Starting phenix.real_space_refine on Sun Jun 22 17:44:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bfu_44507/06_2025/9bfu_44507.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bfu_44507/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9bfu_44507/06_2025/9bfu_44507.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bfu_44507/06_2025/9bfu_44507.map" model { file = "/net/cci-nas-00/data/ceres_data/9bfu_44507/06_2025/9bfu_44507.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bfu_44507/06_2025/9bfu_44507.cif" } resolution = 4.07 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 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): 2.49s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 9, 'ASP:plan': 5, 'TYR:plan': 6, 'ASN:plan1': 1, 'TRP:plan': 6, 'HIS:plan': 5, 'PHE:plan': 2, 'GLU:plan': 18, 'ARG:plan': 17} 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: {'GLN:plan1': 9, 'ASP:plan': 5, 'TYR:plan': 6, 'ASN:plan1': 1, 'TRP:plan': 6, 'HIS:plan': 5, 'PHE:plan': 2, 'GLU:plan': 18, 'ARG:plan': 17} 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: 17.07, per 1000 atoms: 0.66 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: 5.78 Conformation dependent library (CDL) restraints added in 3.2 seconds 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: 5.57 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: 18.64 Time building geometry restraints manager: 6.99 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: 0.00 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: 10.030 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: 1.220 Check model and map are aligned: 0.200 Set scattering table: 0.250 Process input model: 70.270 Find NCS groups from input model: 0.880 Set up NCS constraints: 0.130 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.950 ------------------------------------------------------------------------------- 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 : 3.46 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (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 TRP 0.067 0.003 TRP A 554 HIS 0.013 0.002 HIS A1390 PHE 0.035 0.004 PHE A1086 TYR 0.073 0.003 TYR B 385 ARG 0.026 0.001 ARG A 890 Details of bonding type rmsd link_NAG-ASN : bond 0.01976 ( 24) link_NAG-ASN : angle 8.24492 ( 72) link_BETA1-4 : bond 0.00762 ( 4) link_BETA1-4 : angle 2.29446 ( 12) hydrogen bonds : bond 0.13217 ( 897) hydrogen bonds : angle 7.48618 ( 2562) link_BETA1-6 : bond 0.00737 ( 2) link_BETA1-6 : angle 1.64519 ( 6) SS BOND : bond 0.00667 ( 20) SS BOND : angle 1.72303 ( 40) covalent geometry : bond 0.00712 (26278) covalent geometry : angle 1.23925 (35812) *********************** 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 : 3.157 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: 0.3802 time to fit residues: 99.7438 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 : 2.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 278 optimal weight: 1.9990 chunk 250 optimal weight: 5.9990 chunk 138 optimal weight: 0.7980 chunk 85 optimal weight: 0.6980 chunk 168 optimal weight: 0.0070 chunk 133 optimal weight: 0.9990 chunk 258 optimal weight: 0.8980 chunk 100 optimal weight: 0.8980 chunk 157 optimal weight: 30.0000 chunk 192 optimal weight: 3.9990 chunk 299 optimal weight: 0.9990 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 445 HIS A1746 GLN B 445 HIS B 853 GLN ** B 895 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1588 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.078572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.055694 restraints weight = 96734.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.056348 restraints weight = 57575.