Starting phenix.real_space_refine on Mon Mar 18 16:12:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x2b_22000/03_2024/6x2b_22000_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x2b_22000/03_2024/6x2b_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_22000/03_2024/6x2b_22000.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x2b_22000/03_2024/6x2b_22000.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x2b_22000/03_2024/6x2b_22000_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x2b_22000/03_2024/6x2b_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: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 11.55, per 1000 atoms: 0.55 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: 7.78 Conformation dependent library (CDL) restraints added in 4.6 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: 3.28 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: 9.43 Time building geometry restraints manager: 8.54 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: 1.440 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: 6.870 Check model and map are aligned: 0.330 Set scattering table: 0.200 Process input model: 60.190 Find NCS groups from input model: 1.820 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.590 ------------------------------------------------------------------------------- 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 : 2.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 ILE cc_start: 0.7033 (OUTLIER) cc_final: 0.6462 (pp) REVERT: A 216 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.7997 (pt) outliers start: 45 outliers final: 14 residues processed: 126 average time/residue: 0.3060 time to fit residues: 62.8851 Evaluate side-chains 58 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 42 time to evaluate : 2.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 1004 LEU 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: 0.9980 chunk 145 optimal weight: 0.9990 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: 1.0984 ------------------------------------------------------------------------------- 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: 0.7569 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 21547 Z= 0.184 Angle : 0.591 14.045 29393 Z= 0.314 Chirality : 0.044 0.155 3483 Planarity : 0.004 0.046 3809 Dihedral : 6.323 59.448 3018 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.67 % Favored : 96.29 % Rotamer: Outliers : 1.89 % Allowed : 6.00 % Favored : 92.11 % 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: -0.56 (0.15), residues: 2779 helix: 1.04 (0.20), residues: 682 sheet: -0.40 (0.20), residues: 596 loop : -1.02 (0.15), residues: 1501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 104 HIS 0.005 0.001 HIS B1048 PHE 0.022 0.001 PHE A 497 TYR 0.012 0.001 TYR B 917 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 98 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 57 time to evaluate : 2.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 ILE cc_start: 0.7158 (OUTLIER) cc_final: 0.6591 (pp) REVERT: B 231 ILE cc_start: 0.7480 (mp) cc_final: 0.7192 (mm) REVERT: B 740 MET cc_start: 0.6365 (OUTLIER) cc_final: 0.6158 (mtm) outliers start: 41 outliers final: 21 residues processed: 92 average time/residue: 0.2931 time to fit residues: 46.2340 Evaluate side-chains 64 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 41 time to evaluate : 2.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 856 ILE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1004 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 143 optimal weight: 0.5980 chunk 80 optimal weight: 9.9990 chunk 214 optimal weight: 40.0000 chunk 175 optimal weight: 0.9980 chunk 71 optimal weight: 0.4980 chunk 258 optimal weight: 7.9990 chunk 279 optimal weight: 0.6980 chunk 230 optimal weight: 3.9990 chunk 256 optimal weight: 4.9990 chunk 88 optimal weight: 6.9990 chunk 207 optimal weight: 7.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- 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 ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 926 GLN C 955 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21547 Z= 0.162 Angle : 0.519 14.000 29393 Z= 0.271 Chirality : 0.042 0.145 3483 Planarity : 0.003 0.038 3809 Dihedral : 5.405 56.670 3012 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.32 % Favored : 95.65 % Rotamer: Outliers : 2.17 % Allowed : 6.46 % Favored : 91.37 % 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: -0.13 (0.16), residues: 2779 helix: 1.70 (0.21), residues: 661 sheet: -0.34 (0.20), residues: 627 loop : -0.78 (0.15), residues: 1491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 104 HIS 0.004 0.001 HIS B1048 PHE 0.014 0.001 PHE B1121 TYR 0.016 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 92 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 45 time to evaluate : 2.605 Fit side-chains revert: symmetry clash REVERT: A 101 ILE cc_start: 0.7144 (OUTLIER) cc_final: 0.6590 (pp) outliers start: 47 outliers final: 25 residues processed: 88 average time/residue: 0.2720 time to fit residues: 42.5985 Evaluate side-chains 63 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 37 time to evaluate : 2.