Starting phenix.real_space_refine on Thu Jul 31 19:04:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kfh_22853/07_2025/7kfh_22853.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kfh_22853/07_2025/7kfh_22853.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7kfh_22853/07_2025/7kfh_22853.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kfh_22853/07_2025/7kfh_22853.map" model { file = "/net/cci-nas-00/data/ceres_data/7kfh_22853/07_2025/7kfh_22853.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kfh_22853/07_2025/7kfh_22853.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 48 5.16 5 C 8601 2.51 5 N 2271 2.21 5 O 2655 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 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: 13575 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1793 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 216} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "G" Number of atoms: 1026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1026 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 5, 'TRANS': 127} Chain: "K" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 818 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 100} Chain: "E" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 757 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 4, 'TRANS': 90} Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 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: "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 Restraints were copied for chains: I, H, C, B, J, L, D, F, O, Q, P, R Time building chain proxies: 6.78, per 1000 atoms: 0.50 Number of scatterers: 13575 At special positions: 0 Unit cell: (118.45, 123.6, 123.6, 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 48 16.00 O 2655 8.00 N 2271 7.00 C 8601 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 108 " - pdb=" SG CYS A 135 " distance=2.02 Simple disulfide: pdb=" SG CYS A 121 " - pdb=" SG CYS A 147 " distance=2.02 Simple disulfide: pdb=" SG CYS C 108 " - pdb=" SG CYS C 135 " distance=2.02 Simple disulfide: pdb=" SG CYS B 108 " - pdb=" SG CYS B 135 " distance=2.02 Simple disulfide: pdb=" SG CYS C 121 " - pdb=" SG CYS C 147 " distance=2.03 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 147 " 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 N 3 " - " MAN N 4 " " BMA P 3 " - " MAN P 4 " " BMA R 3 " - " MAN R 4 " ALPHA1-6 " BMA N 3 " - " MAN N 5 " " BMA P 3 " - " MAN P 5 " " BMA R 3 " - " MAN R 5 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " NAG-ASN " NAG A 401 " - " ASN A 238 " " NAG A 402 " - " ASN A 268 " " NAG A 403 " - " ASN A 228 " " NAG B 401 " - " ASN B 238 " " NAG B 402 " - " ASN B 268 " " NAG B 403 " - " ASN B 228 " " NAG C 401 " - " ASN C 238 " " NAG C 402 " - " ASN C 268 " " NAG C 403 " - " ASN C 228 " " NAG M 1 " - " ASN A 257 " " NAG N 1 " - " ASN D 563 " " NAG O 1 " - " ASN B 257 " " NAG P 1 " - " ASN E 563 " " NAG Q 1 " - " ASN C 257 " " NAG R 1 " - " ASN F 563 " Time building additional restraints: 3.93 Conformation dependent library (CDL) restraints added in 1.8 seconds 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3066 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 30 sheets defined 17.3% alpha, 35.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.11 Creating SS restraints... 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 83 Processing helix chain 'A' and resid 249 through 264 Processing helix chain 'A' and resid 278 through 282 removed outlier: 4.481A pdb=" N ASP A 282 " --> pdb=" O PRO A 279 " (cutoff:3.500A) Processing helix chain 'J' and resid 29 through 32 Processing helix chain 'J' and resid 80 through 84 Processing helix chain 'D' and resid 538 through 542 Processing helix chain 'D' and resid 553 through 575 removed outlier: 4.739A pdb=" N GLN D 567 " --> pdb=" O ASN D 563 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ALA D 568 " --> pdb=" O GLU D 564 " (cutoff:3.500A) Processing helix chain 'D' and resid 583 through 597 Processing helix chain 'G' and resid 62 through 65 Processing helix chain 'G' and resid 74 through 76 No H-bonds generated for 'chain 'G' and resid 74 through 76' Processing helix chain 'G' and resid 87 through 91 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 83 Processing helix chain 'B' and resid 249 through 264 Processing helix chain 'B' and resid 278 through 282 removed outlier: 4.483A pdb=" N ASP B 282 " --> pdb=" O PRO B 279 " (cutoff:3.500A) Processing helix chain 'K' and resid 29 through 32 Processing helix chain 'K' and resid 80 through 84 Processing helix chain 'E' and resid 538 through 542 Processing helix chain 'E' and resid 553 through 575 removed outlier: 4.739A pdb=" N GLN E 567 " --> pdb=" O ASN E 563 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ALA E 568 " --> pdb=" O GLU E 564 " (cutoff:3.500A) Processing helix chain 'E' and resid 583 through 597 Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 74 through 76 No H-bonds generated for 'chain 'H' and resid 74 through 76' Processing helix chain 'H' and resid 87 through 91 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 83 Processing helix chain 'C' and resid 249 through 264 Processing helix chain 'C' and resid 278 through 282 removed outlier: 4.482A pdb=" N ASP C 282 " --> pdb=" O PRO C 279 " (cutoff:3.500A) Processing helix chain 'L' and resid 29 through 32 Processing helix chain 'L' and resid 80 through 84 Processing helix chain 'F' and resid 538 through 542 Processing helix chain 'F' and resid 553 through 575 removed outlier: 4.739A pdb=" N GLN F 567 " --> pdb=" O ASN F 563 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ALA F 568 " --> pdb=" O GLU F 564 " (cutoff:3.500A) Processing helix chain 'F' and resid 583 through 597 Processing helix chain 'I' and resid 62 through 65 Processing helix chain 'I' and resid 74 through 76 No H-bonds generated for 'chain 'I' and resid 74 through 76' Processing helix chain 'I' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 43 through 45 removed outlier: 6.700A pdb=" N GLY A 36 " --> pdb=" O ILE A 185 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 544 through 549 removed outlier: 6.313A pdb=" N ASN A 69 " --> pdb=" O GLU A 103 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N VAL A 96 " --> pdb=" O THR D 581 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 86 through 89 Processing sheet with id=AA4, first strand: chain 'A' and resid 105 through 114 removed outlier: 6.273A pdb=" N GLU A 106 " --> pdb=" O TYR A 137 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N HIS A 139 " --> pdb=" O GLU A 106 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N CYS A 108 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N VAL A 141 " --> pdb=" O CYS A 108 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ASN A 110 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N GLY A 143 " --> pdb=" O ASN A 110 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N GLU A 112 " --> pdb=" O GLY A 143 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ARG A 136 " --> pdb=" O THR A 216 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N ILE A 218 " --> pdb=" O ARG A 136 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N VAL A 138 " --> pdb=" O ILE A 218 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N TYR A 220 " --> pdb=" O VAL A 138 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N LYS A 140 " --> pdb=" O TYR A 220 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N ALA A 222 " --> pdb=" O LYS A 140 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N SER A 142 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 14.147A pdb=" N THR A 217 " --> pdb=" O ASP A 237 " (cutoff:3.500A) removed outlier: 10.057A pdb=" N ASP A 237 " --> pdb=" O THR A 217 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N ARG A 219 " --> pdb=" O GLU A 235 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N THR A 240 " --> pdb=" O VAL A 236 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N TYR A 241 " --> pdb=" O TRP A 275 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N