Starting phenix.real_space_refine on Fri Jul 3 10:49:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7kfh_22853/07_2026/7kfh_22853.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kfh_22853/07_2026/7kfh_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7kfh_22853/07_2026/7kfh_22853.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7kfh_22853/07_2026/7kfh_22853.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7kfh_22853/07_2026/7kfh_22853.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kfh_22853/07_2026/7kfh_22853.map" model { file = "/net/cci-nas-00/data/ceres_data/7kfh_22853/07_2026/7kfh_22853.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kfh_22853/07_2026/7kfh_22853.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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: "J" 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: "D" 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: "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: "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 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 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 chiralities: 3 Restraints were copied for chains: B, C, K, L, E, F, H, I, O, Q, P, R Time building chain proxies: 2.19, per 1000 atoms: 0.16 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=15, 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 J 23 " - pdb=" SG CYS J 89 " distance=2.04 Simple disulfide: pdb=" SG CYS D 511 " - pdb=" SG CYS D 556 " distance=2.05 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.02 Simple disulfide: pdb=" SG CYS B 108 " - pdb=" SG CYS B 135 " distance=2.02 Simple disulfide: pdb=" SG CYS C 108 " - pdb=" SG CYS C 135 " distance=2.02 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 147 " distance=2.02 Simple disulfide: pdb=" SG CYS C 121 " - pdb=" SG CYS C 147 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 89 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.04 Simple disulfide: pdb=" SG CYS E 511 " - pdb=" SG CYS E 556 " distance=2.05 Simple disulfide: pdb=" SG CYS F 511 " - pdb=" SG CYS F 556 " distance=2.05 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.02 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " 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: 1.09 Conformation dependent library (CDL) restraints added in 469.7 milliseconds 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: 0.38 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: 2.39 Time building geometry restraints manager: 1.43 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 - 17.75: 7685 17.75 - 35.49: 166 35.49 - 53.24: 78 53.24 - 70.99: 27 70.99 - 88.73: 9 Dihedral angle restraints: 7965 sinusoidal: 3144 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 7962 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: 2.36 - 2.87: 4601 2.87 - 3.38: 11831 3.38 - 3.88: 22877 3.88 - 4.39: 26253 4.39 - 4.90: 43569 Nonbonded interactions: 109131 Sorted by model distance: nonbonded pdb=" N SER C 41 " pdb=" N THR C 42 " model vdw 2.360 2.560 nonbonded pdb=" N SER B 41 " pdb=" N THR B 42 " model vdw 2.362 2.560 nonbonded pdb=" N SER A 41 " pdb=" N THR A 42 " model vdw 2.362 2.560 nonbonded pdb=" N PHE I 55 " pdb=" N GLY I 56 " model vdw 2.411 2.560 nonbonded pdb=" N PHE H 55 " pdb=" N GLY H 56 " model vdw 2.412 2.560 ... (remaining 109126 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } 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: 2.970 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: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 11.810 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 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:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 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 13929 Z= 1.103 Angle : 1.776 11.901 18966 Z= 1.166 Chirality : 0.114 0.563 2157 Planarity : 0.008 0.045 2385 Dihedral : 10.273 88.735 4854 Min Nonbonded Distance : 2.360 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.008 0.001 ARG K 46 TYR 0.060 0.009 TYR H 60 PHE 0.026 0.006 PHE J 84 TRP 0.046 0.009 TRP L 36 HIS 0.005 0.002 HIS F 516 Details of bonding type rmsd/Z covalent geometry : bond 0.02117 / 1.09 (13884) covalent geometry : angle 1.75667 / 1.17 (18846) SS BOND : bond 0.01232 / 0.75 ( 15) SS BOND : angle 1.87656 / 1.19 ( 30) hydrogen bonds : bond 0.15850 / 11.13 ( 513) hydrogen bonds : angle 7.44945 / 5.36 ( 1296) link_ALPHA1-3 : bond 0.08200 / 4.11 ( 3) link_ALPHA1-3 : angle 4.23005 / 1.99 ( 9) link_ALPHA1-6 : bond 0.06335 / 3.18 ( 3) link_ALPHA1-6 : angle 3.87776 / 1.83 ( 9) link_BETA1-4 : bond 0.06563 / 4.36 ( 9) link_BETA1-4 : angle 5.87401 / 3.13 ( 27) link_NAG-ASN : bond 0.07581 / 4.79 ( 15) link_NAG-ASN : angle 2.60121 / 1.74 ( 45) *********************** 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 : 0.490 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: 0.8153 (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: 0.7837 (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: 0.8119 (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: 0.7107 (m-30) REVERT: K 37 TYR cc_start: 0.5216 (m-80) cc_final: 0.4313 (m-80) REVERT: K 47 LEU cc_start: 0.3498 (tp) cc_final: 0.3251 (tt) REVERT: K 48 LEU cc_start: 0.8218 (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: 0.7243 (mtp) REVERT: H 78 THR cc_start: 0.8202 (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: 0.7590 (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: 0.9509 (m) cc_final: 0.9009 (p) REVERT: F 596 ARG cc_start: 0.7748 (mtp-110) cc_final: 0.7519 (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: 0.6994 (tp) REVERT: I 94 TYR cc_start: 0.5017 (m-80) cc_final: 0.4683 (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: 0.1454 time to fit residues: 76.5261 Evaluate side-chains 228 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 225 time to evaluate : 0.492 ------------------------------------------------------------------------------- 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 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 chunk 149 optimal weight: 7.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 549 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.150265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.096717 restraints weight = 21915.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.099197 restraints weight = 14357.