Starting phenix.real_space_refine on Fri Dec 8 05:08:24 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cy7_27069/12_2023/8cy7_27069_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cy7_27069/12_2023/8cy7_27069.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cy7_27069/12_2023/8cy7_27069.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cy7_27069/12_2023/8cy7_27069.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cy7_27069/12_2023/8cy7_27069_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cy7_27069/12_2023/8cy7_27069_trim.pdb" } resolution = 2.9 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= 0.000 sd= 0.017 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: 5 Type Number sf(0) Gaussians S 123 5.16 5 C 18023 2.51 5 N 4654 2.21 5 O 5583 1.98 5 H 26549 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 54932 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 16148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1050, 16148 Classifications: {'peptide': 1050} Link IDs: {'PTRANS': 52, 'TRANS': 997} Chain breaks: 5 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 16161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1050, 16161 Classifications: {'peptide': 1050} Link IDs: {'PTRANS': 52, 'TRANS': 997} Chain breaks: 5 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 16160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1050, 16160 Classifications: {'peptide': 1050} Link IDs: {'PTRANS': 52, 'TRANS': 997} Chain breaks: 5 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 1809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 1809 Classifications: {'peptide': 121} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "E" Number of atoms: 1809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 1809 Classifications: {'peptide': 121} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "F" Number of atoms: 1809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 1809 Classifications: {'peptide': 121} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 238 Unusual residues: {'NAG': 17} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 17 Chain: "B" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Chain: "C" Number of atoms: 252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 252 Unusual residues: {'NAG': 18} Classifications: {'undetermined': 18} Link IDs: {None: 17} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 18 Time building chain proxies: 17.53, per 1000 atoms: 0.32 Number of scatterers: 54932 At special positions: 0 Unit cell: (160.5, 154.08, 196.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 123 16.00 O 5583 8.00 N 4654 7.00 C 18023 6.00 H 26549 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " 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=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " 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=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 95 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 95 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 95 " distance=2.03 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 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1303 " - " ASN A 331 " " NAG A1304 " - " ASN A 603 " " NAG A1306 " - " ASN A 657 " " NAG A1307 " - " ASN A 709 " " NAG A1308 " - " ASN A1074 " " NAG A1309 " - " ASN A 717 " " NAG A1311 " - " ASN A 801 " " NAG A1313 " - " ASN A 149 " " NAG A1314 " - " ASN A 234 " " NAG A1316 " - " ASN A 343 " " NAG B1301 " - " ASN B 61 " " NAG B1304 " - " ASN B 603 " " NAG B1306 " - " ASN B 657 " " NAG B1308 " - " ASN B1074 " " NAG B1310 " - " ASN B 343 " " NAG B1312 " - " ASN B 282 " " NAG B1313 " - " ASN B 234 " " NAG B1314 " - " ASN B 165 " " NAG C1302 " - " ASN C 61 " " NAG C1304 " - " ASN C 282 " " NAG C1305 " - " ASN C 331 " " NAG C1306 " - " ASN C 603 " " NAG C1307 " - " ASN C 616 " " NAG C1308 " - " ASN C 657 " " NAG C1309 " - " ASN C1074 " " NAG C1312 " - " ASN C 149 " " NAG C1313 " - " ASN C 165 " " NAG C1314 " - " ASN C 234 " " NAG G 1 " - " ASN A1134 " " NAG H 1 " - " ASN A 165 " " NAG I 1 " - " ASN A 282 " " NAG J 1 " - " ASN A1098 " " NAG K 1 " - " ASN B 801 " " NAG N 1 " - " ASN B1098 " " NAG P 1 " - " ASN C 801 " " NAG Q 1 " - " ASN C 343 " " NAG R 1 " - " ASN C1098 " Time building additional restraints: 30.48 Conformation dependent library (CDL) restraints added in 4.0 seconds 6942 Ramachandran restraints generated. 3471 Oldfield, 0 Emsley, 3471 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6564 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 54 sheets defined 23.1% alpha, 23.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.40 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 364 through 370 removed outlier: 4.235A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 619 through 623 Processing helix chain 'A' and resid 632 through 637 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 757 removed outlier: 3.830A pdb=" N GLY A 757 " --> pdb=" O LEU A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.527A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 891 removed outlier: 4.055A pdb=" N GLY A 891 " --> pdb=" O PHE A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.484A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.088A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 3.582A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N SER A1147 " --> pdb=" O PRO A1143 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.660A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 372 removed outlier: 4.241A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASN B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N