SER G 112 " --> pdb=" O GLY G 104 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'J' and resid 4 through 7 Processing sheet with id=AA6, first strand: chain 'J' and resid 10 through 13 removed outlier: 6.217A pdb=" N LEU J 34 " --> pdb=" O TYR J 50 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N TYR J 50 " --> pdb=" O LEU J 34 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N TRP J 36 " --> pdb=" O LEU J 48 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'J' and resid 10 through 13 Processing sheet with id=AA8, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AA9, first strand: chain 'G' and resid 10 through 12 removed outlier: 7.146A pdb=" N PHE G 34 " --> pdb=" O GLY G 50 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N GLY G 50 " --> pdb=" O PHE G 34 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N TRP G 36 " --> pdb=" O MET G 48 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 10 through 12 Processing sheet with id=AB2, first strand: chain 'B' and resid 43 through 45 removed outlier: 6.701A pdb=" N GLY B 36 " --> pdb=" O ILE B 185 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 544 through 549 removed outlier: 6.311A pdb=" N ASN B 69 " --> pdb=" O GLU B 103 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N VAL B 96 " --> pdb=" O THR E 581 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 86 through 89 Processing sheet with id=AB5, first strand: chain 'B' and resid 105 through 114 removed outlier: 6.274A pdb=" N GLU B 106 " --> pdb=" O TYR B 137 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N HIS B 139 " --> pdb=" O GLU B 106 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N CYS B 108 " --> pdb=" O HIS B 139 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N VAL B 141 " --> pdb=" O CYS B 108 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ASN B 110 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N GLY B 143 " --> pdb=" O ASN B 110 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N GLU B 112 " --> pdb=" O GLY B 143 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ARG B 136 " --> pdb=" O THR B 216 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N ILE B 218 " --> pdb=" O ARG B 136 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N VAL B 138 " --> pdb=" O ILE B 218 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N TYR B 220 " --> pdb=" O VAL B 138 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N LYS B 140 " --> pdb=" O TYR B 220 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N ALA B 222 " --> pdb=" O LYS B 140 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N SER B 142 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 14.147A pdb=" N THR B 217 " --> pdb=" O ASP B 237 " (cutoff:3.500A) removed outlier: 10.058A pdb=" N ASP B 237 " --> pdb=" O THR B 217 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N ARG B 219 " --> pdb=" O GLU B 235 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N THR B 240 " --> pdb=" O VAL B 236 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N SER H 112 " --> pdb=" O GLY H 104 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'K' and resid 4 through 7 Processing sheet with id=AB7, first strand: chain 'K' and resid 10 through 13 removed outlier: 6.217A pdb=" N LEU K 34 " --> pdb=" O TYR K 50 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N TYR K 50 " --> pdb=" O LEU K 34 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N TRP K 36 " --> pdb=" O LEU K 48 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'K' and resid 10 through 13 Processing sheet with id=AB9, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AC1, first strand: chain 'H' and resid 10 through 12 removed outlier: 7.145A pdb=" N PHE H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N GLY H 50 " --> pdb=" O PHE H 34 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 10 through 12 Processing sheet with id=AC3, first strand: chain 'C' and resid 43 through 45 removed outlier: 6.700A pdb=" N GLY C 36 " --> pdb=" O ILE C 185 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 544 through 549 removed outlier: 6.313A pdb=" N ASN C 69 " --> pdb=" O GLU C 103 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N VAL C 96 " --> pdb=" O THR F 581 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 86 through 89 Processing sheet with id=AC6, first strand: chain 'C' and resid 105 through 114 removed outlier: 6.273A pdb=" N GLU C 106 " --> pdb=" O TYR C 137 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N HIS C 139 " --> pdb=" O GLU C 106 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N CYS C 108 " --> pdb=" O HIS C 139 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N VAL C 141 " --> pdb=" O CYS C 108 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ASN C 110 " --> pdb=" O VAL C 141 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N GLY C 143 " --> pdb=" O ASN C 110 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N GLU C 112 " --> pdb=" O GLY C 143 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ARG C 136 " --> pdb=" O THR C 216 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N ILE C 218 " --> pdb=" O ARG C 136 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N VAL C 138 " --> pdb=" O ILE C 218 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N TYR C 220 " --> pdb=" O VAL C 138 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N LYS C 140 " --> pdb=" O TYR C 220 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N ALA C 222 " --> pdb=" O LYS C 140 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N SER C 142 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 14.147A pdb=" N THR C 217 " --> pdb=" O ASP C 237 " (cutoff:3.500A) removed outlier: 10.059A pdb=" N ASP C 237 " --> pdb=" O THR C 217 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N ARG C 219 " --> pdb=" O GLU C 235 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N THR C 240 " --> pdb=" O VAL C 236 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N SER I 112 " --> pdb=" O GLY I 104 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AC8, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.216A pdb=" N LEU L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N TYR L 50 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'L' and resid 10 through 13 Processing sheet with id=AD1, first strand: chain 'I' and resid 3 through 6 Processing sheet with id=AD2, first strand: chain 'I' and resid 10 through 12 removed outlier: 7.146A pdb=" N PHE I 34 " --> pdb=" O GLY I 50 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N GLY I 50 " --> pdb=" O PHE I 34 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N TRP I 36 " --> pdb=" O MET I 48 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 10 through 12 549 hydrogen bonds defined for protein. 1296 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: 4.66 Time building geometry restraints manager: 4.