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.100780 restraints weight = 11164.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.101570 restraints weight = 9597.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.102332 restraints weight = 8802.689| |-----------------------------------------------------------------------------| r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.3029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13929 Z= 0.165 Angle : 0.703 7.996 18966 Z= 0.370 Chirality : 0.044 0.178 2157 Planarity : 0.005 0.044 2385 Dihedral : 5.298 22.581 1851 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.22 % Favored : 97.60 % Rotamer: Outliers : 2.54 % Allowed : 7.13 % Favored : 90.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.19), residues: 1665 helix: 1.98 (0.34), residues: 162 sheet: 0.80 (0.20), residues: 630 loop : 0.29 (0.20), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 31 TYR 0.017 0.002 TYR L 50 PHE 0.023 0.002 PHE J 72 TRP 0.012 0.001 TRP G 47 HIS 0.002 0.001 HIS E 549 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.16 (13884) covalent geometry : angle 0.67435 / 0.36 (18846) SS BOND : bond 0.00434 / 0.28 ( 15) SS BOND : angle 1.11551 / 0.72 ( 30) hydrogen bonds : bond 0.05011 / 3.44 ( 513) hydrogen bonds : angle 5.75648 / 4.10 ( 1296) link_ALPHA1-3 : bond 0.00760 / 0.38 ( 3) link_ALPHA1-3 : angle 1.41121 / 0.77 ( 9) link_ALPHA1-6 : bond 0.00958 / 0.48 ( 3) link_ALPHA1-6 : angle 1.37663 / 0.78 ( 9) link_BETA1-4 : bond 0.01004 / 0.78 ( 9) link_BETA1-4 : angle 3.90880 / 2.13 ( 27) link_NAG-ASN : bond 0.00560 / 0.43 ( 15) link_NAG-ASN : angle 2.69356 / 1.71 ( 45) *********************** 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 300 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 264 time to evaluate : 0.352 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: 0.8077 (m-30) cc_final: 0.7682 (m-30) REVERT: A 229 GLU cc_start: 0.8158 (pp20) cc_final: 0.7940 (pp20) REVERT: A 258 GLU cc_start: 0.7743 (tp30) cc_final: 0.7342 (tp30) REVERT: J 37 TYR cc_start: 0.7838 (m-80) cc_final: 0.7308 (m-80) REVERT: D 549 HIS cc_start: 0.7895 (p-80) cc_final: 0.7459 (t-170) REVERT: G 10 GLU cc_start: 0.5496 (mm-30) cc_final: 0.5281 (mm-30) REVERT: G 31 ARG cc_start: 0.7693 (mtt90) cc_final: 0.7386 (mtt-85) REVERT: G 65 GLN cc_start: 0.8401 (tp40) cc_final: 0.8051 (tp-100) REVERT: G 81 MET cc_start: 0.7873 (tmm) cc_final: 0.7298 (tmm) REVERT: G 114 LYS cc_start: 0.8412 (ttpt) cc_final: 0.8052 (mtmm) REVERT: K 37 TYR cc_start: 0.7633 (m-80) cc_final: 0.6799 (m-80) REVERT: H 12 LYS cc_start: 0.6344 (OUTLIER) cc_final: 0.5934 (mptt) REVERT: H 65 GLN cc_start: 0.8744 (tp40) cc_final: 0.8477 (mm-40) REVERT: H 114 LYS cc_start: 0.8369 (ttpt) cc_final: 0.7829 (mtmm) REVERT: C 55 ASP cc_start: 0.7848 (m-30) cc_final: 0.7452 (m-30) REVERT: L 37 TYR cc_start: 0.7642 (m-80) cc_final: 0.6230 (m-80) REVERT: L 55 ARG cc_start: 0.7303 (ttm110) cc_final: 0.7039 (mtt90) REVERT: F 545 GLU cc_start: 0.8105 (pm20) cc_final: 0.7897 (pm20) REVERT: I 114 LYS cc_start: 0.8333 (ttpt) cc_final: 0.7875 (mtmm) outliers start: 36 outliers final: 19 residues processed: 283 average time/residue: 0.1281 time to fit residues: 51.5603 Evaluate side-chains 234 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 214 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 267 SER 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 54 ILE Chi-restraints excluded: chain B residue 150 ASP Chi-restraints excluded: chain B residue 184 LEU 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 45 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 C residue 267 SER Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain F residue 593 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 84 optimal weight: 7.9990 chunk 152 optimal weight: 10.0000 chunk 108 optimal weight: 4.9990 chunk 151 optimal weight: 4.9990 chunk 99 optimal weight: 9.9990 chunk 58 optimal weight: 0.0000 chunk 119 optimal weight: 6.9990 chunk 11 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3865 r_free = 0.3865 target = 0.145244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.092861 restraints weight = 22295.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.093865 restraints weight = 16388.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.094195 restraints weight = 11950.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.094484 restraints weight = 11326.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.094643 restraints weight = 11085.723| |-----------------------------------------------------------------------------| r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.3767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 13929 Z= 0.233 Angle : 0.692 8.805 18966 Z= 0.355 Chirality : 0.045 0.195 2157 Planarity : 0.005 0.034 2385 Dihedral : 4.961 18.270 1847 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.18 % Allowed : 1.86 % Favored : 97.96 % Rotamer: Outliers : 4.03 % Allowed : 8.47 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.20), residues: 1665 helix: 1.88 (0.39), residues: 162 sheet: 0.68 (0.21), residues: 612 loop : 0.04 (0.20), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 596 TYR 0.018 0.002 TYR I 117 PHE 0.023 0.002 PHE A 132 TRP 0.011 0.001 TRP A 104 HIS 0.004 0.001 HIS F 549 Details of bonding type rmsd/Z covalent geometry : bond 0.00549 / 0.23 (13884) covalent geometry : angle 0.67214 / 0.35 (18846) SS BOND : bond 0.00467 / 0.30 ( 15) SS BOND : angle 0.95286 / 0.59 ( 30) hydrogen bonds : bond 0.04923 / 3.35 ( 513) hydrogen bonds : angle 5.44856 / 3.88 ( 1296) link_ALPHA1-3 : bond 0.00496 / 0.25 ( 3) link_ALPHA1-3 : angle 1.49362 / 0.84 ( 9) link_ALPHA1-6 : bond 0.00688 / 0.35 ( 3) link_ALPHA1-6 : angle 1.23852 / 0.70 ( 9) link_BETA1-4 : bond 0.00776 / 0.60 ( 9) link_BETA1-4 : angle 3.21321 / 1.75 ( 27) link_NAG-ASN : bond 0.00228 / 0.15 ( 15) link_NAG-ASN : angle 2.27683 / 1.45 ( 45) *********************** 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 289 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 232 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 GLU cc_start: 0.8259 (pp20) cc_final: 0.7920 (pp20) REVERT: A 258 GLU cc_start: 0.7747 (tp30) cc_final: 0.7274 (tp30) REVERT: J 37 TYR cc_start: 0.7791 (m-80) cc_final: 0.7445 (m-80) REVERT: G 31 ARG cc_start: 0.7945 (mtt90) cc_final: 