start: 0.7946 (t70) cc_final: 0.7673 (t70) REVERT: D 1078 ARG cc_start: 0.7935 (ttp-110) cc_final: 0.7470 (ttp-110) REVERT: D 1089 ASP cc_start: 0.7714 (p0) cc_final: 0.7416 (p0) outliers start: 16 outliers final: 2 residues processed: 276 average time/residue: 1.5522 time to fit residues: 465.9181 Evaluate side-chains 192 residues out of total 1551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 189 time to evaluate : 1.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain B residue 826 SER Chi-restraints excluded: chain B residue 1018 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 7.9990 chunk 139 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 94 optimal weight: 0.9990 chunk 74 optimal weight: 20.0000 chunk 144 optimal weight: 3.9990 chunk 55 optimal weight: 6.9990 chunk 87 optimal weight: 4.9990 chunk 107 optimal weight: 7.9990 chunk 167 optimal weight: 9.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 HIS A 270 ASN A 777 GLN A 807 ASN B 850 GLN C 850 GLN C 879 GLN D 850 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 15133 Z= 0.230 Angle : 0.697 20.106 20501 Z= 0.316 Chirality : 0.045 0.331 2244 Planarity : 0.004 0.062 2590 Dihedral : 14.154 164.293 2177 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.08 % Allowed : 20.92 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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: 1.36 (0.19), residues: 1859 helix: 1.67 (0.16), residues: 1005 sheet: 0.39 (0.46), residues: 135 loop : -0.01 (0.24), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 827 HIS 0.005 0.001 HIS A 700 PHE 0.014 0.002 PHE B1061 TYR 0.024 0.002 TYR A 317 ARG 0.004 0.001 ARG D 995 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 221 residues out of total 1551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 189 time to evaluate : 1.753 Fit side-chains revert: symmetry clash REVERT: A 30 LYS cc_start: 0.6364 (mttm) cc_final: 0.5315 (tmtt) REVERT: A 53 GLN cc_start: 0.4445 (OUTLIER) cc_final: 0.4110 (pm20) REVERT: A 61 GLN cc_start: 0.7137 (mt0) cc_final: 0.6764 (mt0) REVERT: A 158 GLU cc_start: 0.6639 (pt0) cc_final: 0.6336 (pt0) REVERT: A 204 PRO cc_start: 0.7288 (Cg_endo) cc_final: 0.6727 (Cg_exo) REVERT: A 264 LEU cc_start: 0.7288 (mp) cc_final: 0.7054 (mt) REVERT: A 300 GLU cc_start: 0.6634 (tp30) cc_final: 0.6170 (tm-30) REVERT: A 321 LYS cc_start: 0.6828 (pttp) cc_final: 0.6586 (pttp) REVERT: A 385 GLN cc_start: 0.7162 (pm20) cc_final: 0.6845 (pm20) REVERT: A 583 MET cc_start: 0.8477 (mmm) cc_final: 0.8234 (mmp) REVERT: A 751 MET cc_start: 0.5625 (ppp) cc_final: 0.5359 (pmm) REVERT: A 864 LYS cc_start: 0.8341 (ttmm) cc_final: 0.8118 (ttpt) REVERT: B 985 MET cc_start: 0.8155 (mmm) cc_final: 0.7869 (mmp) REVERT: B 988 GLN cc_start: 0.7633 (tp40) cc_final: 0.7019 (mm110) REVERT: B 995 ARG cc_start: 0.7794 (OUTLIER) cc_final: 0.7276 (tpt-90) REVERT: B 1067 MET cc_start: 0.7937 (mtp) cc_final: 0.7659 (mtm) REVERT: C 857 MET cc_start: 0.8658 (ttm) cc_final: 0.8347 (mtp) REVERT: C 864 LYS cc_start: 0.8305 (ttmt) cc_final: 0.8023 (mttm) REVERT: C 940 ASP cc_start: 0.8222 (t70) cc_final: 0.7931 (t70) REVERT: C 1067 MET cc_start: 0.7633 (ttm) cc_final: 0.7382 (mtm) REVERT: C 1078 ARG cc_start: 0.8352 (OUTLIER) cc_final: 0.7511 (mtm180) REVERT: C 1089 ASP cc_start: 0.7759 (p0) cc_final: 0.7532 (p0) REVERT: D 881 ARG cc_start: 0.7888 (tpt-90) cc_final: 0.7605 (tpt-90) REVERT: D 940 ASP cc_start: 0.8149 (t70) cc_final: 0.7855 (t70) REVERT: D 1078 ARG cc_start: 0.7914 (ttp-110) cc_final: 0.7517 (ttp-110) REVERT: D 1089 ASP cc_start: 0.7722 (p0) cc_final: 0.7453 (p0) outliers start: 32 outliers final: 9 residues processed: 209 average time/residue: 1.5006 time to fit residues: 341.7722 Evaluate side-chains 186 residues out of total 1551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 174 time to evaluate : 1.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 53 GLN Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 255 ASP Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain B residue 995 ARG Chi-restraints excluded: chain B residue 1018 LYS Chi-restraints excluded: chain C residue 996 GLN Chi-restraints excluded: chain C residue 1078 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 92 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 139 optimal weight: 0.3980 chunk 113 optimal weight: 10.0000 chunk 46 optimal weight: 4.9990 chunk 167 optimal weight: 10.0000 chunk 180 optimal weight: 10.0000 chunk 149 optimal weight: 1.9990 chunk 165 optimal weight: 5.9990 chunk 57 optimal weight: 7.9990 chunk 134 optimal weight: 7.9990 overall best weight: 3.