Starting phenix.real_space_refine on Mon Aug 25 07:31:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bfu_44507/08_2025/9bfu_44507.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bfu_44507/08_2025/9bfu_44507.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9bfu_44507/08_2025/9bfu_44507.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bfu_44507/08_2025/9bfu_44507.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9bfu_44507/08_2025/9bfu_44507.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bfu_44507/08_2025/9bfu_44507.map" } resolution = 4.07 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= 0.006 sd= 0.033 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 88 5.16 5 C 16240 2.51 5 N 4552 2.21 5 O 4816 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25696 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 12642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1652, 12642 Classifications: {'peptide': 1652} Incomplete info: {'truncation_to_alanine': 149} Link IDs: {'PCIS': 2, 'PTRANS': 110, 'TRANS': 1539} Chain breaks: 16 Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 579 Unresolved non-hydrogen angles: 752 Unresolved non-hydrogen dihedrals: 490 Unresolved non-hydrogen chiralities: 51 Planarities with less than four sites: {'GLU:plan': 18, 'ARG:plan': 17, 'ASP:plan': 5, 'TRP:plan': 6, 'HIS:plan': 5, 'GLN:plan1': 9, 'PHE:plan': 2, 'TYR:plan': 6, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 344 Chain: "B" Number of atoms: 12642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1652, 12642 Classifications: {'peptide': 1652} Incomplete info: {'truncation_to_alanine': 149} Link IDs: {'PCIS': 2, 'PTRANS': 110, 'TRANS': 1539} Chain breaks: 16 Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 579 Unresolved non-hydrogen angles: 752 Unresolved non-hydrogen dihedrals: 490 Unresolved non-hydrogen chiralities: 51 Planarities with less than four sites: {'GLU:plan': 18, 'ARG:plan': 17, 'ASP:plan': 5, 'TRP:plan': 6, 'HIS:plan': 5, 'GLN:plan1': 9, 'PHE:plan': 2, 'TYR:plan': 6, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 344 Chain: "C" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 5.44, per 1000 atoms: 0.21 Number of scatterers: 25696 At special positions: 0 Unit cell: (233.23, 118.69, 182.6, 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 88 16.00 O 4816 8.00 N 4552 7.00 C 16240 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=20, symmetry=0 Simple disulfide: pdb=" SG CYS A 220 " - pdb=" SG CYS A 257 " distance=2.03 Simple disulfide: pdb=" SG CYS A 224 " - pdb=" SG CYS A 253 " distance=2.02 Simple disulfide: pdb=" SG CYS A 239 " - pdb=" SG CYS A 248 " distance=2.03 Simple disulfide: pdb=" SG CYS A 270 " - pdb=" SG CYS A 290 " distance=2.03 Simple disulfide: pdb=" SG CYS A 274 " - pdb=" SG CYS A 286 " distance=2.03 Simple disulfide: pdb=" SG CYS A 387 " - pdb=" SG CYS A 393 " distance=2.02 Simple disulfide: pdb=" SG CYS A 981 " - pdb=" SG CYS A 991 " distance=2.03 Simple disulfide: pdb=" SG CYS A1597 " - pdb=" SG CYS A1606 " distance=2.04 Simple disulfide: pdb=" SG CYS A1679 " - pdb=" SG CYS A1713 " distance=2.03 Simple disulfide: pdb=" SG CYS A1695 " - pdb=" SG CYS A1700 " distance=2.03 Simple disulfide: pdb=" SG CYS B 220 " - pdb=" SG CYS B 257 " distance=2.03 Simple disulfide: pdb=" SG CYS B 224 " - pdb=" SG CYS B 253 " distance=2.02 Simple disulfide: pdb=" SG CYS B 239 " - pdb=" SG CYS B 248 " distance=2.03 Simple disulfide: pdb=" SG CYS B 270 " - pdb=" SG CYS B 290 " distance=2.03 Simple disulfide: pdb=" SG CYS B 274 " - pdb=" SG CYS B 286 " distance=2.03 Simple disulfide: pdb=" SG CYS B 387 " - pdb=" SG CYS B 393 " distance=2.02 Simple disulfide: pdb=" SG CYS B 981 " - pdb=" SG CYS B 991 " distance=2.03 Simple disulfide: pdb=" SG CYS B1597 " - pdb=" SG CYS B1606 " distance=2.04 Simple disulfide: pdb=" SG CYS B1679 " - pdb=" SG CYS B1713 " distance=2.03 Simple disulfide: pdb=" SG CYS B1695 " - pdb=" SG CYS B1700 " distance=2.03 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 BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " BETA1-6 " NAG C 1 " - " FUC C 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG E 1 " - " FUC E 3 " NAG-ASN " NAG A2601 " - " ASN A1557 " " NAG A2602 " - " ASN A1550 " " NAG A2603 " - " ASN A1228 " " NAG A2604 " - " ASN A1639 " " NAG A2605 " - " ASN A1725 " " NAG A2606 " - " ASN A 505 " " NAG A2607 " - " ASN A1804 " " NAG A2608 " - " ASN A1889 " " NAG A2609 " - " ASN A1756 " " NAG A2610 " - " ASN A1313 " " NAG B2601 " - " ASN B1557 " " NAG B2602 " - " ASN B1550 " " NAG B2603 " - " ASN B1228 " " NAG B2604 " - " ASN B1639 " " NAG B2605 " - " ASN B1313 " " NAG B2606 " - " ASN B1725 " " NAG B2607 " - " ASN B 505 " " NAG B2608 " - " ASN B1804 " " NAG B2609 " - " ASN B1889 " " NAG B2610 " - " ASN B1756 " " NAG C 1 " - " ASN A1353 " " NAG D 1 " - " ASN A 966 " " NAG E 1 " - " ASN B1353 " " NAG F 1 " - " ASN B 966 " Time building additional restraints: 1.89 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 1.9 microseconds 6472 Ramachandran restraints generated. 3236 Oldfield, 0 Emsley, 3236 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6192 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 77 sheets defined 6.7% alpha, 40.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.29 Creating SS restraints... Processing helix chain 'A' and resid 207 through 227 Processing helix chain 'A' and resid 248 through 257 removed outlier: 3.814A pdb=" N ARG A 252 " --> pdb=" O CYS A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 266 removed outlier: 3.766A pdb=" N ALA A 263 " --> pdb=" O GLN A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 274 Processing helix chain 'A' and resid 283 through 312 removed outlier: 5.373A pdb=" N HIS A 307 " --> pdb=" O LEU A 303 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N LEU A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR A 312 " --> pdb=" O LEU A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 1066 through 1070 removed outlier: 3.568A pdb=" N GLU A1069 " --> pdb=" O THR A1066 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA A1070 " --> pdb=" O PRO A1067 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1066 through 1070' Processing helix chain 'A' and resid 1505 through 1507 No H-bonds generated for 'chain 'A' and resid 1505 through 1507' Processing helix chain 'A' and resid 1610 through 1617 removed outlier: 4.424A pdb=" N GLN A1614 " --> pdb=" O ALA A1610 " (cutoff:3.500A) Processing helix chain 'A' and resid 1619 through 1626 removed outlier: 4.025A pdb=" N GLN A1626 " --> pdb=" O SER A1622 " (cutoff:3.500A) Processing helix chain 'A' and resid 1676 through 1681 removed outlier: 3.629A pdb=" N LEU A1681 " --> pdb=" O LYS A1677 " (cutoff:3.500A) Processing helix chain 'A' and resid 1774 through 1780 removed outlier: 3.533A pdb=" N LYS A1778 " --> pdb=" O SER A1774 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 227 Processing helix chain 'B' and resid 248 through 257 removed outlier: 3.793A pdb=" N ARG B 252 " --> pdb=" O CYS B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 266 removed outlier: 3.773A pdb=" N ALA B 263 " --> pdb=" O GLN B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 274 Processing helix chain 'B' and resid 283 through 312 removed outlier: 5.487A pdb=" N HIS B 307 " --> pdb=" O LEU B 303 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N LEU B 308 " --> pdb=" O ALA B 304 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR B 312 " --> pdb=" O LEU B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 1066 through 1070 removed outlier: 3.557A pdb=" N GLU B1069 " --> pdb=" O THR B1066 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA B1070 " --> pdb=" O PRO B1067 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1066 through 1070' Processing helix chain 'B' and resid 1505 through 1507 No H-bonds generated for 'chain 'B' and resid 1505 through 1507' Processing helix chain 'B' and resid 1610 through 1617 removed outlier: 4.412A pdb=" N GLN B1614 " --> pdb=" O ALA B1610 " (cutoff:3.500A) Processing helix chain 'B' and resid 1619 through 1626 removed outlier: 4.016A pdb=" N GLN B1626 " --> pdb=" O SER B1622 " (cutoff:3.500A) Processing helix chain 'B' and resid 1676 through 1681 removed outlier: 3.652A pdb=" N LEU B1681 " --> pdb=" O LYS B1677 " (cutoff:3.500A) Processing helix chain 'B' and resid 1774 through 1780 removed outlier: 3.533A pdb=" N LYS B1778 " --> pdb=" O SER B1774 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 315 through 317 removed outlier: 4.507A pdb=" N LEU A 329 " --> pdb=" O ILE A 395 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N VAL A 392 " --> pdb=" O ASP A 388 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ASP