Starting phenix.real_space_refine on Thu Jul 31 10:37:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kf9_22847/07_2025/7kf9_22847.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kf9_22847/07_2025/7kf9_22847.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7kf9_22847/07_2025/7kf9_22847.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kf9_22847/07_2025/7kf9_22847.map" model { file = "/net/cci-nas-00/data/ceres_data/7kf9_22847/07_2025/7kf9_22847.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kf9_22847/07_2025/7kf9_22847.cif" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.072 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 42 5.16 5 C 8331 2.51 5 N 2214 2.21 5 O 2574 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 65 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 13161 Number of models: 1 Model: "" Number of chains: 18 Chain: "G" Number of atoms: 1014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1014 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain: "A" Number of atoms: 1724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1724 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 11, 'TRANS': 209} Chain breaks: 1 Chain: "D" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 735 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain breaks: 1 Chain: "J" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 811 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 7, 'TRANS': 102} Chain: "I" Number of atoms: 1014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1014 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain: "C" Number of atoms: 1724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1724 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 11, 'TRANS': 209} Chain breaks: 1 Chain: "F" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 735 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain breaks: 1 Chain: "L" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 811 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 7, 'TRANS': 102} Chain: "H" Number of atoms: 1014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1014 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain: "B" Number of atoms: 1724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1724 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 11, 'TRANS': 209} Chain breaks: 1 Chain: "E" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 735 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain breaks: 1 Chain: "K" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 811 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 7, 'TRANS': 102} Chain: "M" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "N" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "O" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 7.89, per 1000 atoms: 0.60 Number of scatterers: 13161 At special positions: 0 Unit cell: (148.35, 148.35, 106.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 42 16.00 O 2574 8.00 N 2214 7.00 C 8331 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 121 " - pdb=" SG CYS A 147 " distance=2.03 Simple disulfide: pdb=" SG CYS D 511 " - pdb=" SG CYS D 556 " distance=2.04 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 89 " distance=2.02 Simple disulfide: pdb=" SG CYS C 121 " - pdb=" SG CYS C 147 " distance=2.03 Simple disulfide: pdb=" SG CYS F 511 " - pdb=" SG CYS F 556 " distance=2.04 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 147 " distance=2.03 Simple disulfide: pdb=" SG CYS E 511 " - pdb=" SG CYS E 556 " distance=2.04 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 89 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 Links applied ALPHA1-3 " BMA M 3 " - " MAN M 4 " " BMA N 3 " - " MAN N 4 " " BMA O 3 " - " MAN O 4 " ALPHA1-6 " BMA M 3 " - " MAN M 5 " " BMA N 3 " - " MAN N 5 " " BMA O 3 " - " MAN O 5 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " NAG-ASN " NAG A 401 " - " ASN A 257 " " NAG A 402 " - " ASN A 268 " " NAG A 403 " - " ASN A 228 " " NAG B 401 " - " ASN B 257 " " NAG B 402 " - " ASN B 268 " " NAG B 403 " - " ASN B 228 " " NAG C 401 " - " ASN C 257 " " NAG C 402 " - " ASN C 268 " " NAG C 403 " - " ASN C 228 " " NAG M 1 " - " ASN D 563 " " NAG N 1 " - " ASN F 563 " " NAG O 1 " - " ASN E 563 " Time building additional restraints: 3.70 Conformation dependent library (CDL) restraints added in 1.7 seconds 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2982 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 27 sheets defined 16.8% alpha, 38.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.98 Creating SS restraints... Processing helix chain 'G' and resid 63 through 66 Processing helix chain 'G' and resid 88 through 92 Processing helix chain 'A' and resid 59 through 61 No H-bonds generated for 'chain 'A' and resid 59 through 61' Processing helix chain 'A' and resid 71 through 74 Processing helix chain 'A' and resid 78 through 84 removed outlier: 3.787A pdb=" N LYS A 84 " --> pdb=" O PRO A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 264 Processing helix chain 'D' and resid 528 through 532 Processing helix chain 'D' and resid 538 through 542 Processing helix chain 'D' and resid 553 through 575 removed outlier: 4.033A pdb=" N GLN D 567 " --> pdb=" O ASN D 563 " (cutoff:3.500A) Processing helix chain 'D' and resid 583 through 598 removed outlier: 3.908A pdb=" N ARG D 596 " --> pdb=" O PHE D 592 " (cutoff:3.500A) Processing helix chain 'J' and resid 80 through 84 Processing helix chain 'I' and resid 63 through 66 Processing helix chain 'I' and resid 88 through 92 Processing helix chain 'C' and resid 59 through 61 No H-bonds generated for 'chain 'C' and resid 59 through 61' Processing helix chain 'C' and resid 71 through 74 Processing helix chain 'C' and resid 78 through 84 removed outlier: 3.785A pdb=" N LYS C 84 " --> pdb=" O PRO C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 264 Processing helix chain 'F' and resid 528 through 532 Processing helix chain 'F' and resid 538 through 542 Processing helix chain 'F' and resid 553 through 575 removed outlier: 4.033A pdb=" N GLN F 567 " --> pdb=" O ASN F 563 " (cutoff:3.500A) Processing helix chain 'F' and resid 583 through 598 removed outlier: 3.908A pdb=" N ARG F 596 " --> pdb=" O PHE F 592 " (cutoff:3.500A) Processing helix chain 'L' and resid 80 through 84 Processing helix chain 'H' and resid 63 through 66 Processing helix chain 'H' and resid 88 through 92 Processing helix chain 'B' and resid 59 through 61 No H-bonds generated for 'chain 'B' and resid 59 through 61' Processing helix chain 'B' and resid 71 through 74 Processing helix chain 'B' and resid 78 through 84 removed outlier: 3.787A pdb=" N LYS B 84 " --> pdb=" O PRO B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 264 Processing helix chain 'E' and resid 528 through 532 Processing helix chain 'E' and resid 538 through 542 Processing helix chain 'E' and resid 553 through 575 removed outlier: 4.032A pdb=" N GLN E 567 " --> pdb=" O ASN E 563 " (cutoff:3.500A) Processing helix chain 'E' and resid 583 through 598 removed outlier: 3.908A pdb=" N ARG E 596 " --> pdb=" O PHE E 592 " (cutoff:3.500A) Processing helix chain 'K' and resid 80 through 84 Processing sheet with id=AA1, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'G' and resid 11 through 12 removed outlier: 4.217A pdb=" N TYR G 35 " --> pdb=" O