SER B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 390 removed outlier: 4.079A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 407 No H-bonds generated for 'chain 'B' and resid 405 through 407' Processing helix chain 'B' and resid 418 through 423 removed outlier: 3.617A pdb=" N ASN B 422 " --> pdb=" O ILE B 418 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N TYR B 423 " --> pdb=" O ALA B 419 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 418 through 423' Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 616 through 620 Processing helix chain 'B' and resid 632 through 638 removed outlier: 3.719A pdb=" N TYR B 636 " --> pdb=" O THR B 632 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR B 638 " --> pdb=" O ARG B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.624A pdb=" N ILE B 742 " --> pdb=" O CYS B 738 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N CYS B 743 " --> pdb=" O THR B 739 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 757 removed outlier: 3.706A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N TYR B 756 " --> pdb=" O LEU B 752 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLY B 757 " --> pdb=" O LEU B 753 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.765A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 891 removed outlier: 4.057A pdb=" N GLY B 891 " --> pdb=" O PHE B 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.562A 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 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1032 removed outlier: 3.557A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 3.882A pdb=" N SER B1147 " --> pdb=" O PRO B1143 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 385 through 390 removed outlier: 3.553A pdb=" N ASP C 389 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 407 No H-bonds generated for 'chain 'C' and resid 405 through 407' Processing helix chain 'C' and resid 418 through 423 removed outlier: 4.254A pdb=" N TYR C 423 " --> pdb=" O ALA C 419 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 757 removed outlier: 3.664A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N TYR C 756 " --> pdb=" O LEU C 752 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLY C 757 " --> pdb=" O LEU C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 825 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 891 removed outlier: 4.020A pdb=" N GLY C 891 " --> pdb=" O PHE C 888 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.503A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.097A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 4.647A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 90 Processing helix chain 'E' and resid 86 through 90 Processing helix chain 'F' and resid 86 through 90 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 4.028A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 52 removed outlier: 4.245A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 225 through 229 removed outlier: 5.475A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU A 96 " --> pdb=" O ASN A 188 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 125 through 129 Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 316 removed outlier: 6.941A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 326 through 328 Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.894A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 391 through 392 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 553 through 554 removed outlier: 3.703A pdb=" N THR A 553 " --> pdb=" O ASP A 586 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.791A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.409A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 702 through 703 Processing sheet with id=AB4, first strand: chain 'A' and resid 712 through 713 Processing sheet with id=AB5, first strand: chain 'A' and resid 717 through 728 removed outlier: 6.300A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.352A 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 789 removed outlier: 5.866A pdb=" N ILE A 788 " --> pdb=" O ASN B 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 1123 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 27 through 30 removed outlier: 3.956A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 48 through 52 removed outlier: 4.027A 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 removed outlier: 3.651A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 316 removed outlier: 6.938A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 326 through 328 Processing sheet with id=AC6, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.127A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 448 through 453 removed outlier: 6.980A pdb=" N TYR B 449 " --> pdb=" O PHE B 497 " (cutoff:3.500A) removed outlier: 8.645A pdb=" N PHE B 497 " --> pdb=" O TYR B 449 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N TYR B 451 " --> pdb=" O TYR B 495 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 553 through 554 removed outlier: 3.695A pdb=" N THR B 553 " --> pdb=" O ASP B 586 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.587A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 712 through 713 Processing sheet with id=AD2, first strand: chain 'B' and resid 717 through 728 removed outlier: 6.423A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 717 through 728 removed outlier: 6.423A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 735 through 736 Processing sheet with id=AD5, first strand: chain 'B' and resid 788 through 789 removed outlier: 5.628A pdb=" N ILE B 