A 388 " --> pdb=" O VAL A 392 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N ALA B1384 " --> pdb=" O VAL B1378 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N VAL B1378 " --> pdb=" O ALA B1384 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLU B1348 " --> pdb=" O CYS B1340 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N VAL B1342 " --> pdb=" O LEU B1346 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N LEU B1346 " --> pdb=" O VAL B1342 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 380 through 381 Processing sheet with id=AA3, first strand: chain 'A' and resid 380 through 381 Processing sheet with id=AA4, first strand: chain 'A' and resid 443 through 447 removed outlier: 3.560A pdb=" N LEU A 454 " --> pdb=" O PHE A 497 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 484 through 489 removed outlier: 6.812A pdb=" N TYR A 506 " --> pdb=" O PHE A 525 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N PHE A 525 " --> pdb=" O TYR A 506 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N LEU A 508 " --> pdb=" O LYS A 523 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N LYS A 523 " --> pdb=" O LEU A 508 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N LEU A 510 " --> pdb=" O VAL A 521 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N VAL A 521 " --> pdb=" O LEU A 510 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N MET A 512 " --> pdb=" O GLY A 519 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 563 through 568 removed outlier: 6.342A pdb=" N ASN A 563 " --> pdb=" O SER A 556 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N SER A 556 " --> pdb=" O ASN A 563 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N MET A 565 " --> pdb=" O TRP A 554 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N TRP A 554 " --> pdb=" O MET A 565 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 573 through 578 removed outlier: 4.223A pdb=" N LEU A 594 " --> pdb=" O LEU A 611 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N LYS A 598 " --> pdb=" O PRO A 607 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N GLU A 600 " --> pdb=" O VAL A 605 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N VAL A 605 " --> pdb=" O GLU A 600 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 624 through 625 Processing sheet with id=AA9, first strand: chain 'A' and resid 624 through 625 removed outlier: 5.522A pdb=" N ILE A 653 " --> pdb=" O GLU A 668 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N GLU A 668 " --> pdb=" O ILE A 653 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N SER A 655 " --> pdb=" O VAL A 666 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N VAL A 666 " --> pdb=" O SER A 655 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N ASP A 657 " --> pdb=" O GLN A 664 " (cutoff:3.500A) removed outlier: 9.032A pdb=" N GLN A 664 " --> pdb=" O ASP A 657 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 674 through 680 removed outlier: 3.811A pdb=" N GLN A 676 " --> pdb=" O ARG A 689 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N TRP A 688 " --> pdb=" O TRP A 695 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N SER A 693 " --> pdb=" O ASN A 690 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LEU A 694 " --> pdb=" O LEU A 707 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 716 through 719 removed outlier: 3.642A pdb=" N GLN A 719 " --> pdb=" O ILE A 724 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ILE A 724 " --> pdb=" O GLN A 719 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 770 through 772 Processing sheet with id=AB4, first strand: chain 'A' and resid 829 through 835 removed outlier: 5.556A pdb=" N SER A 830 " --> pdb=" O LYS A 845 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LYS A 845 " --> pdb=" O SER A 830 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 874 through 881 removed outlier: 3.770A pdb=" N ASN A 880 " --> pdb=" O TYR A 863 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N TYR A 863 " --> pdb=" O ASN A 880 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU A 899 " --> pdb=" O LEU A 917 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N LEU A 917 " --> pdb=" O LEU A 899 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 949 through 950 removed outlier: 7.474A pdb=" N ARG A 928 " --> pdb=" O LEU A1183 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N LEU A1183 " --> pdb=" O ARG A 928 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ARG A 930 " --> pdb=" O LEU A1181 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N LEU A1181 " --> pdb=" O ARG A 930 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ALA A 932 " --> pdb=" O SER A1179 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 963 through 964 Processing sheet with id=AB8, first strand: chain 'A' and resid 1000 through 1006 removed outlier: 4.525A pdb=" N SER A1002 " --> pdb=" O THR A1015 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL A1022 " --> pdb=" O LEU A1035 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1042 through 1045 removed outlier: 7.111A pdb=" N ARG A1062 " --> pdb=" O THR A1072 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N THR A1072 " --> pdb=" O ARG A1062 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1082 through 1089 removed outlier: 6.890A pdb=" N LEU A1098 " --> pdb=" O ALA A1084 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N PHE A1086 " --> pdb=" O PHE A1096 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N PHE A1096 " --> pdb=" O PHE A1086 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N LEU A1088 " --> pdb=" O GLN A1094 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N GLN A1094 " --> pdb=" O LEU A1088 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TRP A1097 " --> pdb=" O TYR A1108 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N LEU A1105 " --> pdb=" O GLN A1124 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLN A1124 " --> pdb=" O LEU A1105 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N LEU A1107 " --> pdb=" O ILE A1122 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 1131 through 1139 removed outlier: 6.651A pdb=" N SER A1135 " --> pdb=" O LEU A1148 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU A1148 " --> pdb=" O SER A1135 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N ARG A1154 " --> pdb=" O GLU A1149 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 1217 through 1219 Processing sheet with id=AC4, first strand: chain 'A' and resid 1242 through 1248 Processing sheet with id=AC5, first strand: chain 'A' and resid 1299 through 1305 removed outlier: 6.769A pdb=" N VAL A1314 " --> pdb=" O HIS A1363 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N HIS A1363 " --> pdb=" O VAL A1314 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 1345 through 1354 removed outlier: 6.885A pdb=" N CYS A1340 " --> pdb=" O HIS A1347 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N GLU A1349 " --> pdb=" O ILE A1338 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ILE A1338 " --> pdb=" O GLU A1349 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ARG A1351 " --> pdb=" O TYR A1336 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N TYR A1336 " --> pdb=" O ARG A1351 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N ASN A1353 " --> pdb=" O LEU A1334 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N LEU A1334 " --> pdb=" O ASN A1353 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N VAL A1378 " --> pdb=" O ALA A1384 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N ALA A1384 " --> pdb=" O VAL A1378 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ASP B 388 " --> pdb=" O VAL B 392 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N VAL B 392 " --> pdb=" O ASP B 388 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N LEU B 329 " --> pdb=" O ILE B 395 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 1421 through 1422 Processing sheet with id=AC8, first strand: chain 'A' and resid 1421 through 1422 Processing sheet with id=AC9, first strand: chain 'A' and resid 1432 through 1438 removed outlier: 6.771A pdb=" N VAL A1447 " --> pdb=" O GLU A1433 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N LEU A1435 " --> pdb=" O LEU A1445 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N LEU A1445 " --> pdb=" O LEU A1435 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N GLY A1437 " --> pdb=" O ARG A1443 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ARG A1443 " --> pdb=" O GLY A1437 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N GLU A1452 " --> pdb=" O ASN A1448 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LEU A1453 " --> pdb=" O LEU A1465 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 1472 through 1478 removed outlier: 6.888A pdb=" N VAL A1472 " --> pdb=" O LEU A1489 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU A1489 " --> pdb=" O VAL A1472 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ALA A1474 " --> pdb=" O ALA A1487 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N TRP A1518 " --> pdb=" O ILE A1499 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ARG A1501 " --> pdb=" O ARG A1516 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N ARG A1516 " --> pdb=" O ARG A1501 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 1524 through 1525 Processing sheet with id=AD3, first strand: chain 'A' and resid 1524 through 1525 removed outlier: 4.134A pdb=" N GLU A1544 " --> pdb=" O ASN A1550 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ASN A1550 " --> pdb=" O GLU A1544 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 1572 through 1577 removed outlier: 3.554A pdb=" N ARG A1574 " --> pdb=" O VAL A1590 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N VAL A1598 " --> pdb=" O THR A1607 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 1627 through 1629 removed outlier: 6.119A pdb=" N GLY A1646 " --> pdb=" O LEU A1652 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N LEU A1652 " --> pdb=" O GLY A1646 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A' and resid 1702 through 1703 Processing sheet with id=AD7, first strand: chain 'A' and resid 1745 through 1750 removed outlier: 3.714A pdb=" N GLY A1745 " --> pdb=" O LEU A1726 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU A1785 " --> pdb=" O LEU A1772 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'A' and resid 1745 through 1750 removed outlier: 3.714A pdb=" N GLY A1745 " --> pdb=" O LEU A1726 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'A' and resid 1803 through 1811 removed outlier: 5.301A pdb=" N ASN A1804 " --> pdb=" O LEU A1820 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N LEU A1820 " --> pdb=" O ASN A1804 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N GLU A1814 " --> pdb=" O LEU A1810 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'A' and resid 1856 through 1858 removed outlier: 3.901A pdb=" N ASN A1889 " --> pdb=" O ALA A1881 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'A' and resid 1856 through 1858 Processing sheet with id=AE3, first strand: chain 'A' and resid 1906 through 1910 removed outlier: 6.593A pdb=" N SER A1916 " --> pdb=" O LEU A1908 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'A' and resid 1984 through 1987 removed outlier: 4.038A pdb=" N GLN A1939 " --> pdb=" O ARG B1941 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ARG B1941 " --> pdb=" O GLN A1939 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG A1941 " --> pdb=" O GLN B1939 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLN B1939 " --> pdb=" O ARG A1941 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 380 through 381 Processing sheet with id=AE6, first strand: chain 'B' and resid 380 through 381 Processing sheet with id=AE7, first strand: chain 'B' and resid 443 through 447 removed outlier: 3.578A pdb=" N LEU B 454 " --> pdb=" O PHE B 497 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 484 through 489 removed outlier: 6.759A pdb=" N TYR B 506 " --> pdb=" O PHE B 525 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N PHE B 525 " --> pdb=" O TYR B 506 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N LEU B 508 " --> pdb=" O LYS B 523 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N LYS B 523 " --> pdb=" O LEU B 508 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N LEU B 510 " --> pdb=" O VAL B 521 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N VAL B 521 " --> pdb=" O LEU B 510 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N MET B 512 " --> pdb=" O GLY B 519 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 563 through 568 removed outlier: 6.356A pdb=" N ASN B 563 " --> pdb=" O SER B 556 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N SER B 556 " --> pdb=" O ASN B 563 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N MET B 565 " --> pdb=" O TRP B 554 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N TRP B 554 " --> pdb=" O MET B 565 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 573 through 578 removed outlier: 4.162A pdb=" N LEU B 594 " --> pdb=" O LEU B 611 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N LYS B 598 " --> pdb=" O PRO B 607 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N GLU B 600 " --> pdb=" O VAL B 605 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N VAL B 605 " --> pdb=" O GLU B 600 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'B' and resid 624 through 625 Processing sheet with id=AF3, first strand: chain 'B' and resid 624 through 625 removed outlier: 3.525A pdb=" N GLN B 652 " --> pdb=" O MET B 641 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N ILE B 653 " --> pdb=" O GLU B 668 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N GLU B 668 " --> pdb=" O ILE B 653 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N SER B 655 " --> pdb=" O VAL B 666 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N VAL B 666 " --> pdb=" O SER B 655 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N ASP B 657 " --> pdb=" O GLN B 664 " (cutoff:3.500A) removed outlier: 9.048A pdb=" N GLN B 664 " --> pdb=" O ASP B 657 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'B' and resid 674 through 680 removed outlier: 3.815A pdb=" N GLN B 676 " --> pdb=" O ARG B 689 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N TRP B 688 " --> pdb=" O TRP B 695 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER B 693 " --> pdb=" O ASN B 690 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LEU B 694 " --> pdb=" O LEU B 707 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'B' and resid 716 through 719 removed outlier: 3.627A pdb=" N GLN B 719 " --> pdb=" O ILE B 724 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE B 724 " --> pdb=" O GLN B 719 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N PHE B 735 " --> pdb=" O LEU B 748 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU B 748 " --> pdb=" O PHE B 735 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'B' and resid 770 through 772 Processing sheet with id=AF7, first strand: chain 'B' and resid 829 through 835 removed outlier: 5.569A pdb=" N SER B 830 " --> pdb=" O LYS B 845 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LYS B 845 " --> pdb=" O SER B 830 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'B' and resid 874 through 881 removed outlier: 3.758A pdb=" N ASN B 880 " --> pdb=" O TYR B 863 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N TYR B 863 " --> pdb=" O ASN B 880 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU B 899 " --> pdb=" O LEU B 917 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LEU B 917 " --> pdb=" O LEU B 899 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'B' and resid 949 through 950 removed outlier: 7.550A pdb=" N ARG B 928 " --> pdb=" O LEU B1183 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N LEU B1183 " --> pdb=" O ARG B 928 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ARG B 930 " --> pdb=" O LEU B1181 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N LEU B1181 " --> pdb=" O ARG B 930 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ALA B 932 " --> pdb=" O SER B1179 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'B' and resid 963 through 964 Processing sheet with id=AG2, first strand: chain 'B' and resid 1000 through 1006 removed outlier: 4.538A pdb=" N SER B1002 " --> pdb=" O THR B1015 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR B1015 " --> pdb=" O SER B1002 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL B1022 " --> pdb=" O LEU B1035 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'B' and resid 1042 through 1045 removed outlier: 7.091A pdb=" N ARG B1062 " --> pdb=" O THR B1072 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N THR B1072 " --> pdb=" O ARG B1062 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'B' and resid 1082 through 1089 removed outlier: 6.894A pdb=" N LEU B1098 " --> pdb=" O ALA B1084 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N PHE B1086 " --> pdb=" O PHE B1096 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N PHE B1096 " --> pdb=" O PHE B1086 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N LEU B1088 " --> pdb=" O GLN B1094 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N GLN B1094 " --> pdb=" O LEU B1088 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N TRP