VAL G 100 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N TRP G 36 " --> pdb=" O PHE G 52 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N PHE G 52 " --> pdb=" O TRP G 36 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N TRP G 38 " --> pdb=" O ILE G 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 11 through 12 removed outlier: 3.755A pdb=" N VAL G 120 " --> pdb=" O ARG G 99 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 43 through 45 removed outlier: 5.260A pdb=" N GLU A 178 " --> pdb=" O ASN A 107 " (cutoff:3.500A) removed outlier: 8.733A pdb=" N ASN A 107 " --> pdb=" O GLU A 178 " (cutoff:3.500A) removed outlier: 13.553A pdb=" N VAL A 180 " --> pdb=" O ALA A 105 " (cutoff:3.500A) removed outlier: 11.531A pdb=" N ALA A 105 " --> pdb=" O VAL A 180 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N GLU A 106 " --> pdb=" O TYR A 137 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N HIS A 139 " --> pdb=" O GLU A 106 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N CYS A 108 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N VAL A 141 " --> pdb=" O CYS A 108 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ASN A 110 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N GLY A 143 " --> pdb=" O ASN A 110 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N GLU A 112 " --> pdb=" O GLY A 143 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ARG A 136 " --> pdb=" O THR A 216 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N ILE A 218 " --> pdb=" O ARG A 136 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N VAL A 138 " --> pdb=" O ILE A 218 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N TYR A 220 " --> pdb=" O VAL A 138 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LYS A 140 " --> pdb=" O TYR A 220 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N ALA A 222 " --> pdb=" O LYS A 140 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N SER A 142 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 14.582A pdb=" N THR A 217 " --> pdb=" O ASP A 237 " (cutoff:3.500A) removed outlier: 10.544A pdb=" N ASP A 237 " --> pdb=" O THR A 217 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N ARG A 219 " --> pdb=" O GLU A 235 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N THR A 240 " --> pdb=" O VAL A 236 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N TYR A 241 " --> pdb=" O TRP A 275 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 96 through 98 removed outlier: 8.433A pdb=" N ALA A 101 " --> pdb=" O LEU A 63 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N SER A 65 " --> pdb=" O ALA A 101 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N GLU A 103 " --> pdb=" O SER A 65 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N GLY A 67 " --> pdb=" O GLU A 103 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 86 through 89 Processing sheet with id=AA7, first strand: chain 'J' and resid 9 through 12 removed outlier: 6.613A pdb=" N ALA J 10 " --> pdb=" O THR J 109 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N TRP J 36 " --> pdb=" O LEU J 48 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'J' and resid 9 through 12 removed outlier: 6.613A pdb=" N ALA J 10 " --> pdb=" O THR J 109 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'J' and resid 17 through 23 Processing sheet with id=AB1, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'I' and resid 11 through 12 removed outlier: 4.215A pdb=" N TYR I 35 " --> pdb=" O VAL I 100 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N TRP I 36 " --> pdb=" O PHE I 52 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N PHE I 52 " --> pdb=" O TRP I 36 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N TRP I 38 " --> pdb=" O ILE I 50 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 11 through 12 removed outlier: 3.757A pdb=" N VAL I 120 " --> pdb=" O ARG I 99 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 43 through 45 removed outlier: 5.259A pdb=" N GLU C 178 " --> pdb=" O ASN C 107 " (cutoff:3.500A) removed outlier: 8.732A pdb=" N ASN C 107 " --> pdb=" O GLU C 178 " (cutoff:3.500A) removed outlier: 13.553A pdb=" N VAL C 180 " --> pdb=" O ALA C 105 " (cutoff:3.500A) removed outlier: 11.529A pdb=" N ALA C 105 " --> pdb=" O VAL C 180 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N GLU C 106 " --> pdb=" O TYR C 137 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N HIS C 139 " --> pdb=" O GLU C 106 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N CYS C 108 " --> pdb=" O HIS C 139 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N VAL C 141 " --> pdb=" O CYS C 108 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ASN C 110 " --> pdb=" O VAL C 141 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N GLY C 143 " --> pdb=" O ASN C 110 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N GLU C 112 " --> pdb=" O GLY C 143 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N ARG C 136 " --> pdb=" O THR C 216 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N ILE C 218 " --> pdb=" O ARG C 136 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N VAL C 138 " --> pdb=" O ILE C 218 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N TYR C 220 " --> pdb=" O VAL C 138 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LYS C 140 " --> pdb=" O TYR C 220 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N ALA C 222 " --> pdb=" O LYS C 140 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N SER C 142 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 14.583A pdb=" N THR C 217 " --> pdb=" O ASP C 237 " (cutoff:3.500A) removed outlier: 10.544A pdb=" N ASP C 237 " --> pdb=" O THR C 217 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N ARG C 219 " --> pdb=" O GLU C 235 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N THR C 240 " --> pdb=" O VAL C 236 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N TYR C 241 " --> pdb=" O TRP C 275 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 96 through 98 removed outlier: 5.968A pdb=" N ASN C 69 " --> pdb=" O GLU C 103 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 86 through 89 Processing sheet with id=AB7, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.613A pdb=" N ALA L 10 " --> pdb=" O THR L 109 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.613A pdb=" N ALA L 10 " --> pdb=" O THR L 109 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'L' and resid 17 through 23 Processing sheet with id=AC1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AC2, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.216A pdb=" N TYR H 35 " --> pdb=" O VAL H 100 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N TRP H 36 " --> pdb=" O PHE H 52 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N PHE H 52 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N TRP H 38 " --> pdb=" O ILE H 50 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.756A pdb=" N VAL H 120 " --> pdb=" O ARG H 99 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 43 through 45 removed outlier: 5.260A pdb=" N GLU B 178 " --> pdb=" O ASN B 107 " (cutoff:3.500A) removed outlier: 8.733A pdb=" N ASN B 107 " --> pdb=" O GLU B 178 " (cutoff:3.500A) removed outlier: 13.554A pdb=" N VAL B 180 " --> pdb=" O ALA B 105 " (cutoff:3.500A) removed outlier: 11.527A pdb=" N ALA B 105 " --> pdb=" O VAL B 180 