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2776 1.32 - 1.45: 4283 1.45 - 1.59: 6703 1.59 - 1.72: 62 1.72 - 1.85: 60 Bond restraints: 13884 Sorted by residual: bond pdb=" CB HIS D 549 " pdb=" CG HIS D 549 " ideal model delta sigma weight residual 1.497 1.397 0.100 1.40e-02 5.10e+03 5.11e+01 bond pdb=" CB HIS F 549 " pdb=" CG HIS F 549 " ideal model delta sigma weight residual 1.497 1.398 0.099 1.40e-02 5.10e+03 5.02e+01 bond pdb=" CB HIS E 549 " pdb=" CG HIS E 549 " ideal model delta sigma weight residual 1.497 1.398 0.099 1.40e-02 5.10e+03 4.95e+01 bond pdb=" CZ2 TRP F 597 " pdb=" CH2 TRP F 597 " ideal model delta sigma weight residual 1.368 1.490 -0.122 1.90e-02 2.77e+03 4.11e+01 bond pdb=" CZ2 TRP E 597 " pdb=" CH2 TRP E 597 " ideal model delta sigma weight residual 1.368 1.489 -0.121 1.90e-02 2.77e+03 4.08e+01 ... (remaining 13879 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 16173 2.38 - 4.76: 2247 4.76 - 7.14: 363 7.14 - 9.52: 54 9.52 - 11.90: 9 Bond angle restraints: 18846 Sorted by residual: angle pdb=" N PHE I 55 " pdb=" CA PHE I 55 " pdb=" C PHE I 55 " ideal model delta sigma weight residual 113.97 102.49 11.48 1.28e+00 6.10e-01 8.04e+01 angle pdb=" N PHE G 55 " pdb=" CA PHE G 55 " pdb=" C PHE G 55 " ideal model delta sigma weight residual 113.97 102.56 11.41 1.28e+00 6.10e-01 7.95e+01 angle pdb=" N PHE H 55 " pdb=" CA PHE H 55 " pdb=" C PHE H 55 " ideal model delta sigma weight residual 113.97 102.60 11.37 1.28e+00 6.10e-01 7.89e+01 angle pdb=" N SER A 41 " pdb=" CA SER A 41 " pdb=" C SER A 41 " ideal model delta sigma weight residual 114.12 102.22 11.90 1.39e+00 5.18e-01 7.33e+01 angle pdb=" N SER C 41 " pdb=" CA SER C 41 " pdb=" C SER C 41 " ideal model delta sigma weight residual 114.12 102.24 11.88 1.39e+00 5.18e-01 7.30e+01 ... (remaining 18841 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.15: 8307 21.15 - 42.30: 135 42.30 - 63.45: 57 63.45 - 84.60: 35 84.60 - 105.75: 16 Dihedral angle restraints: 8550 sinusoidal: 3729 harmonic: 4821 Sorted by residual: dihedral pdb=" CA PRO H 100 " pdb=" C PRO H 100 " pdb=" N PRO H 101 " pdb=" CA PRO H 101 " ideal model delta harmonic sigma weight residual 180.00 161.42 18.58 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA PRO G 100 " pdb=" C PRO G 100 " pdb=" N PRO G 101 " pdb=" CA PRO G 101 " ideal model delta harmonic sigma weight residual 180.00 161.43 18.57 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA PRO I 100 " pdb=" C PRO I 100 " pdb=" N PRO I 101 " pdb=" CA PRO I 101 " ideal model delta harmonic sigma weight residual 180.00 161.44 18.56 0 5.00e+00 4.00e-02 1.38e+01 ... (remaining 8547 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.113: 1667 0.113 - 0.225: 378 0.225 - 0.338: 64 0.338 - 0.451: 39 0.451 - 0.563: 9 Chirality restraints: 2157 Sorted by residual: chirality pdb=" C1 NAG Q 2 " pdb=" O4 NAG Q 1 " pdb=" C2 NAG Q 2 " pdb=" O5 NAG Q 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.16e+02 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 -2.61 0.21 2.00e-02 2.50e+03 1.10e+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 -2.61 0.21 2.00e-02 2.50e+03 1.10e+02 ... (remaining 2154 not shown) Planarity restraints: 2400 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 238 " 0.096 2.00e-02 2.50e+03 1.02e-01 1.30e+02 pdb=" CG ASN B 238 " -0.041 2.00e-02 2.50e+03 pdb=" OD1 ASN B 238 " -0.018 2.00e-02 2.50e+03 pdb=" ND2 ASN B 238 " -0.160 2.00e-02 2.50e+03 pdb=" C1 NAG B 401 " 0.122 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 238 " -0.096 2.00e-02 2.50e+03 1.02e-01 1.29e+02 pdb=" CG ASN A 238 " 0.041 2.00e-02 2.50e+03 pdb=" OD1 ASN A 238 " 0.018 2.00e-02 2.50e+03 pdb=" ND2 ASN A 238 " 0.160 2.00e-02 2.50e+03 pdb=" C1 NAG A 401 " -0.122 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 238 " -0.096 2.00e-02 2.50e+03 1.01e-01 1.29e+02 pdb=" CG ASN C 238 " 0.039 2.00e-02 2.50e+03 pdb=" OD1 ASN C 238 " 0.018 2.00e-02 2.50e+03 pdb=" ND2 ASN C 238 " 0.160 2.00e-02 2.50e+03 pdb=" C1 NAG C 401 " -0.122 2.00e-02 2.50e+03 ... (remaining 2397 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 79 2.60 - 3.17: 11206 3.17 - 3.75: 20059 3.75 - 4.32: 29891 4.32 - 4.90: 47923 Nonbonded interactions: 109158 Sorted by model distance: nonbonded pdb=" SG CYS G 22 " pdb=" SG CYS G 96 " model vdw 2.024 3.760 nonbonded pdb=" SG CYS I 22 " pdb=" SG CYS I 96 " model vdw 2.024 3.760 nonbonded pdb=" SG CYS H 22 " pdb=" SG CYS H 96 " model vdw 2.024 3.760 nonbonded pdb=" SG CYS L 23 " pdb=" SG CYS L 89 " model vdw 2.039 3.760 nonbonded pdb=" SG CYS J 23 " pdb=" SG CYS J 89 " model vdw 2.040 3.760 ... (remaining 109153 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: 0.09 Found NCS groups: 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 'K' selection = chain 'J' selection = chain 'L' } ncs_group { reference = chain 'E' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'M' selection = chain 'O' selection = chain 'Q' } ncs_group { reference = chain 'N' selection = chain 'P' selection = chain 'R' } 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: 2.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.590 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 32.490 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.050 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:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 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 : 0.021 0.122 13920 Z= 1.103 Angle : 1.776 11.901 18948 Z= 1.166 Chirality : 0.114 0.563 2157 Planarity : 0.008 0.045 2385 Dihedral : 11.997 105.755 5466 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 0.45 Ramachandran Plot: Outliers : 0.36 % Allowed : 1.80 % Favored : 97.84 % Rotamer: Outliers : 0.21 % Allowed : 0.99 % Favored : 98.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.20), residues: 1665 helix: 1.13 (0.31), residues: 159 sheet: 0.97 (0.21), residues: 594 loop : 0.65 (0.20), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.009 TRP L 36 HIS 0.005 0.002 HIS F 516 PHE 0.026 0.006 PHE J 84 TYR 0.060 0.009 TYR H 60 ARG 0.008 0.001 ARG K 46 Details of bonding type rmsd link_NAG-ASN : bond 0.07581 ( 15) link_NAG-ASN : angle 2.60121 ( 45) link_ALPHA1-6 : bond 0.06335 ( 3) link_ALPHA1-6 : angle 3.87776 ( 9) link_BETA1-4 : bond 0.06563 ( 9) link_BETA1-4 : angle 5.87401 ( 27) link_ALPHA1-3 : bond 0.08200 ( 3) link_ALPHA1-3 : angle 4.23005 ( 9) hydrogen bonds : bond 0.15850 ( 513) hydrogen bonds : angle 7.44945 ( 1296) SS BOND : bond 0.00756 ( 6) SS BOND : angle 2.17601 ( 12) covalent geometry : bond 0.02117 (13884) covalent geometry : angle 1.75667 (18846) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 383 time to evaluate : 1.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ASP cc_start: 0.8154 (m-30) cc_final: 0.7343 (m-30) REVERT: A 258 GLU cc_start: 0.7972 (tp30) cc_final: 0.7394 (tp30) REVERT: D 549 HIS cc_start: 0.8104 (p-80) cc_final: 0.7833 (t-170) REVERT: D 581 THR cc_start: 0.9521 (m) cc_final: 0.9132 (p) REVERT: D 596 ARG cc_start: 0.7704 (mtp-110) cc_final: 0.7482 (mtt-85) REVERT: G 48 MET cc_start: 0.7713 (mtp) cc_final: 0.7387 (mtp) REVERT: G 78 THR cc_start: 0.8456 (m) cc_final: 0.7838 (p) REVERT: G 83 LEU cc_start: 0.7106 (tp) cc_final: 0.6651 (tp) REVERT: G 108 TRP cc_start: 0.8336 (p-90) cc_final: 0.8120 (p90) REVERT: G 114 LYS cc_start: 0.8126 (ttpt) cc_final: 0.7553 (mtmm) REVERT: B 55 ASP cc_start: 0.8164 (m-30) cc_final: 0.7106 (m-30) REVERT: K 37 TYR cc_start: 0.5217 (m-80) cc_final: 0.4306 (m-80) REVERT: K 47 LEU cc_start: 0.3496 (tp) cc_final: 0.3250 (tt) REVERT: K 48 LEU cc_start: 0.8217 (mt) cc_final: 0.7862 (mt) REVERT: E 549 HIS cc_start: 0.8025 (p-80) cc_final: 0.7708 (t-170) REVERT: E 550 ASN cc_start: 0.9131 (t0) cc_final: 0.8599 (t0) REVERT: E 581 THR cc_start: 0.9515 (m) cc_final: 0.9246 (p) REVERT: H 48 MET cc_start: 0.7477 (mtp) cc_final: 0.7242 (mtp) REVERT: H 78 THR cc_start: 0.8201 (m) cc_final: 0.7608 (p) REVERT: H 81 MET cc_start: 0.7905 (ttp) cc_final: 0.7634 (tmm) REVERT: H 83 LEU cc_start: 0.7587 (tp) cc_final: 0.7106 (tp) REVERT: H 114 LYS cc_start: 0.8208 (ttpt) cc_final: 0.7589 (ptpt) REVERT: C 109 TYR cc_start: 0.9053 (m-80) cc_final: 0.8765 (m-80) REVERT: C 258 GLU cc_start: 0.7918 (tp30) cc_final: 0.7394 (tp30) REVERT: L 37 TYR cc_start: 0.5533 (m-80) cc_final: 0.4804 (m-80) REVERT: F 550 ASN cc_start: 0.8993 (t0) cc_final: 0.8786 (t0) REVERT: F 581 THR cc_start: 0.9508 (m) cc_final: 0.9009 (p) REVERT: F 596 ARG cc_start: 0.7748 (mtp-110) cc_final: 0.7518 (mtt-85) REVERT: F 597 TRP cc_start: 0.6861 (t-100) cc_final: 0.6339 (t-100) REVERT: I 78 THR cc_start: 0.7994 (m) cc_final: 0.7360 (p) REVERT: I 83 LEU cc_start: 0.7483 (tp) cc_final: 0.7013 (tp) REVERT: I 94 TYR cc_start: 0.5017 (m-80) cc_final: 0.4622 (m-10) REVERT: I 114 LYS cc_start: 0.8161 (ttpt) cc_final: 0.7520 (ptpt) outliers start: 3 outliers final: 3 residues processed: 386 average time/residue: 0.3191 time to fit residues: 166.1291 Evaluate side-chains 229 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 226 time to evaluate : 1.