Starting phenix.real_space_refine on Tue Mar 19 03:39:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tla_25985/03_2024/7tla_25985.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tla_25985/03_2024/7tla_25985.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tla_25985/03_2024/7tla_25985.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tla_25985/03_2024/7tla_25985.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tla_25985/03_2024/7tla_25985.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tla_25985/03_2024/7tla_25985.pdb" } resolution = 3.13 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.080 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 105 5.16 5 C 14738 2.51 5 N 3827 2.21 5 O 4382 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 191": "OE1" <-> "OE2" Residue "A TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 516": "OE1" <-> "OE2" Residue "A TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 661": "OE1" <-> "OE2" Residue "A GLU 773": "OE1" <-> "OE2" Residue "A PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1072": "OE1" <-> "OE2" Residue "A PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1084": "OD1" <-> "OD2" Residue "A GLU 1111": "OE1" <-> "OE2" Residue "A GLU 1144": "OE1" <-> "OE2" Residue "B TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 132": "OE1" <-> "OE2" Residue "B PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 224": "OE1" <-> "OE2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 298": "OE1" <-> "OE2" Residue "B PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 319": "NH1" <-> "NH2" Residue "B TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 619": "OE1" <-> "OE2" Residue "B ASP 627": "OD1" <-> "OD2" Residue "B GLU 661": "OE1" <-> "OE2" Residue "B GLU 773": "OE1" <-> "OE2" Residue "B GLU 780": "OE1" <-> "OE2" Residue "B PHE 898": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1092": "OE1" <-> "OE2" Residue "B GLU 1111": "OE1" <-> "OE2" Residue "B GLU 1144": "OE1" <-> "OE2" Residue "C TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 191": "OE1" <-> "OE2" Residue "C PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 224": "OE1" <-> "OE2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 309": "OE1" <-> "OE2" Residue "C TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 465": "OE1" <-> "OE2" Residue "C PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 578": "OD1" <-> "OD2" Residue "C GLU 619": "OE1" <-> "OE2" Residue "C GLU 661": "OE1" <-> "OE2" Residue "C ASP 745": "OD1" <-> "OD2" Residue "C PHE 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 830": "OD1" <-> "OD2" Residue "C PHE 833": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 898": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1072": "OE1" <-> "OE2" Residue "C GLU 1092": "OE1" <-> "OE2" Residue "C PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1127": "OD1" <-> "OD2" Residue "C GLU 1144": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 23052 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 972, 7602 Classifications: {'peptide': 972} Link IDs: {'PTRANS': 48, 'TRANS': 923} Chain breaks: 11 Chain: "B" Number of atoms: 7757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 992, 7757 Classifications: {'peptide': 992} Link IDs: {'PTRANS': 50, 'TRANS': 941} Chain breaks: 10 Chain: "C" Number of atoms: 7693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 984, 7693 Classifications: {'peptide': 984} Link IDs: {'PTRANS': 48, 'TRANS': 935} Chain breaks: 11 Time building chain proxies: 10.95, per 1000 atoms: 0.48 Number of scatterers: 23052 At special positions: 0 Unit cell: (131.44, 130.38, 170.66, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 105 16.00 O 4382 8.00 N 3827 7.00 C 14738 6.00 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=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 383 " - pdb=" SG CYS B 985 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.02 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.04 Simple disulfide: pdb=" SG CYS A 985 " - pdb=" SG CYS C 383 " distance=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=1.99 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.00 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.05 Simple disulfide: pdb=" SG CYS B 383 " - pdb=" SG CYS C 985 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.02 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.04 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=2.00 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.01 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=2.00 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=2.04 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.01 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=2.02 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=2.05 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.00 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.01 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.78 Conformation dependent library (CDL) restraints added in 4.8 seconds 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5542 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 49 sheets defined 28.0% alpha, 29.