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N GLU B 106 " --> pdb=" O TYR B 137 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N HIS B 139 " --> pdb=" O GLU B 106 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N CYS B 108 " --> pdb=" O HIS B 139 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N VAL B 141 " --> pdb=" O CYS B 108 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ASN B 110 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N GLY B 143 " --> pdb=" O ASN B 110 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N GLU B 112 " --> pdb=" O GLY B 143 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ARG B 136 " --> pdb=" O THR B 216 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N ILE B 218 " --> pdb=" O ARG B 136 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N VAL B 138 " --> pdb=" O ILE B 218 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N TYR B 220 " --> pdb=" O VAL B 138 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LYS B 140 " --> pdb=" O TYR B 220 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N ALA B 222 " --> pdb=" O LYS B 140 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N SER B 142 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 14.583A pdb=" N THR B 217 " --> pdb=" O ASP B 237 " (cutoff:3.500A) removed outlier: 10.545A pdb=" N ASP B 237 " --> pdb=" O THR B 217 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N ARG B 219 " --> pdb=" O GLU B 235 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N THR B 240 " --> pdb=" O VAL B 236 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N TYR B 241 " --> pdb=" O TRP B 275 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 96 through 98 removed outlier: 5.968A pdb=" N ASN B 69 " --> pdb=" O GLU B 103 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 86 through 89 Processing sheet with id=AC7, first strand: chain 'K' and resid 9 through 12 removed outlier: 6.613A pdb=" N ALA K 10 " --> pdb=" O THR K 109 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N TRP K 36 " --> pdb=" O LEU K 48 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'K' and resid 9 through 12 removed outlier: 6.613A pdb=" N ALA K 10 " --> pdb=" O THR K 109 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'K' and resid 17 through 23 516 hydrogen bonds defined for protein. 1263 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: 4.57 Time building geometry restraints manager: 4.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 2727 1.32 - 1.46: 4619 1.46 - 1.59: 6025 1.59 - 1.73: 48 1.73 - 1.87: 45 Bond restraints: 13464 Sorted by residual: bond pdb=" CB HIS A 154 " pdb=" CG HIS A 154 " ideal model delta sigma weight residual 1.497 1.383 0.114 1.40e-02 5.10e+03 6.68e+01 bond pdb=" CB HIS B 154 " pdb=" CG HIS B 154 " ideal model delta sigma weight residual 1.497 1.384 0.113 1.40e-02 5.10e+03 6.57e+01 bond pdb=" CB HIS C 154 " pdb=" CG HIS C 154 " ideal model delta sigma weight residual 1.497 1.384 0.113 1.40e-02 5.10e+03 6.47e+01 bond pdb=" CB LEU L 111 " pdb=" CG LEU L 111 " ideal model delta sigma weight residual 1.530 1.648 -0.118 2.00e-02 2.50e+03 3.47e+01 bond pdb=" CB LEU J 111 " pdb=" CG LEU J 111 " ideal model delta sigma weight residual 1.530 1.648 -0.118 2.00e-02 2.50e+03 3.45e+01 ... (remaining 13459 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.01: 16440 3.01 - 6.01: 1660 6.01 - 9.02: 192 9.02 - 12.02: 8 12.02 - 15.03: 3 Bond angle restraints: 18303 Sorted by residual: angle pdb=" C ALA C 125 " pdb=" N PRO C 126 " pdb=" CA PRO C 126 " ideal model delta sigma weight residual 120.21 128.35 -8.14 9.60e-01 1.09e+00 7.19e+01 angle pdb=" C ALA B 125 " pdb=" N PRO B 126 " pdb=" CA PRO B 126 " ideal model delta sigma weight residual 120.21 128.24 -8.03 9.60e-01 1.09e+00 7.00e+01 angle pdb=" C ALA A 125 " pdb=" N PRO A 126 " pdb=" CA PRO A 126 " ideal model delta sigma weight residual 120.21 128.20 -7.99 9.60e-01 1.09e+00 6.93e+01 angle pdb=" C GLY D 536 " pdb=" N PRO D 537 " pdb=" CA PRO D 537 " ideal model delta sigma weight residual 120.03 127.22 -7.19 9.90e-01 1.02e+00 5.27e+01 angle pdb=" C GLY F 536 " pdb=" N PRO F 537 " pdb=" CA PRO F 537 " ideal model delta sigma weight residual 120.03 127.19 -7.16 9.90e-01 1.02e+00 5.23e+01 ... (remaining 18298 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.36: 7926 21.36 - 42.72: 156 42.72 - 64.07: 45 64.07 - 85.43: 33 85.43 - 106.79: 18 Dihedral angle restraints: 8178 sinusoidal: 3474 harmonic: 4704 Sorted by residual: dihedral pdb=" O4 BMA O 3 " pdb=" C4 BMA O 3 " pdb=" C5 BMA O 3 " pdb=" O5 BMA O 3 " ideal model delta sinusoidal sigma weight residual -71.29 -178.08 106.79 1 3.00e+01 1.11e-03 1.37e+01 dihedral pdb=" O4 BMA M 3 " pdb=" C4 BMA M 3 " pdb=" C5 BMA M 3 " pdb=" O5 BMA M 3 " ideal model delta sinusoidal sigma weight residual -71.29 -178.01 106.72 1 3.00e+01 1.11e-03 1.37e+01 dihedral pdb=" O4 BMA N 3 " pdb=" C4 BMA N 3 " pdb=" C5 BMA N 3 " pdb=" O5 BMA N 3 " ideal model delta sinusoidal sigma weight residual -71.29 -177.95 106.66 1 3.00e+01 1.11e-03 1.37e+01 ... (remaining 8175 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 1374 0.097 - 0.194: 515 0.194 - 0.291: 138 0.291 - 0.388: 42 0.388 - 0.484: 22 Chirality restraints: 2091 Sorted by residual: chirality pdb=" C1 NAG O 2 " pdb=" O4 NAG O 1 " pdb=" C2 NAG O 2 " pdb=" O5 NAG O 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.35e+02 chirality pdb=" C1 NAG N 2 " pdb=" O4 NAG N 1 " pdb=" C2 NAG N 2 " pdb=" O5 NAG N 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.32e+02 chirality pdb=" C1 NAG M 2 " pdb=" O4 NAG M 1 " pdb=" C2 NAG M 2 " pdb=" O5 NAG M 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.23e+02 ... (remaining 2088 not shown) Planarity restraints: 2325 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR I 113 " 0.070 2.00e-02 2.50e+03 3.62e-02 2.62e+01 pdb=" CG TYR I 113 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 TYR I 113 " -0.032 2.00e-02 2.50e+03 pdb=" CD2 TYR I 113 " -0.032 2.00e-02 2.50e+03 pdb=" CE1 TYR I 113 " -0.014 2.00e-02 2.50e+03 pdb=" CE2 TYR I 113 " -0.014 2.00e-02 2.50e+03 pdb=" CZ TYR I 113 " 0.009 2.00e-02 2.50e+03 pdb=" OH TYR I 113 " 0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR H 113 " 0.070 2.00e-02 2.50e+03 3.59e-02 2.58e+01 pdb=" CG TYR H 113 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 TYR H 113 " -0.031 2.00e-02 2.50e+03 pdb=" CD2 TYR H 113 " -0.032 2.00e-02 2.50e+03 pdb=" CE1 TYR H 113 " -0.015 2.00e-02 2.50e+03 pdb=" CE2 TYR H 113 " -0.013 2.00e-02 2.50e+03 pdb=" CZ TYR H 113 " 0.009 2.00e-02 2.50e+03 pdb=" OH TYR H 113 " 0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR G 113 " -0.070 2.00e-02 2.50e+03 3.59e-02 2.57e+01 pdb=" CG TYR G 113 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 TYR G 113 " 0.032 2.00e-02 2.50e+03 pdb=" CD2 TYR G 113 " 0.032 2.00e-02 2.50e+03 pdb=" CE1 TYR G 113 " 0.014 2.00e-02 2.50e+03 pdb=" CE2 TYR G 113 " 0.013 2.00e-02 2.50e+03 pdb=" CZ TYR G 113 " -0.009 2.00e-02 2.50e+03 pdb=" OH TYR G 113 " -0.044 2.00e-02 2.50e+03 ... (remaining 2322 not shown) Histogram of nonbonded interaction distances: 2.47 - 2.96: 6637 2.96 - 3.44: 12335 3.44 - 3.93: 23579 3.93 - 4.41: 27520 4.41 - 4.90: 42979 Nonbonded interactions: 113050 Sorted by model distance: nonbonded pdb=" N ASP K 61 " pdb=" OD1 ASP K 61 " model vdw 2.470 3.120 nonbonded pdb=" N ASP J 61 " pdb=" OD1 ASP J 61 " model vdw 2.471 3.120 nonbonded