B1097 " --> pdb=" O TYR B1108 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN B1123 " --> pdb=" O LEU B1107 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ARG B1109 " --> pdb=" O MET B1121 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N MET B1121 " --> pdb=" O ARG B1109 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'B' and resid 1131 through 1139 removed outlier: 6.576A pdb=" N SER B1135 " --> pdb=" O LEU B1148 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LEU B1148 " --> pdb=" O SER B1135 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N ARG B1154 " --> pdb=" O GLU B1149 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'B' and resid 1217 through 1219 Processing sheet with id=AG7, first strand: chain 'B' and resid 1242 through 1248 Processing sheet with id=AG8, first strand: chain 'B' and resid 1299 through 1305 Processing sheet with id=AG9, first strand: chain 'B' and resid 1421 through 1422 Processing sheet with id=AH1, first strand: chain 'B' and resid 1421 through 1422 Processing sheet with id=AH2, first strand: chain 'B' and resid 1432 through 1438 removed outlier: 6.778A pdb=" N VAL B1447 " --> pdb=" O GLU B1433 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N LEU B1435 " --> pdb=" O LEU B1445 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N LEU B1445 " --> pdb=" O LEU B1435 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N GLY B1437 " --> pdb=" O ARG B1443 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ARG B1443 " --> pdb=" O GLY B1437 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N GLU B1452 " --> pdb=" O ASN B1448 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LEU B1453 " --> pdb=" O LEU B1465 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'B' and resid 1472 through 1478 removed outlier: 6.812A pdb=" N VAL B1472 " --> pdb=" O LEU B1489 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LEU B1489 " --> pdb=" O VAL B1472 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ALA B1474 " --> pdb=" O ALA B1487 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N ALA B1497 " --> pdb=" O SER B1519 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N SER B1519 " --> pdb=" O ALA B1497 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N ILE B1499 " --> pdb=" O VAL B1517 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'B' and resid 1524 through 1525 Processing sheet with id=AH5, first strand: chain 'B' and resid 1524 through 1525 removed outlier: 4.108A pdb=" N GLU B1544 " --> pdb=" O ASN B1550 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ASN B1550 " --> pdb=" O GLU B1544 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'B' and resid 1572 through 1577 removed outlier: 3.675A pdb=" N ARG B1574 " --> pdb=" O VAL B1590 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N VAL B1598 " --> pdb=" O THR B1607 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'B' and resid 1627 through 1629 removed outlier: 6.114A pdb=" N GLY B1646 " --> pdb=" O LEU B1652 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N LEU B1652 " --> pdb=" O GLY B1646 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'B' and resid 1702 through 1703 Processing sheet with id=AH9, first strand: chain 'B' and resid 1745 through 1750 removed outlier: 3.694A pdb=" N GLY B1745 " --> pdb=" O LEU B1726 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU B1785 " --> pdb=" O LEU B1772 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'B' and resid 1745 through 1750 removed outlier: 3.694A pdb=" N GLY B1745 " --> pdb=" O LEU B1726 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'B' and resid 1806 through 1811 removed outlier: 6.535A pdb=" N GLU B1814 " --> pdb=" O LEU B1810 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'B' and resid 1856 through 1858 removed outlier: 3.849A pdb=" N ASN B1889 " --> pdb=" O ALA B1881 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'B' and resid 1856 through 1858 Processing sheet with id=AI5, first strand: chain 'B' and resid 1906 through 1910 removed outlier: 6.586A pdb=" N SER B1916 " --> pdb=" O LEU B1908 " (cutoff:3.500A) 975 hydrogen bonds defined for protein. 2562 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: 8.24 Time building geometry restraints manager: 2.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 8275 1.34 - 1.46: 6057 1.46 - 1.59: 11816 1.59 - 1.71: 2 1.71 - 1.83: 128 Bond restraints: 26278 Sorted by residual: bond pdb=" C ALA A1291 " pdb=" N PRO A1292 " ideal model delta sigma weight residual 1.331 1.420 -0.089 1.28e-02 6.10e+03 4.80e+01 bond pdb=" C ALA B1291 " pdb=" N PRO B1292 " ideal model delta sigma weight residual 1.331 1.418 -0.087 1.28e-02 6.10e+03 4.59e+01 bond pdb=" CB ASN B1804 " pdb=" CG ASN B1804 " ideal model delta sigma weight residual 1.516 1.617 -0.101 2.50e-02 1.60e+03 1.64e+01 bond pdb=" C GLU A1581 " pdb=" N PRO A1582 " ideal model delta sigma weight residual 1.333 1.368 -0.035 1.01e-02 9.80e+03 1.18e+01 bond pdb=" CA SER A1315 " pdb=" CB SER A1315 " ideal model delta sigma weight residual 1.536 1.475 0.060 2.08e-02 2.31e+03 8.44e+00 ... (remaining 26273 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.90: 35138 3.90 - 7.81: 583 7.81 - 11.71: 76 11.71 - 15.62: 10 15.62 - 19.52: 5 Bond angle restraints: 35812 Sorted by residual: angle pdb=" C GLU A 642 " pdb=" N SER A 643 " pdb=" CA SER A 643 " ideal model delta sigma weight residual 122.28 136.05 -13.77 1.77e+00 3.19e-01 6.05e+01 angle pdb=" C ARG A 957 " pdb=" N LEU A 958 " pdb=" CA LEU A 958 " ideal model delta sigma weight residual 122.83 129.54 -6.71 1.08e+00 8.57e-01 3.86e+01 angle pdb=" C ARG B 957 " pdb=" N LEU B 958 " pdb=" CA LEU B 958 " ideal model delta sigma weight residual 122.83 129.53 -6.70 1.08e+00 8.57e-01 3.85e+01 angle pdb=" N ASN B 505 " pdb=" CA ASN B 505 " pdb=" CB ASN B 505 " ideal model delta sigma weight residual 110.41 120.11 -9.70 1.63e+00 3.76e-01 3.54e+01 angle pdb=" C ALA B1308 " pdb=" N LEU B1309 " pdb=" CA LEU B1309 " ideal model delta sigma weight residual 122.40 130.69 -8.29 1.45e+00 4.76e-01 3.27e+01 ... (remaining 35807 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.68: 15029 20.68 - 41.36: 1009 41.36 - 62.03: 106 62.03 - 82.71: 32 82.71 - 103.39: 4 Dihedral angle restraints: 16180 sinusoidal: 6620 harmonic: 9560 Sorted by residual: dihedral pdb=" CA ALA A1493 " pdb=" C ALA A1493 " pdb=" N PRO A1494 " pdb=" CA PRO A1494 " ideal model delta harmonic sigma weight residual 180.00 142.12 37.88 0 5.00e+00 4.00e-02 5.74e+01 dihedral pdb=" CA ALA B1493 " pdb=" C ALA B1493 " pdb=" N PRO B1494 " pdb=" CA PRO B1494 " ideal model delta harmonic sigma weight residual 180.00 142.12 37.88 0 5.00e+00 4.00e-02 5.74e+01 dihedral pdb=" CA LEU B1755 " pdb=" C LEU B1755 " pdb=" N ASN B1756 " pdb=" CA ASN B1756 " ideal model delta harmonic sigma weight residual 180.00 -148.70 -31.30 0 5.00e+00 4.00e-02 3.92e+01 ... (remaining 16177 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.180: 3961 0.180 - 0.360: 87 0.360 - 0.540: 15 0.540 - 0.720: 2 0.720 - 0.900: 1 Chirality restraints: 4066 Sorted by residual: chirality pdb=" C1 NAG B2607 " pdb=" ND2 ASN B 505 " pdb=" C2 NAG B2607 " pdb=" O5 NAG B2607 " both_signs ideal model delta sigma weight residual False -2.40 -1.50 -0.90 2.00e-01 2.50e+01 2.02e+01 chirality pdb=" C2 NAG B2610 " pdb=" C1 NAG B2610 " pdb=" C3 NAG B2610 " pdb=" N2 NAG B2610 " both_signs ideal model delta sigma weight residual False -2.49 -1.95 -0.54 2.00e-01 2.50e+01 7.38e+00 chirality pdb=" C2 NAG A2609 " pdb=" C1 NAG A2609 " pdb=" C3 NAG A2609 " pdb=" N2 NAG A2609 " both_signs ideal model delta sigma weight residual False -2.49 -1.95 -0.54 2.00e-01 2.50e+01 7.35e+00 ... (remaining 4063 not shown) Planarity restraints: 4686 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A2610 " 0.355 2.00e-02 2.50e+03 3.06e-01 1.17e+03 pdb=" C7 NAG A2610 " -0.085 2.00e-02 2.50e+03 pdb=" C8 NAG A2610 " 0.075 2.00e-02 2.50e+03 pdb=" N2 NAG A2610 " -0.540 2.00e-02 2.50e+03 pdb=" O7 NAG A2610 " 0.195 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B2605 " -0.345 2.00e-02 2.50e+03 2.95e-01 1.09e+03 pdb=" C7 NAG B2605 " 0.087 2.00e-02 2.50e+03 pdb=" C8 NAG B2605 " -0.167 2.00e-02 2.50e+03 pdb=" N2 NAG B2605 " 0.521 2.00e-02 2.50e+03 pdb=" O7 NAG B2605 " -0.096 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 505 " 0.072 2.00e-02 2.50e+03 6.81e-02 5.81e+01 pdb=" CG ASN B 505 " -0.081 2.00e-02 2.50e+03 pdb=" OD1 ASN B 505 " 0.015 2.00e-02 2.50e+03 pdb=" ND2 ASN B 505 " -0.078 2.00e-02 2.50e+03 pdb=" C1 NAG B2607 " 0.072 2.00e-02 2.50e+03 ... (remaining 4683 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 8359 2.86 - 3.37: 19192 3.37 - 3.88: 43743 3.88 - 4.39: 46302 4.39 - 4.90: 82316 Nonbonded interactions: 199912 Sorted by model distance: nonbonded pdb=" O GLN A 278 " pdb=" OG1 THR A1245 " model vdw 2.355 3.040 nonbonded pdb=" OG SER A 739 " pdb=" OD1 ASP A 741 " model vdw 2.358 3.040 nonbonded pdb=" OG SER B 739 " pdb=" OD1 ASP B 741 " model vdw 2.358 3.040 nonbonded pdb=" OG SER A1225 " pdb=" O GLY A1227 " model vdw 2.374 3.040 nonbonded pdb=" O LEU B1761 " pdb=" OG1 THR B1794 " model vdw 2.374 3.040 ... (remaining 199907 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 11.