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.34 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.201A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.093A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.781A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 620 removed outlier: 3.607A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.791A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.613A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.652A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 918 Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' 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 removed outlier: 3.678A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.753A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.172A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 364 through 370 removed outlier: 4.058A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 389 removed outlier: 4.108A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.582A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 616 through 618 No H-bonds generated for 'chain 'B' and resid 616 through 618' Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 625 through 629 Processing helix chain 'B' and resid 630 through 635 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.650A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 805 removed outlier: 4.604A pdb=" N GLN B 804 " --> pdb=" O ASN B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.604A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.820A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.688A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.804A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 3.671A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.530A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.988A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 370 removed outlier: 4.085A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 Processing helix chain 'C' and resid 405 through 410 Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.626A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 620 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.937A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.672A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.893A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 830 through 838 removed outlier: 4.332A pdb=" N GLN C 836 " --> pdb=" O GLY C 832 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.601A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.714A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 5.164A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1127 through 1129 No H-bonds generated for 'chain 'C' and resid 1127 through 1129' Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 4.028A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 8.646A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.431A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.431A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.870A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA6, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.643A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 319 removed outlier: 7.081A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.137A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.137A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AB2, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.763A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.415A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 701 through 704 Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.726A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 718 through 728 removed outlier: 7.132A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.504A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 788 through 790 removed outlier: 6.201A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.669A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.407A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR B 95 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.745A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 5.765A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 84 through 85 removed outlier: 4.109A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N ARG B 102 " --> pdb=" O ILE B 119 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE B 119 " --> pdb=" O ARG B 102 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 314 Processing sheet with id=AC7, first strand: chain 'B' and resid 324 through 325 removed outlier: 6.724A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 348 through 349 removed outlier: 7.214A pdb=" N ALA B 348 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 9.541A pdb=" N ARG B 403 " --> pdb=" O ALA B 348 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 348 through 349 removed outlier: 7.214A pdb=" N ALA B 348 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 9.541A pdb=" N ARG B 403 " --> pdb=" O ALA B 348 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.899A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AD3, first strand: chain 'B' and resid 542 through 543 Processing sheet with