pdb=" N ASP L 61 " pdb=" OD1 ASP L 61 " model vdw 2.471 3.120 nonbonded pdb=" N THR B 249 " pdb=" O THR B 249 " model vdw 2.480 2.496 nonbonded pdb=" N THR C 249 " pdb=" O THR C 249 " model vdw 2.480 2.496 ... (remaining 113045 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.10 Found NCS groups: ncs_group { reference = chain 'M' selection = chain 'O' selection = chain 'N' } ncs_group { reference = chain 'K' selection = chain 'J' selection = chain 'L' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'H' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } ncs_group { reference = chain 'E' selection = chain 'D' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.000 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: 0.020 Extract box with map and model: 0.520 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 33.520 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 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 : 0.022 0.148 13497 Z= 1.155 Angle : 1.890 15.027 18393 Z= 1.248 Chirality : 0.117 0.484 2091 Planarity : 0.009 0.053 2313 Dihedral : 12.391 106.789 5169 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 0.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.43 % Allowed : 0.43 % Favored : 99.14 % 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: 0.37 (0.19), residues: 1626 helix: -0.35 (0.29), residues: 195 sheet: -0.12 (0.23), residues: 489 loop : 0.79 (0.19), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.011 TRP H 49 HIS 0.008 0.003 HIS E 549 PHE 0.038 0.006 PHE H 80 TYR 0.070 0.012 TYR I 113 ARG 0.008 0.001 ARG A 85 Details of bonding type rmsd link_NAG-ASN : bond 0.08402 ( 12) link_NAG-ASN : angle 2.04855 ( 36) link_ALPHA1-6 : bond 0.05315 ( 3) link_ALPHA1-6 : angle 2.77680 ( 9) link_BETA1-4 : bond 0.07659 ( 6) link_BETA1-4 : angle 5.58955 ( 18) link_ALPHA1-3 : bond 0.08406 ( 3) link_ALPHA1-3 : angle 4.44207 ( 9) hydrogen bonds : bond 0.16680 ( 489) hydrogen bonds : angle 8.52206 ( 1263) SS BOND : bond 0.00771 ( 9) SS BOND : angle 2.02885 ( 18) covalent geometry : bond 0.02149 (13464) covalent geometry : angle 1.88005 (18303) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 224 time to evaluate : 2.623 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: G 118 MET cc_start: 0.8740 (ttt) cc_final: 0.7477 (tmm) REVERT: A 171 TYR cc_start: 0.9331 (m-80) cc_final: 0.9011 (m-80) REVERT: A 237 ASP cc_start: 0.9043 (t0) cc_final: 0.8730 (m-30) REVERT: J 35 ASP cc_start: 0.9207 (m-30) cc_final: 0.8372 (p0) REVERT: J 53 ASP cc_start: 0.8865 (p0) cc_final: 0.7836 (t0) REVERT: I 118 MET cc_start: 0.8656 (ttt) cc_final: 0.7637 (tmm) REVERT: C 99 TYR cc_start: 0.7360 (m-80) cc_final: 0.6746 (m-80) REVERT: C 109 TYR cc_start: 0.8670 (m-80) cc_final: 0.8437 (m-10) REVERT: C 237 ASP cc_start: 0.9032 (t0) cc_final: 0.8662 (m-30) REVERT: L 35 ASP cc_start: 0.9168 (m-30) cc_final: 0.8444 (p0) REVERT: L 53 ASP cc_start: 0.8886 (p0) cc_final: 0.7882 (t0) REVERT: H 118 MET cc_start: 0.8807 (ttt) cc_final: 0.7804 (tmm) REVERT: B 127 ASP cc_start: 0.9447 (m-30) cc_final: 0.9213 (t0) REVERT: B 237 ASP cc_start: 0.9006 (t0) cc_final: 0.8606 (m-30) REVERT: K 35 ASP cc_start: 0.9210 (m-30) cc_final: 0.8460 (p0) REVERT: K 53 ASP cc_start: 0.8913 (p0) cc_final: 0.7986 (t0) outliers start: 6 outliers final: 0 residues processed: 227 average time/residue: 0.3443 time to fit residues: 112.2191 Evaluate side-chains 77 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 1.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 0.9980 chunk 125 optimal weight: 8.9990 chunk 69 optimal weight: 10.0000 chunk 42 optimal weight: 1.9990 chunk 84 optimal weight: 7.9990 chunk 66 optimal weight: 6.9990 chunk 129 optimal weight: 7.9990 chunk 50 optimal weight: 6.9990 chunk 78 optimal weight: 0.9990 chunk 96 optimal weight: 6.9990 chunk 149 optimal weight: 6.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 ASN ** D 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 28 ASN C 107 ASN L 28 ASN B 107 ASN ** E 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 28 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.037598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.031367 restraints weight = 144803.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.032577 restraints weight = 78433.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.033461 restraints weight = 50410.594| |-----------------------------------------------------------------------------| r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 13497 Z= 0.229 Angle : 0.791 7.660 18393 Z= 0.422 Chirality : 0.048 0.254 2091 Planarity : 0.005 0.031 2313 Dihedral : 9.355 71.150 2292 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.18 % Allowed : 1.66 % Favored : 98.15 % Rotamer: Outliers : 0.07 % Allowed : 2.37 % Favored : 97.56 % 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: 0.13 (0.20), residues: 1626 helix: -0.25 (0.32), residues: 198 sheet: -0.28 (0.20), residues: 606 loop : 0.71 (0.22), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP L 100 HIS 0.002 0.001 HIS A 139 PHE 0.032 0.003 PHE A 252 TYR 0.016 0.002 TYR H 113 ARG 0.006 0.001 ARG C 266 Details of bonding type rmsd link_NAG-ASN : bond 0.00976 ( 12) link_NAG-ASN : angle 1.90778 ( 36) link_ALPHA1-6 : bond 0.00087 ( 3) link_ALPHA1-6 : angle 1.92987 ( 9) link_BETA1-4 : bond 0.00628 ( 6) link_BETA1-4 : angle 3.76662 ( 18) link_ALPHA1-3 : bond 0.00994 ( 3) link_ALPHA1-3 : angle 3.49249 ( 9) hydrogen bonds : bond 0.06022 ( 489) hydrogen bonds : angle 7.32160 ( 1263) SS BOND : bond 0.00514 ( 9) SS BOND : angle 2.49088 ( 18) covalent geometry : bond 0.00468 (13464) covalent geometry : angle 0.77051 (18303) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 127 time to evaluate : 1.510 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: G 118 MET cc_start: 0.8684 (ttt) cc_final: 0.7824 (tmm) REVERT: I 118 MET cc_start: 0.8582 (ttt) cc_final: 0.7597 (tmm) REVERT: C 161 LEU cc_start: 0.9261 (mt) cc_final: 0.9043 (mt) REVERT: C 171 TYR cc_start: 0.9360 (m-80) cc_final: 0.8985 (m-80) REVERT: C 237 ASP cc_start: 0.9058 (t0) cc_final: 0.8806 (m-30) REVERT: L 61 ASP cc_start: 0.9523 (p0) cc_final: 0.9310 (p0) REVERT: H 118 MET cc_start: 0.8604 (ttt) cc_final: 0.7932 (tmm) REVERT: B 171 TYR cc_start: 0.9317 (m-80) cc_final: 0.8816 (m-80) REVERT: B 237 ASP cc_start: 0.8995 (t0) cc_final: 0.8663 (m-30) outliers start: 1 outliers final: 0 residues processed: 128 average time/residue: 0.3060 time to fit residues: 57.0840 Evaluate side-chains 68 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 1.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 154 optimal weight: 0.0970 chunk 128 optimal weight: 1.9990 chunk 146 optimal weight: 9.9990 chunk 58 optimal weight: 7.9990 chunk 66 optimal weight: 8.9990 chunk 34 optimal weight: 5.9990 chunk 3 optimal weight: 4.9990 chunk 77 optimal weight: 9.9990 chunk 104 optimal weight: 10.0000 chunk 156 optimal weight: 6.9990 chunk 160 optimal weight: 10.0000 overall best weight: 4.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 508 GLN ** 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 = 0.3196 r_free = 0.3196 target = 0.035843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.029596 restraints weight = 149840.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.030729 restraints weight = 82026.