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.500 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 25.540 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.060 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: 0.010 Load rotamer database and sin/cos tables:1.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 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 : 0.007 0.101 26328 Z= 0.338 Angle : 1.293 27.350 35942 Z= 0.659 Chirality : 0.073 0.900 4066 Planarity : 0.012 0.306 4662 Dihedral : 13.620 103.387 9928 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 1.83 % Cis-general : 0.00 % Twisted Proline : 0.92 % Twisted General : 0.07 % 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 aren not related in a simple way. whole: -1.97 (0.13), residues: 3236 helix: -3.79 (0.22), residues: 194 sheet: -0.35 (0.14), residues: 1378 loop : -1.84 (0.12), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.001 ARG A 890 TYR 0.073 0.003 TYR B 385 PHE 0.035 0.004 PHE A1086 TRP 0.067 0.003 TRP A 554 HIS 0.013 0.002 HIS A1390 Details of bonding type rmsd covalent geometry : bond 0.00712 (26278) covalent geometry : angle 1.23925 (35812) SS BOND : bond 0.00667 ( 20) SS BOND : angle 1.72303 ( 40) hydrogen bonds : bond 0.13217 ( 897) hydrogen bonds : angle 7.48618 ( 2562) link_BETA1-4 : bond 0.00762 ( 4) link_BETA1-4 : angle 2.29446 ( 12) link_BETA1-6 : bond 0.00737 ( 2) link_BETA1-6 : angle 1.64519 ( 6) link_NAG-ASN : bond 0.01976 ( 24) link_NAG-ASN : angle 8.24492 ( 72) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6472 Ramachandran restraints generated. 3236 Oldfield, 0 Emsley, 3236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6472 Ramachandran restraints generated. 3236 Oldfield, 0 Emsley, 3236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 0.967 Fit side-chains REVERT: A 641 MET cc_start: 0.4303 (tpp) cc_final: 0.3746 (tpp) REVERT: A 688 TRP cc_start: 0.7726 (p90) cc_final: 0.7465 (p90) REVERT: A 715 TRP cc_start: 0.7476 (t60) cc_final: 0.7089 (t60) REVERT: A 913 TRP cc_start: 0.7012 (m100) cc_final: 0.6440 (m100) REVERT: A 1181 LEU cc_start: 0.8822 (tt) cc_final: 0.8578 (tp) REVERT: A 1584 SER cc_start: 0.8933 (m) cc_final: 0.8579 (t) REVERT: A 1702 LEU cc_start: 0.9117 (tp) cc_final: 0.8841 (tt) REVERT: B 386 ASP cc_start: 0.7966 (m-30) cc_final: 0.7491 (t0) REVERT: B 688 TRP cc_start: 0.7643 (p90) cc_final: 0.6704 (p90) REVERT: B 895 ASN cc_start: 0.7973 (t0) cc_final: 0.7674 (t0) REVERT: B 913 TRP cc_start: 0.6645 (m100) cc_final: 0.6155 (m100) REVERT: B 1702 LEU cc_start: 0.9004 (tp) cc_final: 0.8730 (tt) outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.1436 time to fit residues: 37.4129 Evaluate side-chains 104 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 0.6980 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 20.0000 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 2.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 445 HIS A 983 ASN A1371 HIS ** A1399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1746 GLN B 445 HIS ** B 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 895 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1241 GLN ** B1399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1746 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.077254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.054424 restraints weight = 97486.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.054782 restraints weight = 60418.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.054829 restraints weight = 43756.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.055079 restraints weight = 39222.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.055260 restraints weight = 35021.106| |-----------------------------------------------------------------------------| r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.1228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 26328 Z= 0.190 Angle : 0.663 16.104 35942 Z= 0.323 Chirality : 0.043 0.327 4066 Planarity : 0.005 0.048 4662 Dihedral : 6.931 106.932 4200 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.04 % Allowed : 3.11 % Favored : 96.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.83 % 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 aren not related in a simple way. whole: -1.21 (0.14), residues: 3236 helix: -1.07 (0.33), residues: 206 sheet: -0.13 (0.14), residues: 1372 loop : -1.33 (0.13), residues: 1658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 890 TYR 0.014 0.001 TYR A1543 PHE 0.013 0.001 PHE B 639 TRP 0.020 0.001 TRP B 554 HIS 0.005 0.001 HIS A 829 Details of bonding type rmsd covalent geometry : bond 0.00417 (26278) covalent geometry : angle 0.61764 (35812) SS BOND : bond 0.00341 ( 20) SS BOND : angle 1.09769 ( 40) hydrogen bonds : bond 0.03505 ( 897) hydrogen bonds : angle 5.88804 ( 2562) link_BETA1-4 : bond 0.00292 ( 4) link_BETA1-4 : angle 2.05004 ( 12) link_BETA1-6 : bond 0.00278 ( 2) link_BETA1-6 : angle 1.84473 ( 6) link_NAG-ASN : bond 0.00677 ( 24) link_NAG-ASN : angle 5.28680 ( 72) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6472 Ramachandran restraints generated. 3236 Oldfield, 0 Emsley, 3236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6472 Ramachandran restraints generated. 3236 Oldfield, 0 Emsley, 3236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 124 time to evaluate : 0.630 Fit side-chains REVERT: A 715 TRP cc_start: 0.7512 (t60) cc_final: 0.6970 (t60) REVERT: A 1121 MET cc_start: 0.8703 (tpp) cc_final: 0.8024 (tmm) REVERT: A 1584 SER cc_start: 0.9109 (m) cc_final: 0.8744 (t) REVERT: A 1702 LEU cc_start: 0.9107 (tp) cc_final: 0.8872 (tt) REVERT: B 688 TRP cc_start: 0.7751 (p90) cc_final: 0.6750 (p90) REVERT: B 895 ASN cc_start: 0.8084 (t0) cc_final: 0.7667 (t0) REVERT: B 1121 MET cc_start: 0.8398 (tmm) cc_final: 0.7779 (tmm) REVERT: B 1702 LEU cc_start: 0.9123 (tp) cc_final: 0.8885 (tt) outliers start: 1 outliers final: 0 residues processed: 125 average time/residue: 0.1412 time to fit residues: 29.2214 Evaluate side-chains 98 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 153 optimal weight: 7.9990 chunk 268 optimal weight: 0.0970 chunk 237 optimal weight: 10.0000 chunk 280 optimal weight: 0.9980 chunk 164 optimal weight: 20.0000 chunk 203 optimal weight: 3.9990 chunk 235 optimal weight: 3.9990 chunk 145 optimal weight: 2.9990 chunk 53 optimal weight: 0.2980 chunk 20 optimal weight: 9.9990 chunk 12 optimal weight: 0.6980 overall best weight: 1.0180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 445 HIS A1124 GLN A1448 ASN B 445 HIS ** B 895 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1371 HIS B1588 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.077373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.053982 restraints weight = 97815.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.055142 restraints weight = 55106.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.055377 restraints weight = 34156.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.055598 restraints weight = 32733.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.055623 restraints weight = 28623.277| |-----------------------------------------------------------------------------| r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 26328 Z= 0.140 Angle : 0.601 13.907 35942 Z= 0.291 Chirality : 0.043 0.299 4066 Planarity : 0.004 0.044 4662 Dihedral : 6.341 106.172 4200 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.04 % Allowed : 2.64 % Favored : 97.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.83 % 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 aren not related in a simple way. whole: -0.76 (0.14), residues: 3236 helix: 0.41 (0.36), residues: 208 sheet: -0.05 (0.14), residues: 1418 loop : -0.99 (0.14), residues: 1610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 890 TYR 0.012 0.001 TYR A 341 PHE 0.024 0.001 PHE A1239 TRP 0.019 0.001 TRP B 554 HIS 0.004 0.001 HIS B1450 Details of bonding type rmsd covalent geometry : bond 0.00309 (26278) covalent geometry : angle 0.56894 (35812) SS BOND : bond 0.00821 ( 20) SS BOND : angle 0.84373 ( 40) hydrogen bonds : bond 0.03048 ( 897) hydrogen bonds : angle 5.37595 ( 2562) link_BETA1-4 : bond 0.00367 ( 4) link_BETA1-4 : angle 1.87779 ( 12) link_BETA1-6 : bond 0.00244 ( 2) link_BETA1-6 : angle 1.59111 ( 6) link_NAG-ASN : bond 0.00725 ( 24) link_NAG-ASN : angle 4.28762 ( 72) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6472 Ramachandran restraints generated. 