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 HIS A 807 ASN B 850 GLN B 982 ASN C 850 GLN C 988 GLN D 850 GLN D 996 GLN D 997 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 15133 Z= 0.242 Angle : 0.687 18.760 20501 Z= 0.315 Chirality : 0.045 0.265 2244 Planarity : 0.004 0.052 2590 Dihedral : 14.113 172.214 2175 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.95 % Allowed : 20.27 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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: 1.26 (0.19), residues: 1859 helix: 1.58 (0.16), residues: 1007 sheet: 0.20 (0.45), residues: 135 loop : -0.01 (0.24), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 276 HIS 0.004 0.001 HIS A1086 PHE 0.027 0.002 PHE A 134 TYR 0.019 0.002 TYR A 252 ARG 0.005 0.001 ARG D 995 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 210 residues out of total 1551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 180 time to evaluate : 1.604 Fit side-chains revert: symmetry clash REVERT: A 30 LYS cc_start: 0.6328 (mttm) cc_final: 0.5298 (tmtt) REVERT: A 53 GLN cc_start: 0.4622 (OUTLIER) cc_final: 0.4184 (pm20) REVERT: A 61 GLN cc_start: 0.7003 (mt0) cc_final: 0.6541 (mt0) REVERT: A 204 PRO cc_start: 0.7396 (Cg_endo) cc_final: 0.6793 (Cg_exo) REVERT: A 264 LEU cc_start: 0.7416 (mp) cc_final: 0.7148 (mt) REVERT: A 295 LEU cc_start: 0.7223 (OUTLIER) cc_final: 0.7003 (pt) REVERT: A 321 LYS cc_start: 0.6910 (pttp) cc_final: 0.6600 (pttp) REVERT: A 326 LEU cc_start: 0.7194 (mt) cc_final: 0.6931 (mt) REVERT: A 364 TYR cc_start: 0.5902 (t80) cc_final: 0.5598 (t80) REVERT: A 385 GLN cc_start: 0.7207 (pm20) cc_final: 0.6869 (pm20) REVERT: A 732 LYS cc_start: 0.7715 (mttm) cc_final: 0.7383 (mttp) REVERT: A 751 MET cc_start: 0.6054 (OUTLIER) cc_final: 0.5650 (pmm) REVERT: A 978 LYS cc_start: 0.7566 (OUTLIER) cc_final: 0.7216 (mptp) REVERT: A 996 GLN cc_start: 0.7681 (OUTLIER) cc_final: 0.7121 (mt0) REVERT: B 985 MET cc_start: 0.8177 (mmm) cc_final: 0.7874 (mmp) REVERT: B 988 GLN cc_start: 0.7718 (tp40) cc_final: 0.7085 (mm110) REVERT: B 995 ARG cc_start: 0.7792 (OUTLIER) cc_final: 0.7576 (tpt-90) REVERT: B 1067 MET cc_start: 0.7937 (mtp) cc_final: 0.7673 (mtm) REVERT: C 824 ASP cc_start: 0.5797 (OUTLIER) cc_final: 0.5509 (m-30) REVERT: C 864 LYS cc_start: 0.8349 (ttmt) cc_final: 0.8054 (mttm) REVERT: C 940 ASP cc_start: 0.8321 (t70) cc_final: 0.7998 (t70) REVERT: C 988 GLN cc_start: 0.7966 (tp40) cc_final: 0.7730 (tp-100) REVERT: C 1067 MET cc_start: 0.7653 (ttm) cc_final: 0.7371 (mtm) REVERT: C 1078 ARG cc_start: 0.8343 (OUTLIER) cc_final: 0.7441 (mtm180) REVERT: D 996 GLN cc_start: 0.7296 (pt0) cc_final: 0.7038 (pt0) REVERT: D 1078 ARG cc_start: 0.7938 (ttp-110) cc_final: 0.7571 (ttp-110) REVERT: D 1089 ASP cc_start: 0.7757 (p0) cc_final: 0.7486 (p0) outliers start: 30 outliers final: 13 residues processed: 198 average time/residue: 1.4456 time to fit residues: 312.3288 Evaluate side-chains 191 residues out of total 1551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 170 time to evaluate : 1.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 53 GLN Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 751 MET Chi-restraints excluded: chain A residue 978 LYS Chi-restraints excluded: chain A residue 996 GLN Chi-restraints excluded: chain A residue 1089 ASP Chi-restraints excluded: chain B residue 995 ARG Chi-restraints excluded: chain B residue 1018 LYS Chi-restraints excluded: chain C residue 824 ASP Chi-restraints excluded: chain C residue 996 GLN Chi-restraints excluded: chain C residue 1078 ARG Chi-restraints excluded: chain D residue 866 GLU Chi-restraints excluded: chain D residue 892 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 165 optimal weight: 6.9990 chunk 125 optimal weight: 5.9990 chunk 86 optimal weight: 8.9990 chunk 18 optimal weight: 10.0000 chunk 79 optimal weight: 0.1980 chunk 112 optimal weight: 0.9990 chunk 167 optimal weight: 9.9990 chunk 177 optimal weight: 6.9990 chunk 87 optimal weight: 7.9990 chunk 159 optimal weight: 0.6980 chunk 47 optimal weight: 10.0000 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 136 HIS B 850 GLN B 981 ASN B 982 ASN D 850 GLN D 996 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15133 Z= 0.233 Angle : 0.672 17.708 20501 Z= 0.309 Chirality : 0.044 0.254 2244 Planarity : 0.004 0.048 2590 Dihedral : 14.077 175.607 2175 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.21 % Allowed : 20.73 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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: 1.25 (0.19), residues: 1859 helix: 1.57 (0.16), residues: 1011 sheet: 0.11 (0.43), residues: 140 loop : -0.00 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 84 HIS 0.004 0.001 HIS A1086 PHE 0.024 0.002 PHE A 134 TYR 0.025 0.002 TYR A 252 ARG 0.006 0.000 ARG D 995 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 207 residues out of total 1551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 173 time to evaluate : 1.738 Fit side-chains revert: symmetry clash REVERT: A 30 LYS cc_start: 0.6321 (mttm) cc_final: 0.5159 (tmtt) REVERT: A 61 GLN cc_start: 0.6985 (mt0) cc_final: 0.6522 (mt0) REVERT: A 204 PRO cc_start: 0.7383 (Cg_endo) cc_final: 0.6773 (Cg_exo) REVERT: A 256 LEU cc_start: 0.7202 (mt) cc_final: 0.6671 (mt) REVERT: A 264 LEU cc_start: 0.7436 (mp) cc_final: 0.7177 (mt) REVERT: A 321 LYS cc_start: 0.6882 (pttp) cc_final: 0.6522 (pttp) REVERT: A 732 LYS cc_start: 0.7740 (mttm) cc_final: 0.7391 (mttp) REVERT: A 751 MET cc_start: 0.6059 (OUTLIER) cc_final: 0.5697 (pmm) REVERT: A 802 GLU cc_start: 0.7441 (OUTLIER) cc_final: 0.6984 (mt-10) REVERT: A 864 LYS cc_start: 0.8338 (ttmm) cc_final: 0.8107 (ttpt) REVERT: A 978 LYS cc_start: 0.7554 (OUTLIER) cc_final: 0.7200 (mptp) REVERT: A 996 GLN cc_start: 0.7697 (OUTLIER) cc_final: 0.7140 (mt0) REVERT: B 985 MET cc_start: 0.8203 (mmm) cc_final: 0.7912 (mmp) REVERT: B 988 GLN cc_start: 0.7719 (tp40) cc_final: 0.7051 (mm110) REVERT: B 995 ARG cc_start: 0.7795 (OUTLIER) cc_final: 0.7272 (tpt-90) REVERT: B 1067 MET cc_start: 0.7930 (mtp) cc_final: 0.7663 (mtm) REVERT: C 864 LYS cc_start: 0.8373 (OUTLIER) cc_final: 0.8100 (mttm) REVERT: C 1067 MET cc_start: 0.7660 (ttm) cc_final: 0.7386 (mtm) REVERT: C 1078 ARG cc_start: 0.8339 (OUTLIER) cc_final: 0.7438 (mtm180) REVERT: D 996 GLN cc_start: 0.7282 (pt0) cc_final: 0.7052 (pt0) REVERT: D 1089 ASP cc_start: 0.7763 (p0) cc_final: 0.7486 (p0) outliers start: 34 outliers final: 15 residues processed: 191 average time/residue: 1.4999 time to fit residues: 313.9786 Evaluate side-chains 195 residues out of total 1551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 173 time to evaluate : 1.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 699 ASP Chi-restraints excluded: chain A residue 751 MET Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 802 GLU Chi-restraints excluded: chain A residue 867 MET Chi-restraints excluded: chain A residue 978 LYS Chi-restraints excluded: chain A residue 996 GLN Chi-restraints excluded: chain A residue 1089 ASP Chi-restraints excluded: chain B residue 995 ARG Chi-restraints excluded: chain B residue 1018 LYS Chi-restraints excluded: chain C residue 864 LYS Chi-restraints excluded: chain C residue 996 GLN Chi-restraints excluded: chain C residue 1078 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 148 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 chunk 132 optimal weight: 9.9990 chunk 73 optimal weight: 0.9990 chunk 151 optimal weight: 1.9990 chunk 122 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 90 optimal weight: 6.9990 chunk 159 optimal weight: 10.0000 chunk 44 optimal weight: 3.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 136 HIS B 850 GLN B 879 GLN B 982 ASN C 988 GLN D 850 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15133 Z= 0.192 Angle : 0.642 17.615 20501 Z= 0.292 Chirality : 0.043 0.235 2244 Planarity : 0.004 0.047 2590 Dihedral : 13.944 179.975 2175 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.82 % Allowed : 21.38 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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: 1.37 (0.19), residues: 1859 helix: 1.70 (0.16), residues: 1012 sheet: 0.13 (0.44), residues: 135 loop : 0.01 (0.24), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 84 HIS 0.003 0.001 HIS A1086 PHE 0.026 0.002 PHE A 134 TYR 0.030 0.002 TYR A 252 ARG 0.006 0.000 ARG D 995 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 205 residues out of total 1551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 177 time to evaluate : 1.591 Fit side-chains revert: symmetry clash REVERT: A 30 LYS cc_start: 0.6357 (mttm) cc_final: 0.5821 (mttp) REVERT: A 61 GLN cc_start: 0.6914 (mt0) cc_final: 0.6489 (mt0) REVERT: A 204 PRO cc_start: 0.7472 (Cg_endo) cc_final: 0.6869 (Cg_exo) REVERT: A 252 TYR cc_start: 0.7094 (t80) cc_final: 0.6859 (t80) REVERT: A 256 LEU cc_start: 0.7268 (mt) cc_final: 0.6830 (mt) REVERT: A 264 LEU cc_start: 0.7436 (mp) cc_final: 0.7153 (mm) REVERT: A 321 LYS cc_start: 0.6840 (pttp) cc_final: 0.6443 (pttp) REVERT: A 385 GLN cc_start: 0.7118 (pm20) cc_final: 0.6774 (pm20) REVERT: A 732 LYS cc_start: 0.7695 (mttm) cc_final: 0.7329 (mttp) REVERT: A 751 MET cc_start: 0.6076 (OUTLIER) cc_final: 0.5649 (pmm) REVERT: A 864 LYS cc_start: 0.8330 (ttmm) cc_final: 0.8104 (ttpt) REVERT: A 996 GLN cc_start: 0.7661 (OUTLIER) cc_final: 0.7100 (mt0) REVERT: B 881 ARG cc_start: 0.8026 (OUTLIER) cc_final: 0.7272 (tpp80) REVERT: B 988 GLN cc_start: 0.7802 (tp40) cc_final: 0.7046 (mm110) REVERT: B 1067 MET cc_start: 0.7898 (mtp) cc_final: 0.7648 (mtm) REVERT: C 824 ASP cc_start: 0.5707 (OUTLIER) cc_final: 0.5458 (m-30) REVERT: C 864 LYS cc_start: 0.8346 (OUTLIER) cc_final: 0.8061 (mttm) REVERT: C 1067 MET cc_start: 0.7609 (ttm) cc_final: 0.7348 (mtm) REVERT: C 1078 ARG cc_start: 0.8335 (OUTLIER) cc_final: 0.7440 (mtm180) REVERT: D 996 GLN cc_start: 0.7209 (pt0) cc_final: 0.6999 (pt0) REVERT: D 1089 ASP cc_start: 0.7763 (p0) cc_final: 0.7480 (p0) outliers start: 28 outliers final: 12 residues processed: 191 average time/residue: 1.4485 time to fit residues: 302.2562 Evaluate side-chains 188 residues out of total 1551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 170 time to evaluate : 1.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 699 ASP Chi-restraints excluded: chain A residue 751 MET Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 996 GLN Chi-restraints excluded: chain A residue 1089 ASP Chi-restraints excluded: chain B residue 881 ARG Chi-restraints excluded: chain B residue 1018 LYS Chi-restraints excluded: chain C residue 824 ASP Chi-restraints excluded: chain C residue 864 LYS Chi-restraints excluded: chain C residue 996 GLN Chi-restraints excluded: chain C residue 1078 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 59 optimal weight: 10.0000 chunk 160 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 104 optimal weight: 9.9990 chunk 43 optimal weight: 5.9990 chunk 178 optimal weight: 10.0000 chunk 147 optimal weight: 0.8980 chunk 82 optimal weight: 8.9990 chunk 14 optimal weight: 20.0000 chunk 58 optimal weight: 9.9990 chunk 93 optimal weight: 0.7980 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 136 HIS B 850 GLN B 982 ASN C 850 GLN D 850 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15133 Z= 0.232 Angle : 0.672 17.530 20501 Z= 0.309 Chirality : 0.044 0.230 2244 Planarity : 0.004 0.045 2590 Dihedral : 13.795 178.666 2175 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.21 % Allowed : 21.05 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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: 1.24 (0.19), residues: 1859 helix: 1.58 (0.16), residues: 1011 sheet: 0.06 (0.43), residues: 140 loop : -0.00 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 84 HIS 0.004 0.001 HIS A1086 PHE 0.028 0.002 PHE A 134 TYR 0.027 0.002 TYR A 252 ARG 0.006 0.000 ARG D 995 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 207 residues out of total 1551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 173 time to evaluate : 1.669 Fit side-chains revert: symmetry clash REVERT: A 30 LYS cc_start: 0.6329 (mttm) cc_final: 0.5913 (mttp) REVERT: A 61 GLN cc_start: 0.6897 (mt0) cc_final: 0.6493 (mt0) REVERT: A 140 VAL cc_start: 0.3497 (OUTLIER) cc_final: 0.3143 (p) REVERT: A 178 LYS cc_start: 0.5316 (OUTLIER) cc_final: 0.4989 (mtmt) REVERT: A 204 PRO cc_start: 0.7304 (Cg_endo) cc_final: 0.6688 (Cg_exo) REVERT: A 252 TYR cc_start: 0.7151 (t80) cc_final: 0.6893 (t80) REVERT: A 256 LEU cc_start: 0.7247 (mt) cc_final: 0.6870 (mt) REVERT: A 264 LEU cc_start: 0.7452 (mp) cc_final: 0.7162 (mm) REVERT: A 321 LYS cc_start: 0.6819 (pttp) cc_final: 0.6398 (pttp) REVERT: A 385 GLN cc_start: 0.7104 (pm20) cc_final: 0.6782 (pm20) REVERT: A 732 LYS cc_start: 0.7694 (mttm) cc_final: 0.7363 (mttp) REVERT: A 751 MET cc_start: 0.6133 (OUTLIER) cc_final: 0.5788 (pmm) REVERT: A 996 GLN cc_start: 0.7725 (OUTLIER) cc_final: 0.7161 (mt0) REVERT: B 881 ARG cc_start: 0.8067 (OUTLIER) cc_final: 0.7307 (tpp80) REVERT: B 988 GLN cc_start: 0.7818 (tp40) cc_final: 0.7078 (mm110) REVERT: B 995 ARG cc_start: 0.7789 (OUTLIER) cc_final: 0.7572 (tpt-90) REVERT: B 1067 MET cc_start: 0.7933 (mtp) cc_final: 0.7665 (mtm) REVERT: C 824 ASP cc_start: 0.5740 (OUTLIER) cc_final: 0.5500 (m-30) REVERT: C 864 LYS cc_start: 0.8362 (OUTLIER) cc_final: 0.8067 (mttm) REVERT: C 1067 MET cc_start: 0.7659 (ttm) cc_final: 0.7386 (mtm) REVERT: C 1078 ARG cc_start: 0.8353 (OUTLIER) cc_final: 0.7433 (mtm180) REVERT: D 996 GLN cc_start: 0.7206 (pt0) cc_final: 0.7001 (pt0) REVERT: D 1089 ASP cc_start: 0.7787 (p0) cc_final: 0.7509 (p0) outliers start: 34 outliers final: 18 residues processed: 190 average time/residue: 1.4534 time to fit residues: 301.7269 Evaluate side-chains 194 residues out of total 1551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 167 time to evaluate : 1.