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.031552 restraints weight = 53467.154| |-----------------------------------------------------------------------------| r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.3489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13497 Z= 0.209 Angle : 0.716 8.149 18393 Z= 0.374 Chirality : 0.046 0.225 2091 Planarity : 0.005 0.034 2313 Dihedral : 8.097 55.406 2292 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % 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: 0.09 (0.21), residues: 1626 helix: -0.27 (0.32), residues: 198 sheet: -0.36 (0.19), residues: 657 loop : 0.81 (0.24), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP G 121 HIS 0.006 0.002 HIS B 139 PHE 0.018 0.003 PHE I 52 TYR 0.028 0.002 TYR A 99 ARG 0.004 0.001 ARG A 266 Details of bonding type rmsd link_NAG-ASN : bond 0.00449 ( 12) link_NAG-ASN : angle 1.58268 ( 36) link_ALPHA1-6 : bond 0.00036 ( 3) link_ALPHA1-6 : angle 2.03135 ( 9) link_BETA1-4 : bond 0.00667 ( 6) link_BETA1-4 : angle 2.68518 ( 18) link_ALPHA1-3 : bond 0.01025 ( 3) link_ALPHA1-3 : angle 1.60840 ( 9) hydrogen bonds : bond 0.04995 ( 489) hydrogen bonds : angle 6.92728 ( 1263) SS BOND : bond 0.00339 ( 9) SS BOND : angle 2.16454 ( 18) covalent geometry : bond 0.00442 (13464) covalent geometry : angle 0.70409 (18303) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 1.534 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: G 118 MET cc_start: 0.8461 (ttt) cc_final: 0.8063 (tmm) REVERT: A 273 LEU cc_start: 0.9014 (mt) cc_final: 0.8741 (mt) REVERT: D 517 TYR cc_start: 0.7091 (m-10) cc_final: 0.6879 (m-10) REVERT: J 35 ASP cc_start: 0.9502 (m-30) cc_final: 0.9291 (m-30) REVERT: J 74 LEU cc_start: 0.9396 (tt) cc_final: 0.9169 (pp) REVERT: I 118 MET cc_start: 0.8623 (ttt) cc_final: 0.7929 (tmm) REVERT: I 121 TRP cc_start: 0.8061 (m100) cc_final: 0.7756 (m100) REVERT: C 171 TYR cc_start: 0.9405 (m-80) cc_final: 0.9115 (m-80) REVERT: C 237 ASP cc_start: 0.9164 (t0) cc_final: 0.8827 (m-30) REVERT: F 517 TYR cc_start: 0.7159 (m-10) cc_final: 0.6899 (m-10) REVERT: L 35 ASP cc_start: 0.9400 (m-30) cc_final: 0.8751 (p0) REVERT: H 118 MET cc_start: 0.8616 (ttt) cc_final: 0.8240 (tmm) REVERT: B 171 TYR cc_start: 0.9298 (m-80) cc_final: 0.8995 (m-80) REVERT: B 237 ASP cc_start: 0.9151 (t0) cc_final: 0.8793 (m-30) REVERT: B 273 LEU cc_start: 0.8996 (mt) cc_final: 0.8760 (mt) REVERT: K 35 ASP cc_start: 0.9297 (m-30) cc_final: 0.8720 (p0) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.2816 time to fit residues: 43.4680 Evaluate side-chains 68 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 1.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 62 optimal weight: 7.9990 chunk 69 optimal weight: 0.4980 chunk 15 optimal weight: 5.9990 chunk 123 optimal weight: 0.9980 chunk 139 optimal weight: 9.9990 chunk 121 optimal weight: 0.9990 chunk 26 optimal weight: 6.9990 chunk 162 optimal weight: 10.0000 chunk 34 optimal weight: 0.9990 chunk 86 optimal weight: 9.9990 chunk 24 optimal weight: 20.0000 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 508 GLN ** 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 = 0.3213 r_free = 0.3213 target = 0.036213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.029978 restraints weight = 147028.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.031091 restraints weight = 81442.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.031916 restraints weight = 53441.065| |-----------------------------------------------------------------------------| r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.3783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 13497 Z= 0.133 Angle : 0.638 8.760 18393 Z= 0.328 Chirality : 0.046 0.254 2091 Planarity : 0.004 0.031 2313 Dihedral : 7.113 44.875 2292 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % 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: 0.18 (0.21), residues: 1626 helix: -0.11 (0.33), residues: 198 sheet: -0.22 (0.20), residues: 633 loop : 0.73 (0.24), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP G 121 HIS 0.003 0.001 HIS D 516 PHE 0.017 0.002 PHE G 80 TYR 0.017 0.002 TYR B 99 ARG 0.002 0.000 ARG J 26 Details of bonding type rmsd link_NAG-ASN : bond 0.00438 ( 12) link_NAG-ASN : angle 1.25479 ( 36) link_ALPHA1-6 : bond 0.00041 ( 3) link_ALPHA1-6 : angle 2.05239 ( 9) link_BETA1-4 : bond 0.00476 ( 6) link_BETA1-4 : angle 2.60686 ( 18) link_ALPHA1-3 : bond 0.00941 ( 3) link_ALPHA1-3 : angle 2.06851 ( 9) hydrogen bonds : bond 0.04468 ( 489) hydrogen bonds : angle 6.67921 ( 1263) SS BOND : bond 0.00394 ( 9) SS BOND : angle 2.12616 ( 18) covalent geometry : bond 0.00277 (13464) covalent geometry : angle 0.62493 (18303) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 1.429 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: G 118 MET cc_start: 0.8619 (ttt) cc_final: 0.8225 (tmm) REVERT: A 234 PHE cc_start: 0.9255 (t80) cc_final: 0.8871 (t80) REVERT: A 236 VAL cc_start: 0.8594 (t) cc_final: 0.8365 (t) REVERT: A 273 LEU cc_start: 0.8976 (mt) cc_final: 0.8728 (mt) REVERT: J 35 ASP cc_start: 0.9451 (m-30) cc_final: 0.9054 (t70) REVERT: J 53 ASP cc_start: 0.9250 (p0) cc_final: 0.8493 (m-30) REVERT: J 74 LEU cc_start: 0.9409 (tt) cc_final: 0.9132 (pp) REVERT: I 118 MET cc_start: 0.8663 (ttt) cc_final: 0.8047 (tmm) REVERT: C 171 TYR cc_start: 0.9282 (m-80) cc_final: 0.8897 (m-80) REVERT: C 237 ASP cc_start: 0.9084 (t0) cc_final: 0.8666 (m-30) REVERT: F 531 TRP cc_start: 0.7067 (m100) cc_final: 0.6858 (m-10) REVERT: F 548 MET cc_start: 0.5878 (mmt) cc_final: 0.4993 (mmp) REVERT: L 35 ASP cc_start: 0.9421 (m-30) cc_final: 0.9153 (t70) REVERT: H 118 MET cc_start: 0.8601 (ttt) cc_final: 0.8291 (tmm) REVERT: B 171 TYR cc_start: 0.9259 (m-80) cc_final: 0.8896 (m-80) REVERT: B 237 ASP cc_start: 0.9160 (t0) cc_final: 0.8895 (m-30) REVERT: B 273 LEU cc_start: 0.8954 (mt) cc_final: 0.8711 (mt) REVERT: K 35 ASP cc_start: 0.9381 (m-30) cc_final: 0.9021 (t70) REVERT: K 74 LEU cc_start: 0.9052 (pp) cc_final: 0.8839 (pp) outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.2456 time to fit residues: 38.9064 Evaluate side-chains 72 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 1.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 138 optimal weight: 9.9990 chunk 84 optimal weight: 10.0000 chunk 125 optimal weight: 7.9990 chunk 110 optimal weight: 30.0000 chunk 88 optimal weight: 0.9980 chunk 81 optimal weight: 8.9990 chunk 98 optimal weight: 9.9990 chunk 116 optimal weight: 8.9990 chunk 160 optimal weight: 20.0000 chunk 106 optimal weight: 30.0000 chunk 28 optimal weight: 10.0000 overall best weight: 7.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 508 GLN ** 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 = 0.3080 r_free = 0.3080 target = 0.032687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.026716 restraints weight = 152090.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.027707 restraints weight = 85295.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.028403 restraints weight = 56660.195| |-----------------------------------------------------------------------------| r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.4862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.084 13497 Z= 0.344 Angle : 0.868 11.086 18393 Z= 0.439 Chirality : 0.049 0.355 2091 Planarity : 0.005 0.050 2313 Dihedral : 6.929 37.409 2292 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 22.