3236 Oldfield, 0 Emsley, 3236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6472 Ramachandran restraints generated. 3236 Oldfield, 0 Emsley, 3236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 132 time to evaluate : 1.028 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 565 MET cc_start: 0.8106 (tpp) cc_final: 0.7765 (tpp) REVERT: A 1584 SER cc_start: 0.9146 (m) cc_final: 0.8784 (t) REVERT: B 688 TRP cc_start: 0.7770 (p90) cc_final: 0.6646 (p90) REVERT: B 895 ASN cc_start: 0.8129 (t0) cc_final: 0.7655 (t0) REVERT: B 964 MET cc_start: 0.8929 (mmm) cc_final: 0.8726 (mmm) REVERT: B 1121 MET cc_start: 0.8399 (tmm) cc_final: 0.7776 (tmm) outliers start: 1 outliers final: 0 residues processed: 133 average time/residue: 0.1530 time to fit residues: 32.7869 Evaluate side-chains 92 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 10 optimal weight: 3.9990 chunk 195 optimal weight: 6.9990 chunk 139 optimal weight: 0.8980 chunk 37 optimal weight: 0.2980 chunk 1 optimal weight: 0.1980 chunk 179 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 322 optimal weight: 50.0000 chunk 186 optimal weight: 10.0000 chunk 58 optimal weight: 9.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 445 HIS ** A1264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1399 GLN ** A1629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 445 HIS ** B 895 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1390 HIS B1399 GLN B1448 ASN B1513 GLN B1723 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.076532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.053309 restraints weight = 96992.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.054185 restraints weight = 53919.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.054592 restraints weight = 35323.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.054793 restraints weight = 31784.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.054824 restraints weight = 27776.819| |-----------------------------------------------------------------------------| r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 26328 Z= 0.181 Angle : 0.607 12.272 35942 Z= 0.293 Chirality : 0.043 0.293 4066 Planarity : 0.004 0.045 4662 Dihedral : 6.208 105.301 4200 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.83 % 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 aren not related in a simple way. whole: -0.57 (0.14), residues: 3236 helix: 1.17 (0.38), residues: 208 sheet: -0.11 (0.14), residues: 1428 loop : -0.76 (0.15), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 627 TYR 0.013 0.001 TYR B1599 PHE 0.016 0.001 PHE A1086 TRP 0.021 0.001 TRP A 554 HIS 0.004 0.001 HIS A 829 Details of bonding type rmsd covalent geometry : bond 0.00407 (26278) covalent geometry : angle 0.57936 (35812) SS BOND : bond 0.00385 ( 20) SS BOND : angle 1.02350 ( 40) hydrogen bonds : bond 0.02965 ( 897) hydrogen bonds : angle 5.25367 ( 2562) link_BETA1-4 : bond 0.00149 ( 4) link_BETA1-4 : angle 1.93975 ( 12) link_BETA1-6 : bond 0.00334 ( 2) link_BETA1-6 : angle 1.70769 ( 6) link_NAG-ASN : bond 0.00639 ( 24) link_NAG-ASN : angle 3.97780 ( 72) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6472 Ramachandran restraints generated. 3236 Oldfield, 0 Emsley, 3236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6472 Ramachandran restraints generated. 3236 Oldfield, 0 Emsley, 3236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.696 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 565 MET cc_start: 0.8179 (tpp) cc_final: 0.7846 (tpp) REVERT: A 964 MET cc_start: 0.8920 (mmm) cc_final: 0.8718 (mmm) REVERT: B 895 ASN cc_start: 0.8175 (t0) cc_final: 0.7687 (t0) REVERT: B 964 MET cc_start: 0.8937 (mmm) cc_final: 0.8703 (mmm) outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.1495 time to fit residues: 30.4187 Evaluate side-chains 89 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 34 optimal weight: 5.9990 chunk 306 optimal weight: 4.9990 chunk 172 optimal weight: 1.9990 chunk 187 optimal weight: 5.9990 chunk 37 optimal weight: 9.9990 chunk 191 optimal weight: 8.9990 chunk 228 optimal weight: 5.9990 chunk 23 optimal weight: 7.9990 chunk 67 optimal weight: 1.9990 chunk 130 optimal weight: 0.8980 chunk 99 optimal weight: 6.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 445 HIS ** A 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 634 HIS A 683 ASN ** A 986 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 445 HIS ** B 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 683 ASN B 829 HIS ** B 986 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1124 GLN B1513 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.073847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.051529 restraints weight = 97976.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.051543 restraints weight = 59644.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.051542 restraints weight = 45819.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.051695 restraints weight = 42363.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.051876 restraints weight = 38360.120| |-----------------------------------------------------------------------------| r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.065 26328 Z= 0.346 Angle : 0.745 12.394 35942 Z= 0.362 Chirality : 0.046 0.308 4066 Planarity : 0.005 0.051 4662 Dihedral : 6.483 104.230 4200 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.83 % 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 aren not related in a simple way. whole: -0.68 (0.15), residues: 3236 helix: 1.14 (0.38), residues: 210 sheet: -0.34 (0.13), residues: 1456 loop : -0.67 (0.15), residues: 1570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 627 TYR 0.017 0.002 TYR B1599 PHE 0.021 0.002 PHE A1038 TRP 0.021 0.002 TRP B 554 HIS 0.008 0.001 HIS A 829 Details of bonding type rmsd covalent geometry : bond 0.00771 (26278) covalent geometry : angle 0.72274 (35812) SS BOND : bond 0.00608 ( 20) SS BOND : angle 1.77890 ( 40) hydrogen bonds : bond 0.03565 ( 897) hydrogen bonds : angle 5.68236 ( 2562) link_BETA1-4 : bond 0.00401 ( 4) link_BETA1-4 : angle 2.37484 ( 12) link_BETA1-6 : bond 0.00686 ( 2) link_BETA1-6 : angle 1.93085 ( 6) link_NAG-ASN : bond 0.00784 ( 24) link_NAG-ASN : angle 3.81867 ( 72) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6472 Ramachandran restraints generated. 3236 Oldfield, 0 Emsley, 3236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6472 Ramachandran restraints generated. 3236 Oldfield, 0 Emsley, 3236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 1.001 Fit side-chains revert: symmetry clash REVERT: A 565 MET cc_start: 0.8235 (tpp) cc_final: 0.7826 (tpp) REVERT: A 728 MET cc_start: 0.6704 (mmm) cc_final: 0.6132 (mmm) REVERT: A 964 MET cc_start: 0.8952 (mmm) cc_final: 0.8707 (mmm) REVERT: B 447 MET cc_start: 0.7445 (pmm) cc_final: 0.6924 (pmm) REVERT: B 600 GLU cc_start: 0.6559 (tm-30) cc_final: 0.6319 (tm-30) outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.1516 time to fit residues: 29.5828 Evaluate side-chains 85 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 6 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 114 optimal weight: 0.8980 chunk 28 optimal weight: 20.0000 chunk 315 optimal weight: 8.9990 chunk 244 optimal weight: 0.6980 chunk 202 optimal weight: 5.9990 chunk 293 optimal weight: 0.9980 chunk 258 optimal weight: 0.0050 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 445 HIS ** A1629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 445 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.075792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.052529 restraints weight = 97422.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.053531 restraints weight = 53854.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.053891 restraints weight = 34923.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.054132 restraints weight = 30866.