id=AD4, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.671A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 701 through 704 Processing sheet with id=AD6, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.551A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 718 through 728 removed outlier: 7.129A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.394A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.654A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 28 through 31 removed outlier: 8.468A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.338A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.231A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.774A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AE4, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.499A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.298A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE7, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.805A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AE9, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.521A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.803A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.803A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF4, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 5.540A pdb=" N VAL C1122 " --> pdb=" O PHE C1089 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N PHE C1089 " --> pdb=" O VAL C1122 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N GLY C1124 " --> pdb=" O ALA C1087 " (cutoff:3.500A) 1062 hydrogen bonds defined for protein. 2877 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: 11.47 Time building geometry restraints manager: 9.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6040 1.33 - 1.45: 4479 1.45 - 1.58: 12917 1.58 - 1.70: 0 1.70 - 1.82: 129 Bond restraints: 23565 Sorted by residual: bond pdb=" CA PRO A 862 " pdb=" C PRO A 862 " ideal model delta sigma weight residual 1.517 1.540 -0.023 6.70e-03 2.23e+04 1.16e+01 bond pdb=" CA PRO C 862 " pdb=" C PRO C 862 " ideal model delta sigma weight residual 1.517 1.540 -0.023 6.70e-03 2.23e+04 1.15e+01 bond pdb=" CA PRO B 862 " pdb=" C PRO B 862 " ideal model delta sigma weight residual 1.517 1.540 -0.023 6.70e-03 2.23e+04 1.14e+01 bond pdb=" CZ ARG B1039 " pdb=" NH2 ARG B1039 " ideal model delta sigma weight residual 1.330 1.290 0.040 1.30e-02 5.92e+03 9.61e+00 bond pdb=" CZ ARG A1039 " pdb=" NH2 ARG A1039 " ideal model delta sigma weight residual 1.330 1.291 0.039 1.30e-02 5.92e+03 9.11e+00 ... (remaining 23560 not shown) Histogram of bond angle deviations from ideal: 96.47 - 104.22: 312 104.22 - 111.96: 9605 111.96 - 119.70: 9998 119.70 - 127.45: 11979 127.45 - 135.19: 165 Bond angle restraints: 32059 Sorted by residual: angle pdb=" N PRO C 986 " pdb=" CA PRO C 986 " pdb=" C PRO C 986 " ideal model delta sigma weight residual 110.70 118.76 -8.06 1.22e+00 6.72e-01 4.36e+01 angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 118.03 -7.33 1.22e+00 6.72e-01 3.61e+01 angle pdb=" N PRO B 986 " pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 110.70 117.73 -7.03 1.22e+00 6.72e-01 3.32e+01 angle pdb=" CA ASP B 796 " pdb=" CB ASP B 796 " pdb=" CG ASP B 796 " ideal model delta sigma weight residual 112.60 117.99 -5.39 1.00e+00 1.00e+00 2.90e+01 angle pdb=" CB HIS C 519 " pdb=" CG HIS C 519 " pdb=" CD2 HIS C 519 " ideal model delta sigma weight residual 131.20 124.34 6.86 1.30e+00 5.92e-01 2.78e+01 ... (remaining 32054 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.13: 13059 18.13 - 36.25: 792 36.25 - 54.38: 127 54.38 - 72.50: 46 72.50 - 90.63: 32 Dihedral angle restraints: 14056 sinusoidal: 5473 harmonic: 8583 Sorted by residual: dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -165.35 79.35 1 1.00e+01 1.00e-02 7.83e+01 dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -160.97 74.97 1 1.00e+01 1.00e-02 7.11e+01 dihedral pdb=" CB CYS B 738 " pdb=" SG CYS B 738 " pdb=" SG CYS B 760 " pdb=" CB CYS B 760 " ideal model delta sinusoidal sigma weight residual 93.00 153.55 -60.55 1 1.00e+01 1.00e-02 4.88e+01 ... (remaining 14053 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 2191 0.079 - 0.159: 1231 0.159 - 0.238: 199 0.238 - 0.317: 40 0.317 - 0.397: 10 Chirality restraints: 3671 Sorted by residual: chirality pdb=" CA PRO C 986 " pdb=" N PRO C 986 " pdb=" C PRO C 986 " pdb=" CB PRO C 986 " both_signs ideal model delta sigma weight residual False 2.72 2.32 0.40 2.00e-01 2.50e+01 3.94e+00 chirality pdb=" CA ASP A 571 " pdb=" N ASP A 571 " pdb=" C ASP A 571 " pdb=" CB ASP A 571 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.76e+00 chirality pdb=" CA ALA B 123 " pdb=" N ALA B 123 " pdb=" C ALA B 123 " pdb=" CB ALA B 123 " both_signs ideal model delta sigma weight residual False 2.48 2.10 0.38 2.00e-01 2.50e+01 3.66e+00 ... (remaining 3668 not shown) Planarity restraints: 4144 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 495 " -0.153 2.00e-02 2.50e+03 8.42e-02 1.42e+02 pdb=" CG TYR A 495 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 TYR A 495 " 0.061 2.00e-02 2.50e+03 pdb=" CD2 TYR A 495 " 0.076 2.00e-02 2.50e+03 pdb=" CE1 TYR A 495 " 0.054 2.00e-02 2.50e+03 pdb=" CE2 TYR A 495 " 0.040 2.00e-02 2.50e+03 pdb=" CZ TYR A 495 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR A 495 " -0.130 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 707 " -0.113 2.00e-02 2.50e+03 6.81e-02 9.26e+01 pdb=" CG TYR C 707 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 TYR C 707 " 0.062 2.00e-02 2.50e+03 pdb=" CD2 TYR C 707 " 0.037 2.00e-02 2.50e+03 pdb=" CE1 TYR C 707 " 0.038 2.00e-02 2.50e+03 pdb=" CE2 TYR C 707 " 0.065 2.00e-02 2.50e+03 pdb=" CZ TYR C 707 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR C 707 " -0.114 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 423 " -0.126 2.00e-02 2.50e+03 6.70e-02 8.97e+01 pdb=" CG TYR B 423 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 TYR B 423 " 0.064 2.00e-02 2.50e+03 pdb=" CD2 TYR B 423 " 0.049 2.00e-02 2.50e+03 pdb=" CE1 TYR B 423 " 0.028 2.00e-02 2.50e+03 pdb=" CE2 TYR B 423 " 0.037 2.00e-02 2.50e+03 pdb=" CZ TYR B 423 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 423 " -0.097 2.00e-02 2.50e+03 ... (remaining 4141 not shown) Histogram of nonbonded interaction distances: 2.52 - 3.00: 11424 3.00 - 3.47: 22523 3.47 - 3.95: 38851 3.95 - 4.42: 43488 4.42 - 4.90: 74194 Nonbonded interactions: 190480 Sorted by model distance: nonbonded pdb=" OE2 GLU A 918 " pdb=" OG SER C1123 " model vdw 2.522 2.440 nonbonded pdb=" OG SER B1123 " pdb=" OE2 GLU C 918 " model vdw 2.524 2.440 nonbonded pdb=" OE1 GLU B 516 " pdb=" OH TYR C 200 " model vdw 2.525 2.440 nonbonded pdb=" OE1 GLU A 298 " pdb=" OG SER A 316 " model vdw 2.532 2.440 nonbonded pdb=" OH TYR C 756 " pdb=" OD1 ASP C 994 " model vdw 2.543 2.440 ... (remaining 190475 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' selection = (chain 'B' and (resid 27 through 620 or resid 641 through 1147)) selection = (chain 'C' and (resid 27 through 827 or resid 854 through 1147)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 7.260 Check model and map are aligned: 0.310 Set scattering table: 0.190 Process input model: 65.150 Find NCS groups from input model: 1.660 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5969 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.042 23565 Z= 0.800 Angle : 1.760 9.688 32059 Z= 1.195 Chirality : 0.092 0.397 3671 Planarity : 0.014 0.198 4144 Dihedral : 13.367 90.625 8397 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 0.09 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.01 % Favored : 93.71 % Rotamer: Outliers : 1.12 % Allowed : 2.83 % Favored : 96.05 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.14), residues: 2878 helix: -0.85 (0.16), residues: 692 sheet: 0.27 (0.21), residues: 581 loop : -1.02 (0.15), residues: 1605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.101 0.021 TRP A 104 HIS 0.010 0.003 HIS A1083 PHE 0.073 0.012 PHE B 718 TYR 0.153 0.020 TYR A 495 ARG 0.010 0.001 ARG B1019 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 2581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 375 time to evaluate : 2.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: 0.8017 (p0) cc_final: 0.7654 (p0) REVERT: A 200 TYR cc_start: 0.6918 (m-80) cc_final: 0.6231 (m-80) REVERT: A 237 ARG cc_start: 0.6626 (mtt90) cc_final: 0.6169 (mtp180) REVERT: A 239 GLN cc_start: 0.6163 (tt0) cc_final: 0.5872 (tt0) REVERT: A 269 TYR cc_start: 0.7322 (m-80) cc_final: 0.6925 (m-80) REVERT: A 366 SER cc_start: 0.9100 (OUTLIER) cc_final: 0.8870 (p) REVERT: A 442 ASP cc_start: 0.7236 (m-30) cc_final: 0.6978 (m-30) REVERT: A 495 TYR cc_start: 0.6711 (m-80) cc_final: 0.5920 (m-80) REVERT: A 528 LYS cc_start: 0.8254 (tttt) cc_final: 0.8004 (tttm) REVERT: A 529 LYS cc_start: 0.8476 (mttt) cc_final: 0.7640 (mmtt) REVERT: A 558 LYS cc_start: 0.7706 (tttt) cc_final: 0.7117 (mmmt) REVERT: A 614 ASP cc_start: 0.7250 (t70) cc_final: 0.7046 (m-30) REVERT: A 646 ARG cc_start: 0.8127 (mtm180) cc_final: 0.7730 (mtp180) REVERT: A 654 GLU cc_start: 0.6965 (tt0) cc_final: 0.6503 (tp30) REVERT: A 675 GLN cc_start: 0.6524 (mt0) cc_final: 0.5447 (pp30) REVERT: A 776 LYS cc_start: 0.6686 (tttt) cc_final: 0.6437 (tttp) REVERT: A 780 GLU cc_start: 0.6978 (mt-10) cc_final: 0.6660 (mt-10) REVERT: A 786 LYS cc_start: 0.7875 (pttt) cc_final: 0.7473 (pttm) REVERT: A 790 LYS cc_start: 0.7519 (pttt) cc_final: 0.7220 (pttp) REVERT: A 902 MET cc_start: 0.7202 (mmt) cc_final: 0.6846 (mmm) REVERT: A 950 ASP cc_start: 0.6486 (t70) cc_final: 0.6197 (m-30) REVERT: A 957 GLN cc_start: 0.6211 (tp-100) cc_final: 0.5854 (tt0) REVERT: A 995 ARG cc_start: 0.6774 (mtt180) cc_final: 0.6565 (mtp180) REVERT: A 1002 GLN cc_start: 0.6647 (tt0) cc_final: 0.6145 (tp40) REVERT: A 1045 LYS cc_start: 0.7435 (ttpp) cc_final: 0.7229 (mmmt) REVERT: B 29 THR cc_start: 0.7176 (t) cc_final: 0.6930 (t) REVERT: B 81 ASN cc_start: 0.7296 (p0) cc_final: 0.6136 (p0) REVERT: B 118 LEU cc_start: 0.7158 (tp) cc_final: 0.6515 (mt) REVERT: B 128 ILE cc_start: 0.5270 (mt) cc_final: 0.4824 (mt) REVERT: B 198 ASP cc_start: 0.7159 (m-30) cc_final: 0.6777 (p0) REVERT: B 200 TYR cc_start: 0.7156 (m-80) cc_final: 0.6840 (m-80) REVERT: B 231 ILE cc_start: 0.7186 (pt) cc_final: 0.6947 (pt) REVERT: B 307 THR cc_start: 0.8595 (m) cc_final: 0.8153 (t) REVERT: B 309 GLU cc_start: 0.6169 (mp0) cc_final: 0.5905 (mp0) REVERT: B 332 ILE cc_start: 0.5674 (tt) cc_final: 0.5445 (tt) REVERT: B 334 ASN cc_start: 0.6803 (m-40) cc_final: 0.6575 (m110) REVERT: B 335 LEU cc_start: 