0.7652 (mtt-85) REVERT: G 60 TYR cc_start: 0.7995 (m-80) cc_final: 0.7751 (m-80) REVERT: G 65 GLN cc_start: 0.8470 (tp40) cc_final: 0.8048 (mm-40) REVERT: G 81 MET cc_start: 0.8157 (tmm) cc_final: 0.7434 (tmm) REVERT: G 114 LYS cc_start: 0.8573 (ttpt) cc_final: 0.7965 (mtmm) REVERT: B 65 SER cc_start: 0.9171 (OUTLIER) cc_final: 0.8913 (p) REVERT: K 37 TYR cc_start: 0.7641 (m-80) cc_final: 0.6938 (m-80) REVERT: H 12 LYS cc_start: 0.6221 (OUTLIER) cc_final: 0.5888 (mptt) REVERT: H 38 ARG cc_start: 0.7680 (mtp-110) cc_final: 0.7070 (mtp-110) REVERT: H 119 TYR cc_start: 0.8485 (p90) cc_final: 0.8086 (p90) REVERT: L 55 ARG cc_start: 0.7367 (ttm110) cc_final: 0.7047 (mtt90) outliers start: 57 outliers final: 34 residues processed: 265 average time/residue: 0.1252 time to fit residues: 47.4495 Evaluate side-chains 250 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 214 time to evaluate : 0.500 ------------------------------------------------------------------------------- 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 267 SER Chi-restraints excluded: chain J residue 22 SER Chi-restraints excluded: chain J residue 34 LEU 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 D residue 595 GLN Chi-restraints excluded: chain G residue 12 LYS 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 109 PHE Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 103 GLU 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 581 THR Chi-restraints excluded: chain E residue 595 GLN Chi-restraints excluded: chain H residue 12 LYS Chi-restraints excluded: chain H residue 45 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 83 LEU 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 48 MET Chi-restraints excluded: chain I residue 52 ILE Chi-restraints excluded: chain I residue 60 TYR Chi-restraints excluded: chain I residue 109 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 131 optimal weight: 9.9990 chunk 142 optimal weight: 0.8980 chunk 101 optimal weight: 0.9980 chunk 83 optimal weight: 4.9990 chunk 127 optimal weight: 0.8980 chunk 158 optimal weight: 7.9990 chunk 36 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 11 optimal weight: 7.9990 chunk 73 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 HIS C 39 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.140992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.090621 restraints weight = 22294.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.091052 restraints weight = 16319.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.091190 restraints weight = 12138.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.091370 restraints weight = 11422.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.091481 restraints weight = 11010.426| |-----------------------------------------------------------------------------| r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.4178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13929 Z= 0.174 Angle : 0.630 9.585 18966 Z= 0.317 Chirality : 0.044 0.211 2157 Planarity : 0.004 0.066 2385 Dihedral : 4.759 19.774 1847 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.34 % Favored : 97.48 % Rotamer: Outliers : 3.81 % Allowed : 9.11 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.20), residues: 1665 helix: 1.95 (0.39), residues: 162 sheet: 0.49 (0.20), residues: 645 loop : -0.04 (0.21), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG G 38 TYR 0.019 0.002 TYR I 119 PHE 0.020 0.002 PHE F 592 TRP 0.009 0.001 TRP I 47 HIS 0.003 0.001 HIS B 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.17 (13884) covalent geometry : angle 0.61586 / 0.31 (18846) SS BOND : bond 0.00404 / 0.26 ( 15) SS BOND : angle 0.72703 / 0.47 ( 30) hydrogen bonds : bond 0.04190 / 2.85 ( 513) hydrogen bonds : angle 5.04378 / 3.61 ( 1296) link_ALPHA1-3 : bond 0.00530 / 0.27 ( 3) link_ALPHA1-3 : angle 1.39487 / 0.78 ( 9) link_ALPHA1-6 : bond 0.00565 / 0.28 ( 3) link_ALPHA1-6 : angle 1.20472 / 0.68 ( 9) link_BETA1-4 : bond 0.00678 / 0.52 ( 9) link_BETA1-4 : angle 2.62906 / 1.43 ( 27) link_NAG-ASN : bond 0.00195 / 0.13 ( 15) link_NAG-ASN : angle 1.84823 / 1.18 ( 45) *********************** 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 282 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 228 time to evaluate : 0.524 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 229 GLU cc_start: 0.8303 (pp20) cc_final: 0.7897 (pp20) REVERT: A 258 GLU cc_start: 0.7716 (tp30) cc_final: 0.7283 (tp30) REVERT: A 267 SER cc_start: 0.7856 (OUTLIER) cc_final: 0.7147 (p) REVERT: J 48 LEU cc_start: 0.7911 (mt) cc_final: 0.7638 (mp) REVERT: D 587 ARG cc_start: 0.7660 (OUTLIER) cc_final: 0.7330 (mtp180) REVERT: G 38 ARG cc_start: 0.7439 (mtp-110) cc_final: 0.6891 (mtm-85) REVERT: G 65 GLN cc_start: 0.8485 (tp40) cc_final: 0.8081 (mm-40) REVERT: G 81 MET cc_start: 0.8318 (tmm) cc_final: 0.7543 (tmm) REVERT: G 114 LYS cc_start: 0.8570 (ttpt) cc_final: 0.7928 (mtmm) REVERT: B 65 SER cc_start: 0.9129 (OUTLIER) cc_final: 0.8837 (p) REVERT: K 37 TYR cc_start: 0.7711 (m-80) cc_final: 0.7004 (m-80) REVERT: E 587 ARG cc_start: 0.7686 (OUTLIER) cc_final: 0.7342 (ttp-170) REVERT: H 12 LYS cc_start: 0.6011 (OUTLIER) cc_final: 0.5784 (mptt) REVERT: H 119 TYR cc_start: 0.8550 (p90) cc_final: 0.8019 (p90) REVERT: L 37 TYR cc_start: 0.7764 (m-80) cc_final: 0.6144 (m-80) REVERT: L 55 ARG cc_start: 0.7189 (ttm110) cc_final: 0.6888 (mtt90) REVERT: I 120 MET cc_start: 0.8683 (mpp) cc_final: 0.8256 (mpp) outliers start: 54 outliers final: 29 residues processed: 259 average time/residue: 0.1205 time to fit residues: 44.7304 Evaluate side-chains 238 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 204 time to evaluate : 0.415 ------------------------------------------------------------------------------- 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 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 542 ILE Chi-restraints excluded: chain D residue 548 MET Chi-restraints excluded: chain D residue 581 THR Chi-restraints excluded: chain D residue 587 ARG Chi-restraints excluded: chain D residue 595 GLN Chi-restraints excluded: chain G residue 48 MET Chi-restraints excluded: chain G residue 54 ILE Chi-restraints excluded: chain B residue 65 SER 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 520 THR Chi-restraints excluded: chain E residue 581 THR Chi-restraints excluded: chain E residue 587 ARG 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 H residue 83 LEU Chi-restraints excluded: chain H residue 109 PHE Chi-restraints excluded: chain C residue 65 SER 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 F residue 581 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 30 optimal weight: 7.9990 chunk 149 optimal weight: 8.9990 chunk 66 optimal weight: 0.7980 chunk 52 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 47 optimal weight: 8.9990 chunk 27 optimal weight: 20.0000 chunk 77 optimal weight: 20.0000 chunk 157 optimal weight: 5.9990 chunk 147 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 HIS C 39 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.136009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.085151 restraints weight = 22784.