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.054171 restraints weight = 27516.306| |-----------------------------------------------------------------------------| r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 26328 Z= 0.120 Angle : 0.597 13.084 35942 Z= 0.287 Chirality : 0.043 0.295 4066 Planarity : 0.004 0.038 4662 Dihedral : 6.212 105.626 4200 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.83 % 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 aren not related in a simple way. whole: -0.49 (0.15), residues: 3236 helix: 1.48 (0.38), residues: 210 sheet: -0.20 (0.14), residues: 1438 loop : -0.59 (0.15), residues: 1588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1351 TYR 0.012 0.001 TYR B1599 PHE 0.012 0.001 PHE A 639 TRP 0.023 0.001 TRP A 554 HIS 0.004 0.001 HIS B 445 Details of bonding type rmsd covalent geometry : bond 0.00269 (26278) covalent geometry : angle 0.57094 (35812) SS BOND : bond 0.00662 ( 20) SS BOND : angle 1.27305 ( 40) hydrogen bonds : bond 0.02834 ( 897) hydrogen bonds : angle 5.28425 ( 2562) link_BETA1-4 : bond 0.00220 ( 4) link_BETA1-4 : angle 1.90365 ( 12) link_BETA1-6 : bond 0.00270 ( 2) link_BETA1-6 : angle 1.71546 ( 6) link_NAG-ASN : bond 0.00675 ( 24) link_NAG-ASN : angle 3.74723 ( 72) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6472 Ramachandran restraints generated. 3236 Oldfield, 0 Emsley, 3236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6472 Ramachandran restraints generated. 3236 Oldfield, 0 Emsley, 3236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 447 MET cc_start: 0.7443 (pmm) cc_final: 0.7004 (pmm) REVERT: A 565 MET cc_start: 0.8153 (tpp) cc_final: 0.7724 (tpp) REVERT: A 600 GLU cc_start: 0.6665 (tm-30) cc_final: 0.6347 (tm-30) REVERT: A 604 MET cc_start: 0.5255 (tpp) cc_final: 0.4893 (tpp) REVERT: B 447 MET cc_start: 0.7420 (pmm) cc_final: 0.6937 (pmm) REVERT: B 604 MET cc_start: 0.5180 (tpp) cc_final: 0.4832 (tpp) outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.1461 time to fit residues: 29.6182 Evaluate side-chains 92 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 101 optimal weight: 0.8980 chunk 313 optimal weight: 0.0040 chunk 144 optimal weight: 30.0000 chunk 235 optimal weight: 0.5980 chunk 189 optimal weight: 5.9990 chunk 292 optimal weight: 0.6980 chunk 206 optimal weight: 2.9990 chunk 316 optimal weight: 9.9990 chunk 142 optimal weight: 4.9990 chunk 266 optimal weight: 2.9990 chunk 310 optimal weight: 1.9990 overall best weight: 0.8394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 445 HIS A 610 GLN ** A1629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 445 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.075936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.052431 restraints weight = 96953.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.053780 restraints weight = 53541.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.054810 restraints weight = 31353.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.054914 restraints weight = 29133.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.054844 restraints weight = 22708.273| |-----------------------------------------------------------------------------| r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.2792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 26328 Z= 0.125 Angle : 0.581 12.185 35942 Z= 0.278 Chirality : 0.042 0.291 4066 Planarity : 0.004 0.036 4662 Dihedral : 5.997 105.671 4200 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.83 % 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 aren not related in a simple way. whole: -0.37 (0.15), residues: 3236 helix: 1.68 (0.38), residues: 210 sheet: -0.11 (0.14), residues: 1434 loop : -0.54 (0.16), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 626 TYR 0.011 0.001 TYR B1599 PHE 0.022 0.001 PHE B 651 TRP 0.025 0.001 TRP A 554 HIS 0.004 0.001 HIS B 445 Details of bonding type rmsd covalent geometry : bond 0.00285 (26278) covalent geometry : angle 0.55577 (35812) SS BOND : bond 0.00307 ( 20) SS BOND : angle 1.01426 ( 40) hydrogen bonds : bond 0.02756 ( 897) hydrogen bonds : angle 5.09949 ( 2562) link_BETA1-4 : bond 0.00194 ( 4) link_BETA1-4 : angle 1.74480 ( 12) link_BETA1-6 : bond 0.00232 ( 2) link_BETA1-6 : angle 1.70716 ( 6) link_NAG-ASN : bond 0.00615 ( 24) link_NAG-ASN : angle 3.66841 ( 72) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6472 Ramachandran restraints generated. 3236 Oldfield, 0 Emsley, 3236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6472 Ramachandran restraints generated. 3236 Oldfield, 0 Emsley, 3236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 447 MET cc_start: 0.7453 (pmm) cc_final: 0.6961 (pmm) REVERT: A 565 MET cc_start: 0.8132 (tpp) cc_final: 0.7839 (tpp) REVERT: A 600 GLU cc_start: 0.6637 (tm-30) cc_final: 0.6150 (tm-30) REVERT: A 604 MET cc_start: 0.5398 (tpp) cc_final: 0.5040 (tpp) REVERT: A 728 MET cc_start: 0.6952 (mmm) cc_final: 0.6406 (mmm) REVERT: A 964 MET cc_start: 0.8904 (mmm) cc_final: 0.8695 (mmm) REVERT: B 447 MET cc_start: 0.7419 (pmm) cc_final: 0.6941 (pmm) REVERT: B 604 MET cc_start: 0.5329 (tpp) cc_final: 0.4972 (tpp) REVERT: B 728 MET cc_start: 0.6851 (mmm) cc_final: 0.6293 (mmm) REVERT: B 895 ASN cc_start: 0.8030 (t0) cc_final: 0.7725 (t0) outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.1415 time to fit residues: 26.6613 Evaluate side-chains 92 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 55 optimal weight: 10.0000 chunk 182 optimal weight: 0.9980 chunk 207 optimal weight: 8.9990 chunk 275 optimal weight: 0.0370 chunk 41 optimal weight: 4.9990 chunk 209 optimal weight: 5.9990 chunk 213 optimal weight: 7.9990 chunk 18 optimal weight: 0.0970 chunk 273 optimal weight: 1.9990 chunk 169 optimal weight: 0.8980 chunk 94 optimal weight: 0.0970 overall best weight: 0.4254 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 445 HIS B 445 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.076645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.052859 restraints weight = 96458.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.054434 restraints weight = 53323.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.055476 restraints weight = 29861.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.055427 restraints weight = 24512.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.055477 restraints weight = 22192.420| |-----------------------------------------------------------------------------| r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 26328 Z= 0.095 Angle : 0.561 12.371 35942 Z= 0.268 Chirality : 0.042 0.288 4066 Planarity : 0.004 0.037 4662 Dihedral : 5.829 106.022 4200 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.83 % 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 aren not related in a simple way. whole: -0.19 (0.15), residues: 3236 helix: 2.06 (0.38), residues: 208 sheet: 0.02 (0.14), residues: 1432 loop : -0.47 (0.16), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1304 TYR 0.014 0.001 TYR B1722 PHE 0.018 0.001 PHE A1086 TRP 0.028 0.001 TRP A 554 HIS 0.004 0.000 HIS B 445 Details of bonding type rmsd covalent geometry : bond 0.00217 (26278) covalent geometry : angle 0.53684 (35812) SS BOND : bond 0.00286 ( 20) SS BOND : angle 0.93169 ( 40) hydrogen bonds : bond 0.02580 ( 897) hydrogen bonds : angle 4.86686 ( 2562) link_BETA1-4 : bond 0.00316 ( 4) link_BETA1-4 : angle 1.56661 ( 12) link_BETA1-6 : bond 0.00134 ( 2) link_BETA1-6 : angle 1.61793 ( 6) link_NAG-ASN : bond 0.00636 ( 24) link_NAG-ASN : angle 3.56356 ( 72) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6472 Ramachandran restraints generated. 3236 Oldfield, 0 Emsley, 3236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6472 Ramachandran restraints generated. 3236 Oldfield, 0 Emsley, 3236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 447 MET cc_start: 0.7547 (pmm) cc_final: 0.7070 (pmm) REVERT: A 512 MET cc_start: 0.8513 (mtp) cc_final: 0.8231 (ttm) REVERT: A 565 MET cc_start: 0.8022 (tpp) cc_final: 0.7732 (tpp) REVERT: A 600 GLU cc_start: 0.6721 (tm-30) cc_final: 0.6275 (tm-30) REVERT: A 604 MET cc_start: 0.5326 (tpp) cc_final: 0.4962 (tpp) REVERT: A 1247 ASP cc_start: 0.8557 (t70) cc_final: 0.8241 (t70) REVERT: A 1305 LEU cc_start: 0.8868 (tp) cc_final: 0.8539 (pp) REVERT: B 447 MET cc_start: 0.7543 (pmm) cc_final: 0.7047 (pmm) REVERT: B 604 MET cc_start: 0.5348 (tpp) cc_final: 0.4999 (tpp) REVERT: B 895 ASN cc_start: 0.7903 (t0) cc_final: 0.7569 (t0) REVERT: B 964 MET cc_start: 0.8889 (mmm) cc_final: 0.8564 (mmm) outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.1328 time to fit residues: 26.0214 Evaluate side-chains 98 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 27 optimal weight: 1.9990 chunk 285 optimal weight: 4.9990 chunk 23 optimal weight: 0.9990 chunk 44 optimal weight: 10.0000 chunk 49 optimal weight: 8.9990 chunk 281 optimal weight: 2.9990 chunk 210 optimal weight: 0.6980 chunk 191 optimal weight: 10.0000 chunk 145 optimal weight: 0.6980 chunk 129 optimal weight: 7.9990 chunk 186 optimal weight: 7.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 445 HIS ** A1629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 445 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.075449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.052088 restraints weight = 97887.