0.8263 (mt) cc_final: 0.7829 (tt) REVERT: B 351 TYR cc_start: 0.6857 (p90) cc_final: 0.6585 (p90) REVERT: B 518 LEU cc_start: 0.6412 (mt) cc_final: 0.6166 (pp) REVERT: B 529 LYS cc_start: 0.7683 (mttt) cc_final: 0.6927 (mmmm) REVERT: B 556 ASN cc_start: 0.7098 (p0) cc_final: 0.6582 (m110) REVERT: B 661 GLU cc_start: 0.7564 (mt-10) cc_final: 0.7216 (mm-30) REVERT: B 723 THR cc_start: 0.6866 (t) cc_final: 0.6603 (p) REVERT: B 776 LYS cc_start: 0.6495 (tttt) cc_final: 0.5981 (tttm) REVERT: B 786 LYS cc_start: 0.8241 (pttt) cc_final: 0.7979 (pttm) REVERT: B 902 MET cc_start: 0.7492 (mmm) cc_final: 0.6631 (tpt) REVERT: B 950 ASP cc_start: 0.6513 (t70) cc_final: 0.6291 (m-30) REVERT: B 990 GLU cc_start: 0.6481 (mt-10) cc_final: 0.6051 (tt0) REVERT: B 1003 SER cc_start: 0.6932 (t) cc_final: 0.6603 (m) REVERT: B 1045 LYS cc_start: 0.8209 (ttpp) cc_final: 0.7649 (tmtt) REVERT: B 1094 VAL cc_start: 0.7541 (OUTLIER) cc_final: 0.7138 (m) REVERT: B 1114 ILE cc_start: 0.8155 (mm) cc_final: 0.7941 (mm) REVERT: C 32 PHE cc_start: 0.6766 (m-80) cc_final: 0.6164 (m-80) REVERT: C 63 THR cc_start: 0.7142 (m) cc_final: 0.6933 (p) REVERT: C 133 PHE cc_start: 0.6145 (m-80) cc_final: 0.5349 (t80) REVERT: C 239 GLN cc_start: 0.7452 (tt0) cc_final: 0.7102 (tt0) REVERT: C 269 TYR cc_start: 0.7632 (m-80) cc_final: 0.7249 (m-10) REVERT: C 304 LYS cc_start: 0.7556 (mmtm) cc_final: 0.7350 (mmtm) REVERT: C 335 LEU cc_start: 0.7996 (mt) cc_final: 0.7561 (tt) REVERT: C 380 TYR cc_start: 0.6529 (m-80) cc_final: 0.6036 (m-10) REVERT: C 396 TYR cc_start: 0.5062 (m-80) cc_final: 0.4546 (m-10) REVERT: C 558 LYS cc_start: 0.7654 (tttt) cc_final: 0.7363 (mmmt) REVERT: C 568 ASP cc_start: 0.6838 (t0) cc_final: 0.6627 (m-30) REVERT: C 574 ASP cc_start: 0.6281 (t0) cc_final: 0.6080 (t0) REVERT: C 614 ASP cc_start: 0.7515 (t0) cc_final: 0.7180 (m-30) REVERT: C 780 GLU cc_start: 0.7055 (mt-10) cc_final: 0.6300 (mm-30) REVERT: C 786 LYS cc_start: 0.8273 (pttt) cc_final: 0.7824 (ptpp) REVERT: C 902 MET cc_start: 0.7696 (mmt) cc_final: 0.7350 (tpt) REVERT: C 964 LYS cc_start: 0.7200 (mttt) cc_final: 0.6870 (mmtt) REVERT: C 1005 GLN cc_start: 0.7086 (mt0) cc_final: 0.6635 (mm-40) outliers start: 29 outliers final: 9 residues processed: 402 average time/residue: 0.3561 time to fit residues: 219.9235 Evaluate side-chains 227 residues out of total 2581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 216 time to evaluate : 2.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 248 optimal weight: 0.9980 chunk 222 optimal weight: 5.9990 chunk 123 optimal weight: 6.9990 chunk 76 optimal weight: 2.9990 chunk 150 optimal weight: 0.9990 chunk 119 optimal weight: 0.8980 chunk 230 optimal weight: 5.9990 chunk 89 optimal weight: 0.8980 chunk 140 optimal weight: 0.6980 chunk 171 optimal weight: 2.9990 chunk 266 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 751 ASN B 314 GLN B 394 ASN B 914 ASN B 965 GLN C 388 ASN C 613 GLN C 751 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5953 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 23565 Z= 0.202 Angle : 0.616 10.936 32059 Z= 0.327 Chirality : 0.046 0.160 3671 Planarity : 0.004 0.038 4144 Dihedral : 6.066 59.639 3151 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.06 % Favored : 96.84 % Rotamer: Outliers : 1.74 % Allowed : 5.85 % Favored : 92.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.15), residues: 2878 helix: 1.16 (0.20), residues: 694 sheet: 0.09 (0.18), residues: 710 loop : -0.73 (0.15), residues: 1474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 64 HIS 0.003 0.001 HIS A 519 PHE 0.026 0.002 PHE B 168 TYR 0.019 0.002 TYR A 170 ARG 0.009 0.001 ARG B 102 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 255 time to evaluate : 2.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: 0.7895 (p0) cc_final: 0.7188 (p0) REVERT: A 230 PRO cc_start: 0.7770 (Cg_endo) cc_final: 0.7137 (Cg_exo) REVERT: A 237 ARG cc_start: 0.6813 (mtt90) cc_final: 0.6344 (mtm-85) REVERT: A 239 GLN cc_start: 0.6095 (tt0) cc_final: 0.5433 (tt0) REVERT: A 269 TYR cc_start: 0.7179 (m-80) cc_final: 0.6825 (m-10) REVERT: A 528 LYS cc_start: 0.8219 (tttt) cc_final: 0.7652 (ttmm) REVERT: A 529 LYS cc_start: 0.8442 (mttt) cc_final: 0.7677 (mmtt) REVERT: A 558 LYS cc_start: 0.7799 (tttt) cc_final: 0.7132 (mmmt) REVERT: A 591 SER cc_start: 0.7477 (t) cc_final: 0.7024 (p) REVERT: A 619 GLU cc_start: 0.6363 (OUTLIER) cc_final: 0.6116 (mp0) REVERT: A 646 ARG cc_start: 0.8162 (mtm180) cc_final: 0.7894 (mtp180) REVERT: A 654 GLU cc_start: 0.7052 (tt0) cc_final: 0.6386 (tp30) REVERT: A 675 GLN cc_start: 0.6678 (mt0) cc_final: 0.5921 (pp30) REVERT: A 780 GLU cc_start: 0.6914 (mt-10) cc_final: 0.6335 (mm-30) REVERT: A 786 LYS cc_start: 0.7709 (pttt) cc_final: 0.7345 (pttm) REVERT: A 790 LYS cc_start: 0.7423 (pttt) cc_final: 0.6970 (pttp) REVERT: A 804 GLN cc_start: 0.7271 (mm-40) cc_final: 0.6578 (mp10) REVERT: A 902 MET cc_start: 0.6971 (mmt) cc_final: 0.6657 (mmm) REVERT: A 950 ASP cc_start: 0.6523 (t70) cc_final: 0.6225 (m-30) REVERT: A 957 GLN cc_start: 0.6050 (tp-100) cc_final: 0.5813 (tt0) REVERT: A 1002 GLN cc_start: 0.6481 (tt0) cc_final: 0.6072 (tp40) REVERT: A 1003 SER cc_start: 0.6996 (t) cc_final: 0.6656 (p) REVERT: A 1045 LYS cc_start: 0.7294 (ttpp) cc_final: 0.7018 (mmmt) REVERT: A 1092 GLU cc_start: 0.7853 (mt-10) cc_final: 0.7485 (mm-30) REVERT: A 1107 ARG cc_start: 0.7848 (mtm-85) cc_final: 0.7182 (mtt90) REVERT: B 81 ASN cc_start: 0.7353 (p0) cc_final: 0.5977 (p0) REVERT: B 118 LEU cc_start: 0.6774 (tp) cc_final: 0.6288 (mm) REVERT: B 140 PHE cc_start: 0.7402 (p90) cc_final: 0.6922 (p90) REVERT: B 198 ASP cc_start: 0.7247 (m-30) cc_final: 0.6897 (p0) REVERT: B 307 THR cc_start: 0.8437 (m) cc_final: 0.7911 (t) REVERT: B 309 GLU cc_start: 0.5842 (mp0) cc_final: 0.5591 (mp0) REVERT: B 335 LEU cc_start: 0.8014 (mt) cc_final: 0.7708 (tp) REVERT: B 387 LEU cc_start: 0.7299 (mt) cc_final: 0.6983 (mt) REVERT: B 400 PHE cc_start: 0.7156 (p90) cc_final: 0.6942 (p90) REVERT: B 437 ASN cc_start: 0.8650 (p0) cc_final: 0.8333 (t0) REVERT: B 508 TYR cc_start: 0.7531 (m-10) cc_final: 0.7291 (m-10) REVERT: B 529 LYS cc_start: 0.7584 (mttt) cc_final: 0.6901 (mmmm) REVERT: B 568 ASP cc_start: 0.7006 (OUTLIER) cc_final: 0.6427 (m-30) REVERT: B 574 ASP cc_start: 0.6523 (t70) cc_final: 0.5853 (t0) REVERT: B 661 GLU cc_start: 0.7481 (mt-10) cc_final: 0.7234 (mm-30) REVERT: B 721 SER cc_start: 0.7506 (t) cc_final: 0.6870 (p) REVERT: B 776 LYS cc_start: 0.6577 (tttt) cc_final: 0.6213 (ttpt) REVERT: B 786 LYS cc_start: 0.8329 (pttt) cc_final: 0.8076 (pttm) REVERT: B 902 MET cc_start: 0.7209 (mmm) cc_final: 0.6891 (mmm) REVERT: B 950 ASP cc_start: 0.6615 (t70) cc_final: 0.6322 (m-30) REVERT: B 990 GLU cc_start: 0.6172 (mt-10) cc_final: 0.5941 (tt0) REVERT: B 1003 SER cc_start: 0.6956 (t) cc_final: 0.6441 (m) REVERT: B 1045 LYS cc_start: 0.8104 (ttpp) cc_final: 0.7725 (tttm) REVERT: B 1114 ILE cc_start: 0.8041 (mm) cc_final: 0.7798 (mm) REVERT: C 32 PHE cc_start: 0.6240 (m-80) cc_final: 0.6001 (m-80) REVERT: C 133 PHE cc_start: 0.5813 (m-80) cc_final: 0.5283 (t80) REVERT: C 269 TYR cc_start: 0.7858 (m-80) cc_final: 0.7511 (m-10) REVERT: C 316 SER cc_start: 0.7311 (t) cc_final: 0.6941 (p) REVERT: C 335 LEU cc_start: 0.7912 (mt) cc_final: 0.7355 (tt) REVERT: C 425 LEU cc_start: 0.4112 (OUTLIER) cc_final: 0.3883 (pp) REVERT: C 514 SER cc_start: 0.7761 (t) cc_final: 0.7538 (m) REVERT: C 519 HIS cc_start: 0.3840 (OUTLIER) cc_final: 0.3313 (p90) REVERT: C 558 LYS cc_start: 0.7794 (tttt) cc_final: 0.7521 (mmmt) REVERT: C 564 GLN cc_start: 0.6740 (tp40) cc_final: 0.6525 (mm-40) REVERT: C 568 ASP cc_start: 0.6893 (t0) cc_final: 0.6556 (m-30) REVERT: C 614 ASP cc_start: 0.7516 (t0) cc_final: 0.7279 (m-30) REVERT: C 661 GLU cc_start: 0.7747 (mt-10) cc_final: 0.7490 (tt0) REVERT: C 780 GLU cc_start: 0.6879 (mt-10) cc_final: 0.6179 (mm-30) REVERT: C 786 LYS cc_start: 0.8460 (pttt) cc_final: 0.7905 (mtmm) REVERT: C 823 PHE cc_start: 0.7295 (m-80) cc_final: 0.6993 (m-80) REVERT: C 990 GLU cc_start: 0.6448 (mt-10) cc_final: 0.5972 (tm-30) REVERT: C 1005 GLN cc_start: 0.6884 (mt0) cc_final: 0.6652 (tp-100) outliers start: 45 outliers final: 18 residues processed: 286 average time/residue: 0.3447 time to fit residues: 155.0802 Evaluate side-chains 230 residues out of total 2581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 208 time to evaluate : 2.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 811 LYS Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 568 ASP Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 830 ASP Chi-restraints excluded: chain C residue 859 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 148 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 222 optimal weight: 20.0000 chunk 181 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 267 optimal weight: 1.9990 chunk 288 optimal weight: 0.0060 chunk 238 optimal weight: 0.8980 chunk 265 optimal weight: 4.9990 chunk 91 optimal weight: 0.8980 chunk 214 optimal weight: 4.9990 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 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 ASN ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN B 969 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5975 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23565 Z= 0.207 Angle : 0.547 8.017 32059 Z= 0.289 Chirality : 0.045 0.168 3671 Planarity : 0.004 0.043 4144 Dihedral : 5.431 59.762 3142 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.43 % Allowed : 8.37 % Favored : 90.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.15), residues: 2878 helix: 1.58 (0.20), residues: 686 sheet: 0.07 (0.18), residues: 698 loop : -0.74 (0.15), residues: 1494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 353 HIS 0.004 0.001 HIS A 519 PHE 0.021 0.001 PHE B 400 TYR 0.019 0.001 TYR B1067 ARG 0.009 0.000 ARG B 237 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 226 time to evaluate : 2.