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 178 LYS Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 699 ASP Chi-restraints excluded: chain A residue 751 MET Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 791 ASP Chi-restraints excluded: chain A residue 996 GLN Chi-restraints excluded: chain A residue 1089 ASP Chi-restraints excluded: chain B residue 881 ARG Chi-restraints excluded: chain B residue 995 ARG Chi-restraints excluded: chain B residue 1018 LYS Chi-restraints excluded: chain C residue 824 ASP Chi-restraints excluded: chain C residue 864 LYS Chi-restraints excluded: chain C residue 865 GLU Chi-restraints excluded: chain C residue 996 GLN Chi-restraints excluded: chain C residue 1078 ARG Chi-restraints excluded: chain D residue 821 VAL Chi-restraints excluded: chain D residue 866 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 171 optimal weight: 8.9990 chunk 20 optimal weight: 5.9990 chunk 101 optimal weight: 0.8980 chunk 130 optimal weight: 8.9990 chunk 100 optimal weight: 5.9990 chunk 149 optimal weight: 6.9990 chunk 99 optimal weight: 5.9990 chunk 177 optimal weight: 2.9990 chunk 110 optimal weight: 10.0000 chunk 108 optimal weight: 2.9990 chunk 81 optimal weight: 0.0270 overall best weight: 2.5844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 136 HIS B 850 GLN B 982 ASN C 850 GLN C 988 GLN D 850 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15133 Z= 0.210 Angle : 0.653 17.531 20501 Z= 0.298 Chirality : 0.044 0.233 2244 Planarity : 0.004 0.046 2590 Dihedral : 13.006 175.999 2175 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.27 % Allowed : 20.66 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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: 1.33 (0.19), residues: 1859 helix: 1.68 (0.16), residues: 1011 sheet: 0.06 (0.43), residues: 140 loop : -0.00 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 276 HIS 0.004 0.001 HIS A1086 PHE 0.026 0.002 PHE A 134 TYR 0.026 0.002 TYR A 252 ARG 0.007 0.000 ARG D 995 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 209 residues out of total 1551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 174 time to evaluate : 1.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 LYS cc_start: 0.6314 (mttm) cc_final: 0.5906 (mttp) REVERT: A 61 GLN cc_start: 0.6926 (mt0) cc_final: 0.6538 (mt0) REVERT: A 140 VAL cc_start: 0.3306 (OUTLIER) cc_final: 0.2934 (p) REVERT: A 178 LYS cc_start: 0.5337 (OUTLIER) cc_final: 0.4815 (mtmt) REVERT: A 204 PRO cc_start: 0.7303 (Cg_endo) cc_final: 0.6674 (Cg_exo) REVERT: A 252 TYR cc_start: 0.7185 (t80) cc_final: 0.6983 (t80) REVERT: A 256 LEU cc_start: 0.7223 (mt) cc_final: 0.6825 (mt) REVERT: A 264 LEU cc_start: 0.7450 (mp) cc_final: 0.7156 (mm) REVERT: A 385 GLN cc_start: 0.7098 (pm20) cc_final: 0.6779 (pm20) REVERT: A 386 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.7300 (tm-30) REVERT: A 732 LYS cc_start: 0.7710 (mttm) cc_final: 0.7348 (mttp) REVERT: A 751 MET cc_start: 0.6132 (OUTLIER) cc_final: 0.5848 (pmm) REVERT: A 864 LYS cc_start: 0.8323 (ttmm) cc_final: 0.8109 (ttpt) REVERT: A 996 GLN cc_start: 0.7691 (OUTLIER) cc_final: 0.7150 (mt0) REVERT: B 881 ARG cc_start: 0.8042 (OUTLIER) cc_final: 0.7259 (tpp80) REVERT: B 988 GLN cc_start: 0.7823 (tp40) cc_final: 0.7060 (mm110) REVERT: B 995 ARG cc_start: 0.7816 (OUTLIER) cc_final: 0.7614 (tpt-90) REVERT: B 1067 MET cc_start: 0.7899 (mtp) cc_final: 0.7647 (mtm) REVERT: C 824 ASP cc_start: 0.5697 (OUTLIER) cc_final: 0.5470 (m-30) REVERT: C 864 LYS cc_start: 0.8354 (OUTLIER) cc_final: 0.8049 (mttm) REVERT: C 1067 MET cc_start: 0.7648 (ttm) cc_final: 0.7378 (mtm) REVERT: C 1078 ARG cc_start: 0.8350 (OUTLIER) cc_final: 0.7455 (mtm180) REVERT: D 1089 ASP cc_start: 0.7784 (p0) cc_final: 0.7500 (p0) outliers start: 35 outliers final: 17 residues processed: 193 average time/residue: 1.4733 time to fit residues: 310.4386 Evaluate side-chains 198 residues out of total 1551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 171 time to evaluate : 1.