Starting phenix.real_space_refine on Tue Dec 12 13:36:41 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x2b_22000/12_2023/6x2b_22000_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x2b_22000/12_2023/6x2b_22000.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x2b_22000/12_2023/6x2b_22000.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x2b_22000/12_2023/6x2b_22000.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x2b_22000/12_2023/6x2b_22000_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x2b_22000/12_2023/6x2b_22000_neut.pdb" } resolution = 3.6 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= 0.003 sd= 0.048 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 95 5.16 5 C 13483 2.51 5 N 3554 2.21 5 O 3988 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 53": "OD1" <-> "OD2" Residue "A ARG 237": "NH1" <-> "NH2" Residue "A TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 454": "NH1" <-> "NH2" Residue "A PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 819": "OE1" <-> "OE2" Residue "A ASP 867": "OD1" <-> "OD2" Residue "A PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 950": "OD1" <-> "OD2" Residue "A GLU 990": "OE1" <-> "OE2" Residue "A TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1107": "NH1" <-> "NH2" Residue "A PHE 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 287": "OD1" <-> "OD2" Residue "B GLU 324": "OE1" <-> "OE2" Residue "B PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 988": "OE1" <-> "OE2" Residue "B TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 773": "OE1" <-> "OE2" Residue "C GLU 819": "OE1" <-> "OE2" Residue "C ASP 867": "OD1" <-> "OD2" Residue "C PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 898": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 21120 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 963, 7380 Classifications: {'peptide': 963} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 47, 'TRANS': 915} Chain breaks: 12 Unresolved non-hydrogen bonds: 166 Unresolved non-hydrogen angles: 207 Unresolved non-hydrogen dihedrals: 132 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ARG:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 5, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 10, 'ASP:plan': 12} Unresolved non-hydrogen planarities: 114 Chain: "B" Number of atoms: 6870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 949, 6870 Classifications: {'peptide': 949} Incomplete info: {'truncation_to_alanine': 150} Link IDs: {'PTRANS': 46, 'TRANS': 902} Chain breaks: 13 Unresolved non-hydrogen bonds: 576 Unresolved non-hydrogen angles: 742 Unresolved non-hydrogen dihedrals: 481 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'GLN:plan1': 9, 'TYR:plan': 13, 'ASN:plan1': 17, 'TRP:plan': 2, 'ASP:plan': 13, 'PHE:plan': 9, 'GLU:plan': 12, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 382 Chain: "C" Number of atoms: 6870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 949, 6870 Classifications: {'peptide': 949} Incomplete info: {'truncation_to_alanine': 150} Link IDs: {'PTRANS': 46, 'TRANS': 902} Chain breaks: 13 Unresolved non-hydrogen bonds: 576 Unresolved non-hydrogen angles: 742 Unresolved non-hydrogen dihedrals: 481 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'GLN:plan1': 9, 'TYR:plan': 13, 'ASN:plan1': 17, 'TRP:plan': 2, 'ASP:plan': 13, 'PHE:plan': 9, 'GLU:plan': 12, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 382 Time building chain proxies: 11.46, per 1000 atoms: 0.54 Number of scatterers: 21120 At special positions: 0 Unit cell: (128.018, 132.25, 178.802, 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 95 16.00 O 3988 8.00 N 3554 7.00 C 13483 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=34, symmetry=0 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.02 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.05 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.02 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.02 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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 Time building additional restraints: 7.17 Conformation dependent library (CDL) restraints added in 3.7 seconds 5558 Ramachandran restraints generated. 2779 Oldfield, 0 Emsley, 2779 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5376 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 44 sheets defined 27.6% alpha, 25.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.03 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.062A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 389 removed outlier: 3.842A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.334A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 removed outlier: 4.247A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 759 removed outlier: 7.224A pdb=" N SER A 758 " --> pdb=" O GLN A 755 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N PHE A 759 " --> pdb=" O TYR A 756 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 755 through 759' Processing helix chain 'A' and resid 760 through 783 removed outlier: 3.969A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.628A pdb=" N LEU A 821 " --> pdb=" O PHE A 817 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU A 822 " --> pdb=" O ILE A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 4.023A pdb=" N GLN A 872 " --> pdb=" O GLU A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.689A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.571A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.500A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.543A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N THR A 941 " --> pdb=" O SER A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 967 removed outlier: 3.854A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N SER A 967 " --> pdb=" O VAL A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.988A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1129 No H-bonds generated for 'chain 'A' and resid 1127 through 1129' Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'B' and resid 294 through 303 removed outlier: 3.533A pdb=" N THR B 299 " --> pdb=" O PRO B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 4.248A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 370 Processing helix chain 'B' and resid 384 through 389 removed outlier: 3.799A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 3.943A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 620 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 removed outlier: 4.238A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 759 removed outlier: 7.311A pdb=" N SER B 758 " --> pdb=" O GLN B 755 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE B 759 " --> pdb=" O TYR B 756 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 755 through 759' Processing helix chain 'B' and resid 760 through 783 removed outlier: 3.854A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 removed outlier: 3.509A pdb=" N LEU B 821 " --> pdb=" O PHE B 817 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.814A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.652A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 967 removed outlier: 3.679A pdb=" N LEU B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N SER B 967 " --> pdb=" O VAL B 963 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.547A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.941A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.567A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 removed outlier: 3.668A pdb=" N THR C 302 " --> pdb=" O GLU C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 341 Processing helix chain 'C' and resid 364 through 371 removed outlier: 3.985A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 389 removed outlier: 4.080A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.339A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 616 through 620 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 removed outlier: 4.013A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 759 removed outlier: 7.324A pdb=" N SER C 758 " --> pdb=" O GLN C 755 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N PHE C 759 " --> pdb=" O TYR C 756 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 755 through 759' Processing helix chain 'C' and resid 760 through 783 removed outlier: 3.568A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 805 removed outlier: 3.914A pdb=" N GLN C 804 " --> pdb=" O ASN C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.607A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.579A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.532A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.506A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 966 removed outlier: 4.030A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.562A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU C 984 " --> pdb=" O ILE C 980 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.653A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1116 through 1118 No H-bonds generated for 'chain 'C' and resid 1116 through 1118' Processing helix chain 'C' and resid 1141 through 1147 removed outlier: 3.797A pdb=" N ASP C1146 " --> pdb=" O GLN C1142 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.481A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 44 removed outlier: 5.604A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 7.539A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.519A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.244A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.060A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 356 removed outlier: 3.819A pdb=" N ALA A 397 " --> pdb=" O LYS A 356 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.849A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.060A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.307A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AB4, first strand: chain 'A' and resid 718 through 722 Processing sheet with id=AB5, first strand: chain 'A' and resid 718 through 722 removed outlier: 5.805A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB7, first strand: chain 'A' and resid 788 through 790 removed outlier: 6.292A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.076A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC1, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.592A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER B 94 " --> pdb=" O ARG B 190 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 9.644A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 50 through 55 removed outlier: 3.856A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 317 removed outlier: 6.837A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLN B 613 " --> pdb=" O GLY B 594 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 325 through 327 removed outlier: 5.807A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 354 through 358 removed outlier: 6.861A pdb=" N ASN B 437 " --> pdb=" O PHE B 374 " (cutoff:3.500A) removed outlier: 8.315A pdb=" N PHE B 374 " --> pdb=" O ASN B 437 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AC8, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.222A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.625A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 702 through 704 removed outlier: 6.527A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.618A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1123 Processing sheet with