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 ASN Chi-restraints excluded: chain B residue 238 ASN Chi-restraints excluded: chain C residue 238 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 136 optimal weight: 5.9990 chunk 122 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 chunk 65 optimal weight: 0.8980 chunk 126 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 94 optimal weight: 0.6980 chunk 147 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 GLN F 549 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.148991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.099031 restraints weight = 21875.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.098321 restraints weight = 13982.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.098226 restraints weight = 12104.747| |-----------------------------------------------------------------------------| r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.3142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 13920 Z= 0.190 Angle : 0.726 8.344 18948 Z= 0.378 Chirality : 0.046 0.226 2157 Planarity : 0.005 0.044 2385 Dihedral : 8.866 72.773 2463 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.18 % Allowed : 1.98 % Favored : 97.84 % Rotamer: Outliers : 2.54 % Allowed : 7.63 % Favored : 89.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.86 (0.20), residues: 1665 helix: 1.90 (0.34), residues: 162 sheet: 0.69 (0.21), residues: 615 loop : 0.35 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 86 HIS 0.003 0.001 HIS C 39 PHE 0.021 0.002 PHE J 72 TYR 0.017 0.002 TYR L 50 ARG 0.009 0.001 ARG I 31 Details of bonding type rmsd link_NAG-ASN : bond 0.00497 ( 15) link_NAG-ASN : angle 2.75188 ( 45) link_ALPHA1-6 : bond 0.00792 ( 3) link_ALPHA1-6 : angle 1.66601 ( 9) link_BETA1-4 : bond 0.00882 ( 9) link_BETA1-4 : angle 4.29501 ( 27) link_ALPHA1-3 : bond 0.01097 ( 3) link_ALPHA1-3 : angle 3.11270 ( 9) hydrogen bonds : bond 0.05061 ( 513) hydrogen bonds : angle 5.70012 ( 1296) SS BOND : bond 0.00226 ( 6) SS BOND : angle 0.57765 ( 12) covalent geometry : bond 0.00418 (13884) covalent geometry : angle 0.69279 (18846) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 256 time to evaluate : 1.563 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: A 55 ASP cc_start: 0.8158 (m-30) cc_final: 0.7585 (m-30) REVERT: J 37 TYR cc_start: 0.7863 (m-80) cc_final: 0.7338 (m-80) REVERT: G 10 GLU cc_start: 0.5506 (mm-30) cc_final: 0.5250 (mm-30) REVERT: G 60 TYR cc_start: 0.7857 (m-80) cc_final: 0.7589 (m-80) REVERT: G 65 GLN cc_start: 0.8384 (tp40) cc_final: 0.8105 (tp-100) REVERT: G 81 MET cc_start: 0.7943 (tmm) cc_final: 0.7267 (tmm) REVERT: G 114 LYS cc_start: 0.8452 (ttpt) cc_final: 0.7982 (mtmm) REVERT: K 37 TYR cc_start: 0.7669 (m-80) cc_final: 0.6954 (m-80) REVERT: H 12 LYS cc_start: 0.6345 (OUTLIER) cc_final: 0.5920 (mptt) REVERT: H 65 GLN cc_start: 0.8841 (tp40) cc_final: 0.8559 (mm-40) REVERT: H 114 LYS cc_start: 0.8306 (ttpt) cc_final: 0.7786 (mtmm) REVERT: C 55 ASP cc_start: 0.7910 (m-30) cc_final: 0.7379 (m-30) REVERT: L 37 TYR cc_start: 0.7636 (m-80) cc_final: 0.6241 (m-80) REVERT: L 55 ARG cc_start: 0.7244 (ttm110) cc_final: 0.7018 (mtt90) REVERT: F 545 GLU cc_start: 0.8159 (pm20) cc_final: 0.7919 (pm20) REVERT: I 114 LYS cc_start: 0.8368 (ttpt) cc_final: 0.7803 (mtmm) outliers start: 36 outliers final: 19 residues processed: 277 average time/residue: 0.2882 time to fit residues: 111.4646 Evaluate side-chains 227 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 207 time to evaluate : 1.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 238 ASN Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain D residue 548 MET Chi-restraints excluded: chain D residue 593 LEU Chi-restraints excluded: chain G residue 52 ILE Chi-restraints excluded: chain G residue 54 ILE Chi-restraints excluded: chain B residue 150 ASP Chi-restraints excluded: chain B residue 238 ASN Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain E residue 593 LEU Chi-restraints excluded: chain H residue 12 LYS Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain C residue 238 ASN Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain I residue 52 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 96 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 48 optimal weight: 7.9990 chunk 98 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 chunk 158 optimal weight: 9.9990 chunk 28 optimal weight: 20.0000 chunk 88 optimal weight: 3.9990 chunk 109 optimal weight: 0.0670 chunk 50 optimal weight: 4.9990 chunk 148 optimal weight: 1.9990 overall best weight: 2.4124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 59 ASN H 59 ASN C 39 HIS I 59 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.138221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.083929 restraints weight = 22457.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.086350 restraints weight = 16299.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.086708 restraints weight = 11407.810| |-----------------------------------------------------------------------------| r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.4031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 13920 Z= 0.281 Angle : 0.744 7.369 18948 Z= 0.379 Chirality : 0.048 0.159 2157 Planarity : 0.005 0.042 2385 Dihedral : 8.146 59.648 2463 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.10 % Favored : 97.72 % Rotamer: Outliers : 4.03 % Allowed : 8.90 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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 (0.20), residues: 1665 helix: 1.58 (0.39), residues: 162 sheet: 0.21 (0.20), residues: 648 loop : 0.06 (0.20), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 47 HIS 0.006 0.002 HIS F 549 PHE 0.030 0.003 PHE A 132 TYR 0.018 0.002 TYR I 117 ARG 0.008 0.001 ARG G 31 Details of bonding type rmsd link_NAG-ASN : bond 0.00228 ( 15) link_NAG-ASN : angle 2.24970 ( 45) link_ALPHA1-6 : bond 0.00751 ( 3) link_ALPHA1-6 : angle 1.20663 ( 9) link_BETA1-4 : bond 0.00814 ( 9) link_BETA1-4 : angle 3.63989 ( 27) link_ALPHA1-3 : bond 0.00967 ( 3) link_ALPHA1-3 : angle 2.06176 ( 9) hydrogen bonds : bond 0.05287 ( 513) hydrogen bonds : angle 5.52701 ( 1296) SS BOND : bond 0.00390 ( 6) SS BOND : angle 0.30319 ( 12) covalent geometry : bond 0.00665 (13884) covalent geometry : angle 0.72286 (18846) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 217 time to evaluate : 1.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 37 TYR cc_start: 0.7863 (m-80) cc_final: 0.7366 (m-80) REVERT: G 31 ARG cc_start: 0.7850 (mtt90) cc_final: 0.7636 (mtt-85) REVERT: G 65 GLN cc_start: 0.8508 (tp40) cc_final: 0.8098 (mm-40) REVERT: G 81 MET cc_start: 0.8308 (tmm) cc_final: 0.7530 (tmm) REVERT: G 114 LYS cc_start: 0.8571 (ttpt) cc_final: 0.7887 (mtmm) REVERT: K 37 TYR cc_start: 0.7676 (m-80) cc_final: 0.7104 (m-80) REVERT: K 55 ARG cc_start: 0.6913 (mtt90) cc_final: 0.6629 (mpt180) REVERT: H 12 LYS cc_start: 0.6201 (OUTLIER) cc_final: 0.5901 (mptt) REVERT: H 119 TYR cc_start: 0.8591 (p90) cc_final: 0.7996 (p90) REVERT: L 55 ARG cc_start: 0.7386 (ttm110) cc_final: 0.6946 (mtt90) REVERT: F 510 LYS cc_start: 0.8625 (mttt) cc_final: 0.7881 (mmtt) outliers start: 57 outliers final: 32 residues processed: 255 average time/residue: 0.2922 time to fit residues: 104.7523 Evaluate side-chains 237 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 204 time to evaluate : 1.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 238 ASN Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain D residue 542 ILE Chi-restraints excluded: chain D residue 548 MET Chi-restraints excluded: chain D residue 581 THR Chi-restraints excluded: chain G residue 12 LYS Chi-restraints excluded: chain G residue 48 MET Chi-restraints excluded: chain G residue 54 ILE Chi-restraints excluded: chain G residue 109 PHE Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 238 ASN Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain E residue 520 THR Chi-restraints excluded: chain E residue 548 MET Chi-restraints excluded: chain E residue 581 THR Chi-restraints excluded: chain E residue 587 ARG Chi-restraints excluded: chain E residue 593 LEU Chi-restraints excluded: chain H residue 12 LYS Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain C residue 238 ASN Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain F residue 581 THR Chi-restraints excluded: chain I residue 52 ILE Chi-restraints excluded: chain I residue 60 TYR Chi-restraints excluded: chain I residue 109 PHE Chi-restraints excluded: chain I residue 121 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 144 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 146 optimal weight: 0.8980 chunk 156 optimal weight: 10.0000 chunk 120 optimal weight: 0.7980 chunk 136 optimal weight: 9.9990 chunk 114 optimal weight: 0.7980 chunk 154 optimal weight: 0.8980 chunk 105 optimal weight: 0.0770 chunk 151 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 39 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.141574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.087826 restraints weight = 21933.