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 178 LYS Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 386 GLU Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 699 ASP Chi-restraints excluded: chain A residue 751 MET Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 791 ASP Chi-restraints excluded: chain A residue 996 GLN Chi-restraints excluded: chain A residue 1089 ASP Chi-restraints excluded: chain B residue 881 ARG Chi-restraints excluded: chain B residue 995 ARG Chi-restraints excluded: chain B residue 1018 LYS Chi-restraints excluded: chain C residue 824 ASP Chi-restraints excluded: chain C residue 864 LYS Chi-restraints excluded: chain C residue 865 GLU Chi-restraints excluded: chain C residue 996 GLN Chi-restraints excluded: chain C residue 1078 ARG Chi-restraints excluded: chain D residue 821 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 109 optimal weight: 8.9990 chunk 70 optimal weight: 9.9990 chunk 105 optimal weight: 5.9990 chunk 53 optimal weight: 10.0000 chunk 34 optimal weight: 20.0000 chunk 112 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 87 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 chunk 139 optimal weight: 9.9990 chunk 161 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 136 HIS B 850 GLN B 982 ASN C 850 GLN C 988 GLN D 850 GLN D1081 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 15133 Z= 0.289 Angle : 0.712 17.592 20501 Z= 0.331 Chirality : 0.046 0.244 2244 Planarity : 0.004 0.044 2590 Dihedral : 12.450 171.633 2175 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.14 % Allowed : 20.60 % Favored : 77.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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: 1.10 (0.19), residues: 1859 helix: 1.44 (0.16), residues: 1011 sheet: 0.01 (0.43), residues: 140 loop : -0.05 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 827 HIS 0.005 0.002 HIS A1086 PHE 0.026 0.002 PHE A 134 TYR 0.024 0.003 TYR A 252 ARG 0.007 0.001 ARG D 995 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 201 residues out of total 1551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 168 time to evaluate : 1.606 Fit side-chains revert: symmetry clash REVERT: A 30 LYS cc_start: 0.6213 (mttm) cc_final: 0.5769 (mttp) REVERT: A 61 GLN cc_start: 0.6934 (mt0) cc_final: 0.6566 (mt0) REVERT: A 140 VAL cc_start: 0.3445 (OUTLIER) cc_final: 0.3056 (p) REVERT: A 178 LYS cc_start: 0.5270 (OUTLIER) cc_final: 0.4897 (mtmt) REVERT: A 204 PRO cc_start: 0.7266 (Cg_endo) cc_final: 0.6654 (Cg_exo) REVERT: A 256 LEU cc_start: 0.7220 (mt) cc_final: 0.6862 (mt) REVERT: A 264 LEU cc_start: 0.7429 (mp) cc_final: 0.7162 (mm) REVERT: A 385 GLN cc_start: 0.7061 (pm20) cc_final: 0.6745 (pm20) REVERT: A 386 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.7173 (tm-30) REVERT: A 732 LYS cc_start: 0.7693 (mttm) cc_final: 0.7369 (mttp) REVERT: A 751 MET cc_start: 0.6213 (OUTLIER) cc_final: 0.5912 (pmm) REVERT: A 802 GLU cc_start: 0.7462 (OUTLIER) cc_final: 0.6959 (mt-10) REVERT: A 864 LYS cc_start: 0.8371 (ttmm) cc_final: 0.8121 (ttpt) REVERT: A 996 GLN cc_start: 0.7759 (OUTLIER) cc_final: 0.7201 (mt0) REVERT: B 881 ARG cc_start: 0.8101 (OUTLIER) cc_final: 0.7342 (tpp80) REVERT: B 988 GLN cc_start: 0.7843 (tp40) cc_final: 0.7222 (mm110) REVERT: B 995 ARG cc_start: 0.7806 (OUTLIER) cc_final: 0.7601 (tpt-90) REVERT: B 1067 MET cc_start: 0.7965 (mtp) cc_final: 0.7706 (mtm) REVERT: C 824 ASP cc_start: 0.5722 (OUTLIER) cc_final: 0.5522 (m-30) REVERT: C 864 LYS cc_start: 0.8358 (OUTLIER) cc_final: 0.8065 (mttm) REVERT: C 1067 MET cc_start: 0.7676 (ttm) cc_final: 0.7401 (mtm) REVERT: C 1078 ARG cc_start: 0.8371 (OUTLIER) cc_final: 0.7447 (mtm180) REVERT: D 1089 ASP cc_start: 0.7692 (p0) cc_final: 0.7427 (p0) outliers start: 33 outliers final: 17 residues processed: 189 average time/residue: 1.5588 time to fit residues: 320.3776 Evaluate side-chains 196 residues out of total 1551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 168 time to evaluate : 1.