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 0.22 % Allowed : 1.79 % Favored : 97.99 % 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: -0.40 (0.21), residues: 1626 helix: -0.80 (0.31), residues: 198 sheet: -0.60 (0.19), residues: 657 loop : 0.46 (0.23), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP D 531 HIS 0.006 0.002 HIS D 516 PHE 0.018 0.003 PHE A 234 TYR 0.023 0.003 TYR B 99 ARG 0.005 0.001 ARG A 164 Details of bonding type rmsd link_NAG-ASN : bond 0.00471 ( 12) link_NAG-ASN : angle 2.05184 ( 36) link_ALPHA1-6 : bond 0.00682 ( 3) link_ALPHA1-6 : angle 2.07895 ( 9) link_BETA1-4 : bond 0.00394 ( 6) link_BETA1-4 : angle 2.11071 ( 18) link_ALPHA1-3 : bond 0.00625 ( 3) link_ALPHA1-3 : angle 3.06235 ( 9) hydrogen bonds : bond 0.04943 ( 489) hydrogen bonds : angle 7.12159 ( 1263) SS BOND : bond 0.00912 ( 9) SS BOND : angle 1.62052 ( 18) covalent geometry : bond 0.00716 (13464) covalent geometry : angle 0.85712 (18303) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 86 time to evaluate : 1.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 118 MET cc_start: 0.8716 (ttt) cc_final: 0.8100 (tmm) REVERT: A 234 PHE cc_start: 0.9189 (t80) cc_final: 0.8855 (t80) REVERT: D 517 TYR cc_start: 0.8059 (m-80) cc_final: 0.7769 (m-80) REVERT: D 548 MET cc_start: 0.8093 (mmt) cc_final: 0.7652 (mmt) REVERT: J 74 LEU cc_start: 0.9454 (tt) cc_final: 0.9251 (pp) REVERT: I 118 MET cc_start: 0.8700 (ttt) cc_final: 0.8267 (tmm) REVERT: C 171 TYR cc_start: 0.9420 (m-80) cc_final: 0.9212 (m-80) REVERT: C 237 ASP cc_start: 0.9224 (t0) cc_final: 0.8836 (m-30) REVERT: H 118 MET cc_start: 0.8763 (ttt) cc_final: 0.8191 (tmm) REVERT: B 171 TYR cc_start: 0.9331 (m-80) cc_final: 0.8985 (m-80) REVERT: B 234 PHE cc_start: 0.9173 (t80) cc_final: 0.8915 (t80) REVERT: B 237 ASP cc_start: 0.9162 (t0) cc_final: 0.8722 (m-30) REVERT: E 517 TYR cc_start: 0.7622 (m-80) cc_final: 0.7145 (m-10) REVERT: E 548 MET cc_start: 0.8122 (mmp) cc_final: 0.7900 (mmt) outliers start: 3 outliers final: 0 residues processed: 89 average time/residue: 0.2390 time to fit residues: 33.0225 Evaluate side-chains 61 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 1.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 59 optimal weight: 10.0000 chunk 51 optimal weight: 20.0000 chunk 75 optimal weight: 3.9990 chunk 36 optimal weight: 9.9990 chunk 49 optimal weight: 10.0000 chunk 41 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 132 optimal weight: 4.9990 chunk 2 optimal weight: 6.9990 chunk 113 optimal weight: 10.0000 chunk 10 optimal weight: 7.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 506 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 = 0.3148 r_free = 0.3148 target = 0.034187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.028200 restraints weight = 140984.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.029241 restraints weight = 77593.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.029966 restraints weight = 50535.109| |-----------------------------------------------------------------------------| r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.5014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13497 Z= 0.190 Angle : 0.660 7.267 18393 Z= 0.339 Chirality : 0.045 0.275 2091 Planarity : 0.004 0.034 2313 Dihedral : 6.323 31.919 2292 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 15.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % 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: -0.43 (0.21), residues: 1626 helix: -0.75 (0.32), residues: 198 sheet: -0.50 (0.20), residues: 627 loop : 0.24 (0.23), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 275 HIS 0.002 0.001 HIS C 139 PHE 0.017 0.002 PHE A 234 TYR 0.014 0.002 TYR F 517 ARG 0.006 0.001 ARG K 17 Details of bonding type rmsd link_NAG-ASN : bond 0.00345 ( 12) link_NAG-ASN : angle 1.69597 ( 36) link_ALPHA1-6 : bond 0.00120 ( 3) link_ALPHA1-6 : angle 1.83519 ( 9) link_BETA1-4 : bond 0.00211 ( 6) link_BETA1-4 : angle 2.05955 ( 18) link_ALPHA1-3 : bond 0.01040 ( 3) link_ALPHA1-3 : angle 2.21971 ( 9) hydrogen bonds : bond 0.04329 ( 489) hydrogen bonds : angle 6.78890 ( 1263) SS BOND : bond 0.00712 ( 9) SS BOND : angle 2.04493 ( 18) covalent geometry : bond 0.00401 (13464) covalent geometry : angle 0.64784 (18303) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 1.577 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: G 118 MET cc_start: 0.8774 (ttt) cc_final: 0.8060 (tmm) REVERT: A 171 TYR cc_start: 0.9111 (m-80) cc_final: 0.8788 (m-10) REVERT: A 234 PHE cc_start: 0.9125 (t80) cc_final: 0.8807 (t80) REVERT: D 517 TYR cc_start: 0.7835 (m-80) cc_final: 0.7480 (m-80) REVERT: D 548 MET cc_start: 0.7892 (mmt) cc_final: 0.7104 (mmt) REVERT: J 35 ASP cc_start: 0.9373 (m-30) cc_final: 0.9118 (t0) REVERT: I 118 MET cc_start: 0.8695 (ttt) cc_final: 0.8289 (tmm) REVERT: C 33 ILE cc_start: 0.8881 (tp) cc_final: 0.7995 (tp) REVERT: C 171 TYR cc_start: 0.9392 (m-80) cc_final: 0.9058 (m-80) REVERT: C 234 PHE cc_start: 0.9216 (t80) cc_final: 0.8939 (t80) REVERT: C 237 ASP cc_start: 0.9235 (t0) cc_final: 0.8761 (m-30) REVERT: F 548 MET cc_start: 0.7672 (mmp) cc_final: 0.7303 (mmt) REVERT: H 118 MET cc_start: 0.8810 (ttt) cc_final: 0.8145 (tmm) REVERT: B 171 TYR cc_start: 0.9372 (m-80) cc_final: 0.8985 (m-80) REVERT: B 234 PHE cc_start: 0.9177 (t80) cc_final: 0.8953 (t80) REVERT: B 237 ASP cc_start: 0.9205 (t0) cc_final: 0.8742 (m-30) REVERT: E 548 MET cc_start: 0.8018 (mmp) cc_final: 0.7310 (mtm) REVERT: K 35 ASP cc_start: 0.9299 (m-30) cc_final: 0.9032 (t0) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.2216 time to fit residues: 32.3364 Evaluate side-chains 65 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 1.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 74 optimal weight: 6.9990 chunk 77 optimal weight: 10.0000 chunk 48 optimal weight: 0.3980 chunk 17 optimal weight: 3.9990 chunk 151 optimal weight: 2.9990 chunk 38 optimal weight: 9.9990 chunk 64 optimal weight: 10.0000 chunk 121 optimal weight: 7.9990 chunk 73 optimal weight: 5.9990 chunk 124 optimal weight: 20.0000 chunk 132 optimal weight: 7.9990 overall best weight: 4.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 595 GLN ** F 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 595 GLN ** E 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 595 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.033383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.027227 restraints weight = 151757.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.028241 restraints weight = 85532.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.028953 restraints weight = 57001.919| |-----------------------------------------------------------------------------| r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.5378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13497 Z= 0.193 Angle : 0.658 7.808 18393 Z= 0.335 Chirality : 0.045 0.269 2091 Planarity : 0.004 0.040 2313 Dihedral : 6.041 27.233 2292 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 16.