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.090390 restraints weight = 13862.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.091982 restraints weight = 10576.743| |-----------------------------------------------------------------------------| r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.4295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 13920 Z= 0.124 Angle : 0.605 8.137 18948 Z= 0.301 Chirality : 0.044 0.161 2157 Planarity : 0.004 0.078 2385 Dihedral : 7.193 48.015 2463 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.10 % Favored : 97.72 % Rotamer: Outliers : 3.11 % Allowed : 9.60 % Favored : 87.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.31 (0.20), residues: 1665 helix: 1.93 (0.40), residues: 162 sheet: 0.36 (0.21), residues: 621 loop : -0.15 (0.20), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 47 HIS 0.002 0.001 HIS A 154 PHE 0.020 0.001 PHE L 72 TYR 0.020 0.002 TYR I 117 ARG 0.010 0.001 ARG E 596 Details of bonding type rmsd link_NAG-ASN : bond 0.00389 ( 15) link_NAG-ASN : angle 2.00566 ( 45) link_ALPHA1-6 : bond 0.00836 ( 3) link_ALPHA1-6 : angle 1.23885 ( 9) link_BETA1-4 : bond 0.00773 ( 9) link_BETA1-4 : angle 2.96060 ( 27) link_ALPHA1-3 : bond 0.01202 ( 3) link_ALPHA1-3 : angle 1.86960 ( 9) hydrogen bonds : bond 0.03975 ( 513) hydrogen bonds : angle 4.94539 ( 1296) SS BOND : bond 0.00225 ( 6) SS BOND : angle 0.48099 ( 12) covalent geometry : bond 0.00272 (13884) covalent geometry : angle 0.58642 (18846) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 223 time to evaluate : 1.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 SER cc_start: 0.7886 (OUTLIER) cc_final: 0.7144 (p) REVERT: J 37 TYR cc_start: 0.7915 (m-80) cc_final: 0.7572 (m-80) REVERT: D 587 ARG cc_start: 0.7555 (OUTLIER) cc_final: 0.7236 (mtp180) REVERT: G 65 GLN cc_start: 0.8447 (tp40) cc_final: 0.8011 (mm-40) REVERT: G 81 MET cc_start: 0.8192 (tmm) cc_final: 0.7429 (tmm) REVERT: G 114 LYS cc_start: 0.8582 (ttpt) cc_final: 0.8023 (ptmt) REVERT: B 103 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.8306 (tt0) REVERT: K 37 TYR cc_start: 0.7743 (m-80) cc_final: 0.6994 (m-80) REVERT: H 12 LYS cc_start: 0.6016 (OUTLIER) cc_final: 0.5812 (mptt) REVERT: H 64 PHE cc_start: 0.7325 (m-80) cc_final: 0.7089 (m-10) REVERT: I 48 MET cc_start: 0.7673 (ptm) cc_final: 0.7194 (ptm) outliers start: 44 outliers final: 23 residues processed: 247 average time/residue: 0.2827 time to fit residues: 98.6997 Evaluate side-chains 223 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 196 time to evaluate : 1.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 238 ASN Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 101 GLN Chi-restraints excluded: chain D residue 542 ILE Chi-restraints excluded: chain D residue 548 MET Chi-restraints excluded: chain D residue 587 ARG Chi-restraints excluded: chain G residue 48 MET Chi-restraints excluded: chain G residue 52 ILE Chi-restraints excluded: chain G residue 54 ILE Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 238 ASN Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain E residue 587 ARG Chi-restraints excluded: chain E residue 593 LEU Chi-restraints excluded: chain H residue 12 LYS Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain I residue 60 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 130 optimal weight: 0.5980 chunk 95 optimal weight: 6.9990 chunk 153 optimal weight: 7.9990 chunk 26 optimal weight: 9.9990 chunk 91 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 138 optimal weight: 4.9990 chunk 85 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 39 GLN G 39 GLN E 595 GLN C 39 HIS L 39 GLN I 39 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.140032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.087186 restraints weight = 22287.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.089071 restraints weight = 16136.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.089898 restraints weight = 12087.944| |-----------------------------------------------------------------------------| r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.4564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13920 Z= 0.148 Angle : 0.611 7.841 18948 Z= 0.302 Chirality : 0.044 0.164 2157 Planarity : 0.004 0.044 2385 Dihedral : 6.469 46.805 2461 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.22 % Favored : 97.60 % Rotamer: Outliers : 3.46 % Allowed : 10.81 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.25 (0.20), residues: 1665 helix: 2.02 (0.40), residues: 162 sheet: 0.20 (0.21), residues: 636 loop : -0.12 (0.21), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 104 HIS 0.003 0.001 HIS A 154 PHE 0.018 0.001 PHE L 72 TYR 0.017 0.001 TYR I 117 ARG 0.009 0.001 ARG D 596 Details of bonding type rmsd link_NAG-ASN : bond 0.00198 ( 15) link_NAG-ASN : angle 1.96117 ( 45) link_ALPHA1-6 : bond 0.00858 ( 3) link_ALPHA1-6 : angle 1.17942 ( 9) link_BETA1-4 : bond 0.00698 ( 9) link_BETA1-4 : angle 2.99874 ( 27) link_ALPHA1-3 : bond 0.01141 ( 3) link_ALPHA1-3 : angle 2.01702 ( 9) hydrogen bonds : bond 0.04000 ( 513) hydrogen bonds : angle 4.77788 ( 1296) SS BOND : bond 0.00275 ( 6) SS BOND : angle 0.34464 ( 12) covalent geometry : bond 0.00341 (13884) covalent geometry : angle 0.59175 (18846) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 211 time to evaluate : 1.641 Fit side-chains REVERT: A 174 THR cc_start: 0.9337 (m) cc_final: 0.9011 (p) REVERT: A 267 SER cc_start: 0.7854 (OUTLIER) cc_final: 0.7132 (p) REVERT: J 37 TYR cc_start: 0.7940 (m-80) cc_final: 0.7735 (m-10) REVERT: G 38 ARG cc_start: 0.7316 (mtm110) cc_final: 0.7037 (mtm110) REVERT: G 65 GLN cc_start: 0.8390 (tp40) cc_final: 0.7970 (mm-40) REVERT: G 81 MET cc_start: 0.8342 (tmm) cc_final: 0.7410 (tmm) REVERT: G 111 GLU cc_start: 0.8331 (pp20) cc_final: 0.8005 (pp20) REVERT: H 119 TYR cc_start: 0.8464 (p90) cc_final: 0.7813 (p90) REVERT: C 112 GLU cc_start: 0.7562 (mt-10) cc_final: 0.7335 (mt-10) REVERT: L 63 PHE cc_start: 0.7778 (m-80) cc_final: 0.7169 (m-80) REVERT: I 119 TYR cc_start: 0.8562 (p90) cc_final: 0.8277 (p90) REVERT: I 128 THR cc_start: 0.7307 (OUTLIER) cc_final: 0.6873 (p) outliers start: 49 outliers final: 29 residues processed: 246 average time/residue: 0.2801 time to fit residues: 97.7168 Evaluate side-chains 229 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 198 time to evaluate : 1.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain J residue 22 SER Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 101 GLN Chi-restraints excluded: chain D residue 548 MET Chi-restraints excluded: chain D residue 581 THR Chi-restraints excluded: chain D residue 593 LEU Chi-restraints excluded: chain G residue 48 MET Chi-restraints excluded: chain G residue 54 ILE Chi-restraints excluded: chain G residue 60 TYR Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain E residue 520 THR Chi-restraints excluded: chain E residue 587 ARG Chi-restraints excluded: chain E residue 595 GLN Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain F residue 581 THR Chi-restraints excluded: chain I residue 60 TYR Chi-restraints excluded: chain I residue 128 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 0 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 149 optimal weight: 6.9990 chunk 106 optimal weight: 0.9990 chunk 6 optimal weight: 0.3980 chunk 144 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 81 optimal weight: 20.0000 chunk 153 optimal weight: 9.9990 overall best weight: 1.