id=AD5, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD6, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.963A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.611A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 50 through 55 removed outlier: 3.882A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.681A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.319A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.830A pdb=" N TYR C 396 " --> pdb=" O SER C 514 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE C 402 " --> pdb=" O TYR C 508 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 361 through 362 removed outlier: 3.927A pdb=" N CYS C 361 " --> pdb=" O THR C 523 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N CYS C 525 " --> pdb=" O CYS C 361 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AE4, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.039A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.549A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 711 through 719 removed outlier: 6.568A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 719 removed outlier: 6.568A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 1120 through 1123 Processing sheet with id=AE8, first strand: chain 'C' and resid 1094 through 1097 935 hydrogen bonds defined for protein. 2556 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: 9.30 Time building geometry restraints manager: 7.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6176 1.34 - 1.46: 3511 1.46 - 1.58: 11741 1.58 - 1.70: 0 1.70 - 1.82: 119 Bond restraints: 21547 Sorted by residual: bond pdb=" C ASN C 606 " pdb=" N GLN C 607 " ideal model delta sigma weight residual 1.330 1.380 -0.050 1.32e-02 5.74e+03 1.45e+01 bond pdb=" CZ ARG C 34 " pdb=" NH2 ARG C 34 " ideal model delta sigma weight residual 1.330 1.288 0.042 1.30e-02 5.92e+03 1.02e+01 bond pdb=" CZ ARG A 357 " pdb=" NH2 ARG A 357 " ideal model delta sigma weight residual 1.330 1.289 0.041 1.30e-02 5.92e+03 9.74e+00 bond pdb=" CZ ARG C 905 " pdb=" NH2 ARG C 905 " ideal model delta sigma weight residual 1.330 1.290 0.040 1.30e-02 5.92e+03 9.68e+00 bond pdb=" CZ ARG A 328 " pdb=" NH2 ARG A 328 " ideal model delta sigma weight residual 1.330 1.290 0.040 1.30e-02 5.92e+03 9.63e+00 ... (remaining 21542 not shown) Histogram of bond angle deviations from ideal: 97.28 - 104.91: 358 104.91 - 112.53: 9984 112.53 - 120.15: 9959 120.15 - 127.77: 9022 127.77 - 135.39: 70 Bond angle restraints: 29393 Sorted by residual: angle pdb=" CA ASP C 40 " pdb=" CB ASP C 40 " pdb=" CG ASP C 40 " ideal model delta sigma weight residual 112.60 118.53 -5.93 1.00e+00 1.00e+00 3.51e+01 angle pdb=" C GLY C1093 " pdb=" N VAL C1094 " pdb=" CA VAL C1094 " ideal model delta sigma weight residual 122.11 128.55 -6.44 1.12e+00 7.97e-01 3.31e+01 angle pdb=" CA PHE C 759 " pdb=" CB PHE C 759 " pdb=" CG PHE C 759 " ideal model delta sigma weight residual 113.80 119.53 -5.73 1.00e+00 1.00e+00 3.28e+01 angle pdb=" CA ASP A 578 " pdb=" CB ASP A 578 " pdb=" CG ASP A 578 " ideal model delta sigma weight residual 112.60 118.32 -5.72 1.00e+00 1.00e+00 3.27e+01 angle pdb=" CA PHE C 275 " pdb=" CB PHE C 275 " pdb=" CG PHE C 275 " ideal model delta sigma weight residual 113.80 119.35 -5.55 1.00e+00 1.00e+00 3.08e+01 ... (remaining 29388 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 11899 17.77 - 35.54: 726 35.54 - 53.31: 139 53.31 - 71.08: 36 71.08 - 88.85: 20 Dihedral angle restraints: 12820 sinusoidal: 4525 harmonic: 8295 Sorted by residual: dihedral pdb=" CB CYS A1032 " pdb=" SG CYS A1032 " pdb=" SG CYS A1043 " pdb=" CB CYS A1043 " ideal model delta sinusoidal sigma weight residual 93.00 165.28 -72.28 1 1.00e+01 1.00e-02 6.68e+01 dihedral pdb=" CB CYS C1032 " pdb=" SG CYS C1032 " pdb=" SG CYS C1043 " pdb=" CB CYS C1043 " ideal model delta sinusoidal sigma weight residual 93.00 157.17 -64.17 1 1.00e+01 1.00e-02 5.42e+01 dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -146.21 60.21 1 1.00e+01 1.00e-02 4.83e+01 ... (remaining 12817 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 2550 0.096 - 0.193: 837 0.193 - 0.289: 81 0.289 - 0.385: 14 0.385 - 0.481: 1 Chirality restraints: 3483 Sorted by residual: chirality pdb=" CA ASP B 571 " pdb=" N ASP B 571 " pdb=" C ASP B 571 " pdb=" CB ASP B 571 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.79e+00 chirality pdb=" CA ASP C1041 " pdb=" N ASP C1041 " pdb=" C ASP C1041 " pdb=" CB ASP C1041 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.69e+00 chirality pdb=" CA TRP A 104 " pdb=" N TRP A 104 " pdb=" C TRP A 104 " pdb=" CB TRP A 104 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.27e+00 ... (remaining 3480 not shown) Planarity restraints: 3809 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 886 " -0.102 2.00e-02 2.50e+03 6.79e-02 1.15e+02 pdb=" CG TRP A 886 " 0.002 2.00e-02 2.50e+03 pdb=" CD1 TRP A 886 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP A 886 " 0.084 2.00e-02 2.50e+03 pdb=" NE1 TRP A 886 " 0.043 2.00e-02 2.50e+03 pdb=" CE2 TRP A 886 " 0.048 2.00e-02 2.50e+03 pdb=" CE3 TRP A 886 " 0.101 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 886 " -0.039 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 886 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 886 " -0.111 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 104 " -0.106 2.00e-02 2.50e+03 6.20e-02 9.61e+01 pdb=" CG TRP B 104 " -0.014 2.00e-02 2.50e+03 pdb=" CD1 TRP B 104 " 0.038 2.00e-02 2.50e+03 pdb=" CD2 TRP B 104 " 0.046 2.00e-02 2.50e+03 pdb=" NE1 TRP B 104 " 0.042 2.00e-02 2.50e+03 pdb=" CE2 TRP B 104 " 0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP B 104 " 0.110 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 104 " -0.058 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 104 " 0.014 2.00e-02 2.50e+03 pdb=" CH2 TRP B 104 " -0.078 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 904 " -0.111 2.00e-02 2.50e+03 6.55e-02 8.59e+01 