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.056628 restraints weight = 38131.470| |-----------------------------------------------------------------------------| r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.1083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 26328 Z= 0.127 Angle : 0.637 16.122 35942 Z= 0.308 Chirality : 0.043 0.321 4066 Planarity : 0.005 0.050 4662 Dihedral : 6.902 107.177 4200 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.04 % Allowed : 2.83 % Favored : 97.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.14), residues: 3236 helix: -1.30 (0.32), residues: 206 sheet: -0.05 (0.14), residues: 1368 loop : -1.41 (0.13), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 554 HIS 0.005 0.001 HIS A 829 PHE 0.012 0.001 PHE A1239 TYR 0.017 0.001 TYR B 385 ARG 0.008 0.000 ARG B 890 Details of bonding type rmsd link_NAG-ASN : bond 0.00756 ( 24) link_NAG-ASN : angle 5.36214 ( 72) link_BETA1-4 : bond 0.00395 ( 4) link_BETA1-4 : angle 1.88082 ( 12) hydrogen bonds : bond 0.03370 ( 897) hydrogen bonds : angle 5.83742 ( 2562) link_BETA1-6 : bond 0.00338 ( 2) link_BETA1-6 : angle 1.72275 ( 6) SS BOND : bond 0.00308 ( 20) SS BOND : angle 0.96769 ( 40) covalent geometry : bond 0.00267 (26278) covalent geometry : angle 0.58876 (35812) *********************** 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 136 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 135 time to evaluate : 2.901 Fit side-chains revert: symmetry clash REVERT: A 715 TRP cc_start: 0.7404 (t60) cc_final: 0.6985 (t60) REVERT: A 719 GLN cc_start: 0.8296 (mp10) cc_final: 0.7605 (mp10) REVERT: A 913 TRP cc_start: 0.7180 (m100) cc_final: 0.6513 (m100) REVERT: A 1121 MET cc_start: 0.8687 (tpp) cc_final: 0.7984 (tmm) REVERT: A 1584 SER cc_start: 0.9045 (m) cc_final: 0.8694 (t) REVERT: A 1702 LEU cc_start: 0.9052 (tp) cc_final: 0.8843 (tt) REVERT: B 853 GLN cc_start: 0.8154 (OUTLIER) cc_final: 0.7895 (pm20) REVERT: B 895 ASN cc_start: 0.7978 (t0) cc_final: 0.7555 (t0) REVERT: B 1121 MET cc_start: 0.8406 (tmm) cc_final: 0.7774 (tmm) REVERT: B 1702 LEU cc_start: 0.9047 (tp) cc_final: 0.8840 (tt) outliers start: 1 outliers final: 0 residues processed: 136 average time/residue: 0.3772 time to fit residues: 84.9696 Evaluate side-chains 101 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 100 time to evaluate : 3.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 187 optimal weight: 5.9990 chunk 299 optimal weight: 0.8980 chunk 237 optimal weight: 10.0000 chunk 74 optimal weight: 2.9990 chunk 257 optimal weight: 2.9990 chunk 188 optimal weight: 4.9990 chunk 310 optimal weight: 5.9990 chunk 210 optimal weight: 0.0870 chunk 272 optimal weight: 0.0270 chunk 83 optimal weight: 0.2980 chunk 251 optimal weight: 6.9990 overall best weight: 0.8618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 445 HIS A1124 GLN A1371 HIS ** A1777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 445 HIS ** B 895 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1371 HIS ** B1777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.077948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.055197 restraints weight = 96727.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.055977 restraints weight = 53855.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.056024 restraints weight = 36087.473| |-----------------------------------------------------------------------------| r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 26328 Z= 0.129 Angle : 0.595 14.067 35942 Z= 0.287 Chirality : 0.042 0.302 4066 Planarity : 0.004 0.045 4662 Dihedral : 6.286 106.025 4200 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.04 % Allowed : 2.13 % Favored : 97.