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 856 ILE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 1004 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 255 optimal weight: 8.9990 chunk 194 optimal weight: 0.9980 chunk 134 optimal weight: 50.0000 chunk 28 optimal weight: 0.9980 chunk 123 optimal weight: 50.0000 chunk 173 optimal weight: 9.9990 chunk 259 optimal weight: 0.4980 chunk 274 optimal weight: 6.9990 chunk 135 optimal weight: 10.0000 chunk 245 optimal weight: 0.5980 chunk 73 optimal weight: 4.9990 overall best weight: 1.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 644 GLN A 957 GLN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN B 965 GLN C 955 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.2544 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= 0.179 Angle : 0.496 15.114 29393 Z= 0.257 Chirality : 0.042 0.142 3483 Planarity : 0.003 0.049 3809 Dihedral : 4.986 57.700 3010 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.71 % Favored : 96.26 % Rotamer: Outliers : 2.03 % Allowed : 7.34 % Favored : 90.63 % 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: 1.94 (0.21), residues: 656 sheet: -0.31 (0.20), residues: 656 loop : -0.64 (0.16), residues: 1467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 104 HIS 0.004 0.001 HIS B1048 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 86 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 42 time to evaluate : 2.956 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 101 ILE cc_start: 0.7365 (OUTLIER) cc_final: 0.6886 (pp) REVERT: A 239 GLN cc_start: 0.6789 (OUTLIER) cc_final: 0.6359 (tp40) REVERT: C 117 LEU cc_start: 0.6687 (tp) cc_final: 0.6460 (tt) outliers start: 44 outliers final: 26 residues processed: 84 average time/residue: 0.2822 time to fit residues: 43.1372 Evaluate side-chains 62 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 34 time to evaluate : 2.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 856 ILE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 570 LEU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1104 VAL 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: 0.9990 chunk 3 optimal weight: 10.0000 chunk 204 optimal weight: 10.0000 chunk 113 optimal weight: 2.9990 chunk 234 optimal weight: 0.8980 chunk 189 optimal weight: 0.4980 chunk 0 optimal weight: 9.9990 chunk 140 optimal weight: 7.9990 chunk 246 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- 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 239 GLN ** 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** ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 21547 Z= 0.182 Angle : 0.491 13.572 29393 Z= 0.252 Chirality : 0.042 0.143 3483 Planarity : 0.003 0.051 3809 Dihedral : 4.796 58.454 3008 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.92 % Favored : 96.04 % Rotamer: Outliers : 1.94 % Allowed : 8.22 % Favored : 89.84 % 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: 0.16 (0.16), residues: 2779 helix: 2.15 (0.21), residues: 642 sheet: -0.36 (0.19), residues: 698 loop : -0.56 (0.16), residues: 1439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 104 HIS 0.004 0.001 HIS B1048 PHE 0.015 0.001 PHE B 342 TYR 0.015 0.001 TYR A1067 ARG 0.003 0.000 ARG A 983 *********************** 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 78 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 36 time to evaluate : 2.146 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 101 ILE cc_start: 0.7269 (OUTLIER) cc_final: 0.6767 (pp) REVERT: A 239 GLN cc_start: 0.6757 (OUTLIER) cc_final: 0.6361 (tp40) REVERT: C 869 MET cc_start: 0.6528 (ptp) cc_final: 0.6288 (ptp) outliers start: 42 outliers final: 30 residues processed: 76 average time/residue: 0.2407 time to fit residues: 34.1105 Evaluate side-chains 67 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 35 time to evaluate : 2.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 856 ILE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 1004 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 92 optimal weight: 2.9990 chunk 247 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 chunk 161 optimal weight: 4.9990 chunk 67 optimal weight: 7.9990 chunk 274 optimal weight: 6.9990 chunk 228 optimal weight: 50.0000 chunk 127 optimal weight: 7.9990 chunk 22 optimal weight: 10.0000 chunk 90 optimal weight: 0.7980 chunk 144 optimal weight: 7.