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 39 GLN C 39 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.139824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.086778 restraints weight = 22722.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.089189 restraints weight = 14786.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.090732 restraints weight = 11475.703| |-----------------------------------------------------------------------------| r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.4791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 13920 Z= 0.217 Angle : 0.654 7.386 18948 Z= 0.324 Chirality : 0.045 0.159 2157 Planarity : 0.004 0.056 2385 Dihedral : 6.301 50.150 2457 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.70 % Favored : 97.12 % Rotamer: Outliers : 3.67 % Allowed : 11.51 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.07 (0.20), residues: 1665 helix: 1.85 (0.40), residues: 162 sheet: -0.03 (0.20), residues: 657 loop : -0.13 (0.21), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 104 HIS 0.004 0.001 HIS B 154 PHE 0.021 0.002 PHE E 592 TYR 0.015 0.001 TYR I 117 ARG 0.008 0.001 ARG E 596 Details of bonding type rmsd link_NAG-ASN : bond 0.00115 ( 15) link_NAG-ASN : angle 1.79091 ( 45) link_ALPHA1-6 : bond 0.00861 ( 3) link_ALPHA1-6 : angle 1.06537 ( 9) link_BETA1-4 : bond 0.00630 ( 9) link_BETA1-4 : angle 3.00932 ( 27) link_ALPHA1-3 : bond 0.01040 ( 3) link_ALPHA1-3 : angle 2.23634 ( 9) hydrogen bonds : bond 0.04327 ( 513) hydrogen bonds : angle 4.85154 ( 1296) SS BOND : bond 0.00313 ( 6) SS BOND : angle 0.18875 ( 12) covalent geometry : bond 0.00513 (13884) covalent geometry : angle 0.63727 (18846) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 210 time to evaluate : 1.712 Fit side-chains revert: symmetry clash REVERT: A 267 SER cc_start: 0.8000 (OUTLIER) cc_final: 0.7225 (p) REVERT: J 37 TYR cc_start: 0.7973 (m-80) cc_final: 0.7772 (m-10) REVERT: G 65 GLN cc_start: 0.8445 (tp40) cc_final: 0.8039 (mm-40) REVERT: G 81 MET cc_start: 0.8321 (tmm) cc_final: 0.7399 (tmm) REVERT: G 111 GLU cc_start: 0.8279 (pp20) cc_final: 0.7999 (pp20) REVERT: G 119 TYR cc_start: 0.8517 (p90) cc_final: 0.8255 (p90) REVERT: K 37 TYR cc_start: 0.7694 (m-10) cc_final: 0.7149 (m-10) REVERT: H 38 ARG cc_start: 0.7353 (mtp-110) cc_final: 0.6624 (mtm110) REVERT: H 86 LEU cc_start: 0.7087 (mt) cc_final: 0.6728 (mp) REVERT: H 119 TYR cc_start: 0.8564 (p90) cc_final: 0.8317 (p90) REVERT: L 37 TYR cc_start: 0.7682 (m-80) cc_final: 0.7094 (m-10) REVERT: L 63 PHE cc_start: 0.7775 (m-80) cc_final: 0.7185 (m-80) REVERT: I 95 PHE cc_start: 0.6662 (m-80) cc_final: 0.6449 (m-80) REVERT: I 119 TYR cc_start: 0.8632 (p90) cc_final: 0.8345 (p90) REVERT: I 120 MET cc_start: 0.8414 (mpp) cc_final: 0.8015 (mpp) REVERT: I 128 THR cc_start: 0.7373 (OUTLIER) cc_final: 0.6948 (p) outliers start: 52 outliers final: 39 residues processed: 242 average time/residue: 0.2860 time to fit residues: 97.6687 Evaluate side-chains 237 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 196 time to evaluate : 1.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 101 GLN Chi-restraints excluded: chain D residue 548 MET Chi-restraints excluded: chain D residue 581 THR Chi-restraints excluded: chain D residue 593 LEU Chi-restraints excluded: chain G residue 48 MET Chi-restraints excluded: chain G residue 54 ILE Chi-restraints excluded: chain G residue 60 TYR Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain E residue 520 THR Chi-restraints excluded: chain E residue 581 THR Chi-restraints excluded: chain E residue 587 ARG Chi-restraints excluded: chain E residue 593 LEU Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain H residue 109 PHE Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain F residue 581 THR Chi-restraints excluded: chain I residue 60 TYR Chi-restraints excluded: chain I residue 109 PHE Chi-restraints excluded: chain I residue 128 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 6 optimal weight: 0.8980 chunk 55 optimal weight: 4.9990 chunk 97 optimal weight: 8.9990 chunk 79 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 chunk 99 optimal weight: 6.9990 chunk 34 optimal weight: 0.9990 chunk 139 optimal weight: 3.9990 chunk 135 optimal weight: 20.0000 chunk 153 optimal weight: 0.6980 chunk 50 optimal weight: 9.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 39 HIS L 27 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.139542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.089446 restraints weight = 22694.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.088732 restraints weight = 15768.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.089041 restraints weight = 13140.222| |-----------------------------------------------------------------------------| r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.5002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 13920 Z= 0.204 Angle : 0.645 7.177 18948 Z= 0.320 Chirality : 0.045 0.151 2157 Planarity : 0.004 0.051 2385 Dihedral : 6.184 51.415 2457 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.58 % Favored : 97.24 % Rotamer: Outliers : 4.10 % Allowed : 11.79 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.06 (0.21), residues: 1665 helix: 1.87 (0.40), residues: 162 sheet: -0.02 (0.20), residues: 672 loop : -0.16 (0.21), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.001 TRP H 36 HIS 0.004 0.001 HIS B 154 PHE 0.018 0.002 PHE E 592 TYR 0.017 0.002 TYR L 50 ARG 0.013 0.001 ARG G 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00102 ( 15) link_NAG-ASN : angle 1.66771 ( 45) link_ALPHA1-6 : bond 0.00896 ( 3) link_ALPHA1-6 : angle 1.10461 ( 9) link_BETA1-4 : bond 0.00591 ( 9) link_BETA1-4 : angle 2.77021 ( 27) link_ALPHA1-3 : bond 0.00974 ( 3) link_ALPHA1-3 : angle 2.00098 ( 9) hydrogen bonds : bond 0.04264 ( 513) hydrogen bonds : angle 4.86221 ( 1296) SS BOND : bond 0.00320 ( 6) SS BOND : angle 0.36869 ( 12) covalent geometry : bond 0.00479 (13884) covalent geometry : angle 0.63064 (18846) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 210 time to evaluate : 1.529 Fit side-chains REVERT: A 267 SER cc_start: 0.8050 (OUTLIER) cc_final: 0.7272 (p) REVERT: J 37 TYR cc_start: 0.7930 (m-80) cc_final: 0.7207 (m-80) REVERT: J 63 PHE cc_start: 0.7407 (m-80) cc_final: 0.6685 (m-80) REVERT: G 10 GLU cc_start: 0.7196 (tt0) cc_final: 0.6979 (mm-30) REVERT: G 12 LYS cc_start: 0.7443 (tptt) cc_final: 0.7206 (tppt) REVERT: G 31 ARG cc_start: 0.8155 (mtt90) cc_final: 0.7893 (mtt-85) REVERT: G 36 TRP cc_start: 0.7988 (m100) cc_final: 0.7616 (m100) REVERT: G 65 GLN cc_start: 0.8417 (tp40) cc_final: 0.8113 (mm-40) REVERT: G 81 MET cc_start: 0.8235 (tmm) cc_final: 0.8007 (tmm) REVERT: G 111 GLU cc_start: 0.8498 (pp20) cc_final: 0.8124 (pp20) REVERT: G 114 LYS cc_start: 0.8590 (ttpt) cc_final: 0.8049 (ptmt) REVERT: G 119 TYR cc_start: 0.8579 (p90) cc_final: 0.8313 (p90) REVERT: G 120 MET cc_start: 0.8423 (mpp) cc_final: 0.8128 (mpp) REVERT: K 37 TYR cc_start: 0.7644 (m-10) cc_final: 0.6566 (m-10) REVERT: H 86 LEU cc_start: 0.7055 (mt) cc_final: 0.6738 (mp) REVERT: H 114 LYS cc_start: 0.8369 (ttpt) cc_final: 0.7813 (ptpt) REVERT: H 120 MET cc_start: 0.8321 (mpp) cc_final: 0.7978 (mpp) REVERT: L 37 TYR cc_start: 0.7737 (m-80) cc_final: 0.7302 (m-10) REVERT: L 63 PHE cc_start: 0.7709 (m-80) cc_final: 0.7115 (m-80) REVERT: I 119 TYR cc_start: 0.8676 (p90) cc_final: 0.8406 (p90) REVERT: I 120 MET cc_start: 0.8413 (mpp) cc_final: 0.8195 (mpp) REVERT: I 128 THR cc_start: 0.7399 (OUTLIER) cc_final: 0.6998 (p) outliers start: 58 outliers final: 44 residues processed: 243 average time/residue: 0.3012 time to fit residues: 104.8999 Evaluate side-chains 247 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 201 time to evaluate : 1.