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'B' and resid 1120 through 1123 removed outlier: 3.564A pdb=" N CYS B1082 " --> pdb=" O VAL B1133 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD8, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.881A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA C 93 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 48 through 55 removed outlier: 4.357A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.842A pdb=" N TRP C 104 " --> pdb=" O ILE C 119 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 311 through 317 removed outlier: 4.164A pdb=" N GLY C 311 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.881A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE5, first strand: chain 'C' and resid 538 through 543 removed outlier: 3.686A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ILE C 584 " --> pdb=" O SER C 555 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 664 through 667 removed outlier: 6.441A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 712 through 713 Processing sheet with id=AE8, first strand: chain 'C' and resid 717 through 728 removed outlier: 6.463A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU C1063 " --> pdb=" O PHE C1052 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N PHE C1052 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1120 through 1123 Processing sheet with id=AF1, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AF2, first strand: chain 'D' and resid 4 through 8 Processing sheet with id=AF3, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.079A pdb=" N ARG D 37 " --> pdb=" O PHE D 46 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N PHE D 46 " --> pdb=" O ARG D 37 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 10 through 13 removed outlier: 7.296A pdb=" N GLY D 99 " --> pdb=" O VAL D 108 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N VAL D 108 " --> pdb=" O GLY D 99 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 4 through 8 Processing sheet with id=AF6, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.184A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N SER E 120 " --> pdb=" O GLY E 10 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N VAL E 12 " --> pdb=" O SER E 120 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ARG E 37 " --> pdb=" O PHE E 46 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N PHE E 46 " --> pdb=" O ARG E 37 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.184A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N SER E 120 " --> pdb=" O GLY E 10 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N VAL E 12 " --> pdb=" O SER E 120 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N GLY E 99 " --> pdb=" O VAL E 108 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N VAL E 108 " --> pdb=" O GLY E 99 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'F' and resid 5 through 8 Processing sheet with id=AF9, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.101A pdb=" N GLY F 10 " --> pdb=" O THR F 118 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N SER F 120 " --> pdb=" O GLY F 10 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N VAL F 12 " --> pdb=" O SER F 120 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ARG F 37 " --> pdb=" O PHE F 46 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N PHE F 46 " --> pdb=" O ARG F 37 " (cutoff:3.500A) 1079 hydrogen bonds defined for protein. 2946 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 18.53 Time building geometry restraints manager: 32.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 26537 1.03 - 1.23: 92 1.23 - 1.42: 12252 1.42 - 1.62: 16531 1.62 - 1.81: 156 Bond restraints: 55568 Sorted by residual: bond pdb=" C1 NAG C1304 " pdb=" O5 NAG C1304 " ideal model delta sigma weight residual 1.406 1.459 -0.053 2.00e-02 2.50e+03 7.01e+00 bond pdb=" C1 NAG I 1 " pdb=" O5 NAG I 1 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.71e+00 bond pdb=" C1 NAG P 1 " pdb=" O5 NAG P 1 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.53e+00 bond pdb=" C1 NAG B1306 " pdb=" O5 NAG B1306 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.52e+00 bond pdb=" C1 NAG L 2 " pdb=" O5 NAG L 2 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.17e+00 ... (remaining 55563 not shown) Histogram of bond angle deviations from ideal: 68.70 - 85.02: 380 85.02 - 101.34: 38 101.34 - 117.66: 72182 117.66 - 133.98: 26974 133.98 - 150.29: 14 Bond angle restraints: 99588 Sorted by residual: angle pdb="HD21 ASN B 657 " pdb=" ND2 ASN B 657 " pdb="HD22 ASN B 657 " ideal model delta sigma weight residual 120.00 73.91 46.09 3.00e+00 1.11e-01 2.36e+02 angle pdb="HD21 ASN B 801 " pdb=" ND2 ASN B 801 " pdb="HD22 ASN B 801 " ideal model delta sigma weight residual 120.00 74.14 45.86 3.00e+00 1.11e-01 2.34e+02 angle pdb="HD21 ASN A1134 " pdb=" ND2 ASN A1134 " pdb="HD22 ASN A1134 " ideal model delta sigma weight residual 120.00 74.15 45.85 3.00e+00 1.11e-01 2.34e+02 angle pdb="HD21 ASN C 801 " pdb=" ND2 ASN C 801 " pdb="HD22 ASN C 801 " ideal model delta sigma weight residual 120.00 74.20 45.80 3.00e+00 1.11e-01 2.33e+02 angle pdb="HD21 ASN A 801 " pdb=" ND2 ASN A 801 " pdb="HD22 ASN A 801 " ideal model delta sigma weight residual 120.00 74.25 45.75 3.00e+00 1.11e-01 2.33e+02 ... (remaining 99583 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.51: 26057 25.51 - 51.02: 907 51.02 - 76.52: 132 76.52 - 102.03: 21 102.03 - 127.54: 1 Dihedral angle restraints: 27118 sinusoidal: 14857 harmonic: 12261 Sorted by residual: dihedral pdb=" CB CYS B 131 " pdb=" SG CYS B 131 " pdb=" SG CYS B 166 " pdb=" CB CYS B 166 " ideal model delta sinusoidal sigma