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.14), residues: 3236 helix: 0.12 (0.36), residues: 208 sheet: 0.01 (0.14), residues: 1418 loop : -1.06 (0.14), residues: 1610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 554 HIS 0.004 0.001 HIS B 340 PHE 0.022 0.001 PHE A1239 TYR 0.012 0.001 TYR A 341 ARG 0.009 0.000 ARG B 890 Details of bonding type rmsd link_NAG-ASN : bond 0.00724 ( 24) link_NAG-ASN : angle 4.29511 ( 72) link_BETA1-4 : bond 0.00270 ( 4) link_BETA1-4 : angle 1.83064 ( 12) hydrogen bonds : bond 0.03010 ( 897) hydrogen bonds : angle 5.31332 ( 2562) link_BETA1-6 : bond 0.00124 ( 2) link_BETA1-6 : angle 1.61763 ( 6) SS BOND : bond 0.00344 ( 20) SS BOND : angle 0.84680 ( 40) covalent geometry : bond 0.00287 (26278) covalent geometry : angle 0.56221 (35812) *********************** 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 : 2.844 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 565 MET cc_start: 0.8108 (tpp) cc_final: 0.7745 (tpp) REVERT: A 715 TRP cc_start: 0.7479 (t60) cc_final: 0.6902 (t60) REVERT: A 1584 SER cc_start: 0.9101 (m) cc_final: 0.8743 (t) REVERT: B 895 ASN cc_start: 0.8075 (t0) cc_final: 0.7593 (t0) REVERT: B 1121 MET cc_start: 0.8421 (tmm) cc_final: 0.7836 (tmm) REVERT: B 1406 TYR cc_start: 0.9176 (p90) cc_final: 0.8833 (p90) outliers start: 1 outliers final: 0 residues processed: 133 average time/residue: 0.3756 time to fit residues: 83.3046 Evaluate side-chains 97 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 2.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 62 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 chunk 125 optimal weight: 5.9990 chunk 95 optimal weight: 0.6980 chunk 304 optimal weight: 0.6980 chunk 81 optimal weight: 0.6980 chunk 142 optimal weight: 9.9990 chunk 28 optimal weight: 5.9990 chunk 306 optimal weight: 0.7980 chunk 83 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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** A1448 ASN B 445 HIS ** B 895 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1513 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.077925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.054587 restraints weight = 97368.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.055813 restraints weight = 53929.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.056263 restraints weight = 33309.573| |-----------------------------------------------------------------------------| r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 26328 Z= 0.115 Angle : 0.572 13.190 35942 Z= 0.273 Chirality : 0.042 0.305 4066 Planarity : 0.004 0.039 4662 Dihedral : 6.059 105.599 4200 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.14), residues: 3236 helix: 1.05 (0.38), residues: 208 sheet: 0.05 (0.14), residues: 1418 loop : -0.86 (0.14), residues: 1610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 554 HIS 0.002 0.000 HIS A 445 PHE 0.016 0.001 PHE A1239 TYR 0.011 0.001 TYR A 341 ARG 0.006 0.000 ARG B1574 Details of bonding type rmsd link_NAG-ASN : bond 0.00681 ( 24) link_NAG-ASN : angle 3.99663 ( 72) link_BETA1-4 : bond 0.00308 ( 4) link_BETA1-4 : angle 1.71900 ( 12) hydrogen bonds : bond 0.02757 ( 897) hydrogen bonds : angle 5.08732 ( 2562) link_BETA1-6 : bond 0.00153 ( 2) link_BETA1-6 : angle 1.56550 ( 6) SS BOND : bond 0.00416 ( 20) SS BOND : angle 0.88265 ( 40) covalent geometry : bond 0.00260 (26278) covalent geometry : angle 0.54225 (35812) *********************** 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 134 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 2.992 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 565 MET cc_start: 0.8127 (tpp) cc_final: 0.7799 (tpp) REVERT: A 728 MET cc_start: 0.6688 (mmm) cc_final: 0.6163 (mmm) REVERT: A 1121 MET cc_start: 0.8428 (tmm) cc_final: 0.7835 (tmm) REVERT: A 1584 SER cc_start: 0.9121 (m) cc_final: 0.8773 (t) REVERT: B 284 MET cc_start: 0.9293 (mmm) cc_final: 0.8910 (mmm) REVERT: B 728 MET cc_start: 0.6685 (mmm) cc_final: 0.6091 (mmm) REVERT: B 895 ASN cc_start: 0.8114 (t0) cc_final: 0.7646 (t0) REVERT: B 1121 MET cc_start: 0.8422 (tmm) cc_final: 0.7796 (tmm) REVERT: B 1373 GLN cc_start: 0.8746 (mm-40) cc_final: 0.8193 (mm-40) REVERT: B 1406 TYR cc_start: 0.9158 (p90) cc_final: 0.8884 (p90) outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.3920 time to fit residues: 87.6749 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 : 2.