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.053186 restraints weight = 54055.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.053631 restraints weight = 33364.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.053945 restraints weight = 29557.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.053870 restraints weight = 25422.447| |-----------------------------------------------------------------------------| r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 26328 Z= 0.178 Angle : 0.596 12.739 35942 Z= 0.285 Chirality : 0.042 0.280 4066 Planarity : 0.004 0.035 4662 Dihedral : 5.867 105.510 4200 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.83 % 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 aren not related in a simple way. whole: -0.23 (0.15), residues: 3236 helix: 1.97 (0.38), residues: 208 sheet: -0.07 (0.14), residues: 1446 loop : -0.41 (0.16), residues: 1582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1234 TYR 0.010 0.001 TYR B1599 PHE 0.027 0.001 PHE B1086 TRP 0.029 0.001 TRP A 554 HIS 0.005 0.001 HIS A 829 Details of bonding type rmsd covalent geometry : bond 0.00406 (26278) covalent geometry : angle 0.57389 (35812) SS BOND : bond 0.00293 ( 20) SS BOND : angle 1.10818 ( 40) hydrogen bonds : bond 0.02796 ( 897) hydrogen bonds : angle 4.96129 ( 2562) link_BETA1-4 : bond 0.00135 ( 4) link_BETA1-4 : angle 1.78258 ( 12) link_BETA1-6 : bond 0.00219 ( 2) link_BETA1-6 : angle 1.67124 ( 6) link_NAG-ASN : bond 0.00592 ( 24) link_NAG-ASN : angle 3.48147 ( 72) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6472 Ramachandran restraints generated. 3236 Oldfield, 0 Emsley, 3236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6472 Ramachandran restraints generated. 3236 Oldfield, 0 Emsley, 3236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.961 Fit side-chains REVERT: A 386 ASP cc_start: 0.8651 (t70) cc_final: 0.8381 (t0) REVERT: A 447 MET cc_start: 0.7499 (pmm) cc_final: 0.7025 (pmm) REVERT: A 565 MET cc_start: 0.7996 (tpp) cc_final: 0.7744 (tpp) REVERT: A 600 GLU cc_start: 0.6761 (tm-30) cc_final: 0.6556 (tm-30) REVERT: A 604 MET cc_start: 0.5520 (tpp) cc_final: 0.5168 (tpp) REVERT: A 641 MET cc_start: 0.4107 (tpp) cc_final: 0.3581 (tpp) REVERT: A 728 MET cc_start: 0.6897 (mmm) cc_final: 0.6383 (mmm) REVERT: A 1247 ASP cc_start: 0.8590 (t70) cc_final: 0.8309 (t70) REVERT: A 1305 LEU cc_start: 0.8957 (tp) cc_final: 0.8506 (pp) REVERT: B 447 MET cc_start: 0.7436 (pmm) cc_final: 0.6921 (pmm) REVERT: B 604 MET cc_start: 0.5376 (tpp) cc_final: 0.5018 (tpp) REVERT: B 728 MET cc_start: 0.6872 (mmm) cc_final: 0.6349 (mmm) REVERT: B 964 MET cc_start: 0.8911 (mmm) cc_final: 0.8686 (mmm) outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.1439 time to fit residues: 26.9394 Evaluate side-chains 94 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 17 optimal weight: 0.6980 chunk 237 optimal weight: 0.9980 chunk 288 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 59 optimal weight: 0.1980 chunk 319 optimal weight: 30.0000 chunk 192 optimal weight: 2.9990 chunk 296 optimal weight: 0.9990 chunk 28 optimal weight: 20.0000 chunk 199 optimal weight: 8.9990 chunk 236 optimal weight: 0.6980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 445 HIS B 445 HIS B 898 GLN B1241 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.076156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.053050 restraints weight = 97381.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.053870 restraints weight = 53233.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.054213 restraints weight = 34377.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.054376 restraints weight = 33215.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.054514 restraints weight = 28614.139| |-----------------------------------------------------------------------------| r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 26328 Z= 0.113 Angle : 0.575 12.304 35942 Z= 0.274 Chirality : 0.042 0.283 4066 Planarity : 0.004 0.035 4662 Dihedral : 5.912 106.175 4200 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.83 % 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 aren not related in a simple way. whole: -0.12 (0.15), residues: 3236 helix: 2.01 (0.38), residues: 210 sheet: 0.01 (0.14), residues: 1420 loop : -0.35 (0.16), residues: 1606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 210 TYR 0.012 0.001 TYR B1722 PHE 0.014 0.001 PHE B1086 TRP 0.031 0.001 TRP A 554 HIS 0.004 0.001 HIS B 445 Details of bonding type rmsd covalent geometry : bond 0.00261 (26278) covalent geometry : angle 0.55259 (35812) SS BOND : bond 0.00415 ( 20) SS BOND : angle 1.07170 ( 40) hydrogen bonds : bond 0.02593 ( 897) hydrogen bonds : angle 4.84849 ( 2562) link_BETA1-4 : bond 0.00288 ( 4) link_BETA1-4 : angle 1.56954 ( 12) link_BETA1-6 : bond 0.00096 ( 2) link_BETA1-6 : angle 1.58200 ( 6) link_NAG-ASN : bond 0.00629 ( 24) link_NAG-ASN : angle 3.43247 ( 72) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6472 Ramachandran restraints generated. 3236 Oldfield, 0 Emsley, 3236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6472 Ramachandran restraints generated. 3236 Oldfield, 0 Emsley, 3236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.791 Fit side-chains REVERT: A 447 MET cc_start: 0.7340 (pmm) cc_final: 0.6916 (pmm) REVERT: A 565 MET cc_start: 0.7922 (tpp) cc_final: 0.7707 (tpp) REVERT: A 600 GLU cc_start: 0.6701 (tm-30) cc_final: 0.6467 (tm-30) REVERT: A 604 MET cc_start: 0.5566 (tpp) cc_final: 0.5215 (tpp) REVERT: A 728 MET cc_start: 0.6987 (mmm) cc_final: 0.6464 (mmm) REVERT: A 913 TRP cc_start: 0.7455 (m100) cc_final: 0.6462 (m100) REVERT: A 1247 ASP cc_start: 0.8547 (t70) cc_final: 0.8251 (t70) REVERT: A 1305 LEU cc_start: 0.8903 (tp) cc_final: 0.8498 (pp) REVERT: B 284 MET cc_start: 0.9234 (mmm) cc_final: 0.8997 (mmm) REVERT: B 447 MET cc_start: 0.7362 (pmm) cc_final: 0.6910 (pmm) REVERT: B 728 MET cc_start: 0.6886 (mmm) cc_final: 0.6356 (mmm) REVERT: B 913 TRP cc_start: 0.7405 (m100) cc_final: 0.5700 (m100) outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.1504 time to fit residues: 29.2740 Evaluate side-chains 89 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 278 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 128 optimal weight: 4.9990 chunk 70 optimal weight: 0.0030 chunk 199 optimal weight: 5.9990 chunk 165 optimal weight: 5.9990 chunk 209 optimal weight: 5.9990 chunk 102 optimal weight: 4.9990 chunk 303 optimal weight: 2.9990 chunk 37 optimal weight: 20.0000 overall best weight: 1.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 445 HIS ** A1264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 445 HIS ** B 986 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1390 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.075023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.051732 restraints weight = 97261.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.052937 restraints weight = 53707.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.053163 restraints weight = 33350.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.053465 restraints weight = 30284.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.053479 restraints weight = 26266.756| |-----------------------------------------------------------------------------| r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.3172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 26328 Z= 0.188 Angle : 0.604 12.041 35942 Z= 0.290 Chirality : 0.043 0.272 4066 Planarity : 0.004 0.041 4662 Dihedral : 5.938 105.679 4200 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.83 % 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 aren not related in a simple way. whole: -0.19 (0.15), residues: 3236 helix: 1.96 (0.38), residues: 210 sheet: -0.06 (0.14), residues: 1444 loop : -0.36 (0.16), residues: 1582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 210 TYR 0.012 0.001 TYR A1599 PHE 0.020 0.001 PHE B1086 TRP 0.030 0.001 TRP A 554 HIS 0.005 0.001 HIS B 829 Details of bonding type rmsd covalent geometry : bond 0.00427 (26278) covalent geometry : angle 0.58354 (35812) SS BOND : bond 0.00443 ( 20) SS BOND : angle 1.25038 ( 40) hydrogen bonds : bond 0.02841 ( 897) hydrogen bonds : angle 4.97600 ( 2562) link_BETA1-4 : bond 0.00101 ( 4) link_BETA1-4 : angle 1.81340 ( 12) link_BETA1-6 : bond 0.00154 ( 2) link_BETA1-6 : angle 1.62398 ( 6) link_NAG-ASN : bond 0.00598 ( 24) link_NAG-ASN : angle 3.37020 ( 72) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3567.30 seconds wall clock time: 62 minutes 32.56 seconds (3752.56 seconds total)