weight residual 93.00 134.64 -41.64 1 1.00e+01 1.00e-02 2.43e+01 dihedral pdb=" CA VAL C 620 " pdb=" C VAL C 620 " pdb=" N PRO C 621 " pdb=" CA PRO C 621 " ideal model delta harmonic sigma weight residual -180.00 -155.70 -24.30 0 5.00e+00 4.00e-02 2.36e+01 dihedral pdb=" C ILE B 624 " pdb=" N ILE B 624 " pdb=" CA ILE B 624 " pdb=" CB ILE B 624 " ideal model delta harmonic sigma weight residual -122.00 -133.29 11.29 0 2.50e+00 1.60e-01 2.04e+01 ... (remaining 27115 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.349: 4575 0.349 - 0.698: 39 0.698 - 1.047: 0 1.047 - 1.396: 6 1.396 - 1.745: 43 Chirality restraints: 4663 Sorted by residual: chirality pdb=" CG LEU B 878 " pdb=" CB LEU B 878 " pdb=" CD1 LEU B 878 " pdb=" CD2 LEU B 878 " both_signs ideal model delta sigma weight residual False -2.59 -0.85 -1.74 2.00e-01 2.50e+01 7.61e+01 chirality pdb=" CG LEU B1004 " pdb=" CB LEU B1004 " pdb=" CD1 LEU B1004 " pdb=" CD2 LEU B1004 " both_signs ideal model delta sigma weight residual False -2.59 -0.86 -1.73 2.00e-01 2.50e+01 7.51e+01 chirality pdb=" CG LEU C1004 " pdb=" CB LEU C1004 " pdb=" CD1 LEU C1004 " pdb=" CD2 LEU C1004 " both_signs ideal model delta sigma weight residual False -2.59 -0.86 -1.73 2.00e-01 2.50e+01 7.50e+01 ... (remaining 4660 not shown) Planarity restraints: 8345 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL C 620 " -0.050 5.00e-02 4.00e+02 7.66e-02 9.38e+00 pdb=" N PRO C 621 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO C 621 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO C 621 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 861 " 0.025 5.00e-02 4.00e+02 3.73e-02 2.22e+00 pdb=" N PRO C 862 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO C 862 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 862 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 861 " 0.023 5.00e-02 4.00e+02 3.47e-02 1.93e+00 pdb=" N PRO B 862 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO B 862 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 862 " 0.019 5.00e-02 4.00e+02 ... (remaining 8342 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.16: 2106 2.16 - 2.77: 101164 2.77 - 3.38: 142505 3.38 - 3.99: 183049 3.99 - 4.60: 282005 Nonbonded interactions: 710829 Sorted by model distance: nonbonded pdb=" H ASN C1125 " pdb=" HA ASN C1125 " model vdw 1.551 1.816 nonbonded pdb=" H LYS B 187 " pdb=" HA LYS B 187 " model vdw 1.564 1.816 nonbonded pdb=" H HIS C 66 " pdb=" HA HIS C 66 " model vdw 1.567 1.816 nonbonded pdb=" H ILE B 584 " pdb=" HA ILE B 584 " model vdw 1.568 1.816 nonbonded pdb=" H HIS B1088 " pdb=" HA HIS B1088 " model vdw 1.568 1.816 ... (remaining 710824 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 25 through 615 or (resid 616 and (name N or name CA or nam \ e C or name O or name CB or name CG or name OD1 or name ND2 or name H or name HA \ or name HB2 or name HB3 or name HD21)) or resid 617 through 801 or (resid 802 a \ nd (name N or name CA or name C or name O or name CB or name CG or name CD1 or n \ ame CD2 or name CE1 or name CE2 or name CZ or name HA or name HB2 or name HB3 or \ name HD1 or name HD2 or name HE1 or name HE2 or name HZ )) or resid 803 through \ 1147 or resid 1301 through 1315)) selection = (chain 'B' and (resid 25 through 320 or (resid 321 and (name N or name CA or nam \ e C or name O or name CB or name H or name HA )) or resid 322 through 615 or (re \ sid 616 and (name N or name CA or name C or name O or name CB or name CG or name \ OD1 or name ND2 or name H or name HA or name HB2 or name HB3 or name HD21)) or \ resid 617 through 656 or (resid 657 and (name N or name CA or name C or name O o \ r name CB or name CG or name OD1 or name ND2 or name H or name HA or name HB2 or \ name HB3 or name HD21)) or resid 658 through 800 or (resid 801 and (name N or n \ ame CA or name C or name O or name CB or name CG or name OD1 or name ND2 or name \ HA or name HB2 or name HB3 or name HD21 or name HD22)) or resid 802 or (resid 8 \ 03 and (name N or name CA or name C or name O or name CB or name OG or name HA o \ r name HB2 or name HB3 or name HG )) or resid 804 through 1133 or (resid 1134 th \ rough 1135 and (name N or name CA or name C or name O or name CB or name CG or n \ ame OD1 or name ND2 or name HA or name HB2 or name HB3 or name HD21 or name HD22 \ )) or resid 1136 through 1147 or resid 1301 through 1315)) selection = (chain 'C' and (resid 25 through 320 or (resid 321 and (name N or name CA or nam \ e C or name O or name CB or name H or name HA )) or resid 322 through 800 or (re \ sid 801 and (name N or name CA or name C or name O or name CB or name CG or name \ OD1 or name ND2 or name HA or name HB2 or name HB3 or name HD21 or name HD22)) \ or resid 802 or (resid 803 and (name N or name CA or name C or name O or name CB \ or name OG or name HA or name HB2 or name HB3 or name HG )) or resid 804 throug \ h 1133 or (resid 1134 through 1135 and (name N or name CA or name C or name O or \ name CB or name CG or name OD1 or name ND2 or name HA or name HB2 or name HB3 o \ r name HD21 or name HD22)) or resid 1136 through 1147 or resid 1301 through 1315 \ )) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.810 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: 0.620 Extract box with map and model: 14.040 Check model and map are aligned: 0.610 Set scattering table: 0.390 Process input model: 123.130 Find NCS groups from input model: 2.250 Set up NCS constraints: 0.400 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 152.