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 146 optimal weight: 7.9990 chunk 291 optimal weight: 3.9990 chunk 158 optimal weight: 10.0000 chunk 225 optimal weight: 10.0000 chunk 210 optimal weight: 0.8980 chunk 61 optimal weight: 5.9990 chunk 306 optimal weight: 0.9990 chunk 29 optimal weight: 10.0000 chunk 53 optimal weight: 8.9990 chunk 295 optimal weight: 0.9980 chunk 207 optimal weight: 9.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 445 HIS A 683 ASN ** A1264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1399 GLN ** A1629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 445 HIS B 683 ASN B 829 HIS ** B 986 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1241 GLN B1399 GLN ** B1448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1513 GLN B1723 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.075019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.051924 restraints weight = 97713.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.052529 restraints weight = 59125.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.052745 restraints weight = 38770.433| |-----------------------------------------------------------------------------| r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 26328 Z= 0.290 Angle : 0.683 11.694 35942 Z= 0.331 Chirality : 0.045 0.291 4066 Planarity : 0.005 0.037 4662 Dihedral : 6.181 104.161 4200 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.14), residues: 3236 helix: 1.33 (0.38), residues: 208 sheet: -0.11 (0.14), residues: 1432 loop : -0.71 (0.15), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 554 HIS 0.007 0.001 HIS A 829 PHE 0.020 0.002 PHE A1086 TYR 0.017 0.002 TYR B1543 ARG 0.005 0.001 ARG B1424 Details of bonding type rmsd link_NAG-ASN : bond 0.00772 ( 24) link_NAG-ASN : angle 3.78778 ( 72) link_BETA1-4 : bond 0.00211 ( 4) link_BETA1-4 : angle 2.24570 ( 12) hydrogen bonds : bond 0.03331 ( 897) hydrogen bonds : angle 5.40297 ( 2562) link_BETA1-6 : bond 0.00599 ( 2) link_BETA1-6 : angle 1.87165 ( 6) SS BOND : bond 0.00539 ( 20) SS BOND : angle 1.45884 ( 40) covalent geometry : bond 0.00655 (26278) covalent geometry : angle 0.65980 (35812) *********************** 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 114 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 3.365 Fit side-chains REVERT: A 565 MET cc_start: 0.8258 (tpp) cc_final: 0.7799 (tpp) REVERT: A 964 MET cc_start: 0.8900 (mmm) cc_final: 0.8653 (mmm) outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.4650 time to fit residues: 87.8733 Evaluate side-chains 87 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 3.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 229 optimal weight: 0.9990 chunk 134 optimal weight: 0.9980 chunk 245 optimal weight: 2.9990 chunk 294 optimal weight: 6.9990 chunk 204 optimal weight: 0.9980 chunk 230 optimal weight: 7.9990 chunk 96 optimal weight: 0.8980 chunk 130 optimal weight: 0.0010 chunk 320 optimal weight: 10.0000 chunk 118 optimal weight: 0.8980 chunk 214 optimal weight: 4.9990 overall best weight: 0.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 445 HIS A 683 ASN B 445 HIS B1448 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.076658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.053598 restraints weight = 96596.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.054323 restraints weight = 58684.