pdb=" CG TYR A 904 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR A 904 " 0.040 2.00e-02 2.50e+03 pdb=" CD2 TYR A 904 " 0.050 2.00e-02 2.50e+03 pdb=" CE1 TYR A 904 " 0.044 2.00e-02 2.50e+03 pdb=" CE2 TYR A 904 " 0.043 2.00e-02 2.50e+03 pdb=" CZ TYR A 904 " 0.021 2.00e-02 2.50e+03 pdb=" OH TYR A 904 " -0.113 2.00e-02 2.50e+03 ... (remaining 3806 not shown) Histogram of nonbonded interaction distances: 2.53 - 3.00: 10860 3.00 - 3.48: 21081 3.48 - 3.95: 33688 3.95 - 4.43: 37433 4.43 - 4.90: 62418 Nonbonded interactions: 165480 Sorted by model distance: nonbonded pdb=" OD1 ASP A 364 " pdb=" OG SER A 366 " model vdw 2.530 2.440 nonbonded pdb=" OG1 THR B 323 " pdb=" OE1 GLU B 324 " model vdw 2.548 2.440 nonbonded pdb=" OD1 ASP B 294 " pdb=" OG SER B 297 " model vdw 2.549 2.440 nonbonded pdb=" OE2 GLU A 918 " pdb=" OG SER C1123 " model vdw 2.549 2.440 nonbonded pdb=" OD1 ASP A 294 " pdb=" OG SER A 297 " model vdw 2.550 2.440 ... (remaining 165475 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 52 or (resid 53 and (name N or name CA or name \ C or name O or name CB )) or resid 54 through 66 or resid 82 through 95 or (resi \ d 96 and (name N or name CA or name C or name O or name CB )) or resid 97 throug \ h 112 or (resid 113 and (name N or name CA or name C or name O or name CB )) or \ resid 116 through 124 or (resid 125 and (name N or name CA or name C or name O o \ r name CB )) or resid 126 through 131 or (resid 132 and (name N or name CA or na \ me C or name O or name CB )) or resid 133 or (resid 134 through 138 and (name N \ or name CA or name C or name O or name CB )) or resid 139 through 140 or resid 1 \ 67 through 171 or (resid 172 and (name N or name CA or name C or name O or name \ CB )) or resid 186 through 196 or resid 200 through 211 or (resid 215 and (name \ N or name CA or name C or name O or name CB )) or resid 216 through 217 or (resi \ d 218 and (name N or name CA or name C or name O or name CB )) or resid 219 thro \ ugh 223 or (resid 224 and (name N or name CA or name C or name O or name CB )) o \ r resid 225 through 238 or (resid 239 and (name N or name CA or name C or name O \ or name CB )) or resid 240 through 308 or (resid 309 and (name N or name CA or \ name C or name O or name CB )) or resid 310 through 332 or (resid 333 through 33 \ 4 and (name N or name CA or name C or name O or name CB )) or resid 335 through \ 345 or (resid 346 through 360 and (name N or name CA or name C or name O or name \ CB )) or resid 361 or (resid 362 through 378 and (name N or name CA or name C o \ r name O or name CB )) or resid 379 or (resid 380 and (name N or name CA or name \ C or name O or name CB )) or resid 381 or (resid 382 through 383 and (name N or \ name CA or name C or name O or name CB )) or resid 384 or (resid 385 through 39 \ 0 and (name N or name CA or name C or name O or name CB )) or resid 391 or (resi \ d 392 through 403 and (name N or name CA or name C or name O or name CB )) or (r \ esid 404 through 411 and (name N or name CA or name C or name O or name CB )) or \ resid 412 through 413 or (resid 414 through 415 and (name N or name CA or name \ C or name O or name CB )) or resid 416 or (resid 417 through 425 and (name N or \ name CA or name C or name O or name CB )) or resid 426 through 427 or (resid 428 \ through 430 and (name N or name CA or name C or name O or name CB )) or resid 4 \ 31 through 432 or (resid 433 through 454 and (name N or name CA or name C or nam \ e O or name CB )) or (resid 462 and (name N or name CA or name C or name O or na \ me CB )) or resid 463 or (resid 464 through 466 and (name N or name CA or name C \ or name O or name CB )) or resid 491 or (resid 492 through 495 and (name N or n \ ame CA or name C or name O or name CB )) or resid 496 or (resid 497 through 498 \ and (name N or name CA or name C or name O or name CB )) or resid 499 or (resid \ 500 through 503 and (name N or name CA or name C or name O or name CB )) or (res \ id 504 through 506 and (name N or name CA or name C or name O or name CB )) or r \ esid 507 or (resid 508 through 515 and (name N or name CA or name C or name O or \ name CB )) or (resid 522 through 524 and (name N or name CA or name C or name O \ or name CB )) or resid 525 through 528 or (resid 529 and (name N or name CA or \ name C or name O or name CB )) or resid 530 through 553 or (resid 554 and (name \ N or name CA or name C or name O or name CB )) or resid 555 through 793 or (resi \ d 794 and (name N or name CA or name C or name O or name CB )) or resid 795 or ( \ resid 796 and (name N or name CA or name C or name O or name CB )) or resid 797 \ through 1141 or (resid 1142 and (name N or name CA or name C or name O or name C \ B )) or resid 1143 through 1144 or (resid 1145 through 1146 and (name N or name \ CA or name C or name O or name CB )) or resid 1147)) selection = (chain 'B' and (resid 27 through 66 or resid 82 through 98 or (resid 99 and (nam \ e N or name CA or name C or name O or name CB )) or resid 100 through 110 or (re \ sid 111 and (name N or name CA or name C or name O or name CB )) or resid 112 th \ rough 113 or resid 116 through 128 or (resid 129 and (name N or name CA or name \ C or name O or name CB )) or resid 130 through 134 or (resid 135 through 138 and \ (name N or name CA or name C or name O or name CB )) or resid 139 through 140 o \ r resid 167 through 187 or (resid 188 and (name N or name CA or name C or name O \ or name CB )) or resid 189 through 195 or (resid 196 and (name N or name CA or \ name C or name O or name CB )) or resid 200 through 241 or (resid 242 through 26 \ 4 and (name N or name CA or name C or name O or name CB )) or resid 265 through \ 280 or (resid 281 and (name N or name CA or name C or name O or name CB )) or re \ sid 282 through 442 or resid 448 through 501 or resid 503 through 567 or (resid \ 568 and (name N or name CA