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 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 : 0.003 0.053 29019 Z= 0.223 Angle : 0.757 15.504 39504 Z= 0.368 Chirality : 0.172 1.745 4663 Planarity : 0.003 0.077 5011 Dihedral : 13.015 127.538 11496 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.75 % Favored : 96.11 % Rotamer: Outliers : 0.26 % Allowed : 0.13 % Favored : 99.60 % Cbeta Deviations : 0.30 % 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: 0.96 (0.15), residues: 3471 helix: 3.33 (0.21), residues: 647 sheet: 0.91 (0.19), residues: 712 loop : -0.33 (0.14), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP C 886 HIS 0.001 0.000 HIS A 207 PHE 0.010 0.001 PHE B 592 TYR 0.010 0.000 TYR A1067 ARG 0.001 0.000 ARG A 328 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6942 Ramachandran restraints generated. 3471 Oldfield, 0 Emsley, 3471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6942 Ramachandran restraints generated. 3471 Oldfield, 0 Emsley, 3471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 147 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue LYS 147 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue LYS 147 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Evaluate side-chains 157 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 149 time to evaluate : 3.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 8 residues processed: 157 average time/residue: 1.8226 time to fit residues: 356.2004 Evaluate side-chains 96 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 88 time to evaluate : 3.087 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 8 residues processed: 0 time to fit residues: 3.9243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 296 optimal weight: 2.9990 chunk 266 optimal weight: 7.9990 chunk 147 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 179 optimal weight: 1.9990 chunk 142 optimal weight: 30.0000 chunk 275 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 167 optimal weight: 0.7980 chunk 204 optimal weight: 1.9990 chunk 318 optimal weight: 50.0000 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1135 ASN ** B 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 81 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.1211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 29019 Z= 0.317 Angle : 0.773 15.549 39504 Z= 0.383 Chirality : 0.172 1.769 4663 Planarity : 0.004 0.081 5011 Dihedral : 8.662 118.481 5322 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.84 % Favored : 95.04 % Rotamer: Outliers : 0.53 % Allowed : 3.99 % Favored : 95.48 % Cbeta Deviations : 0.24 % 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: 0.71 (0.15), residues: 3471 helix: 3.02 (0.21), residues: 672 sheet: 0.73 (0.19), residues: 737 loop : -0.50 (0.14), residues: 2062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 100 HIS 0.004 0.001 HIS B1048 PHE 0.018 0.001 PHE C 392 TYR 0.016 0.001 TYR B1067 ARG 0.018 0.000 ARG E 37 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6942 Ramachandran restraints generated. 3471 Oldfield, 0 Emsley, 3471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6942 Ramachandran restraints generated. 3471 Oldfield, 0 Emsley, 3471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 147 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue LYS 147 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue LYS 147 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Evaluate side-chains 105 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 89 time to evaluate : 3.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 12 residues processed: 103 average time/residue: 1.6051 time to fit residues: 212.7208 Evaluate side-chains 95 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 83 time to evaluate : 3.140 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 11 residues processed: 1 average time/residue: 0.7486 time to fit residues: 5.1295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 177 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 265 optimal weight: 2.9990 chunk 217 optimal weight: 5.9990 chunk 87 optimal weight: 4.9990 chunk 319 optimal weight: 4.9990 chunk 344 optimal weight: 20.0000 chunk 284 optimal weight: 1.9990 chunk 316 optimal weight: 30.0000 chunk 108 optimal weight: 1.9990 chunk 256 optimal weight: 7.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1135 ASN ** B 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 29019 Z= 0.295 Angle : 0.752 15.516 39504 Z= 0.373 Chirality : 0.172 1.767 4663 Planarity : 0.003 0.067 5011 Dihedral : 8.014 115.831 5322 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.49 % Favored : 95.39 % Rotamer: Outliers : 0.83 % Allowed : 4.95 % Favored : 94.22 % Cbeta Deviations : 0.27 % 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: 0.61 (0.15), residues: 3471 helix: 2.92 (0.21), residues: 665 sheet: 0.66 (0.19), residues: 748 loop : -0.56 (0.14), residues: 2058 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 100 HIS 0.004 0.001 HIS B1048 PHE 0.020 0.001 PHE E 46 TYR 0.016 0.001 TYR B1067 ARG 0.004 0.000 ARG B 634 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6942 Ramachandran restraints generated. 3471 Oldfield, 0 Emsley, 3471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6942 Ramachandran restraints generated. 3471 Oldfield, 0 Emsley, 3471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 147 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue LYS 147 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue LYS 147 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Evaluate side-chains 114 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 89 time to evaluate : 3.