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.085406 restraints weight = 15859.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.085526 restraints weight = 11782.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.085590 restraints weight = 12030.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.085837 restraints weight = 11197.290| |-----------------------------------------------------------------------------| r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.4711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.072 13929 Z= 0.326 Angle : 0.775 8.856 18966 Z= 0.388 Chirality : 0.049 0.159 2157 Planarity : 0.005 0.056 2385 Dihedral : 5.097 19.043 1847 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.46 % Favored : 97.36 % Rotamer: Outliers : 4.24 % Allowed : 10.03 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.20), residues: 1665 helix: 1.33 (0.39), residues: 159 sheet: -0.20 (0.20), residues: 660 loop : -0.20 (0.21), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 31 TYR 0.019 0.002 TYR B 214 PHE 0.027 0.003 PHE C 132 TRP 0.011 0.001 TRP C 104 HIS 0.006 0.002 HIS B 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00779 / 0.33 (13884) covalent geometry : angle 0.76072 / 0.39 (18846) SS BOND : bond 0.00499 / 0.32 ( 15) SS BOND : angle 0.72895 / 0.46 ( 30) hydrogen bonds : bond 0.05223 / 3.58 ( 513) hydrogen bonds : angle 5.20285 / 3.70 ( 1296) link_ALPHA1-3 : bond 0.00257 / 0.13 ( 3) link_ALPHA1-3 : angle 1.99427 / 1.05 ( 9) link_ALPHA1-6 : bond 0.00390 / 0.19 ( 3) link_ALPHA1-6 : angle 1.23815 / 0.70 ( 9) link_BETA1-4 : bond 0.00620 / 0.48 ( 9) link_BETA1-4 : angle 3.10632 / 1.73 ( 27) link_NAG-ASN : bond 0.00309 / 0.24 ( 15) link_NAG-ASN : angle 1.81781 / 1.18 ( 45) *********************** 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 269 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 209 time to evaluate : 0.407 Fit side-chains REVERT: A 174 THR cc_start: 0.9401 (m) cc_final: 0.9004 (p) REVERT: A 267 SER cc_start: 0.8214 (OUTLIER) cc_final: 0.7265 (p) REVERT: J 2 ILE cc_start: 0.6799 (mt) cc_final: 0.6593 (mt) REVERT: D 510 LYS cc_start: 0.8552 (mttt) cc_final: 0.7617 (mmtt) REVERT: G 3 GLN cc_start: 0.7587 (pm20) cc_final: 0.7372 (pm20) REVERT: G 64 PHE cc_start: 0.7864 (m-80) cc_final: 0.7653 (m-80) REVERT: G 65 GLN cc_start: 0.8515 (tp40) cc_final: 0.8061 (mm-40) REVERT: G 81 MET cc_start: 0.8447 (tmm) cc_final: 0.7554 (tmm) REVERT: G 111 GLU cc_start: 0.8286 (pp20) cc_final: 0.7986 (pp20) REVERT: B 65 SER cc_start: 0.9211 (OUTLIER) cc_final: 0.8893 (p) REVERT: K 63 PHE cc_start: 0.7384 (m-80) cc_final: 0.7179 (m-80) REVERT: E 510 LYS cc_start: 0.8674 (mttt) cc_final: 0.7720 (mmtt) REVERT: H 83 LEU cc_start: 0.6936 (OUTLIER) cc_final: 0.6712 (tp) REVERT: H 86 LEU cc_start: 0.7130 (mt) cc_final: 0.6745 (mp) REVERT: L 37 TYR cc_start: 0.7741 (m-80) cc_final: 0.7248 (m-10) REVERT: F 510 LYS cc_start: 0.8603 (mttt) cc_final: 0.7718 (mmtt) REVERT: I 119 TYR cc_start: 0.8602 (p90) cc_final: 0.8193 (p90) outliers start: 60 outliers final: 36 residues processed: 245 average time/residue: 0.1243 time to fit residues: 43.1224 Evaluate side-chains 235 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 196 time to evaluate : 0.475 ------------------------------------------------------------------------------- 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 267 SER Chi-restraints excluded: chain J residue 22 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 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 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 65 SER Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 239 LEU 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 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 83 LEU Chi-restraints excluded: chain H residue 109 PHE Chi-restraints excluded: chain H residue 111 GLU 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 267 SER Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain F residue 545 GLU 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 111 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 102 optimal weight: 5.9990 chunk 9 optimal weight: 0.2980 chunk 54 optimal weight: 2.9990 chunk 122 optimal weight: 0.7980 chunk 101 optimal weight: 4.9990 chunk 107 optimal weight: 7.9990 chunk 146 optimal weight: 0.8980 chunk 127 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 124 optimal weight: 1.9990 chunk 35 optimal weight: 0.0980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 HIS E 595 GLN F 595 GLN I 59 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.142021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.091405 restraints weight = 22346.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.092405 restraints weight = 15912.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.092671 restraints weight = 11564.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.092778 restraints weight = 10820.