or name C or name O or name CB )) or resid 569 throug \ h 570 or (resid 571 and (name N or name CA or name C or name O or name CB )) or \ resid 572 through 581 or (resid 582 through 583 and (name N or name CA or name C \ or name O or name CB )) or resid 584 through 585 or (resid 586 and (name N or n \ ame CA or name C or name O or name CB )) or resid 587 through 613 or (resid 614 \ and (name N or name CA or name C or name O or name CB )) or resid 615 through 61 \ 8 or (resid 619 and (name N or name CA or name C or name O or name CB )) or resi \ d 620 through 676 or resid 690 through 744 or (resid 745 and (name N or name CA \ or name C or name O or name CB )) or resid 746 through 827 or resid 855 through \ 920 or (resid 921 and (name N or name CA or name C or name O or name CB )) or re \ sid 922 through 1072 or (resid 1073 and (name N or name CA or name C or name O o \ r name CB )) or resid 1074 through 1117 or (resid 1118 and (name N or name CA or \ name C or name O or name CB )) or resid 1119 through 1143 or (resid 1144 throug \ h 1146 and (name N or name CA or name C or name O or name CB )) or resid 1147)) selection = (chain 'C' and (resid 27 through 66 or resid 82 through 98 or (resid 99 and (nam \ e N or name CA or name C or name O or name CB )) or resid 100 through 110 or (re \ sid 111 and (name N or name CA or name C or name O or name CB )) or resid 112 th \ rough 113 or resid 116 through 128 or (resid 129 and (name N or name CA or name \ C or name O or name CB )) or resid 130 through 134 or (resid 135 through 138 and \ (name N or name CA or name C or name O or name CB )) or resid 139 through 140 o \ r resid 167 through 187 or (resid 188 and (name N or name CA or name C or name O \ or name CB )) or resid 189 through 195 or (resid 196 and (name N or name CA or \ name C or name O or name CB )) or resid 200 through 241 or (resid 242 through 26 \ 4 and (name N or name CA or name C or name O or name CB )) or resid 265 through \ 280 or (resid 281 and (name N or name CA or name C or name O or name CB )) or re \ sid 282 through 442 or resid 448 through 501 or resid 503 through 567 or (resid \ 568 and (name N or name CA or name C or name O or name CB )) or resid 569 throug \ h 570 or (resid 571 and (name N or name CA or name C or name O or name CB )) or \ resid 572 through 581 or (resid 582 through 583 and (name N or name CA or name C \ or name O or name CB )) or resid 584 through 585 or (resid 586 and (name N or n \ ame CA or name C or name O or name CB )) or resid 587 through 613 or (resid 614 \ and (name N or name CA or name C or name O or name CB )) or resid 615 through 61 \ 8 or (resid 619 and (name N or name CA or name C or name O or name CB )) or resi \ d 620 through 676 or resid 690 through 744 or (resid 745 and (name N or name CA \ or name C or name O or name CB )) or resid 746 through 827 or resid 855 through \ 920 or (resid 921 and (name N or name CA or name C or name O or name CB )) or re \ sid 922 through 1072 or (resid 1073 and (name N or name CA or name C or name O o \ r name CB )) or resid 1074 through 1117 or (resid 1118 and (name N or name CA or \ name C or name O or name CB )) or resid 1119 through 1143 or (resid 1144 throug \ h 1146 and (name N or name CA or name C or name O or name CB )) or resid 1147)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.950 Check model and map are aligned: 0.330 Set scattering table: 0.220 Process input model: 56.490 Find NCS groups from input model: 1.830 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 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 : 0.012 0.050 21547 Z= 0.773 Angle : 1.744 8.160 29393 Z= 1.174 Chirality : 0.088 0.481 3483 Planarity : 0.013 0.147 3809 Dihedral : 13.172 88.847 7342 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 0.34 Ramachandran Plot: Outliers : 0.43 % Allowed : 6.69 % Favored : 92.88 % Rotamer: Outliers : 2.08 % Allowed : 4.71 % Favored : 93.21 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.14), residues: 2779 helix: -0.92 (0.17), residues: 649 sheet: -0.41 (0.23), residues: 450 loop : -1.46 (0.14), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.111 0.023 TRP A 886 HIS 0.018 0.004 HIS A1048 PHE 0.087 0.013 PHE C1121 TYR 0.113 0.020 TYR A 904 ARG 0.016 0.002 ARG A 44 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5558 Ramachandran restraints generated. 2779 Oldfield, 0 Emsley, 2779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5558 Ramachandran restraints generated. 2779 Oldfield, 0 Emsley, 2779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 84 time to evaluate : 2.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 45 outliers final: 14 residues processed: 126 average time/residue: 0.3043 time to fit residues: 62.8977 Evaluate side-chains 56 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 42 time to evaluate : 2.421 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1942 time to fit residues: 8.2313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 239 optimal weight: 5.9990 chunk 215 optimal weight: 40.0000 chunk 119 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 145 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 222 optimal weight: 10.0000 chunk 86 optimal weight: 0.6980 chunk 135 optimal weight: 9.9990 chunk 165 optimal weight: 0.7980 chunk 257 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 564 GLN A 751 ASN A 777 ASN A 913 GLN A 955 ASN ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1023 ASN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 644 GLN B 751 ASN B 777 ASN C 777 ASN C 953 ASN C 955 ASN C 960 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 21547 Z= 0.196 Angle : 0.595 13.833 29393 Z= 0.315 Chirality : 0.044 0.157 3483 Planarity : 0.004 0.045 3809 Dihedral : 5.513 22.728 2992 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.67 % Favored : 96.29 % Rotamer: Outliers : 1.48 % Allowed : 6.14 % Favored : 92.