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 14 residues processed: 107 average time/residue: 1.7393 time to fit residues: 236.6635 Evaluate side-chains 94 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 80 time to evaluate : 3.179 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 13 residues processed: 1 average time/residue: 0.6033 time to fit residues: 5.0707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 315 optimal weight: 30.0000 chunk 240 optimal weight: 8.9990 chunk 165 optimal weight: 0.5980 chunk 35 optimal weight: 5.9990 chunk 152 optimal weight: 3.9990 chunk 214 optimal weight: 0.0770 chunk 320 optimal weight: 8.9990 chunk 339 optimal weight: 7.9990 chunk 167 optimal weight: 1.9990 chunk 303 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 overall best weight: 1.3344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1135 ASN ** B 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 717 ASN ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 29019 Z= 0.227 Angle : 0.736 15.542 39504 Z= 0.363 Chirality : 0.171 1.756 4663 Planarity : 0.003 0.066 5011 Dihedral : 7.666 114.417 5322 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.35 % Favored : 95.53 % Rotamer: Outliers : 0.96 % Allowed : 5.84 % Favored : 93.20 % Cbeta Deviations : 0.24 % 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: 0.59 (0.15), residues: 3471 helix: 2.93 (0.21), residues: 664 sheet: 0.61 (0.19), residues: 747 loop : -0.56 (0.14), residues: 2060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 100 HIS 0.006 0.001 HIS C 69 PHE 0.012 0.001 PHE A 898 TYR 0.014 0.001 TYR B1067 ARG 0.002 0.000 ARG E 37 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6942 Ramachandran restraints generated. 3471 Oldfield, 0 Emsley, 3471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6942 Ramachandran restraints generated. 3471 Oldfield, 0 Emsley, 3471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 147 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue LYS 147 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue LYS 147 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Evaluate side-chains 110 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 81 time to evaluate : 3.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 16 residues processed: 104 average time/residue: 1.6309 time to fit residues: 220.1393 Evaluate side-chains 92 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 76 time to evaluate : 3.285 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 16 residues processed: 0 time to fit residues: 4.0553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 282 optimal weight: 1.9990 chunk 192 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 252 optimal weight: 3.9990 chunk 139 optimal weight: 30.0000 chunk 289 optimal weight: 1.9990 chunk 234 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 173 optimal weight: 3.9990 chunk 304 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1135 ASN C1106 GLN E 1 GLN ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 29019 Z= 0.379 Angle : 0.793 15.793 39504 Z= 0.394 Chirality : 0.173 1.798 4663 Planarity : 0.004 0.132 5011 Dihedral : 7.525 113.891 5322 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.22 % Favored : 93.66 % Rotamer: Outliers : 1.06 % Allowed : 7.07 % Favored : 91.88 % Cbeta Deviations : 0.30 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.61 % 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 (0.15), residues: 3471 helix: 2.68 (0.21), residues: 665 sheet: 0.25 (0.18), residues: 763 loop : -0.75 (0.14), residues: 2043 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 35 HIS 0.005 0.001 HIS C 69 PHE 0.041 0.002 PHE D 67 TYR 0.020 0.001 TYR B1067 ARG 0.003 0.000 ARG B 634 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6942 Ramachandran restraints generated. 3471 Oldfield, 0 Emsley, 3471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6942 Ramachandran restraints generated. 3471 Oldfield, 0 Emsley, 3471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 147 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue LYS 147 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue LYS 147 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Evaluate side-chains 115 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 83 time to evaluate : 3.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 19 residues processed: 107 average time/residue: 1.5625 time to fit residues: 217.2358 Evaluate side-chains 94 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 75 time to evaluate : 3.244 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 18 residues processed: 2 average time/residue: 1.3389 time to fit residues: 7.6225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 114 optimal weight: 6.9990 chunk 305 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 199 optimal weight: 0.5980 chunk 83 optimal weight: 0.5980 chunk 339 optimal weight: 40.0000 chunk 281 optimal weight: 0.6980 chunk 157 optimal weight: 2.9990 chunk 28 optimal weight: 7.9990 chunk 112 optimal weight: 6.9990 chunk 178 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 29019 Z= 0.195 Angle : 0.740 16.888 39504 Z= 0.365 Chirality : 0.172 1.818 4663 Planarity : 0.003 0.047 5011 Dihedral : 7.205 112.556 5322 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.32 % Favored : 95.53 % Rotamer: Outliers : 0.79 % Allowed : 7.49 % Favored : 91.71 % Cbeta Deviations : 0.30 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.61 % 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: 0.41 (0.15), residues: 3471 helix: 2.86 (0.21), residues: 663 sheet: 0.37 (0.19), residues: 755 loop : -0.65 (0.14), residues: 2053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 100 HIS 0.004 0.001 HIS C 69 PHE 0.014 0.001 PHE D 67 TYR 0.012 0.001 TYR B1067 ARG 0.004 0.000 ARG A 983 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6942 Ramachandran restraints generated. 