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.092984 restraints weight = 10737.435| |-----------------------------------------------------------------------------| r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.4824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13929 Z= 0.120 Angle : 0.600 7.564 18966 Z= 0.299 Chirality : 0.043 0.157 2157 Planarity : 0.004 0.035 2385 Dihedral : 4.635 20.398 1845 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.46 % Favored : 97.36 % Rotamer: Outliers : 3.25 % Allowed : 12.43 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.20), residues: 1665 helix: 2.04 (0.41), residues: 162 sheet: -0.03 (0.21), residues: 636 loop : -0.15 (0.21), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 596 TYR 0.018 0.002 TYR I 117 PHE 0.023 0.001 PHE F 592 TRP 0.009 0.001 TRP H 47 HIS 0.002 0.001 HIS C 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (13884) covalent geometry : angle 0.58997 / 0.30 (18846) SS BOND : bond 0.00385 / 0.26 ( 15) SS BOND : angle 0.75560 / 0.49 ( 30) hydrogen bonds : bond 0.03836 / 2.64 ( 513) hydrogen bonds : angle 4.74974 / 3.38 ( 1296) link_ALPHA1-3 : bond 0.00725 / 0.36 ( 3) link_ALPHA1-3 : angle 1.22668 / 0.69 ( 9) link_ALPHA1-6 : bond 0.00471 / 0.24 ( 3) link_ALPHA1-6 : angle 1.19472 / 0.68 ( 9) link_BETA1-4 : bond 0.00598 / 0.45 ( 9) link_BETA1-4 : angle 2.02603 / 1.10 ( 27) link_NAG-ASN : bond 0.00268 / 0.18 ( 15) link_NAG-ASN : angle 1.56563 / 1.00 ( 45) *********************** 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 265 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 219 time to evaluate : 0.488 Fit side-chains revert: symmetry clash REVERT: A 174 THR cc_start: 0.9350 (m) cc_final: 0.9039 (p) REVERT: A 267 SER cc_start: 0.8037 (OUTLIER) cc_final: 0.7268 (p) REVERT: J 63 PHE cc_start: 0.7299 (m-80) cc_final: 0.6686 (m-80) REVERT: G 3 GLN cc_start: 0.7779 (pm20) cc_final: 0.7560 (pm20) REVERT: G 38 ARG cc_start: 0.7370 (mtp-110) cc_final: 0.7092 (mtm-85) REVERT: G 64 PHE cc_start: 0.7730 (m-80) cc_final: 0.7474 (m-80) REVERT: G 65 GLN cc_start: 0.8392 (tp40) cc_final: 0.8054 (mm-40) REVERT: G 81 MET cc_start: 0.8291 (tmm) cc_final: 0.8042 (tmm) REVERT: G 111 GLU cc_start: 0.8419 (pp20) cc_final: 0.8122 (pp20) REVERT: G 114 LYS cc_start: 0.8623 (ttpt) cc_final: 0.8049 (ptmt) REVERT: G 119 TYR cc_start: 0.8467 (p90) cc_final: 0.8263 (p90) REVERT: G 120 MET cc_start: 0.8440 (mpp) cc_final: 0.8041 (mpp) REVERT: B 65 SER cc_start: 0.9037 (OUTLIER) cc_final: 0.8770 (p) REVERT: K 37 TYR cc_start: 0.7846 (m-10) cc_final: 0.6866 (m-10) REVERT: E 587 ARG cc_start: 0.7707 (OUTLIER) cc_final: 0.7283 (ttp-170) REVERT: H 83 LEU cc_start: 0.6837 (OUTLIER) cc_final: 0.6505 (tp) REVERT: H 86 LEU cc_start: 0.7079 (mt) cc_final: 0.6797 (mp) REVERT: H 114 LYS cc_start: 0.8486 (ttpt) cc_final: 0.7917 (ptpt) REVERT: H 119 TYR cc_start: 0.8609 (p90) cc_final: 0.8203 (p90) REVERT: H 120 MET cc_start: 0.8549 (mpp) cc_final: 0.8136 (mpp) REVERT: L 37 TYR cc_start: 0.7709 (m-80) cc_final: 0.7440 (m-10) REVERT: I 119 TYR cc_start: 0.8609 (p90) cc_final: 0.8229 (p90) outliers start: 46 outliers final: 35 residues processed: 246 average time/residue: 0.1087 time to fit residues: 38.4785 Evaluate side-chains 241 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 202 time to evaluate : 0.322 ------------------------------------------------------------------------------- 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 239 LEU Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain J residue 22 SER Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 48 LEU 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 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 G residue 109 PHE Chi-restraints excluded: chain B residue 65 SER 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 K residue 34 LEU Chi-restraints excluded: chain K residue 48 LEU 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 H residue 83 LEU Chi-restraints excluded: chain H residue 109 PHE 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 284 THR Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain F residue 595 GLN Chi-restraints excluded: chain I residue 60 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 66 optimal weight: 0.7980 chunk 93 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 131 optimal weight: 5.9990 chunk 126 optimal weight: 1.9990 chunk 140 optimal weight: 6.9990 chunk 57 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 136 optimal weight: 4.9990 chunk 135 optimal weight: 10.0000 chunk 146 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 39 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.139617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.089250 restraints weight = 22372.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.090102 restraints weight = 16762.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.090190 restraints weight = 11915.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.090301 restraints weight = 11675.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.090474 restraints weight = 10962.665| |-----------------------------------------------------------------------------| r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.4917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 13929 Z= 0.204 Angle : 0.647 8.504 18966 Z= 0.321 Chirality : 0.045 0.163 2157 Planarity : 0.004 0.067 2385 Dihedral : 4.606 19.309 1845 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.58 % Favored : 97.24 % Rotamer: Outliers : 3.18 % Allowed : 12.92 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.00 (0.21), residues: 1665 helix: 1.94 (0.41), residues: 159 sheet: -0.06 (0.21), residues: 636 loop : -0.21 (0.21), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 38 TYR 0.024 0.002 TYR J 50 PHE 0.024 0.002 PHE E 592 TRP 0.008 0.001 TRP H 47 HIS 0.004 0.001 HIS B 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00487 / 0.20 (13884) covalent geometry : angle 0.63610 / 0.32 (18846) SS BOND : bond 0.00395 / 0.26 ( 15) SS BOND : angle 0.62161 / 0.40 ( 30) hydrogen bonds : bond 0.04270 / 2.92 ( 513) hydrogen bonds : angle 4.78929 / 3.41 ( 1296) link_ALPHA1-3 : bond 0.00371 / 0.19 ( 3) link_ALPHA1-3 : angle 1.51283 / 0.83 ( 9) link_ALPHA1-6 : bond 0.00398 / 0.20 ( 3) link_ALPHA1-6 : angle 1.19015 / 0.67 ( 9) link_BETA1-4 : bond 0.00520 / 0.41 ( 9) link_BETA1-4 : angle 2.40043 / 1.32 ( 27) link_NAG-ASN : bond 0.00105 / 0.08 ( 15) link_NAG-ASN : angle 1.51361 / 0.98 ( 45) *********************** 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 245 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 200 time to evaluate : 0.382 Fit side-chains REVERT: A 267 SER cc_start: 0.8159 (OUTLIER) cc_final: 0.7308 (p) REVERT: J 63 PHE cc_start: 0.7391 (m-80) cc_final: 0.6755 (m-80) REVERT: G 3 GLN cc_start: 0.7831 (pm20) cc_final: 0.7597 (pm20) REVERT: G 38 ARG cc_start: 0.7632 (mtp-110) cc_final: 0.7306 (mtm-85) REVERT: G 64 PHE cc_start: 0.7756 (m-80) cc_final: 0.7549 (m-80) REVERT: G 65 GLN cc_start: 0.8397 (tp40) cc_final: 