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- 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 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 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 21547 Z= 0.358 Angle : 0.569 15.181 29393 Z= 0.291 Chirality : 0.043 0.186 3483 Planarity : 0.004 0.051 3809 Dihedral : 5.059 59.883 3008 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.68 % Favored : 95.29 % Rotamer: Outliers : 2.03 % Allowed : 8.73 % Favored : 89.24 % 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: 0.01 (0.16), residues: 2779 helix: 2.05 (0.21), residues: 637 sheet: -0.50 (0.19), residues: 671 loop : -0.63 (0.16), residues: 1471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 104 HIS 0.005 0.001 HIS B1048 PHE 0.019 0.002 PHE C 92 TYR 0.017 0.002 TYR A1067 ARG 0.004 0.000 ARG A 815 *********************** 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 83 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 39 time to evaluate : 2.425 Fit side-chains REVERT: A 101 ILE cc_start: 0.7166 (OUTLIER) cc_final: 0.6642 (pp) REVERT: A 239 GLN cc_start: 0.7028 (OUTLIER) cc_final: 0.6447 (tp40) outliers start: 44 outliers final: 28 residues processed: 80 average time/residue: 0.2770 time to fit residues: 40.6996 Evaluate side-chains 63 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 33 time to evaluate : 2.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 264 optimal weight: 7.9990 chunk 30 optimal weight: 7.9990 chunk 156 optimal weight: 5.9990 chunk 200 optimal weight: 0.1980 chunk 155 optimal weight: 0.9980 chunk 231 optimal weight: 1.9990 chunk 153 optimal weight: 0.2980 chunk 273 optimal weight: 0.8980 chunk 171 optimal weight: 0.7980 chunk 166 optimal weight: 0.7980 chunk 126 optimal weight: 50.0000 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN B 935 GLN C 872 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 21547 Z= 0.127 Angle : 0.473 14.365 29393 Z= 0.242 Chirality : 0.041 0.192 3483 Planarity : 0.003 0.053 3809 Dihedral : 4.641 58.290 3008 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.42 % Favored : 96.55 % Rotamer: Outliers : 1.85 % Allowed : 9.23 % Favored : 88.92 % 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: 0.29 (0.16), residues: 2779 helix: 2.26 (0.21), residues: 642 sheet: -0.24 (0.19), residues: 683 loop : -0.49 (0.16), residues: 1454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 104 HIS 0.002 0.000 HIS C 207 PHE 0.012 0.001 PHE B1121 TYR 0.013 0.001 TYR A1067 ARG 0.004 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 81 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 41 time to evaluate : 2.531 Fit side-chains revert: symmetry clash REVERT: A 101 ILE cc_start: 0.7143 (OUTLIER) cc_final: 0.6599 (pp) REVERT: A 239 GLN cc_start: 0.6882 (OUTLIER) cc_final: 0.6472 (tp40) outliers start: 40 outliers final: 28 residues processed: 76 average time/residue: 0.2558 time to fit residues: 36.3868 Evaluate side-chains 66 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 36 time to evaluate : 2.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1104 VAL 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: 0.6980 chunk 163 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 53 optimal weight: 10.0000 chunk 174 optimal weight: 0.9980 chunk 186 optimal weight: 4.9990 chunk 135 optimal weight: 8.9990 chunk 25 optimal weight: 9.9990 chunk 215 optimal weight: 50.0000 chunk 249 optimal weight: 6.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- 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 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 317 ASN ** 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.3051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 21547 Z= 0.270 Angle : 0.526 13.782 29393 Z= 0.269 Chirality : 0.042 0.139 3483 Planarity : 0.003 0.054 3809 Dihedral : 4.767 57.822 3008 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.61 % Favored : 95.36 % Rotamer: Outliers : 1.99 % Allowed : 9.14 % Favored : 88.87 % 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: 0.22 (0.16), residues: 2779 helix: 2.19 (0.21), residues: 641 sheet: -0.38 (0.19), residues: 694 loop : -0.48 (0.16), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 104 HIS 0.004 0.001 HIS B1048 PHE 0.015 0.001 PHE C 342 TYR 0.015 0.001 TYR A1067 ARG 0.003 0.000 ARG B 765 *********************** 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 81 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 38 time to evaluate : 2.541 Fit side-chains revert: symmetry clash REVERT: A 101 ILE cc_start: 0.7322 (OUTLIER) cc_final: 0.6758 (pp) REVERT: A 239 GLN cc_start: 0.7016 (OUTLIER) cc_final: 0.6570 (tp40) REVERT: C 117 LEU cc_start: 0.6743 (tp) cc_final: 0.6534 (tt) REVERT: C 342 PHE cc_start: 0.5537 (t80) cc_final: 0.5301 (t80) outliers start: 43 outliers final: 30 residues processed: 77 average time/residue: 0.2723 time to fit residues: 37.7911 Evaluate side-chains 66 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 34 time to evaluate : 2.