3471 Oldfield, 0 Emsley, 3471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6942 Ramachandran restraints generated. 3471 Oldfield, 0 Emsley, 3471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 147 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue LYS 147 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue LYS 147 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Evaluate side-chains 98 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 74 time to evaluate : 3.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 21 residues processed: 95 average time/residue: 1.5692 time to fit residues: 196.1634 Evaluate side-chains 97 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 76 time to evaluate : 3.110 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 21 residues processed: 2 average time/residue: 0.7754 time to fit residues: 6.3537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 327 optimal weight: 30.0000 chunk 38 optimal weight: 30.0000 chunk 193 optimal weight: 3.9990 chunk 248 optimal weight: 6.9990 chunk 192 optimal weight: 2.9990 chunk 285 optimal weight: 8.9990 chunk 189 optimal weight: 3.9990 chunk 338 optimal weight: 20.0000 chunk 211 optimal weight: 0.8980 chunk 206 optimal weight: 0.9990 chunk 156 optimal weight: 4.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 GLN ** B 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.2936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 29019 Z= 0.403 Angle : 0.799 16.020 39504 Z= 0.397 Chirality : 0.173 1.781 4663 Planarity : 0.003 0.059 5011 Dihedral : 7.250 111.675 5322 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.60 % Favored : 93.29 % Rotamer: Outliers : 0.86 % Allowed : 8.02 % Favored : 91.12 % Cbeta Deviations : 0.30 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.61 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.15), residues: 3471 helix: 2.56 (0.21), residues: 671 sheet: 0.09 (0.18), residues: 775 loop : -0.82 (0.14), residues: 2025 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 886 HIS 0.005 0.001 HIS A1048 PHE 0.022 0.002 PHE A 898 TYR 0.019 0.001 TYR B1067 ARG 0.004 0.000 ARG A 983 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6942 Ramachandran restraints generated. 3471 Oldfield, 0 Emsley, 3471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6942 Ramachandran restraints generated. 3471 Oldfield, 0 Emsley, 3471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 147 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue LYS 147 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue LYS 147 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Evaluate side-chains 107 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 81 time to evaluate : 3.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 20 residues processed: 104 average time/residue: 1.6400 time to fit residues: 225.8127 Evaluate side-chains 97 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 77 time to evaluate : 3.196 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 19 residues processed: 2 average time/residue: 1.3604 time to fit residues: 7.8718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 209 optimal weight: 0.3980 chunk 135 optimal weight: 9.9990 chunk 202 optimal weight: 0.8980 chunk 101 optimal weight: 0.8980 chunk 66 optimal weight: 0.5980 chunk 65 optimal weight: 0.5980 chunk 215 optimal weight: 1.9990 chunk 230 optimal weight: 0.8980 chunk 167 optimal weight: 1.9990 chunk 31 optimal weight: 10.0000 chunk 265 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 29019 Z= 0.180 Angle : 0.742 15.385 39504 Z= 0.366 Chirality : 0.171 1.745 4663 Planarity : 0.003 0.102 5011 Dihedral : 7.033 111.245 5322 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.70 % Favored : 95.19 % Rotamer: Outliers : 0.76 % Allowed : 8.15 % Favored : 91.09 % Cbeta Deviations : 0.30 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.61 % 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: 0.31 (0.15), residues: 3471 helix: 2.75 (0.21), residues: 670 sheet: 0.26 (0.19), residues: 760 loop : -0.71 (0.14), residues: 2041 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 64 HIS 0.004 0.001 HIS C 69 PHE 0.022 0.001 PHE A 855 TYR 0.011 0.001 TYR B1067 ARG 0.012 0.000 ARG B 815 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6942 Ramachandran restraints generated. 3471 Oldfield, 0 Emsley, 3471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6942 Ramachandran restraints generated. 3471 Oldfield, 0 Emsley, 3471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 147 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue LYS 147 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue LYS 147 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Evaluate side-chains 99 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 76 time to evaluate : 3.