0.8106 (mm-40) REVERT: G 81 MET cc_start: 0.8215 (tmm) cc_final: 0.7955 (tmm) REVERT: G 111 GLU cc_start: 0.8501 (pp20) cc_final: 0.8142 (pp20) REVERT: G 114 LYS cc_start: 0.8621 (ttpt) cc_final: 0.8102 (ptmt) REVERT: G 119 TYR cc_start: 0.8544 (p90) cc_final: 0.8305 (p90) REVERT: G 120 MET cc_start: 0.8437 (mpp) cc_final: 0.8051 (mpp) REVERT: B 65 SER cc_start: 0.9093 (OUTLIER) cc_final: 0.8770 (p) REVERT: K 37 TYR cc_start: 0.7923 (m-10) cc_final: 0.6771 (m-10) REVERT: E 587 ARG cc_start: 0.7768 (OUTLIER) cc_final: 0.7311 (ttp-170) REVERT: H 83 LEU cc_start: 0.6700 (OUTLIER) cc_final: 0.6468 (tp) REVERT: H 86 LEU cc_start: 0.7133 (mt) cc_final: 0.6911 (mp) REVERT: H 114 LYS cc_start: 0.8431 (ttpt) cc_final: 0.7950 (ptpt) REVERT: H 119 TYR cc_start: 0.8662 (p90) cc_final: 0.8225 (p90) REVERT: H 120 MET cc_start: 0.8550 (mpp) cc_final: 0.8059 (mpp) REVERT: L 37 TYR cc_start: 0.7870 (m-80) cc_final: 0.7624 (m-10) REVERT: L 63 PHE cc_start: 0.7656 (m-80) cc_final: 0.6759 (m-80) REVERT: I 119 TYR cc_start: 0.8667 (p90) cc_final: 0.8292 (p90) outliers start: 45 outliers final: 37 residues processed: 228 average time/residue: 0.1158 time to fit residues: 37.9357 Evaluate side-chains 236 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 195 time to evaluate : 0.499 ------------------------------------------------------------------------------- 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 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 70 THR 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 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 G residue 109 PHE Chi-restraints excluded: chain B residue 65 SER 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 284 THR Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 48 LEU Chi-restraints excluded: chain E residue 581 THR Chi-restraints excluded: chain E residue 587 ARG 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 83 LEU Chi-restraints excluded: chain H residue 109 PHE 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 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 91 GLN Chi-restraints excluded: chain F residue 595 GLN Chi-restraints excluded: chain I residue 60 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 46 optimal weight: 1.9990 chunk 26 optimal weight: 0.3980 chunk 28 optimal weight: 6.9990 chunk 131 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 156 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 128 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 27 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 = 0.3814 r_free = 0.3814 target = 0.138977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.088448 restraints weight = 22428.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.089373 restraints weight = 15661.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.089243 restraints weight = 11358.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.089542 restraints weight = 11761.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.089736 restraints weight = 10883.989| |-----------------------------------------------------------------------------| r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.5102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 13929 Z= 0.215 Angle : 0.663 8.078 18966 Z= 0.330 Chirality : 0.045 0.155 2157 Planarity : 0.004 0.037 2385 Dihedral : 4.637 20.501 1845 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.36 % Favored : 96.46 % Rotamer: Outliers : 3.81 % Allowed : 12.57 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.21), residues: 1665 helix: 1.09 (0.40), residues: 177 sheet: 0.04 (0.22), residues: 585 loop : -0.26 (0.20), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 38 TYR 0.022 0.002 TYR J 50 PHE 0.021 0.002 PHE E 592 TRP 0.008 0.001 TRP C 104 HIS 0.004 0.001 HIS B 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00509 / 0.22 (13884) covalent geometry : angle 0.65421 / 0.33 (18846) SS BOND : bond 0.00385 / 0.25 ( 15) SS BOND : angle 0.54811 / 0.36 ( 30) hydrogen bonds : bond 0.04350 / 2.98 ( 513) hydrogen bonds : angle 4.82119 / 3.42 ( 1296) link_ALPHA1-3 : bond 0.00456 / 0.23 ( 3) link_ALPHA1-3 : angle 1.48836 / 0.82 ( 9) link_ALPHA1-6 : bond 0.00448 / 0.22 ( 3) link_ALPHA1-6 : angle 1.17391 / 0.66 ( 9) link_BETA1-4 : bond 0.00533 / 0.41 ( 9) link_BETA1-4 : angle 2.34116 / 1.29 ( 27) link_NAG-ASN : bond 0.00118 / 0.09 ( 15) link_NAG-ASN : angle 1.42945 / 0.93 ( 45) *********************** 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 260 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 206 time to evaluate : 0.520 Fit side-chains REVERT: A 267 SER cc_start: 0.8224 (OUTLIER) cc_final: 0.7268 (p) REVERT: J 63 PHE cc_start: 0.7388 (m-80) cc_final: 0.6676 (m-80) REVERT: G 3 GLN cc_start: 0.7674 (pm20) cc_final: 0.7443 (pm20) REVERT: G 36 TRP cc_start: 0.8179 (m100) cc_final: 0.7403 (m100) REVERT: G 38 ARG cc_start: 0.7547 (mtp-110) cc_final: 0.7023 (mtm-85) REVERT: G 64 PHE cc_start: 0.7761 (m-80) cc_final: 0.7492 (m-80) REVERT: G 65 GLN cc_start: 0.8430 (tp40) cc_final: 0.8155 (mm-40) REVERT: G 81 MET cc_start: 0.8355 (tmm) cc_final: 0.8104 (tmm) REVERT: G 94 TYR cc_start: 0.8099 (m-10) cc_final: 0.7885 (m-10) REVERT: G 95 PHE cc_start: 0.6343 (m-80) cc_final: 0.5579 (m-80) REVERT: G 111 GLU cc_start: 0.8470 (pp20) cc_final: 0.8122 (pp20) REVERT: G 114 LYS cc_start: 0.8680 (ttpt) cc_final: 0.8068 (ptmt) REVERT: G 119 TYR cc_start: 0.8584 (p90) cc_final: 0.8281 (p90) REVERT: G 120 MET cc_start: 0.8460 (mpp) cc_final: 0.8040 (mpp) REVERT: B 65 SER cc_start: 0.9068 (OUTLIER) cc_final: 0.8737 (p) REVERT: K 37 TYR cc_start: 0.7894 (m-10) cc_final: 0.6920 (m-10) REVERT: E 587 ARG cc_start: 0.7759 (OUTLIER) cc_final: 0.7323 (ttp-170) REVERT: H 114 LYS cc_start: 0.8470 (ttpt) cc_final: 0.7895 (ptpt) REVERT: H 120 MET cc_start: 0.8395 (mpp) cc_final: 0.8045 (mpp) REVERT: L 37 TYR cc_start: 0.7723 (m-80) cc_final: 0.7489 (m-10) REVERT: L 63 PHE cc_start: 0.7654 (m-80) cc_final: 0.6760 (m-80) REVERT: L 84 PHE cc_start: 0.6928 (m-80) cc_final: 0.6691 (m-80) REVERT: I 46 GLU cc_start: 0.7408 (pm20) cc_final: 0.7071 (pm20) REVERT: I 119 TYR cc_start: 0.8727 (p90) cc_final: 0.8335 (p90) outliers start: 54 outliers final: 40 residues processed: 239 average time/residue: 0.1219 time to fit residues: 41.9258 Evaluate side-chains 246 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 203 time to evaluate : 0.466 ------------------------------------------------------------------------------- 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 239 LEU Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 273 LEU 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 542 ILE 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 60 TYR Chi-restraints excluded: chain G residue 109 PHE Chi-restraints excluded: chain B residue 65 SER 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 284 THR Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 48 LEU 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 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 H residue 111 GLU 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 48 LEU Chi-restraints excluded: chain L residue 91 GLN Chi-restraints excluded: chain I residue 60 TYR Chi-restraints excluded: chain I residue 109 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 136 optimal weight: 10.0000 chunk 22 optimal weight: 1.9990 chunk 84 optimal weight: 9.9990 chunk 79 optimal weight: 8.9990 chunk 27 optimal weight: 20.0000 chunk 161 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 87 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 chunk 49 optimal weight: 9.9990 chunk 128 optimal weight: 3.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.138346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.088623 restraints weight = 22537.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.088058 restraints weight = 15507.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.088792 restraints weight = 12654.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.089408 restraints weight = 12146.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.089393 restraints weight = 10495.169| |-----------------------------------------------------------------------------| r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.5266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 13929 Z= 0.223 Angle : 0.677 9.385 18966 Z= 0.336 Chirality : 0.045 0.153 2157 Planarity : 0.004 0.038 2385 Dihedral : 4.684 19.651 1845 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.30 % Favored : 96.52 % Rotamer: Outliers : 3.39 % Allowed : 12.99 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.21), residues: 1665 helix: 1.05 (0.40), residues: 177 sheet: 0.03 (0.22), residues: 582 loop : -0.33 (0.20), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG I 38 TYR 0.022 0.002 TYR J 50 PHE 0.021 0.002 PHE E 592 TRP 0.014 0.001 TRP I 47 HIS 0.005 0.001 HIS F 549 Details of bonding type rmsd/Z covalent geometry : bond 0.00530 / 0.22 (13884) covalent geometry : angle 0.66864 / 0.33 (18846) SS BOND : bond 0.00405 / 0.27 ( 15) SS BOND : angle 0.58678 / 0.39 ( 30) hydrogen bonds : bond 0.04399 / 3.02 ( 513) hydrogen bonds : angle 4.85886 / 3.44 ( 1296) link_ALPHA1-3 : bond 0.00471 / 0.24 ( 3) link_ALPHA1-3 : angle 1.55947 / 0.86 ( 9) link_ALPHA1-6 : bond 0.00423 / 0.21 ( 3) link_ALPHA1-6 : angle 1.15497 / 0.65 ( 9) link_BETA1-4 : bond 0.00537 / 0.42 ( 9) link_BETA1-4 : angle 2.32005 / 1.27 ( 27) link_NAG-ASN : bond 0.00137 / 0.11 ( 15) link_NAG-ASN : angle 1.40472 / 0.91 ( 45) *********************** 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 257 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 209 time to evaluate : 0.518 Fit side-chains REVERT: A 267 SER cc_start: 0.8272 (OUTLIER) cc_final: 0.7274 (p) REVERT: J 37 TYR cc_start: 0.7704 (m-10) cc_final: 0.7035 (m-10) REVERT: J 63 PHE cc_start: 0.7398 (m-80) cc_final: 0.6706 (m-80) REVERT: G 36 TRP cc_start: 0.8120 (m100) cc_final: 0.7649 (m100) REVERT: G 65 GLN cc_start: 0.8384 (tp40) cc_final: 0.8162 (mm-40) REVERT: G 95 PHE cc_start: 0.6396 (m-80) cc_final: 0.5964 (m-80) REVERT: G 111 GLU cc_start: 0.8458 (pp20) cc_final: 0.8116 (pp20) REVERT: G 119 TYR cc_start: 0.8629 (p90) cc_final: 0.8323 (p90) REVERT: G 120 MET cc_start: 0.8430 (mpp) cc_final: 0.8112 (mpp) REVERT: B 65 SER cc_start: 0.9045 (OUTLIER) cc_final: 0.8748 (p) REVERT: K 37 TYR cc_start: 0.7957 (m-10) cc_final: 0.6977 (m-10) REVERT: E 587 ARG cc_start: 0.7778 (OUTLIER) cc_final: 0.7339 (ttp-170) REVERT: H 114 LYS cc_start: 0.8491 (ttpt) cc_final: 0.7907 (ptpt) REVERT: H 120 MET cc_start: 0.8341 (mpp) cc_final: 0.8038 (mpp) REVERT: C 98 ASN cc_start: 0.9310 (OUTLIER) cc_final: 0.9108 (p0) REVERT: L 63 PHE cc_start: 0.7642 (m-80) cc_final: 0.6793 (m-80) REVERT: L 84 PHE cc_start: 0.6767 (m-80) cc_final: 0.6550 (m-80) REVERT: F 596 ARG cc_start: 0.7933 (mtt90) cc_final: 0.7724 (mtt90) REVERT: I 38 ARG cc_start: 0.8068 (mtm110) cc_final: 0.7773 (mtm110) REVERT: I 46 GLU cc_start: 0.7364 (pm20) cc_final: 0.7071 (pm20) REVERT: I 119 TYR cc_start: 0.8762 (p90) cc_final: 0.8372 (p90) outliers start: 48 outliers final: 40 residues processed: 240 average time/residue: 0.1126 time to fit residues: 39.4133 Evaluate side-chains 245 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 201 time to evaluate : 0.504 ------------------------------------------------------------------------------- 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 239 LEU Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 273 LEU 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 52 ILE Chi-restraints excluded: chain G residue 60 TYR Chi-restraints excluded: chain G residue 109 PHE Chi-restraints excluded: chain B residue 65 SER 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 284 THR 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 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 H residue 111 GLU Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 103 GLU 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 48 LEU Chi-restraints excluded: chain L residue 91 GLN Chi-restraints excluded: chain F residue 581 THR Chi-restraints excluded: chain I residue 60 TYR Chi-restraints excluded: chain I residue 109 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 37 optimal weight: 0.9980 chunk 151 optimal weight: 4.9990 chunk 101 optimal weight: 8.9990 chunk 95 optimal weight: 7.9990 chunk 86 optimal weight: 2.9990 chunk 46 optimal weight: 0.0970 chunk 110 optimal weight: 0.6980 chunk 122 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 59 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.140418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.088621 restraints weight = 22310.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.091011 restraints weight = 14607.