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % 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: -0.44 (0.21), residues: 1626 helix: -0.65 (0.33), residues: 198 sheet: -0.50 (0.20), residues: 627 loop : 0.20 (0.23), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 275 HIS 0.002 0.001 HIS E 516 PHE 0.016 0.002 PHE A 234 TYR 0.024 0.002 TYR B 99 ARG 0.005 0.000 ARG K 17 Details of bonding type rmsd link_NAG-ASN : bond 0.00394 ( 12) link_NAG-ASN : angle 1.74301 ( 36) link_ALPHA1-6 : bond 0.00080 ( 3) link_ALPHA1-6 : angle 1.79924 ( 9) link_BETA1-4 : bond 0.00204 ( 6) link_BETA1-4 : angle 2.11505 ( 18) link_ALPHA1-3 : bond 0.00914 ( 3) link_ALPHA1-3 : angle 2.08993 ( 9) hydrogen bonds : bond 0.04249 ( 489) hydrogen bonds : angle 6.83992 ( 1263) SS BOND : bond 0.00772 ( 9) SS BOND : angle 2.37220 ( 18) covalent geometry : bond 0.00408 (13464) covalent geometry : angle 0.64410 (18303) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 1.572 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: G 118 MET cc_start: 0.8674 (ttt) cc_final: 0.8036 (tmm) REVERT: A 171 TYR cc_start: 0.9134 (m-80) cc_final: 0.8576 (m-10) REVERT: A 234 PHE cc_start: 0.9206 (t80) cc_final: 0.8922 (t80) REVERT: D 517 TYR cc_start: 0.7598 (m-80) cc_final: 0.6537 (m-10) REVERT: D 548 MET cc_start: 0.7742 (mmt) cc_final: 0.6797 (mpp) REVERT: J 35 ASP cc_start: 0.9404 (m-30) cc_final: 0.9145 (t70) REVERT: I 118 MET cc_start: 0.8704 (ttt) cc_final: 0.8204 (tmm) REVERT: C 171 TYR cc_start: 0.9387 (m-80) cc_final: 0.8987 (m-80) REVERT: C 237 ASP cc_start: 0.9241 (t0) cc_final: 0.8979 (m-30) REVERT: F 517 TYR cc_start: 0.7377 (m-10) cc_final: 0.7158 (m-10) REVERT: F 548 MET cc_start: 0.7893 (mmp) cc_final: 0.7482 (mmt) REVERT: H 118 MET cc_start: 0.8793 (ttt) cc_final: 0.8127 (tmm) REVERT: B 33 ILE cc_start: 0.8965 (tp) cc_final: 0.8102 (tp) REVERT: B 171 TYR cc_start: 0.9344 (m-80) cc_final: 0.8941 (m-80) REVERT: B 234 PHE cc_start: 0.9265 (t80) cc_final: 0.9047 (t80) REVERT: B 237 ASP cc_start: 0.9190 (t0) cc_final: 0.8745 (m-30) REVERT: K 35 ASP cc_start: 0.9346 (m-30) cc_final: 0.9057 (t0) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.2346 time to fit residues: 31.9963 Evaluate side-chains 65 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 1.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 14 optimal weight: 20.0000 chunk 124 optimal weight: 20.0000 chunk 27 optimal weight: 9.9990 chunk 37 optimal weight: 0.8980 chunk 9 optimal weight: 10.0000 chunk 91 optimal weight: 4.9990 chunk 105 optimal weight: 20.0000 chunk 96 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 chunk 153 optimal weight: 8.9990 chunk 120 optimal weight: 1.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 506 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 = 0.3111 r_free = 0.3111 target = 0.033538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.027338 restraints weight = 149580.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.028369 restraints weight = 83512.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.029089 restraints weight = 55444.472| |-----------------------------------------------------------------------------| r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.5539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13497 Z= 0.156 Angle : 0.625 7.751 18393 Z= 0.319 Chirality : 0.045 0.243 2091 Planarity : 0.004 0.042 2313 Dihedral : 5.731 23.500 2292 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % 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: -0.39 (0.21), residues: 1626 helix: -0.52 (0.34), residues: 198 sheet: -0.50 (0.20), residues: 627 loop : 0.24 (0.24), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 275 HIS 0.006 0.001 HIS E 549 PHE 0.023 0.002 PHE C 234 TYR 0.011 0.001 TYR I 96 ARG 0.004 0.000 ARG K 17 Details of bonding type rmsd link_NAG-ASN : bond 0.00349 ( 12) link_NAG-ASN : angle 1.64339 ( 36) link_ALPHA1-6 : bond 0.00112 ( 3) link_ALPHA1-6 : angle 1.71031 ( 9) link_BETA1-4 : bond 0.00195 ( 6) link_BETA1-4 : angle 2.05411 ( 18) link_ALPHA1-3 : bond 0.00967 ( 3) link_ALPHA1-3 : angle 1.71601 ( 9) hydrogen bonds : bond 0.04052 ( 489) hydrogen bonds : angle 6.65005 ( 1263) SS BOND : bond 0.00499 ( 9) SS BOND : angle 2.20782 ( 18) covalent geometry : bond 0.00335 (13464) covalent geometry : angle 0.61251 (18303) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 1.582 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: G 118 MET cc_start: 0.8745 (ttt) cc_final: 0.8096 (tmm) REVERT: A 161 LEU cc_start: 0.9496 (mt) cc_final: 0.9258 (mt) REVERT: A 234 PHE cc_start: 0.9228 (t80) cc_final: 0.8949 (t80) REVERT: D 517 TYR cc_start: 0.7847 (m-80) cc_final: 0.7463 (m-10) REVERT: J 35 ASP cc_start: 0.9449 (m-30) cc_final: 0.9192 (t0) REVERT: I 118 MET cc_start: 0.8657 (ttt) cc_final: 0.7836 (tmm) REVERT: I 121 TRP cc_start: 0.8381 (m100) cc_final: 0.7859 (m100) REVERT: C 161 LEU cc_start: 0.9461 (mt) cc_final: 0.9212 (mt) REVERT: C 171 TYR cc_start: 0.9396 (m-80) cc_final: 0.8946 (m-80) REVERT: C 237 ASP cc_start: 0.9343 (t0) cc_final: 0.8862 (m-30) REVERT: H 118 MET cc_start: 0.8717 (ttt) cc_final: 0.8045 (tmm) REVERT: B 171 TYR cc_start: 0.9352 (m-80) cc_final: 0.8965 (m-80) REVERT: B 234 PHE cc_start: 0.9287 (t80) cc_final: 0.9076 (t80) REVERT: B 237 ASP cc_start: 0.9100 (t0) cc_final: 0.8679 (m-30) REVERT: E 548 MET cc_start: 0.7513 (mpp) cc_final: 0.7111 (mtp) REVERT: K 35 ASP cc_start: 0.9362 (m-30) cc_final: 0.9099 (t0) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.2318 time to fit residues: 31.4030 Evaluate side-chains 67 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 1.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 68 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 45 optimal weight: 20.0000 chunk 103 optimal weight: 0.8980 chunk 150 optimal weight: 6.9990 chunk 89 optimal weight: 7.9990 chunk 54 optimal weight: 8.9990 chunk 18 optimal weight: 0.6980 chunk 122 optimal weight: 20.0000 chunk 29 optimal weight: 7.9990 chunk 61 optimal weight: 4.9990 overall best weight: 1.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 506 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 = 0.3139 r_free = 0.3139 target = 0.034137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.027869 restraints weight = 145412.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.028907 restraints weight = 81205.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.029663 restraints weight = 54083.005| |-----------------------------------------------------------------------------| r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.5662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13497 Z= 0.117 Angle : 0.593 8.000 18393 Z= 0.301 Chirality : 0.044 0.250 2091 Planarity : 0.004 0.038 2313 Dihedral : 5.517 22.758 2292 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.21), residues: 1626 helix: -0.36 (0.35), residues: 198 sheet: -0.47 (0.20), residues: 627 loop : 0.27 (0.24), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 275 HIS 0.003 0.001 HIS D 516 PHE 0.017 0.002 PHE A 234 TYR 0.014 0.001 TYR A 171 ARG 0.005 0.000 ARG G 104 Details of bonding type rmsd link_NAG-ASN : bond 0.00350 ( 12) link_NAG-ASN : angle 2.24231 ( 36) link_ALPHA1-6 : bond 0.00227 ( 3) link_ALPHA1-6 : angle 1.62294 ( 9) link_BETA1-4 : bond 0.00234 ( 6) link_BETA1-4 : angle 2.08629 ( 18) link_ALPHA1-3 : bond 0.00971 ( 3) link_ALPHA1-3 : angle 1.47980 ( 9) hydrogen bonds : bond 0.03796 ( 489) hydrogen bonds : angle 6.46885 ( 1263) SS BOND : bond 0.00436 ( 9) SS BOND : angle 2.05144 ( 18) covalent geometry : bond 0.00250 (13464) covalent geometry : angle 0.57706 (18303) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 1.387 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: G 118 MET cc_start: 0.8689 (ttt) cc_final: 0.8117 (tmm) REVERT: A 33 ILE cc_start: 0.8907 (tp) cc_final: 0.7872 (tp) REVERT: A 161 LEU cc_start: 0.9534 (mt) cc_final: 0.9326 (mt) REVERT: A 234 PHE cc_start: 0.9244 (t80) cc_final: 0.8926 (t80) REVERT: A 273 LEU cc_start: 0.8970 (mt) cc_final: 0.8684 (mp) REVERT: D 517 TYR cc_start: 0.7680 (m-80) cc_final: 0.7043 (m-10) REVERT: D 548 MET cc_start: 0.8030 (mmp) cc_final: 0.7152 (mmt) REVERT: J 35 ASP cc_start: 0.9484 (m-30) cc_final: 0.9172 (t70) REVERT: I 118 MET cc_start: 0.8629 (ttt) cc_final: 0.7827 (tmm) REVERT: I 121 TRP cc_start: 0.8265 (m100) cc_final: 0.7861 (m100) REVERT: C 161 LEU cc_start: 0.9506 (mt) cc_final: 0.9292 (mt) REVERT: C 171 TYR cc_start: 0.9320 (m-80) cc_final: 0.8821 (m-80) REVERT: C 234 PHE cc_start: 0.9213 (t80) cc_final: 0.8909 (t80) REVERT: C 237 ASP cc_start: 0.9326 (t0) cc_final: 0.8812 (m-30) REVERT: F 545 GLU cc_start: 0.9254 (pm20) cc_final: 0.9044 (pp20) REVERT: H 118 MET cc_start: 0.8708 (ttt) cc_final: 0.8033 (tmm) REVERT: B 171 TYR cc_start: 0.9389 (m-80) cc_final: 0.9025 (m-80) REVERT: B 234 PHE cc_start: 0.9304 (t80) cc_final: 0.9049 (t80) REVERT: B 237 ASP cc_start: 0.9070 (t0) cc_final: 0.8813 (m-30) REVERT: B 273 LEU cc_start: 0.8845 (mt) cc_final: 0.8626 (mt) REVERT: E 548 MET cc_start: 0.7650 (mpp) cc_final: 0.7056 (mtp) REVERT: K 35 ASP cc_start: 0.9422 (m-30) cc_final: 0.9109 (t0) outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.2392 time to fit residues: 34.8916 Evaluate side-chains 71 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 1.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 141 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 151 optimal weight: 0.8980 chunk 106 optimal weight: 40.0000 chunk 36 optimal weight: 0.0570 chunk 102 optimal weight: 5.9990 chunk 112 optimal weight: 10.0000 chunk 14 optimal weight: 20.0000 chunk 91 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 82 optimal weight: 6.9990 overall best weight: 1.9902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 516 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.034287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.028057 restraints weight = 146160.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.029089 restraints weight = 82297.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.029834 restraints weight = 55064.913| |-----------------------------------------------------------------------------| r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.5801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13497 Z= 0.124 Angle : 0.590 8.408 18393 Z= 0.300 Chirality : 0.044 0.333 2091 Planarity : 0.004 0.041 2313 Dihedral : 5.276 22.868 2292 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % 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: -0.34 (0.21), residues: 1626 helix: -0.60 (0.33), residues: 216 sheet: -0.38 (0.20), residues: 606 loop : 0.23 (0.24), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 275 HIS 0.003 0.001 HIS E 549 PHE 0.021 0.002 PHE A 234 TYR 0.010 0.001 TYR B 109 ARG 0.003 0.000 ARG K 17 Details of bonding type rmsd link_NAG-ASN : bond 0.00322 ( 12) link_NAG-ASN : angle 1.72556 ( 36) link_ALPHA1-6 : bond 0.00205 ( 3) link_ALPHA1-6 : angle 1.61075 ( 9) link_BETA1-4 : bond 0.00209 ( 6) link_BETA1-4 : angle 2.04743 ( 18) link_ALPHA1-3 : bond 0.00908 ( 3) link_ALPHA1-3 : angle 1.50251 ( 9) hydrogen bonds : bond 0.03777 ( 489) hydrogen bonds : angle 6.41673 ( 1263) SS BOND : bond 0.00419 ( 9) SS BOND : angle 1.97123 ( 18) covalent geometry : bond 0.00272 (13464) covalent geometry : angle 0.57761 (18303) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 1.391 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: G 118 MET cc_start: 0.8697 (ttt) cc_final: 0.8064 (tmm) REVERT: A 234 PHE cc_start: 0.9200 (t80) cc_final: 0.8895 (t80) REVERT: A 273 LEU cc_start: 0.8978 (mt) cc_final: 0.8668 (mt) REVERT: D 517 TYR cc_start: 0.7689 (m-80) cc_final: 0.7017 (m-10) REVERT: D 548 MET cc_start: 0.8071 (mmp) cc_final: 0.7260 (mmt) REVERT: J 35 ASP cc_start: 0.9474 (m-30) cc_final: 0.9141 (t70) REVERT: I 118 MET cc_start: 0.8621 (ttt) cc_final: 0.7862 (tmm) REVERT: I 121 TRP cc_start: 0.8248 (m100) cc_final: 0.7843 (m100) REVERT: C 161 LEU cc_start: 0.9535 (mt) cc_final: 0.9329 (mt) REVERT: C 171 TYR cc_start: 0.9329 (m-80) cc_final: 0.8786 (m-80) REVERT: C 234 PHE cc_start: 0.9197 (t80) cc_final: 0.8916 (t80) REVERT: C 237 ASP cc_start: 0.9325 (t0) cc_final: 0.8780 (m-30) REVERT: F 531 TRP cc_start: 0.7003 (m100) cc_final: 0.6593 (m-10) REVERT: F 548 MET cc_start: 0.7873 (mmp) cc_final: 0.7543 (mmt) REVERT: H 118 MET cc_start: 0.8742 (ttt) cc_final: 0.8069 (tmm) REVERT: B 171 TYR cc_start: 0.9398 (m-80) cc_final: 0.9041 (m-80) REVERT: B 237 ASP cc_start: 0.9342 (t0) cc_final: 0.8809 (m-30) REVERT: B 273 LEU cc_start: 0.8845 (mt) cc_final: 0.8611 (mt) REVERT: E 548 MET cc_start: 0.7611 (mpp) cc_final: 0.7051 (mtp) REVERT: K 35 ASP cc_start: 0.9415 (m-30) cc_final: 0.9103 (t0) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.2654 time to fit residues: 37.2879 Evaluate side-chains 69 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 1.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 163 optimal weight: 8.9990 chunk 5 optimal weight: 9.9990 chunk 161 optimal weight: 30.0000 chunk 101 optimal weight: 20.0000 chunk 12 optimal weight: 20.0000 chunk 48 optimal weight: 0.8980 chunk 104 optimal weight: 0.0040 chunk 10 optimal weight: 5.9990 chunk 45 optimal weight: 9.9990 chunk 43 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 overall best weight: 2.1798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 506 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 = 0.3143 r_free = 0.3143 target = 0.034254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.028010 restraints weight = 146725.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.029058 restraints weight = 82096.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.029811 restraints weight = 54401.717| |-----------------------------------------------------------------------------| r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.5869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13497 Z= 0.125 Angle : 0.580 7.980 18393 Z= 0.296 Chirality : 0.044 0.283 2091 Planarity : 0.004 0.034 2313 Dihedral : 5.189 22.909 2292 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % 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: -0.34 (0.21), residues: 1626 helix: -0.57 (0.33), residues: 216 sheet: -0.41 (0.21), residues: 606 loop : 0.24 (0.24), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 104 HIS 0.017 0.001 HIS E 516 PHE 0.025 0.002 PHE B 234 TYR 0.010 0.001 TYR E 517 ARG 0.003 0.000 ARG K 17 Details of bonding type rmsd link_NAG-ASN : bond 0.00321 ( 12) link_NAG-ASN : angle 1.68325 ( 36) link_ALPHA1-6 : bond 0.00208 ( 3) link_ALPHA1-6 : angle 1.60214 ( 9) link_BETA1-4 : bond 0.00212 ( 6) link_BETA1-4 : angle 2.01099 ( 18) link_ALPHA1-3 : bond 0.00878 ( 3) link_ALPHA1-3 : angle 1.44869 ( 9) hydrogen bonds : bond 0.03738 ( 489) hydrogen bonds : angle 6.37030 ( 1263) SS BOND : bond 0.00423 ( 9) SS BOND : angle 1.97404 ( 18) covalent geometry : bond 0.00271 (13464) covalent geometry : angle 0.56772 (18303) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4200.53 seconds wall clock time: 77 minutes 13.11 seconds (4633.11 seconds total)