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: 0.8137 (p0) cc_final: 0.7452 (p0) REVERT: A 170 TYR cc_start: 0.5538 (t80) cc_final: 0.5170 (t80) REVERT: A 230 PRO cc_start: 0.7827 (Cg_endo) cc_final: 0.7606 (Cg_exo) REVERT: A 237 ARG cc_start: 0.6629 (mtt90) cc_final: 0.6178 (mtm-85) REVERT: A 239 GLN cc_start: 0.6197 (tt0) cc_final: 0.5689 (tt0) REVERT: A 269 TYR cc_start: 0.7204 (m-80) cc_final: 0.6821 (m-10) REVERT: A 528 LYS cc_start: 0.8203 (tttt) cc_final: 0.7638 (ttmm) REVERT: A 529 LYS cc_start: 0.8421 (mttt) cc_final: 0.7665 (mmtt) REVERT: A 558 LYS cc_start: 0.7849 (tttt) cc_final: 0.7165 (mmmt) REVERT: A 619 GLU cc_start: 0.6357 (OUTLIER) cc_final: 0.6152 (mp0) REVERT: A 661 GLU cc_start: 0.7430 (mt-10) cc_final: 0.6823 (mm-30) REVERT: A 675 GLN cc_start: 0.6838 (mt0) cc_final: 0.6029 (pp30) REVERT: A 786 LYS cc_start: 0.7732 (pttt) cc_final: 0.7341 (pttm) REVERT: A 790 LYS cc_start: 0.7582 (pttt) cc_final: 0.7059 (pttp) REVERT: A 950 ASP cc_start: 0.6531 (t70) cc_final: 0.6283 (m-30) REVERT: A 957 GLN cc_start: 0.6000 (tp-100) cc_final: 0.5758 (tt0) REVERT: A 1002 GLN cc_start: 0.6424 (tt0) cc_final: 0.6032 (tp40) REVERT: A 1003 SER cc_start: 0.7105 (t) cc_final: 0.6752 (p) REVERT: A 1045 LYS cc_start: 0.7322 (ttpp) cc_final: 0.7032 (mmmt) REVERT: A 1073 LYS cc_start: 0.6604 (tttt) cc_final: 0.6338 (ttmm) REVERT: A 1092 GLU cc_start: 0.7870 (mt-10) cc_final: 0.7446 (mm-30) REVERT: A 1107 ARG cc_start: 0.7803 (mtm-85) cc_final: 0.7086 (mtt90) REVERT: B 81 ASN cc_start: 0.7383 (p0) cc_final: 0.6351 (p0) REVERT: B 118 LEU cc_start: 0.6824 (tp) cc_final: 0.6373 (mm) REVERT: B 140 PHE cc_start: 0.7485 (p90) cc_final: 0.7106 (p90) REVERT: B 198 ASP cc_start: 0.7243 (m-30) cc_final: 0.6923 (p0) REVERT: B 200 TYR cc_start: 0.6926 (m-80) cc_final: 0.6596 (m-80) REVERT: B 307 THR cc_start: 0.8418 (m) cc_final: 0.7895 (t) REVERT: B 309 GLU cc_start: 0.5980 (mp0) cc_final: 0.5716 (mp0) REVERT: B 335 LEU cc_start: 0.8022 (mt) cc_final: 0.7662 (tp) REVERT: B 351 TYR cc_start: 0.7164 (p90) cc_final: 0.6884 (p90) REVERT: B 400 PHE cc_start: 0.7275 (p90) cc_final: 0.6999 (p90) REVERT: B 441 LEU cc_start: 0.8611 (mm) cc_final: 0.8346 (mt) REVERT: B 492 LEU cc_start: 0.7226 (pt) cc_final: 0.6973 (mt) REVERT: B 568 ASP cc_start: 0.6839 (OUTLIER) cc_final: 0.5887 (m-30) REVERT: B 574 ASP cc_start: 0.6605 (t70) cc_final: 0.5967 (t0) REVERT: B 661 GLU cc_start: 0.7547 (mt-10) cc_final: 0.7253 (mm-30) REVERT: B 721 SER cc_start: 0.7245 (t) cc_final: 0.6657 (p) REVERT: B 776 LYS cc_start: 0.6584 (tttt) cc_final: 0.6241 (ttpt) REVERT: B 786 LYS cc_start: 0.8334 (pttt) cc_final: 0.8086 (pttm) REVERT: B 902 MET cc_start: 0.7278 (mmm) cc_final: 0.6968 (mmm) REVERT: B 950 ASP cc_start: 0.6673 (t70) cc_final: 0.6257 (m-30) REVERT: B 1003 SER cc_start: 0.6977 (t) cc_final: 0.6491 (m) REVERT: B 1045 LYS cc_start: 0.8116 (ttpp) cc_final: 0.7630 (tttm) REVERT: C 32 PHE cc_start: 0.6270 (m-80) cc_final: 0.5865 (m-80) REVERT: C 133 PHE cc_start: 0.5859 (m-80) cc_final: 0.5312 (t80) REVERT: C 239 GLN cc_start: 0.7629 (tt0) cc_final: 0.7254 (tt0) REVERT: C 269 TYR cc_start: 0.8005 (m-80) cc_final: 0.7613 (m-10) REVERT: C 316 SER cc_start: 0.7420 (t) cc_final: 0.7074 (p) REVERT: C 335 LEU cc_start: 0.8076 (mt) cc_final: 0.7293 (tt) REVERT: C 425 LEU cc_start: 0.4170 (OUTLIER) cc_final: 0.3944 (pp) REVERT: C 558 LYS cc_start: 0.7735 (tttt) cc_final: 0.7411 (mmmt) REVERT: C 614 ASP cc_start: 0.7680 (t0) cc_final: 0.7451 (m-30) REVERT: C 643 PHE cc_start: 0.5896 (t80) cc_final: 0.5649 (t80) REVERT: C 661 GLU cc_start: 0.7714 (mt-10) cc_final: 0.7428 (tt0) REVERT: C 780 GLU cc_start: 0.6779 (mt-10) cc_final: 0.6051 (mm-30) REVERT: C 786 LYS cc_start: 0.8487 (pttt) cc_final: 0.7968 (ptpp) REVERT: C 811 LYS cc_start: 0.6159 (mmtp) cc_final: 0.5903 (tttm) REVERT: C 823 PHE cc_start: 0.7431 (m-80) cc_final: 0.7131 (m-80) REVERT: C 902 MET cc_start: 0.7365 (mmm) cc_final: 0.6946 (tpt) REVERT: C 990 GLU cc_start: 0.6451 (mt-10) cc_final: 0.5972 (tm-30) outliers start: 37 outliers final: 23 residues processed: 252 average time/residue: 0.3348 time to fit residues: 135.6309 Evaluate side-chains 226 residues out of total 2581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 200 time to evaluate : 2.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 811 LYS Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 568 ASP Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 854 LYS Chi-restraints excluded: chain C residue 859 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 264 optimal weight: 5.9990 chunk 201 optimal weight: 9.9990 chunk 138 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 127 optimal weight: 7.9990 chunk 179 optimal weight: 0.7980 chunk 268 optimal weight: 3.9990 chunk 284 optimal weight: 4.9990 chunk 140 optimal weight: 8.9990 chunk 254 optimal weight: 0.9980 chunk 76 optimal weight: 7.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 607 GLN A 613 GLN A 913 GLN B 52 GLN B 165 ASN ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN B 935 GLN C 388 ASN C 914 ASN C1010 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6012 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 23565 Z= 0.432 Angle : 0.609 8.067 32059 Z= 0.319 Chirality : 0.048 0.230 3671 Planarity : 0.004 0.052 4144 Dihedral : 5.493 57.156 3142 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.25 % Allowed : 9.53 % Favored : 88.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.15), residues: 2878 helix: 1.26 (0.20), residues: 693 sheet: 0.00 (0.18), residues: 692 loop : -0.94 (0.15), residues: 1493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 353 HIS 0.006 0.001 HIS A 519 PHE 0.017 0.002 PHE B 400 TYR 0.022 0.002 TYR C1067 ARG 0.004 0.001 ARG B 102 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 203 time to evaluate : 2.