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.092560 restraints weight = 11308.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.093358 restraints weight = 9703.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.093952 restraints weight = 8916.381| |-----------------------------------------------------------------------------| r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.5339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13929 Z= 0.132 Angle : 0.624 10.623 18966 Z= 0.307 Chirality : 0.043 0.148 2157 Planarity : 0.004 0.034 2385 Dihedral : 4.461 20.409 1845 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.24 % Favored : 96.58 % Rotamer: Outliers : 2.82 % Allowed : 13.91 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.21), residues: 1665 helix: 1.39 (0.41), residues: 177 sheet: 0.07 (0.22), residues: 585 loop : -0.22 (0.21), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG I 38 TYR 0.024 0.002 TYR J 50 PHE 0.019 0.001 PHE E 592 TRP 0.012 0.001 TRP H 47 HIS 0.003 0.001 HIS F 549 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 (13884) covalent geometry : angle 0.61700 / 0.31 (18846) SS BOND : bond 0.00347 / 0.25 ( 15) SS BOND : angle 0.59144 / 0.38 ( 30) hydrogen bonds : bond 0.03823 / 2.63 ( 513) hydrogen bonds : angle 4.70042 / 3.34 ( 1296) link_ALPHA1-3 : bond 0.00564 / 0.28 ( 3) link_ALPHA1-3 : angle 1.27431 / 0.72 ( 9) link_ALPHA1-6 : bond 0.00452 / 0.23 ( 3) link_ALPHA1-6 : angle 1.23177 / 0.70 ( 9) link_BETA1-4 : bond 0.00550 / 0.41 ( 9) link_BETA1-4 : angle 1.93391 / 1.05 ( 27) link_NAG-ASN : bond 0.00106 / 0.07 ( 15) link_NAG-ASN : angle 1.34312 / 0.85 ( 45) ********************** 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 247 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 207 time to evaluate : 0.548 Fit side-chains REVERT: A 267 SER cc_start: 0.8154 (OUTLIER) cc_final: 0.7266 (p) REVERT: J 63 PHE cc_start: 0.7293 (m-80) cc_final: 0.6629 (m-80) REVERT: G 3 GLN cc_start: 0.7790 (pm20) cc_final: 0.7526 (pm20) REVERT: G 65 GLN cc_start: 0.8354 (tp40) cc_final: 0.8118 (mm-40) REVERT: G 106 ARG cc_start: 0.7987 (mtp-110) cc_final: 0.7412 (mmm-85) REVERT: G 111 GLU cc_start: 0.8457 (pp20) cc_final: 0.8099 (pp20) REVERT: G 119 TYR cc_start: 0.8618 (p90) cc_final: 0.8369 (p90) REVERT: G 120 MET cc_start: 0.8428 (mpp) cc_final: 0.8116 (mpp) REVERT: B 65 SER cc_start: 0.8933 (OUTLIER) cc_final: 0.8698 (p) REVERT: K 37 TYR cc_start: 0.7977 (m-10) cc_final: 0.7073 (m-10) REVERT: E 587 ARG cc_start: 0.7781 (OUTLIER) cc_final: 0.7347 (ttp-170) REVERT: H 81 MET cc_start: 0.7535 (tmm) cc_final: 0.7222 (tmm) REVERT: H 114 LYS cc_start: 0.8429 (ttpt) cc_final: 0.7895 (ptpt) REVERT: H 120 MET cc_start: 0.8274 (mpp) cc_final: 0.8051 (mpp) REVERT: L 37 TYR cc_start: 0.7532 (m-10) cc_final: 0.7037 (m-10) REVERT: L 63 PHE cc_start: 0.7541 (m-80) cc_final: 0.7108 (m-80) REVERT: L 84 PHE cc_start: 0.6737 (m-80) cc_final: 0.6521 (m-80) REVERT: F 596 ARG cc_start: 0.7811 (mtt90) cc_final: 0.7589 (mtt90) REVERT: I 38 ARG cc_start: 0.8045 (mtm110) cc_final: 0.7772 (mtm110) REVERT: I 46 GLU cc_start: 0.7388 (pm20) cc_final: 0.7084 (pm20) REVERT: I 119 TYR cc_start: 0.8731 (p90) cc_final: 0.8424 (p90) outliers start: 40 outliers final: 32 residues processed: 234 average time/residue: 0.1198 time to fit residues: 40.8304 Evaluate side-chains 231 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 196 time to evaluate : 0.482 ------------------------------------------------------------------------------- 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 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 52 ILE Chi-restraints excluded: chain G residue 60 TYR Chi-restraints excluded: chain B residue 65 SER 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 284 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 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 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 48 LEU Chi-restraints excluded: chain I residue 60 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 88 optimal weight: 0.0000 chunk 16 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 47 optimal weight: 10.0000 chunk 43 optimal weight: 7.9990 chunk 28 optimal weight: 2.9990 chunk 132 optimal weight: 8.9990 chunk 156 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 97 optimal weight: 8.9990 overall best weight: 1.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.138421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.085818 restraints weight = 22659.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.088224 restraints weight = 14814.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.089711 restraints weight = 11466.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.090471 restraints weight = 9880.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 61)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.091185 restraints weight = 9052.053| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.5445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 13929 Z= 0.210 Angle : 0.681 10.795 18966 Z= 0.334 Chirality : 0.045 0.153 2157 Planarity : 0.004 0.037 2385 Dihedral : 4.548 19.343 1845 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.60 % Favored : 96.22 % Rotamer: Outliers : 2.75 % Allowed : 14.05 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.21), residues: 1665 helix: 1.17 (0.40), residues: 177 sheet: 0.07 (0.22), residues: 612 loop : -0.26 (0.21), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG I 38 TYR 0.028 0.002 TYR G 94 PHE 0.020 0.002 PHE E 592 TRP 0.011 0.001 TRP I 47 HIS 0.005 0.001 HIS F 549 Details of bonding type rmsd/Z covalent geometry : bond 0.00500 / 0.21 (13884) covalent geometry : angle 0.67273 / 0.33 (18846) SS BOND : bond 0.00387 / 0.26 ( 15) SS BOND : angle 0.57232 / 0.38 ( 30) hydrogen bonds : bond 0.04303 / 2.95 ( 513) hydrogen bonds : angle 4.81133 / 3.41 ( 1296) link_ALPHA1-3 : bond 0.00323 / 0.16 ( 3) link_ALPHA1-3 : angle 1.57531 / 0.86 ( 9) link_ALPHA1-6 : bond 0.00393 / 0.20 ( 3) link_ALPHA1-6 : angle 1.18803 / 0.67 ( 9) link_BETA1-4 : bond 0.00536 / 0.42 ( 9) link_BETA1-4 : angle 2.32586 / 1.28 ( 27) link_NAG-ASN : bond 0.00158 / 0.12 ( 15) link_NAG-ASN : angle 1.32893 / 0.86 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2231.70 seconds wall clock time: 39 minutes 27.73 seconds (2367.73 seconds total)