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.054343 restraints weight = 38224.370| |-----------------------------------------------------------------------------| r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 26328 Z= 0.117 Angle : 0.575 12.079 35942 Z= 0.277 Chirality : 0.042 0.305 4066 Planarity : 0.004 0.037 4662 Dihedral : 5.979 105.180 4200 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.15), residues: 3236 helix: 1.54 (0.38), residues: 210 sheet: -0.09 (0.14), residues: 1458 loop : -0.58 (0.15), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 554 HIS 0.004 0.001 HIS B 445 PHE 0.024 0.001 PHE A1239 TYR 0.011 0.001 TYR B1599 ARG 0.003 0.000 ARG B 900 Details of bonding type rmsd link_NAG-ASN : bond 0.00672 ( 24) link_NAG-ASN : angle 3.70536 ( 72) link_BETA1-4 : bond 0.00234 ( 4) link_BETA1-4 : angle 1.72840 ( 12) hydrogen bonds : bond 0.02757 ( 897) hydrogen bonds : angle 5.08398 ( 2562) link_BETA1-6 : bond 0.00241 ( 2) link_BETA1-6 : angle 1.63307 ( 6) SS BOND : bond 0.00337 ( 20) SS BOND : angle 1.00379 ( 40) covalent geometry : bond 0.00262 (26278) covalent geometry : angle 0.54875 (35812) *********************** 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 127 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 3.040 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 523 LYS cc_start: 0.8926 (mmmt) cc_final: 0.8593 (tppt) REVERT: A 565 MET cc_start: 0.8188 (tpp) cc_final: 0.7749 (tpp) REVERT: A 728 MET cc_start: 0.6755 (mmm) cc_final: 0.6207 (mmm) REVERT: B 600 GLU cc_start: 0.6645 (tm-30) cc_final: 0.6337 (tm-30) REVERT: B 728 MET cc_start: 0.6734 (mmm) cc_final: 0.6206 (mmm) outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.3923 time to fit residues: 81.4598 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 : 3.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 184 optimal weight: 0.0570 chunk 279 optimal weight: 0.0980 chunk 48 optimal weight: 0.8980 chunk 99 optimal weight: 0.7980 chunk 3 optimal weight: 0.0270 chunk 258 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 145 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 325 optimal weight: 0.9980 chunk 225 optimal weight: 8.9990 overall best weight: 0.3756 ------------------------------------------------------------------------------- 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 ** A1120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 445 HIS B1124 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.077222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.054058 restraints weight = 96978.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.054851 restraints weight = 57194.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.055515 restraints weight = 36134.631| |-----------------------------------------------------------------------------| r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 26328 Z= 0.096 Angle : 0.556 12.253 35942 Z= 0.266 Chirality : 0.042 0.303 4066 Planarity : 0.004 0.035 4662 Dihedral : 5.770 105.237 4200 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.15), residues: 3236 helix: 1.80 (0.38), residues: 208 sheet: -0.01 (0.14), residues: 1424 loop : -0.55 (0.15), residues: 1604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 554 HIS 0.003 0.000 HIS B 445 PHE 0.011 0.001 PHE A 639 TYR 0.013 0.001 TYR B 897 ARG 0.007 0.000 ARG B1154 Details of bonding type rmsd link_NAG-ASN : bond 0.00650 ( 24) link_NAG-ASN : angle 3.61137 ( 72) link_BETA1-4 : bond 0.00275 ( 4) link_BETA1-4 : angle 1.57850 ( 12) hydrogen bonds : bond 0.02578 ( 897) hydrogen bonds : angle 4.90588 ( 2562) link_BETA1-6 : bond 0.00155 ( 2) link_BETA1-6 : angle 1.59961 ( 6) SS BOND : bond 0.00290 ( 20) SS BOND : angle 1.02821 ( 40) covalent geometry : bond 0.00223 (26278) covalent geometry : angle 0.53057 (35812) *********************** 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 130 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 2.