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain D residue 548 MET Chi-restraints excluded: chain D residue 581 THR Chi-restraints excluded: chain D residue 593 LEU Chi-restraints excluded: chain G residue 48 MET Chi-restraints excluded: chain G residue 54 ILE Chi-restraints excluded: chain G residue 60 TYR Chi-restraints excluded: chain G residue 109 PHE Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain E residue 520 THR Chi-restraints excluded: chain E residue 581 THR Chi-restraints excluded: chain E residue 587 ARG Chi-restraints excluded: chain E residue 593 LEU Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain H residue 109 PHE Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain I residue 60 TYR Chi-restraints excluded: chain I residue 109 PHE Chi-restraints excluded: chain I residue 111 GLU Chi-restraints excluded: chain I residue 128 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 52 optimal weight: 3.9990 chunk 119 optimal weight: 5.9990 chunk 59 optimal weight: 0.0060 chunk 138 optimal weight: 9.9990 chunk 157 optimal weight: 2.9990 chunk 84 optimal weight: 10.0000 chunk 49 optimal weight: 10.0000 chunk 54 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 126 optimal weight: 0.2980 chunk 17 optimal weight: 0.9990 overall best weight: 1.6602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 27 GLN L 27 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.139324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.086533 restraints weight = 22738.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.088899 restraints weight = 14822.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.090446 restraints weight = 11503.493| |-----------------------------------------------------------------------------| r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.5134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 13920 Z= 0.198 Angle : 0.651 7.944 18948 Z= 0.322 Chirality : 0.045 0.154 2157 Planarity : 0.004 0.035 2385 Dihedral : 6.070 51.613 2457 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.06 % Favored : 96.76 % Rotamer: Outliers : 3.53 % Allowed : 12.64 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.05 (0.21), residues: 1665 helix: 1.17 (0.40), residues: 180 sheet: 0.03 (0.21), residues: 627 loop : -0.24 (0.21), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP H 36 HIS 0.004 0.001 HIS A 154 PHE 0.016 0.002 PHE F 592 TYR 0.016 0.002 TYR L 50 ARG 0.013 0.001 ARG H 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00095 ( 15) link_NAG-ASN : angle 1.60120 ( 45) link_ALPHA1-6 : bond 0.00891 ( 3) link_ALPHA1-6 : angle 1.12701 ( 9) link_BETA1-4 : bond 0.00580 ( 9) link_BETA1-4 : angle 2.68529 ( 27) link_ALPHA1-3 : bond 0.01058 ( 3) link_ALPHA1-3 : angle 2.00661 ( 9) hydrogen bonds : bond 0.04245 ( 513) hydrogen bonds : angle 4.85968 ( 1296) SS BOND : bond 0.00297 ( 6) SS BOND : angle 0.26114 ( 12) covalent geometry : bond 0.00466 (13884) covalent geometry : angle 0.63786 (18846) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 206 time to evaluate : 1.448 Fit side-chains REVERT: A 267 SER cc_start: 0.8097 (OUTLIER) cc_final: 0.7304 (p) REVERT: J 37 TYR cc_start: 0.7981 (m-80) cc_final: 0.7557 (m-10) REVERT: J 63 PHE cc_start: 0.7468 (m-80) cc_final: 0.6754 (m-80) REVERT: J 84 PHE cc_start: 0.6722 (m-80) cc_final: 0.6516 (m-80) REVERT: G 10 GLU cc_start: 0.7164 (tt0) cc_final: 0.6778 (mm-30) REVERT: G 36 TRP cc_start: 0.7943 (m100) cc_final: 0.7708 (m100) REVERT: G 65 GLN cc_start: 0.8389 (tp40) cc_final: 0.8183 (mm-40) REVERT: G 81 MET cc_start: 0.8192 (tmm) cc_final: 0.7982 (tmm) REVERT: G 111 GLU cc_start: 0.8467 (pp20) cc_final: 0.8132 (pp20) REVERT: G 114 LYS cc_start: 0.8647 (ttpt) cc_final: 0.8310 (ttmm) REVERT: G 119 TYR cc_start: 0.8639 (p90) cc_final: 0.8361 (p90) REVERT: K 37 TYR cc_start: 0.7579 (m-10) cc_final: 0.6585 (m-10) REVERT: H 38 ARG cc_start: 0.7427 (mtm110) cc_final: 0.6506 (mtm-85) REVERT: H 83 LEU cc_start: 0.6592 (tp) cc_final: 0.6290 (tt) REVERT: H 86 LEU cc_start: 0.7054 (mt) cc_final: 0.6823 (mp) REVERT: H 114 LYS cc_start: 0.8369 (ttpt) cc_final: 0.7844 (ptpt) REVERT: H 120 MET cc_start: 0.8282 (mpp) cc_final: 0.8052 (mpp) REVERT: L 37 TYR cc_start: 0.7796 (m-80) cc_final: 0.7451 (m-10) REVERT: L 63 PHE cc_start: 0.7655 (m-80) cc_final: 0.7123 (m-80) REVERT: I 119 TYR cc_start: 0.8699 (p90) cc_final: 0.8433 (p90) REVERT: I 128 THR cc_start: 0.7495 (OUTLIER) cc_final: 0.7164 (p) outliers start: 50 outliers final: 43 residues processed: 234 average time/residue: 0.2836 time to fit residues: 92.8303 Evaluate side-chains 244 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 199 time to evaluate : 1.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain D residue 548 MET Chi-restraints excluded: chain D residue 581 THR Chi-restraints excluded: chain D residue 593 LEU Chi-restraints excluded: chain G residue 48 MET Chi-restraints excluded: chain G residue 54 ILE Chi-restraints excluded: chain G residue 109 PHE Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain E residue 520 THR Chi-restraints excluded: chain E residue 581 THR Chi-restraints excluded: chain E residue 587 ARG Chi-restraints excluded: chain E residue 593 LEU Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain H residue 109 PHE Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain F residue 581 THR Chi-restraints excluded: chain I residue 60 TYR Chi-restraints excluded: chain I residue 109 PHE Chi-restraints excluded: chain I residue 128 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 112 optimal weight: 3.9990 chunk 19 optimal weight: 0.6980 chunk 132 optimal weight: 1.9990 chunk 155 optimal weight: 7.9990 chunk 42 optimal weight: 3.9990 chunk 92 optimal weight: 0.9980 chunk 51 optimal weight: 7.9990 chunk 113 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 59 optimal weight: 0.5980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.140534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.088303 restraints weight = 22419.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.090669 restraints weight = 14528.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.092129 restraints weight = 11236.432| |-----------------------------------------------------------------------------| r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.5242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13920 Z= 0.144 Angle : 0.623 9.335 18948 Z= 0.306 Chirality : 0.044 0.151 2157 Planarity : 0.004 0.037 2385 Dihedral : 5.790 48.577 2457 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.88 % Favored : 96.94 % Rotamer: Outliers : 3.25 % Allowed : 12.85 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.15 (0.21), residues: 1665 helix: 2.10 (0.40), residues: 162 sheet: 0.09 (0.22), residues: 615 loop : -0.18 (0.21), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP H 36 HIS 0.002 0.001 HIS A 154 PHE 0.016 0.001 PHE F 592 TYR 0.050 0.002 TYR H 94 ARG 0.016 0.001 ARG G 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00146 ( 15) link_NAG-ASN : angle 1.50896 ( 45) link_ALPHA1-6 : bond 0.00839 ( 3) link_ALPHA1-6 : angle 1.26590 ( 9) link_BETA1-4 : bond 0.00581 ( 9) link_BETA1-4 : angle 2.46270 ( 27) link_ALPHA1-3 : bond 0.01044 ( 3) link_ALPHA1-3 : angle 1.58163 ( 9) hydrogen bonds : bond 0.03917 ( 513) hydrogen bonds : angle 4.74211 ( 1296) SS BOND : bond 0.00211 ( 6) SS BOND : angle 0.31567 ( 12) covalent geometry : bond 0.00336 (13884) covalent geometry : angle 0.61145 (18846) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 207 time to evaluate : 1.450 Fit side-chains REVERT: A 267 SER cc_start: 0.8065 (OUTLIER) cc_final: 0.7220 (p) REVERT: J 37 TYR cc_start: 0.7787 (m-80) cc_final: 0.7513 (m-80) REVERT: J 63 PHE cc_start: 0.7343 (m-80) cc_final: 0.6700 (m-80) REVERT: G 10 GLU cc_start: 0.7087 (tt0) cc_final: 0.6587 (mm-30) REVERT: G 36 TRP cc_start: 0.7952 (m100) cc_final: 0.7736 (m100) REVERT: G 111 GLU cc_start: 0.8519 (pp20) cc_final: 0.8222 (pp20) REVERT: G 114 LYS cc_start: 0.8668 (ttpt) cc_final: 0.8313 (ttmm) REVERT: G 119 TYR cc_start: 0.8639 (p90) cc_final: 0.8351 (p90) REVERT: K 37 TYR cc_start: 0.7535 (m-10) cc_final: 0.6695 (m-10) REVERT: H 38 ARG cc_start: 0.7844 (mtm110) cc_final: 0.7388 (mtp-110) REVERT: H 63 LYS cc_start: 0.8334 (ptmt) cc_final: 0.8078 (ptmt) REVERT: H 64 PHE cc_start: 0.7327 (m-80) cc_final: 0.7042 (m-10) REVERT: H 83 LEU cc_start: 0.6619 (tp) cc_final: 0.6231 (tt) REVERT: H 114 LYS cc_start: 0.8342 (ttpt) cc_final: 0.7809 (ptpt) REVERT: H 120 MET cc_start: 0.8279 (mpp) cc_final: 0.8076 (mpp) REVERT: L 63 PHE cc_start: 0.7644 (m-80) cc_final: 0.7188 (m-80) REVERT: I 38 ARG cc_start: 0.8243 (ttp-110) cc_final: 0.7196 (mtp-110) REVERT: I 46 GLU cc_start: 0.7678 (pm20) cc_final: 0.7464 (pm20) REVERT: I 48 MET cc_start: 0.7777 (ptm) cc_final: 0.7171 (ptp) REVERT: I 119 TYR cc_start: 0.8720 (p90) cc_final: 0.8492 (p90) REVERT: I 128 THR cc_start: 0.7393 (OUTLIER) cc_final: 0.7070 (p) outliers start: 46 outliers final: 40 residues processed: 237 average time/residue: 0.2804 time to fit residues: 93.6940 Evaluate side-chains 239 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 197 time to evaluate : 1.