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 158 GLU Chi-restraints excluded: chain A residue 178 LYS Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 386 GLU Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 751 MET Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 791 ASP Chi-restraints excluded: chain A residue 802 GLU Chi-restraints excluded: chain A residue 996 GLN Chi-restraints excluded: chain A residue 1089 ASP Chi-restraints excluded: chain B residue 881 ARG Chi-restraints excluded: chain B residue 995 ARG Chi-restraints excluded: chain B residue 1018 LYS Chi-restraints excluded: chain C residue 824 ASP Chi-restraints excluded: chain C residue 864 LYS Chi-restraints excluded: chain C residue 865 GLU Chi-restraints excluded: chain C residue 996 GLN Chi-restraints excluded: chain C residue 1078 ARG Chi-restraints excluded: chain D residue 821 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 169 optimal weight: 4.9990 chunk 155 optimal weight: 6.9990 chunk 165 optimal weight: 0.9990 chunk 99 optimal weight: 0.8980 chunk 71 optimal weight: 0.9990 chunk 129 optimal weight: 6.9990 chunk 50 optimal weight: 7.9990 chunk 149 optimal weight: 4.9990 chunk 156 optimal weight: 0.9990 chunk 164 optimal weight: 5.9990 chunk 108 optimal weight: 1.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 136 HIS B 850 GLN C 850 GLN C 988 GLN D 850 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 15133 Z= 0.154 Angle : 0.620 17.462 20501 Z= 0.280 Chirality : 0.042 0.240 2244 Planarity : 0.003 0.049 2590 Dihedral : 11.457 170.167 2175 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.75 % Allowed : 20.60 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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: 1.45 (0.19), residues: 1859 helix: 1.80 (0.16), residues: 1010 sheet: 0.09 (0.44), residues: 135 loop : 0.01 (0.23), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 84 HIS 0.004 0.001 HIS A 332 PHE 0.027 0.001 PHE A 134 TYR 0.021 0.002 TYR A 317 ARG 0.007 0.000 ARG D 995 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 202 residues out of total 1551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 175 time to evaluate : 1.675 Fit side-chains revert: symmetry clash REVERT: A 30 LYS cc_start: 0.6293 (mttm) cc_final: 0.5909 (mttp) REVERT: A 61 GLN cc_start: 0.6943 (mt0) cc_final: 0.6610 (mt0) REVERT: A 107 ILE cc_start: 0.5839 (OUTLIER) cc_final: 0.5418 (tt) REVERT: A 140 VAL cc_start: 0.3509 (OUTLIER) cc_final: 0.3122 (p) REVERT: A 178 LYS cc_start: 0.5355 (OUTLIER) cc_final: 0.4888 (mtmt) REVERT: A 204 PRO cc_start: 0.7496 (Cg_endo) cc_final: 0.6855 (Cg_exo) REVERT: A 249 GLU cc_start: 0.5725 (mp0) cc_final: 0.5389 (mp0) REVERT: A 256 LEU cc_start: 0.7286 (mt) cc_final: 0.7028 (mt) REVERT: A 264 LEU cc_start: 0.7477 (mp) cc_final: 0.7191 (mm) REVERT: A 732 LYS cc_start: 0.7686 (mttm) cc_final: 0.7310 (mttp) REVERT: A 751 MET cc_start: 0.6250 (OUTLIER) cc_final: 0.5913 (pmm) REVERT: A 864 LYS cc_start: 0.8317 (ttmm) cc_final: 0.8092 (ttpt) REVERT: A 996 GLN cc_start: 0.7658 (OUTLIER) cc_final: 0.7112 (mt0) REVERT: B 988 GLN cc_start: 0.7779 (tp40) cc_final: 0.6984 (mm110) REVERT: B 1067 MET cc_start: 0.7881 (mtp) cc_final: 0.7574 (mtm) REVERT: C 864 LYS cc_start: 0.8330 (OUTLIER) cc_final: 0.8013 (mttm) REVERT: C 1067 MET cc_start: 0.7564 (ttm) cc_final: 0.7318 (mtm) REVERT: C 1078 ARG cc_start: 0.8341 (OUTLIER) cc_final: 0.7484 (mtm180) REVERT: D 1089 ASP cc_start: 0.7798 (p0) cc_final: 0.7511 (p0) outliers start: 27 outliers final: 11 residues processed: 192 average time/residue: 1.5018 time to fit residues: 314.2840 Evaluate side-chains 190 residues out of total 1551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 172 time to evaluate : 1.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 178 LYS Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 751 MET Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 996 GLN Chi-restraints excluded: chain A residue 1089 ASP Chi-restraints excluded: chain B residue 1018 LYS Chi-restraints excluded: chain C residue 864 LYS Chi-restraints excluded: chain C residue 996 GLN Chi-restraints excluded: chain C residue 1078 ARG Chi-restraints excluded: chain D residue 821 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 174 optimal weight: 6.9990 chunk 106 optimal weight: 3.9990 chunk 82 optimal weight: 6.9990 chunk 121 optimal weight: 2.9990 chunk 183 optimal weight: 6.9990 chunk 168 optimal weight: 7.9990 chunk 145 optimal weight: 20.0000 chunk 15 optimal weight: 7.9990 chunk 112 optimal weight: 4.9990 chunk 89 optimal weight: 0.7980 chunk 115 optimal weight: 0.8980 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 136 HIS B 850 GLN C 988 GLN D 850 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15133 Z= 0.225 Angle : 0.669 17.458 20501 Z= 0.307 Chirality : 0.044 0.241 2244 Planarity : 0.004 0.049 2590 Dihedral : 11.254 171.161 2175 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.43 % Allowed : 21.05 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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: 