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 565 MET cc_start: 0.8164 (tpp) cc_final: 0.7743 (tpp) REVERT: A 728 MET cc_start: 0.6909 (mmm) cc_final: 0.6399 (mmm) REVERT: A 1035 LEU cc_start: 0.9182 (tt) cc_final: 0.8967 (tp) REVERT: A 1247 ASP cc_start: 0.8691 (t70) cc_final: 0.8421 (t70) REVERT: B 284 MET cc_start: 0.9223 (mmm) cc_final: 0.8913 (mmm) REVERT: B 447 MET cc_start: 0.7541 (pmm) cc_final: 0.7071 (pmm) REVERT: B 719 GLN cc_start: 0.7883 (mp10) cc_final: 0.7207 (mp10) REVERT: B 728 MET cc_start: 0.6785 (mmm) cc_final: 0.6244 (mmm) REVERT: B 1247 ASP cc_start: 0.8622 (t70) cc_final: 0.8401 (t70) outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.3608 time to fit residues: 78.1717 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 : 2.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 117 optimal weight: 0.6980 chunk 63 optimal weight: 6.9990 chunk 33 optimal weight: 20.0000 chunk 46 optimal weight: 10.0000 chunk 141 optimal weight: 3.9990 chunk 227 optimal weight: 6.9990 chunk 198 optimal weight: 20.0000 chunk 120 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 86 optimal weight: 0.0370 overall best weight: 0.7462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 445 HIS A 683 ASN ** A1120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 445 HIS B 898 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.076928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.054025 restraints weight = 96976.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.054646 restraints weight = 55351.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.054707 restraints weight = 37655.903| |-----------------------------------------------------------------------------| r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 26328 Z= 0.114 Angle : 0.559 12.183 35942 Z= 0.268 Chirality : 0.042 0.299 4066 Planarity : 0.004 0.057 4662 Dihedral : 5.699 105.029 4200 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.15), residues: 3236 helix: 2.04 (0.38), residues: 208 sheet: 0.01 (0.14), residues: 1422 loop : -0.45 (0.15), residues: 1606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 554 HIS 0.003 0.000 HIS B 445 PHE 0.024 0.001 PHE B1239 TYR 0.010 0.001 TYR B1722 ARG 0.010 0.000 ARG B1154 Details of bonding type rmsd link_NAG-ASN : bond 0.00630 ( 24) link_NAG-ASN : angle 3.51859 ( 72) link_BETA1-4 : bond 0.00217 ( 4) link_BETA1-4 : angle 1.60767 ( 12) hydrogen bonds : bond 0.02608 ( 897) hydrogen bonds : angle 4.83857 ( 2562) link_BETA1-6 : bond 0.00166 ( 2) link_BETA1-6 : angle 1.57357 ( 6) SS BOND : bond 0.00293 ( 20) SS BOND : angle 1.02148 ( 40) covalent geometry : bond 0.00262 (26278) covalent geometry : angle 0.53532 (35812) *********************** 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 124 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 2.917 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 565 MET cc_start: 0.8140 (tpp) cc_final: 0.7856 (tpp) REVERT: A 728 MET cc_start: 0.7123 (mmm) cc_final: 0.6618 (mmm) REVERT: A 964 MET cc_start: 0.8894 (mmm) cc_final: 0.8675 (mmm) REVERT: A 1035 LEU cc_start: 0.9212 (tt) cc_final: 0.8993 (tp) REVERT: A 1247 ASP cc_start: 0.8640 (t70) cc_final: 0.8355 (t70) REVERT: B 447 MET cc_start: 0.7580 (pmm) cc_final: 0.7090 (pmm) REVERT: B 600 GLU cc_start: 0.6159 (tm-30) cc_final: 0.5842 (tm-30) REVERT: B 719 GLN cc_start: 0.7911 (mp10) cc_final: 0.7226 (mp10) REVERT: B 728 MET cc_start: 0.7113 (mmm) cc_final: 0.6594 (mmm) REVERT: B 895 ASN cc_start: 0.7763 (t0) cc_final: 0.7521 (t0) REVERT: B 964 MET cc_start: 0.8847 (mmm) cc_final: 0.8614 (mmm) outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.3715 time to fit residues: 77.7816 Evaluate side-chains 95 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 3.