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 19 residues processed: 96 average time/residue: 1.4898 time to fit residues: 189.3272 Evaluate side-chains 94 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 75 time to evaluate : 3.213 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 19 residues processed: 1 average time/residue: 0.7632 time to fit residues: 5.1762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 307 optimal weight: 0.0060 chunk 324 optimal weight: 50.0000 chunk 295 optimal weight: 1.9990 chunk 315 optimal weight: 8.9990 chunk 189 optimal weight: 3.9990 chunk 137 optimal weight: 0.7980 chunk 247 optimal weight: 20.0000 chunk 96 optimal weight: 1.9990 chunk 284 optimal weight: 2.9990 chunk 298 optimal weight: 2.9990 chunk 314 optimal weight: 0.9980 overall best weight: 1.1600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.3007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 29019 Z= 0.220 Angle : 0.745 15.539 39504 Z= 0.367 Chirality : 0.172 1.758 4663 Planarity : 0.003 0.089 5011 Dihedral : 6.839 109.649 5322 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.01 % Favored : 94.90 % Rotamer: Outliers : 0.79 % Allowed : 8.09 % Favored : 91.12 % Cbeta Deviations : 0.30 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.61 % 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 (0.15), residues: 3471 helix: 2.83 (0.21), residues: 669 sheet: 0.30 (0.19), residues: 756 loop : -0.69 (0.14), residues: 2046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 886 HIS 0.004 0.001 HIS C 69 PHE 0.028 0.001 PHE E 46 TYR 0.012 0.001 TYR B1067 ARG 0.014 0.000 ARG B 815 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6942 Ramachandran restraints generated. 3471 Oldfield, 0 Emsley, 3471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6942 Ramachandran restraints generated. 3471 Oldfield, 0 Emsley, 3471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 147 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue LYS 147 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue LYS 147 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Evaluate side-chains 98 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 74 time to evaluate : 3.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 20 residues processed: 94 average time/residue: 1.5043 time to fit residues: 187.1684 Evaluate side-chains 94 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 74 time to evaluate : 3.267 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 19 residues processed: 2 average time/residue: 1.2195 time to fit residues: 7.2893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 207 optimal weight: 0.8980 chunk 333 optimal weight: 20.0000 chunk 203 optimal weight: 1.9990 chunk 158 optimal weight: 1.9990 chunk 231 optimal weight: 1.9990 chunk 349 optimal weight: 10.0000 chunk 321 optimal weight: 30.0000 chunk 278 optimal weight: 2.9990 chunk 28 optimal weight: 20.0000 chunk 215 optimal weight: 0.5980 chunk 170 optimal weight: 0.7980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 GLN ** B 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 29019 Z= 0.217 Angle : 0.742 15.523 39504 Z= 0.366 Chirality : 0.172 1.756 4663 Planarity : 0.003 0.091 5011 Dihedral : 6.715 108.827 5322 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.52 % Favored : 95.39 % Rotamer: Outliers : 0.59 % Allowed : 8.29 % Favored : 91.12 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.61 % 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: 0.38 (0.15), residues: 3471 helix: 2.90 (0.21), residues: 667 sheet: 0.33 (0.19), residues: 754 loop : -0.70 (0.14), residues: 2050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 886 HIS 0.004 0.001 HIS C 69 PHE 0.017 0.001 PHE A 855 TYR 0.013 0.001 TYR B1067 ARG 0.011 0.000 ARG B 815 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6942 Ramachandran restraints generated. 3471 Oldfield, 0 Emsley, 3471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6942 Ramachandran restraints generated. 3471 Oldfield, 0 Emsley, 3471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 147 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue LYS 147 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue LYS 147 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Evaluate side-chains 93 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 75 time to evaluate : 3.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 20 residues processed: 93 average time/residue: 1.5614 time to fit residues: 191.8283 Evaluate side-chains 94 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 74 time to evaluate : 3.116 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 20 residues processed: 2 average time/residue: 1.2127 time to fit residues: 7.1995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 221 optimal weight: 7.9990 chunk 296 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 256 optimal weight: 1.9990 chunk 41 optimal weight: 0.0010 chunk 77 optimal weight: 1.9990 chunk 278 optimal weight: 3.9990 chunk 116 optimal weight: 9.9990 chunk 286 optimal weight: 0.0570 chunk 35 optimal weight: 20.0000 chunk 51 optimal weight: 4.9990 overall best weight: 1.2110 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 GLN ** B 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.117221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.074763 restraints weight = 235139.775| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 3.66 r_work: 0.3194 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 29019 Z= 0.219 Angle : 0.743 15.526 39504 Z= 0.366 Chirality : 0.172 1.757 4663 Planarity : 0.003 0.086 5011 Dihedral : 6.615 107.850 5322 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.01 % Favored : 94.90 % Rotamer: Outliers : 0.63 % Allowed : 8.29 % Favored : 91.09 % Cbeta Deviations : 0.30 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.61 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.15), residues: 3471 helix: 2.92 (0.21), residues: 665 sheet: 0.32 (0.19), residues: 756 loop : -0.69 (0.14), residues: 2050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 886 HIS 0.003 0.001 HIS C 69 PHE 0.036 0.001 PHE A 855 TYR 0.014 0.001 TYR B 380 ARG 0.010 0.000 ARG B 815 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8389.90 seconds wall clock time: 147 minutes 22.50 seconds (8842.50 seconds total)