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.15), residues: 2779 helix: 1.03 (0.20), residues: 676 sheet: -0.39 (0.20), residues: 594 loop : -1.02 (0.15), residues: 1509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 104 HIS 0.006 0.001 HIS B1048 PHE 0.021 0.001 PHE A 497 TYR 0.012 0.001 TYR A 904 ARG 0.006 0.001 ARG B 765 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5558 Ramachandran restraints generated. 2779 Oldfield, 0 Emsley, 2779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5558 Ramachandran restraints generated. 2779 Oldfield, 0 Emsley, 2779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 57 time to evaluate : 2.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 13 residues processed: 84 average time/residue: 0.3067 time to fit residues: 45.4233 Evaluate side-chains 55 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 42 time to evaluate : 2.410 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1925 time to fit residues: 8.0890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 143 optimal weight: 0.6980 chunk 80 optimal weight: 0.0970 chunk 214 optimal weight: 50.0000 chunk 175 optimal weight: 8.9990 chunk 71 optimal weight: 0.4980 chunk 258 optimal weight: 0.7980 chunk 279 optimal weight: 7.9990 chunk 230 optimal weight: 0.9980 chunk 256 optimal weight: 0.2980 chunk 88 optimal weight: 6.9990 chunk 207 optimal weight: 7.9990 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN A 762 GLN ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1048 HIS B 926 GLN C 955 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 21547 Z= 0.128 Angle : 0.516 14.032 29393 Z= 0.270 Chirality : 0.042 0.143 3483 Planarity : 0.003 0.035 3809 Dihedral : 4.621 24.377 2992 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.92 % Favored : 96.04 % Rotamer: Outliers : 0.97 % Allowed : 6.79 % Favored : 92.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.16), residues: 2779 helix: 1.73 (0.21), residues: 656 sheet: -0.31 (0.20), residues: 637 loop : -0.77 (0.16), residues: 1486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 104 HIS 0.004 0.001 HIS B1048 PHE 0.014 0.001 PHE C 759 TYR 0.015 0.001 TYR A1067 ARG 0.006 0.000 ARG B 765 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5558 Ramachandran restraints generated. 2779 Oldfield, 0 Emsley, 2779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5558 Ramachandran restraints generated. 2779 Oldfield, 0 Emsley, 2779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 51 time to evaluate : 2.564 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 3 residues processed: 68 average time/residue: 0.3105 time to fit residues: 37.3841 Evaluate side-chains 43 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 40 time to evaluate : 2.821 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2594 time to fit residues: 5.1792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 255 optimal weight: 9.9990 chunk 194 optimal weight: 0.9990 chunk 134 optimal weight: 50.0000 chunk 28 optimal weight: 7.9990 chunk 123 optimal weight: 9.9990 chunk 173 optimal weight: 0.9980 chunk 259 optimal weight: 2.9990 chunk 274 optimal weight: 5.9990 chunk 135 optimal weight: 3.9990 chunk 245 optimal weight: 0.0370 chunk 73 optimal weight: 1.9990 overall best weight: 1.4064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 957 GLN B 957 GLN C 955 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 21547 Z= 0.167 Angle : 0.491 12.756 29393 Z= 0.254 Chirality : 0.041 0.139 3483 Planarity : 0.003 0.041 3809 Dihedral : 4.249 16.686 2992 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.78 % Favored : 96.19 % Rotamer: Outliers : 0.88 % Allowed : 7.99 % Favored : 91.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.16), residues: 2779 helix: 1.97 (0.21), residues: 655 sheet: -0.34 (0.19), residues: 701 loop : -0.63 (0.16), residues: 1423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 104 HIS 0.005 0.001 HIS A1048 PHE 0.013 0.001 PHE B1121 TYR 0.015 0.001 TYR A1067 ARG 0.006 0.000 ARG A 983 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5558 Ramachandran restraints generated. 2779 Oldfield, 0 Emsley, 2779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5558 Ramachandran restraints generated. 2779 Oldfield, 0 Emsley, 2779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 45 time to evaluate : 2.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 6 residues processed: 62 average time/residue: 0.3158 time to fit residues: 36.1639 Evaluate side-chains 42 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 36 time to evaluate : 2.397 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 6 average time/residue: 0.1940 time to fit residues: 5.4334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 228 optimal weight: 50.0000 chunk 155 optimal weight: 7.9990 chunk 3 optimal weight: 9.9990 chunk 204 optimal weight: 20.0000 chunk 113 optimal weight: 10.0000 chunk 234 optimal weight: 7.9990 chunk 189 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 140 optimal weight: 9.9990 chunk 246 optimal weight: 6.9990 chunk 69 optimal weight: 3.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 655 HIS ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.2692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.099 21547 Z= 0.492 Angle : 0.656 14.661 29393 Z= 0.337 Chirality : 0.045 0.152 3483 Planarity : 0.004 0.041 3809 Dihedral : 4.701 23.750 2992 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.29 % Favored : 94.67 % Rotamer: Outliers : 1.39 % Allowed : 8.96 % Favored : 89.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.16), residues: 2779 helix: 1.76 (0.20), residues: 638 sheet: -0.59 (0.19), residues: 677 loop : -0.72 (0.16), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 886 HIS 0.006 0.002 HIS B1048 PHE 0.028 0.002 PHE A 133 TYR 0.022 0.002 TYR C 266 ARG 0.005 0.001 ARG A 815 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5558 Ramachandran restraints generated. 