1.33 (0.19), residues: 1859 helix: 1.68 (0.16), residues: 1007 sheet: 0.09 (0.43), residues: 140 loop : -0.02 (0.23), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 827 HIS 0.004 0.001 HIS A1086 PHE 0.026 0.002 PHE A 134 TYR 0.021 0.002 TYR A 304 ARG 0.008 0.000 ARG D 995 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 193 residues out of total 1551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 171 time to evaluate : 1.647 Fit side-chains revert: symmetry clash REVERT: A 30 LYS cc_start: 0.6289 (mttm) cc_final: 0.5874 (mttp) REVERT: A 61 GLN cc_start: 0.6923 (mt0) cc_final: 0.6609 (mt0) REVERT: A 107 ILE cc_start: 0.5738 (OUTLIER) cc_final: 0.5348 (tt) REVERT: A 140 VAL cc_start: 0.3548 (OUTLIER) cc_final: 0.3159 (p) REVERT: A 178 LYS cc_start: 0.5321 (OUTLIER) cc_final: 0.4959 (mtmt) REVERT: A 204 PRO cc_start: 0.7362 (Cg_endo) cc_final: 0.6726 (Cg_exo) REVERT: A 249 GLU cc_start: 0.5808 (mp0) cc_final: 0.5484 (mp0) REVERT: A 256 LEU cc_start: 0.7265 (mt) cc_final: 0.6991 (mt) REVERT: A 264 LEU cc_start: 0.7463 (mp) cc_final: 0.7178 (mm) REVERT: A 732 LYS cc_start: 0.7672 (mttm) cc_final: 0.7333 (mttp) REVERT: A 751 MET cc_start: 0.6219 (OUTLIER) cc_final: 0.5898 (pmm) REVERT: A 864 LYS cc_start: 0.8338 (ttmm) cc_final: 0.8098 (ttpt) REVERT: A 996 GLN cc_start: 0.7697 (OUTLIER) cc_final: 0.7160 (mt0) REVERT: B 985 MET cc_start: 0.8134 (mmm) cc_final: 0.7896 (mmp) REVERT: B 988 GLN cc_start: 0.7826 (tp40) cc_final: 0.7073 (mm110) REVERT: B 1067 MET cc_start: 0.7913 (mtp) cc_final: 0.7664 (mtm) REVERT: C 824 ASP cc_start: 0.5683 (OUTLIER) cc_final: 0.5452 (m-30) REVERT: C 864 LYS cc_start: 0.8347 (OUTLIER) cc_final: 0.8075 (mttm) REVERT: C 1067 MET cc_start: 0.7641 (ttm) cc_final: 0.7369 (mtm) REVERT: C 1078 ARG cc_start: 0.8354 (OUTLIER) cc_final: 0.7468 (mtm180) REVERT: D 1089 ASP cc_start: 0.7784 (p0) cc_final: 0.7503 (p0) outliers start: 22 outliers final: 12 residues processed: 185 average time/residue: 1.4634 time to fit residues: 296.1947 Evaluate side-chains 189 residues out of total 1551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 169 time to evaluate : 1.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 178 LYS Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 751 MET Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 996 GLN Chi-restraints excluded: chain A residue 1089 ASP Chi-restraints excluded: chain B residue 1018 LYS Chi-restraints excluded: chain C residue 824 ASP Chi-restraints excluded: chain C residue 864 LYS Chi-restraints excluded: chain C residue 996 GLN Chi-restraints excluded: chain C residue 1078 ARG Chi-restraints excluded: chain D residue 821 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 9.9990 chunk 44 optimal weight: 10.0000 chunk 134 optimal weight: 6.9990 chunk 21 optimal weight: 20.0000 chunk 40 optimal weight: 3.9990 chunk 146 optimal weight: 10.0000 chunk 61 optimal weight: 3.9990 chunk 150 optimal weight: 10.0000 chunk 18 optimal weight: 10.0000 chunk 26 optimal weight: 0.0570 chunk 128 optimal weight: 10.0000 overall best weight: 5.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 136 HIS B 850 GLN C 850 GLN C 988 GLN D 850 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.142599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.105174 restraints weight = 24160.908| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 1.71 r_work: 0.2965 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2850 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2850 r_free = 0.2850 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2850 r_free = 0.2850 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2850 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8869 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 15133 Z= 0.345 Angle : 0.754 17.722 20501 Z= 0.353 Chirality : 0.049 0.265 2244 Planarity : 0.005 0.047 2590 Dihedral : 11.227 171.941 2175 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.69 % Allowed : 20.66 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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 (0.19), residues: 1859 helix: 1.36 (0.16), residues: 1013 sheet: -0.30 (0.42), residues: 150 loop : -0.06 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 827 HIS 0.005 0.002 HIS A 113 PHE 0.027 0.002 PHE A 134 TYR 0.021 0.003 TYR A 192 ARG 0.007 0.001 ARG D 995 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6074.75 seconds wall clock time: 109 minutes 23.85 seconds (6563.85 seconds total)