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 262 optimal weight: 0.8980 chunk 239 optimal weight: 10.0000 chunk 255 optimal weight: 7.9990 chunk 153 optimal weight: 0.7980 chunk 111 optimal weight: 7.9990 chunk 200 optimal weight: 20.0000 chunk 78 optimal weight: 0.9980 chunk 230 optimal weight: 6.9990 chunk 241 optimal weight: 9.9990 chunk 254 optimal weight: 1.9990 chunk 167 optimal weight: 7.9990 overall best weight: 2.3384 ------------------------------------------------------------------------------- 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 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.3116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 21547 Z= 0.233 Angle : 0.505 13.376 29393 Z= 0.259 Chirality : 0.041 0.139 3483 Planarity : 0.003 0.055 3809 Dihedral : 4.722 57.089 3008 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.28 % Favored : 95.68 % Rotamer: Outliers : 1.66 % Allowed : 9.56 % Favored : 88.78 % 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: 0.24 (0.16), residues: 2779 helix: 2.20 (0.21), residues: 642 sheet: -0.35 (0.19), residues: 682 loop : -0.48 (0.16), residues: 1455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 104 HIS 0.004 0.001 HIS B1048 PHE 0.016 0.001 PHE C 342 TYR 0.015 0.001 TYR A1067 ARG 0.004 0.000 ARG B 765 *********************** 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 73 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 37 time to evaluate : 2.535 Fit side-chains revert: symmetry clash REVERT: A 101 ILE cc_start: 0.7133 (OUTLIER) cc_final: 0.6536 (pp) REVERT: A 239 GLN cc_start: 0.7054 (OUTLIER) cc_final: 0.6514 (tp40) REVERT: C 117 LEU cc_start: 0.6790 (tp) cc_final: 0.6576 (tt) outliers start: 36 outliers final: 33 residues processed: 71 average time/residue: 0.2540 time to fit residues: 33.5822 Evaluate side-chains 71 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 36 time to evaluate : 2.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 269 optimal weight: 9.9990 chunk 164 optimal weight: 6.9990 chunk 127 optimal weight: 30.0000 chunk 187 optimal weight: 0.9980 chunk 282 optimal weight: 5.9990 chunk 260 optimal weight: 2.9990 chunk 225 optimal weight: 50.0000 chunk 23 optimal weight: 4.9990 chunk 174 optimal weight: 0.7980 chunk 138 optimal weight: 8.9990 chunk 178 optimal weight: 7.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- 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 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 21547 Z= 0.301 Angle : 0.543 13.079 29393 Z= 0.278 Chirality : 0.042 0.155 3483 Planarity : 0.004 0.057 3809 Dihedral : 4.854 56.382 3008 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.93 % Favored : 95.03 % Rotamer: Outliers : 1.62 % Allowed : 9.51 % Favored : 88.87 % 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: 0.16 (0.16), residues: 2779 helix: 2.07 (0.21), residues: 652 sheet: -0.42 (0.19), residues: 687 loop : -0.50 (0.17), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 104 HIS 0.004 0.001 HIS C 49 PHE 0.015 0.001 PHE A1089 TYR 0.016 0.001 TYR A1067 ARG 0.003 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 70 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 35 time to evaluate : 2.586 Fit side-chains revert: symmetry clash REVERT: A 101 ILE cc_start: 0.7238 (OUTLIER) cc_final: 0.6638 (pp) REVERT: A 239 GLN cc_start: 0.7142 (OUTLIER) cc_final: 0.6418 (tp40) REVERT: C 117 LEU cc_start: 0.6823 (tp) cc_final: 0.6612 (tt) REVERT: C 342 PHE cc_start: 0.5802 (t80) cc_final: 0.5387 (t80) outliers start: 35 outliers final: 31 residues processed: 69 average time/residue: 0.2546 time to fit residues: 32.8111 Evaluate side-chains 68 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 35 time to evaluate : 2.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 240 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 chunk 207 optimal weight: 0.9980 chunk 33 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 225 optimal weight: 0.5980 chunk 94 optimal weight: 0.8980 chunk 231 optimal weight: 5.9990 chunk 28 optimal weight: 0.2980 chunk 41 optimal weight: 3.9990 chunk 198 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.065224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.046468 restraints weight = 93968.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.048113 restraints weight = 43391.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.049168 restraints weight = 26224.873| |-----------------------------------------------------------------------------| r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.3309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 21547 Z= 0.134 Angle : 0.472 12.501 29393 Z= 0.242 Chirality : 0.041 0.139 3483 Planarity : 0.003 0.061 3809 Dihedral : 4.512 55.780 3008 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.07 % Favored : 95.90 % Rotamer: Outliers : 1.39 % Allowed : 9.74 % Favored : 88.87 % 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: 2.35 (0.21), residues: 645 sheet: -0.37 (0.20), residues: 669 loop : -0.38 (0.16), residues: 1465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 104 HIS 0.003 0.001 HIS B1064 PHE 0.011 0.001 PHE B1121 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: 2881.62 seconds wall clock time: 54 minutes 6.09 seconds (3246.09 seconds total)