2779 Oldfield, 0 Emsley, 2779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5558 Ramachandran restraints generated. 2779 Oldfield, 0 Emsley, 2779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 37 time to evaluate : 2.237 Fit side-chains revert: symmetry clash outliers start: 30 outliers final: 9 residues processed: 64 average time/residue: 0.2721 time to fit residues: 32.4883 Evaluate side-chains 44 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 35 time to evaluate : 2.534 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1986 time to fit residues: 6.8068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 92 optimal weight: 3.9990 chunk 247 optimal weight: 7.9990 chunk 54 optimal weight: 6.9990 chunk 161 optimal weight: 2.9990 chunk 67 optimal weight: 6.9990 chunk 274 optimal weight: 0.0060 chunk 228 optimal weight: 50.0000 chunk 127 optimal weight: 20.0000 chunk 22 optimal weight: 6.9990 chunk 90 optimal weight: 1.9990 chunk 144 optimal weight: 2.9990 overall best weight: 2.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 317 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 644 GLN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 965 GLN C 872 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 21547 Z= 0.241 Angle : 0.516 13.716 29393 Z= 0.267 Chirality : 0.042 0.218 3483 Planarity : 0.003 0.049 3809 Dihedral : 4.359 18.831 2992 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.92 % Favored : 96.04 % Rotamer: Outliers : 0.88 % Allowed : 9.60 % Favored : 89.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.16), residues: 2779 helix: 2.07 (0.21), residues: 638 sheet: -0.51 (0.19), residues: 671 loop : -0.65 (0.16), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 104 HIS 0.003 0.001 HIS B1048 PHE 0.017 0.001 PHE A 133 TYR 0.015 0.001 TYR A1067 ARG 0.004 0.000 ARG B 765 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5558 Ramachandran restraints generated. 2779 Oldfield, 0 Emsley, 2779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5558 Ramachandran restraints generated. 2779 Oldfield, 0 Emsley, 2779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 39 time to evaluate : 2.414 Fit side-chains outliers start: 19 outliers final: 7 residues processed: 54 average time/residue: 0.2793 time to fit residues: 28.4431 Evaluate side-chains 42 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 35 time to evaluate : 2.436 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2135 time to fit residues: 5.8521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 264 optimal weight: 10.0000 chunk 30 optimal weight: 6.9990 chunk 156 optimal weight: 6.9990 chunk 200 optimal weight: 8.9990 chunk 155 optimal weight: 1.9990 chunk 231 optimal weight: 3.9990 chunk 153 optimal weight: 7.9990 chunk 273 optimal weight: 0.9980 chunk 171 optimal weight: 0.9990 chunk 166 optimal weight: 0.9980 chunk 126 optimal weight: 40.0000 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 644 GLN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.2961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21547 Z= 0.192 Angle : 0.489 12.828 29393 Z= 0.252 Chirality : 0.041 0.142 3483 Planarity : 0.003 0.053 3809 Dihedral : 4.128 17.446 2992 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.46 % Favored : 95.50 % Rotamer: Outliers : 0.51 % Allowed : 10.20 % Favored : 89.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.16), residues: 2779 helix: 2.22 (0.21), residues: 638 sheet: -0.43 (0.19), residues: 692 loop : -0.56 (0.16), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 104 HIS 0.003 0.001 HIS A1048 PHE 0.014 0.001 PHE B1121 TYR 0.015 0.001 TYR A1067 ARG 0.003 0.000 ARG B 765 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5558 Ramachandran restraints generated. 2779 Oldfield, 0 Emsley, 2779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5558 Ramachandran restraints generated. 2779 Oldfield, 0 Emsley, 2779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 41 time to evaluate : 2.432 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 0 residues processed: 50 average time/residue: 0.3067 time to fit residues: 28.1338 Evaluate side-chains 37 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 2.340 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.0723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 169 optimal weight: 8.9990 chunk 109 optimal weight: 7.9990 chunk 163 optimal weight: 0.7980 chunk 82 optimal weight: 3.9990 chunk 53 optimal weight: 10.0000 chunk 174 optimal weight: 0.5980 chunk 186 optimal weight: 4.9990 chunk 135 optimal weight: 6.9990 chunk 25 optimal weight: 9.9990 chunk 215 optimal weight: 40.0000 chunk 249 optimal weight: 6.9990 overall best weight: 3.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 644 GLN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.3038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.098 21547 Z= 0.328 Angle : 0.553 12.236 29393 Z= 0.284 Chirality : 0.042 0.176 3483 Planarity : 0.004 0.056 3809 Dihedral : 4.277 18.053 2992 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.86 % Favored : 95.11 % Rotamer: Outliers : 0.51 % Allowed : 10.53 % Favored : 88.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.16), residues: 2779 helix: 2.09 (0.21), residues: 639 sheet: -0.49 (0.19), residues: 699 loop : -0.55 (0.16), residues: 1441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 104 HIS 0.005 0.001 HIS B1048 PHE 0.016 0.001 PHE C 92 TYR 0.017 0.001 TYR A1067 ARG 0.003 0.000 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5558 Ramachandran restraints generated. 2779 Oldfield, 0 Emsley, 2779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5558 Ramachandran restraints generated. 