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain D residue 548 MET Chi-restraints excluded: chain D residue 593 LEU Chi-restraints excluded: chain G residue 48 MET Chi-restraints excluded: chain G residue 52 ILE Chi-restraints excluded: chain G residue 54 ILE Chi-restraints excluded: chain G residue 60 TYR Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain E residue 581 THR Chi-restraints excluded: chain E residue 587 ARG Chi-restraints excluded: chain E residue 593 LEU Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain H residue 109 PHE Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain F residue 581 THR Chi-restraints excluded: chain I residue 60 TYR Chi-restraints excluded: chain I residue 128 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 64 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 42 optimal weight: 8.9990 chunk 77 optimal weight: 5.9990 chunk 104 optimal weight: 6.9990 chunk 124 optimal weight: 0.7980 chunk 136 optimal weight: 9.9990 chunk 81 optimal weight: 10.0000 chunk 148 optimal weight: 0.6980 chunk 26 optimal weight: 6.9990 chunk 57 optimal weight: 2.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 27 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.139487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.091652 restraints weight = 22556.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.090455 restraints weight = 22432.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.091395 restraints weight = 20182.849| |-----------------------------------------------------------------------------| r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.5343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13920 Z= 0.185 Angle : 0.661 13.424 18948 Z= 0.323 Chirality : 0.045 0.156 2157 Planarity : 0.004 0.042 2385 Dihedral : 5.726 48.570 2457 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.06 % Favored : 96.76 % Rotamer: Outliers : 3.25 % Allowed : 12.99 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.10 (0.21), residues: 1665 helix: 1.29 (0.40), residues: 180 sheet: 0.23 (0.23), residues: 579 loop : -0.21 (0.21), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 36 HIS 0.004 0.001 HIS B 154 PHE 0.016 0.002 PHE E 592 TYR 0.018 0.001 TYR L 50 ARG 0.014 0.001 ARG G 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00080 ( 15) link_NAG-ASN : angle 1.44200 ( 45) link_ALPHA1-6 : bond 0.00915 ( 3) link_ALPHA1-6 : angle 1.18027 ( 9) link_BETA1-4 : bond 0.00521 ( 9) link_BETA1-4 : angle 2.56796 ( 27) link_ALPHA1-3 : bond 0.01015 ( 3) link_ALPHA1-3 : angle 1.89094 ( 9) hydrogen bonds : bond 0.04194 ( 513) hydrogen bonds : angle 4.77237 ( 1296) SS BOND : bond 0.00250 ( 6) SS BOND : angle 0.25701 ( 12) covalent geometry : bond 0.00436 (13884) covalent geometry : angle 0.64962 (18846) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 202 time to evaluate : 1.531 Fit side-chains REVERT: A 267 SER cc_start: 0.8117 (OUTLIER) cc_final: 0.7224 (p) REVERT: G 10 GLU cc_start: 0.7014 (tt0) cc_final: 0.6718 (mm-30) REVERT: G 38 ARG cc_start: 0.7908 (mtm110) cc_final: 0.7616 (mtm110) REVERT: G 81 MET cc_start: 0.7845 (tmm) cc_final: 0.7581 (tmm) REVERT: G 111 GLU cc_start: 0.8536 (pp20) cc_final: 0.8290 (pp20) REVERT: G 114 LYS cc_start: 0.8591 (ttpt) cc_final: 0.8348 (ttmm) REVERT: G 119 TYR cc_start: 0.8662 (p90) cc_final: 0.8416 (p90) REVERT: K 37 TYR cc_start: 0.7551 (m-10) cc_final: 0.6791 (m-10) REVERT: E 587 ARG cc_start: 0.7834 (OUTLIER) cc_final: 0.7348 (ttp-170) REVERT: H 114 LYS cc_start: 0.8329 (ttpt) cc_final: 0.7861 (ptpt) REVERT: L 63 PHE cc_start: 0.7655 (m-80) cc_final: 0.7203 (m-80) REVERT: L 84 PHE cc_start: 0.7022 (m-80) cc_final: 0.6714 (m-80) REVERT: I 128 THR cc_start: 0.7497 (OUTLIER) cc_final: 0.7164 (p) outliers start: 46 outliers final: 42 residues processed: 229 average time/residue: 0.2916 time to fit residues: 94.1416 Evaluate side-chains 239 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 194 time to evaluate : 1.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 48 LEU Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain D residue 548 MET Chi-restraints excluded: chain D residue 581 THR Chi-restraints excluded: chain D residue 593 LEU Chi-restraints excluded: chain G residue 48 MET Chi-restraints excluded: chain G residue 52 ILE Chi-restraints excluded: chain G residue 54 ILE Chi-restraints excluded: chain G residue 60 TYR Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain E residue 520 THR Chi-restraints excluded: chain E residue 581 THR Chi-restraints excluded: chain E residue 587 ARG Chi-restraints excluded: chain E residue 593 LEU Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain H residue 109 PHE Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain F residue 581 THR Chi-restraints excluded: chain I residue 60 TYR Chi-restraints excluded: chain I residue 128 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 120 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 132 optimal weight: 10.0000 chunk 53 optimal weight: 6.9990 chunk 111 optimal weight: 2.9990 chunk 27 optimal weight: 20.0000 chunk 8 optimal weight: 1.9990 chunk 138 optimal weight: 9.9990 chunk 46 optimal weight: 0.0070 chunk 51 optimal weight: 0.7980 overall best weight: 1.1602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 27 GLN K 39 GLN H 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.140103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.092422 restraints weight = 22639.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.091586 restraints weight = 15493.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.091510 restraints weight = 12253.073| |-----------------------------------------------------------------------------| r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.5443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13920 Z= 0.154 Angle : 0.646 12.005 18948 Z= 0.315 Chirality : 0.044 0.177 2157 Planarity : 0.004 0.046 2385 Dihedral : 5.620 47.500 2457 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.12 % Favored : 96.70 % Rotamer: Outliers : 3.46 % Allowed : 12.99 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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 (0.21), residues: 1665 helix: 1.38 (0.40), residues: 180 sheet: 0.24 (0.23), residues: 576 loop : -0.20 (0.21), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.072 0.002 TRP G 36 HIS 0.003 0.001 HIS B 154 PHE 0.017 0.001 PHE F 592 TYR 0.019 0.001 TYR I 94 ARG 0.015 0.001 ARG G 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00101 ( 15) link_NAG-ASN : angle 1.38941 ( 45) link_ALPHA1-6 : bond 0.00891 ( 3) link_ALPHA1-6 : angle 1.27211 ( 9) link_BETA1-4 : bond 0.00520 ( 9) link_BETA1-4 : angle 2.39635 ( 27) link_ALPHA1-3 : bond 0.01053 ( 3) link_ALPHA1-3 : angle 1.59276 ( 9) hydrogen bonds : bond 0.03944 ( 513) hydrogen bonds : angle 4.74659 ( 1296) SS BOND : bond 0.00213 ( 6) SS BOND : angle 0.29874 ( 12) covalent geometry : bond 0.00360 (13884) covalent geometry : angle 0.63609 (18846) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4512.58 seconds wall clock time: 79 minutes 25.05 seconds (4765.05 seconds total)