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 113 optimal weight: 0.5980 chunk 259 optimal weight: 0.0970 chunk 266 optimal weight: 0.8980 chunk 58 optimal weight: 9.9990 chunk 92 optimal weight: 0.0370 chunk 100 optimal weight: 0.2980 chunk 60 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 chunk 320 optimal weight: 40.0000 chunk 111 optimal weight: 0.9990 chunk 231 optimal weight: 0.9990 overall best weight: 0.3856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 445 HIS ** A1120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1588 ASN ** 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 = 0.3538 r_free = 0.3538 target = 0.077457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.054548 restraints weight = 97062.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.055250 restraints weight = 55898.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.055325 restraints weight = 36859.253| |-----------------------------------------------------------------------------| r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 26328 Z= 0.091 Angle : 0.552 12.317 35942 Z= 0.264 Chirality : 0.042 0.299 4066 Planarity : 0.004 0.032 4662 Dihedral : 5.621 105.204 4200 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.15), residues: 3236 helix: 2.30 (0.38), residues: 206 sheet: 0.12 (0.14), residues: 1424 loop : -0.48 (0.15), residues: 1606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 554 HIS 0.003 0.000 HIS B 445 PHE 0.012 0.001 PHE A1239 TYR 0.012 0.001 TYR B 385 ARG 0.006 0.000 ARG B1154 Details of bonding type rmsd link_NAG-ASN : bond 0.00648 ( 24) link_NAG-ASN : angle 3.43998 ( 72) link_BETA1-4 : bond 0.00290 ( 4) link_BETA1-4 : angle 1.46393 ( 12) hydrogen bonds : bond 0.02491 ( 897) hydrogen bonds : angle 4.72299 ( 2562) link_BETA1-6 : bond 0.00116 ( 2) link_BETA1-6 : angle 1.51704 ( 6) SS BOND : bond 0.00346 ( 20) SS BOND : angle 0.99110 ( 40) covalent geometry : bond 0.00210 (26278) covalent geometry : angle 0.52899 (35812) *********************** 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 129 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 6.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 565 MET cc_start: 0.8045 (tpp) cc_final: 0.7775 (tpp) REVERT: A 641 MET cc_start: 0.3597 (tpp) cc_final: 0.2986 (tpp) REVERT: A 1035 LEU cc_start: 0.9192 (tt) cc_final: 0.8988 (mp) REVERT: A 1247 ASP cc_start: 0.8628 (t70) cc_final: 0.8313 (t70) REVERT: B 447 MET cc_start: 0.7583 (pmm) cc_final: 0.7060 (pmm) REVERT: B 600 GLU cc_start: 0.6210 (tm-30) cc_final: 0.5879 (tm-30) REVERT: B 719 GLN cc_start: 0.7953 (mp10) cc_final: 0.7263 (mp10) REVERT: B 895 ASN cc_start: 0.7608 (t0) cc_final: 0.7294 (t0) REVERT: B 964 MET cc_start: 0.8861 (mmm) cc_final: 0.8634 (mmm) REVERT: B 1247 ASP cc_start: 0.8611 (t70) cc_final: 0.8338 (t70) outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 0.4510 time to fit residues: 99.8861 Evaluate side-chains 99 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 3.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 192 optimal weight: 0.9980 chunk 224 optimal weight: 9.9990 chunk 302 optimal weight: 0.9990 chunk 64 optimal weight: 10.0000 chunk 39 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 306 optimal weight: 0.0370 chunk 30 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 chunk 324 optimal weight: 40.0000 chunk 173 optimal weight: 0.7980 overall best weight: 0.9662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 445 HIS ** A1120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1264 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 = 0.3520 r_free = 0.3520 target = 0.076669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.053515 restraints weight = 96927.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.054567 restraints weight = 53712.