2779 Oldfield, 0 Emsley, 2779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 37 time to evaluate : 2.440 Fit side-chains outliers start: 11 outliers final: 2 residues processed: 45 average time/residue: 0.2837 time to fit residues: 25.3379 Evaluate side-chains 37 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 35 time to evaluate : 2.501 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1942 time to fit residues: 3.9976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 262 optimal weight: 2.9990 chunk 239 optimal weight: 4.9990 chunk 255 optimal weight: 3.9990 chunk 153 optimal weight: 4.9990 chunk 111 optimal weight: 8.9990 chunk 200 optimal weight: 0.8980 chunk 78 optimal weight: 0.7980 chunk 230 optimal weight: 0.9980 chunk 241 optimal weight: 0.9980 chunk 254 optimal weight: 0.9990 chunk 167 optimal weight: 6.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.3155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.071 21547 Z= 0.145 Angle : 0.482 11.911 29393 Z= 0.248 Chirality : 0.041 0.142 3483 Planarity : 0.003 0.057 3809 Dihedral : 3.952 17.246 2992 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.74 % Favored : 96.22 % Rotamer: Outliers : 0.23 % Allowed : 10.76 % Favored : 89.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.16), residues: 2779 helix: 2.31 (0.21), residues: 642 sheet: -0.25 (0.20), residues: 669 loop : -0.48 (0.16), residues: 1468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 104 HIS 0.003 0.001 HIS A1048 PHE 0.013 0.001 PHE B 898 TYR 0.013 0.001 TYR A1067 ARG 0.007 0.000 ARG B 577 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5558 Ramachandran restraints generated. 2779 Oldfield, 0 Emsley, 2779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5558 Ramachandran restraints generated. 2779 Oldfield, 0 Emsley, 2779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 42 time to evaluate : 2.440 Fit side-chains outliers start: 5 outliers final: 1 residues processed: 46 average time/residue: 0.3053 time to fit residues: 25.7349 Evaluate side-chains 39 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 38 time to evaluate : 2.335 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2623 time to fit residues: 3.7185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 269 optimal weight: 10.0000 chunk 164 optimal weight: 0.0970 chunk 127 optimal weight: 50.0000 chunk 187 optimal weight: 3.9990 chunk 282 optimal weight: 4.9990 chunk 260 optimal weight: 0.9980 chunk 225 optimal weight: 50.0000 chunk 23 optimal weight: 10.0000 chunk 174 optimal weight: 0.2980 chunk 138 optimal weight: 0.9990 chunk 178 optimal weight: 10.0000 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 644 GLN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN B 935 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.3273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 21547 Z= 0.163 Angle : 0.477 11.736 29393 Z= 0.245 Chirality : 0.041 0.142 3483 Planarity : 0.003 0.056 3809 Dihedral : 3.848 16.832 2992 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.07 % Favored : 95.90 % Rotamer: Outliers : 0.05 % Allowed : 10.99 % Favored : 88.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.16), residues: 2779 helix: 2.34 (0.21), residues: 643 sheet: -0.32 (0.20), residues: 665 loop : -0.39 (0.16), residues: 1471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 104 HIS 0.003 0.001 HIS A1048 PHE 0.015 0.001 PHE B1121 TYR 0.014 0.001 TYR A1067 ARG 0.004 0.000 ARG B 765 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5558 Ramachandran restraints generated. 2779 Oldfield, 0 Emsley, 2779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5558 Ramachandran restraints generated. 2779 Oldfield, 0 Emsley, 2779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 42 time to evaluate : 2.579 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 43 average time/residue: 0.3558 time to fit residues: 27.9645 Evaluate side-chains 38 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 2.468 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.3398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 240 optimal weight: 0.2980 chunk 69 optimal weight: 7.9990 chunk 207 optimal weight: 0.8980 chunk 33 optimal weight: 9.9990 chunk 62 optimal weight: 2.9990 chunk 225 optimal weight: 0.0570 chunk 94 optimal weight: 3.9990 chunk 231 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 41 optimal weight: 4.9990 chunk 198 optimal weight: 2.9990 overall best weight: 1.0100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 644 GLN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.065360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.046584 restraints weight = 95671.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.048269 restraints weight = 43704.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.049367 restraints weight = 26314.668| |-----------------------------------------------------------------------------| r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.3376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 21547 Z= 0.141 Angle : 0.466 11.496 29393 Z= 0.238 Chirality : 0.041 0.142 3483 Planarity : 0.003 0.062 3809 Dihedral : 3.737 16.828 2992 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.92 % Favored : 96.04 % Rotamer: Outliers : 0.05 % Allowed : 10.99 % Favored : 88.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.16), residues: 2779 helix: 2.34 (0.21), residues: 656 sheet: -0.06 (0.20), residues: 665 loop : -0.42 (0.16), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 104 HIS 0.003 0.000 HIS A1048 PHE 0.019 0.001 PHE C 342 TYR 0.013 0.001 TYR A1067 ARG 0.005 0.000 ARG B 765 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2850.26 seconds wall clock time: 54 minutes 7.74 seconds (3247.74 seconds total)