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.054522 restraints weight = 34822.651| |-----------------------------------------------------------------------------| r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 26328 Z= 0.132 Angle : 0.566 11.964 35942 Z= 0.271 Chirality : 0.042 0.293 4066 Planarity : 0.004 0.034 4662 Dihedral : 5.609 104.829 4200 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.15), residues: 3236 helix: 2.26 (0.38), residues: 208 sheet: 0.03 (0.14), residues: 1438 loop : -0.42 (0.15), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 554 HIS 0.003 0.001 HIS B 445 PHE 0.013 0.001 PHE A 639 TYR 0.023 0.001 TYR B 402 ARG 0.003 0.000 ARG B1234 Details of bonding type rmsd link_NAG-ASN : bond 0.00609 ( 24) link_NAG-ASN : angle 3.35446 ( 72) link_BETA1-4 : bond 0.00187 ( 4) link_BETA1-4 : angle 1.61519 ( 12) hydrogen bonds : bond 0.02654 ( 897) hydrogen bonds : angle 4.72939 ( 2562) link_BETA1-6 : bond 0.00157 ( 2) link_BETA1-6 : angle 1.56895 ( 6) SS BOND : bond 0.00367 ( 20) SS BOND : angle 1.18118 ( 40) covalent geometry : bond 0.00304 (26278) covalent geometry : angle 0.54425 (35812) ********************** 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 122 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 2.899 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 523 LYS cc_start: 0.8866 (mmmt) cc_final: 0.7876 (mmtm) REVERT: A 565 MET cc_start: 0.7986 (tpp) cc_final: 0.7749 (tpp) REVERT: A 728 MET cc_start: 0.6997 (mmm) cc_final: 0.6541 (mmm) REVERT: A 1247 ASP cc_start: 0.8627 (t70) cc_final: 0.8345 (t70) REVERT: B 447 MET cc_start: 0.7500 (pmm) cc_final: 0.7004 (pmm) REVERT: B 565 MET cc_start: 0.8208 (tpp) cc_final: 0.7896 (tpp) REVERT: B 600 GLU cc_start: 0.6314 (tm-30) cc_final: 0.5818 (tm-30) REVERT: B 719 GLN cc_start: 0.7911 (mp10) cc_final: 0.7222 (mp10) REVERT: B 728 MET cc_start: 0.6913 (mmm) cc_final: 0.6463 (mmm) REVERT: B 895 ASN cc_start: 0.7474 (t0) cc_final: 0.7046 (t0) outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.3628 time to fit residues: 75.7623 Evaluate side-chains 95 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 2.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 255 optimal weight: 0.0670 chunk 127 optimal weight: 0.9990 chunk 193 optimal weight: 5.9990 chunk 48 optimal weight: 7.9990 chunk 133 optimal weight: 0.8980 chunk 145 optimal weight: 0.6980 chunk 51 optimal weight: 9.9990 chunk 53 optimal weight: 6.9990 chunk 96 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 32 optimal weight: 9.9990 overall best weight: 0.7120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 445 HIS ** A1120 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 = 0.3527 r_free = 0.3527 target = 0.076960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.053809 restraints weight = 97411.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.054724 restraints weight = 53745.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.055124 restraints weight = 34433.071| |-----------------------------------------------------------------------------| r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 26328 Z= 0.108 Angle : 0.555 12.211 35942 Z= 0.265 Chirality : 0.042 0.296 4066 Planarity : 0.004 0.034 4662 Dihedral : 5.559 105.166 4200 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.00 % Allowed : 0.08 % Favored : 99.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.15), residues: 3236 helix: 2.42 (0.38), residues: 206 sheet: 0.10 (0.14), residues: 1422 loop : -0.40 (0.15), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 554 HIS 0.003 0.000 HIS B 445 PHE 0.012 0.001 PHE A 639 TYR 0.015 0.001 TYR B 402 ARG 0.003 0.000 ARG B1234 Details of bonding type rmsd link_NAG-ASN : bond 0.00642 ( 24) link_NAG-ASN : angle 3.30230 ( 72) link_BETA1-4 : bond 0.00297 ( 4) link_BETA1-4 : angle 1.47664 ( 12) hydrogen bonds : bond 0.02519 ( 897) hydrogen bonds : angle 4.66192 ( 2562) link_BETA1-6 : bond 0.00099 ( 2) link_BETA1-6 : angle 1.51429 ( 6) SS BOND : bond 0.00318 ( 20) SS BOND : angle 0.99934 ( 40) covalent geometry : bond 0.00250 (26278) covalent geometry : angle 0.53390 (35812) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8547.21 seconds wall clock time: 150 minutes 56.46 seconds (9056.46 seconds total)