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: 0.8234 (p0) cc_final: 0.7516 (p0) REVERT: A 237 ARG cc_start: 0.6647 (mtt90) cc_final: 0.6179 (mtm-85) REVERT: A 239 GLN cc_start: 0.6259 (tt0) cc_final: 0.5749 (tt0) REVERT: A 269 TYR cc_start: 0.7190 (m-80) cc_final: 0.6819 (m-10) REVERT: A 529 LYS cc_start: 0.8415 (mttt) cc_final: 0.7680 (mmtt) REVERT: A 558 LYS cc_start: 0.7952 (tttt) cc_final: 0.7229 (mmmt) REVERT: A 675 GLN cc_start: 0.6787 (mt0) cc_final: 0.6018 (pp30) REVERT: A 786 LYS cc_start: 0.7713 (pttt) cc_final: 0.7302 (pttm) REVERT: A 790 LYS cc_start: 0.7766 (pttt) cc_final: 0.7182 (pttp) REVERT: A 804 GLN cc_start: 0.7335 (mm-40) cc_final: 0.6485 (mp10) REVERT: A 957 GLN cc_start: 0.6142 (tp-100) cc_final: 0.5879 (tt0) REVERT: A 1002 GLN cc_start: 0.6362 (tt0) cc_final: 0.6025 (tp40) REVERT: A 1003 SER cc_start: 0.7102 (t) cc_final: 0.6879 (m) REVERT: A 1045 LYS cc_start: 0.7368 (ttpp) cc_final: 0.7005 (mmmt) REVERT: A 1073 LYS cc_start: 0.6579 (tttt) cc_final: 0.6294 (ttmm) REVERT: A 1107 ARG cc_start: 0.7646 (mtm-85) cc_final: 0.7067 (mtt180) REVERT: B 118 LEU cc_start: 0.6795 (tp) cc_final: 0.6384 (mm) REVERT: B 140 PHE cc_start: 0.7633 (p90) cc_final: 0.7326 (p90) REVERT: B 198 ASP cc_start: 0.7391 (m-30) cc_final: 0.7085 (p0) REVERT: B 200 TYR cc_start: 0.7016 (m-80) cc_final: 0.6654 (m-80) REVERT: B 307 THR cc_start: 0.8393 (m) cc_final: 0.7863 (t) REVERT: B 309 GLU cc_start: 0.5973 (mp0) cc_final: 0.5702 (mp0) REVERT: B 400 PHE cc_start: 0.7264 (p90) cc_final: 0.6978 (p90) REVERT: B 492 LEU cc_start: 0.7178 (pt) cc_final: 0.6920 (mt) REVERT: B 574 ASP cc_start: 0.6699 (t70) cc_final: 0.6482 (t0) REVERT: B 661 GLU cc_start: 0.7625 (mt-10) cc_final: 0.7321 (mm-30) REVERT: B 776 LYS cc_start: 0.6336 (tttt) cc_final: 0.5916 (ttpt) REVERT: B 786 LYS cc_start: 0.8395 (pttt) cc_final: 0.8155 (pttm) REVERT: B 902 MET cc_start: 0.7204 (mmm) cc_final: 0.6658 (tpt) REVERT: B 950 ASP cc_start: 0.6757 (t70) cc_final: 0.6429 (m-30) REVERT: B 1045 LYS cc_start: 0.8102 (ttpp) cc_final: 0.7631 (tttm) REVERT: C 32 PHE cc_start: 0.6426 (m-80) cc_final: 0.5967 (m-80) REVERT: C 133 PHE cc_start: 0.5887 (m-80) cc_final: 0.5350 (t80) REVERT: C 269 TYR cc_start: 0.7960 (m-80) cc_final: 0.7553 (m-10) REVERT: C 281 GLU cc_start: 0.6742 (pm20) cc_final: 0.6368 (pm20) REVERT: C 316 SER cc_start: 0.7477 (t) cc_final: 0.7124 (p) REVERT: C 335 LEU cc_start: 0.7728 (mt) cc_final: 0.7209 (tt) REVERT: C 425 LEU cc_start: 0.4264 (OUTLIER) cc_final: 0.4042 (pp) REVERT: C 558 LYS cc_start: 0.7797 (tttt) cc_final: 0.7511 (mmmt) REVERT: C 614 ASP cc_start: 0.7757 (t0) cc_final: 0.7498 (m-30) REVERT: C 643 PHE cc_start: 0.5865 (t80) cc_final: 0.5636 (t80) REVERT: C 661 GLU cc_start: 0.7620 (mt-10) cc_final: 0.7402 (tt0) REVERT: C 786 LYS cc_start: 0.8509 (pttt) cc_final: 0.7970 (ptpp) REVERT: C 811 LYS cc_start: 0.6115 (mmtp) cc_final: 0.5769 (tttm) REVERT: C 902 MET cc_start: 0.7325 (mmm) cc_final: 0.6665 (tpt) REVERT: C 912 THR cc_start: 0.7624 (OUTLIER) cc_final: 0.7140 (p) REVERT: C 990 GLU cc_start: 0.6501 (mt-10) cc_final: 0.6020 (tm-30) outliers start: 58 outliers final: 39 residues processed: 247 average time/residue: 0.3282 time to fit residues: 130.3367 Evaluate side-chains 229 residues out of total 2581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 188 time to evaluate : 2.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 811 LYS Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 854 LYS Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 236 optimal weight: 6.9990 chunk 161 optimal weight: 0.3980 chunk 4 optimal weight: 0.9990 chunk 211 optimal weight: 7.9990 chunk 117 optimal weight: 0.8980 chunk 242 optimal weight: 5.9990 chunk 196 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 145 optimal weight: 0.4980 chunk 255 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 914 ASN ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5982 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 23565 Z= 0.156 Angle : 0.505 7.757 32059 Z= 0.264 Chirality : 0.044 0.188 3671 Planarity : 0.004 0.072 4144 Dihedral : 5.045 58.280 3142 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.01 % Allowed : 10.31 % Favored : 87.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.15), residues: 2878 helix: 1.72 (0.20), residues: 689 sheet: 0.08 (0.18), residues: 656 loop : -0.74 (0.15), residues: 1533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 353 HIS 0.003 0.001 HIS C 519 PHE 0.019 0.001 PHE B 400 TYR 0.022 0.001 TYR B 508 ARG 0.004 0.000 ARG B 102 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 224 time to evaluate : 2.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: 0.8316 (p0) cc_final: 0.7676 (p0) REVERT: A 237 ARG cc_start: 0.6710 (mtt90) cc_final: 0.6241 (mtm-85) REVERT: A 239 GLN cc_start: 0.6187 (tt0) cc_final: 0.5589 (tt0) REVERT: A 269 TYR cc_start: 0.7307 (m-80) cc_final: 0.6859 (m-10) REVERT: A 529 LYS cc_start: 0.8416 (mttt) cc_final: 0.7665 (mmtt) REVERT: A 558 LYS cc_start: 0.7931 (tttt) cc_final: 0.7188 (mmmt) REVERT: A 675 GLN cc_start: 0.6775 (mt0) cc_final: 0.6052 (pp30) REVERT: A 780 GLU cc_start: 0.6816 (mt-10) cc_final: 0.6385 (mm-30) REVERT: A 786 LYS cc_start: 0.7740 (pttt) cc_final: 0.7339 (pttm) REVERT: A 790 LYS cc_start: 0.7796 (pttt) cc_final: 0.7244 (pttp) REVERT: A 804 GLN cc_start: 0.7304 (mm-40) cc_final: 0.6535 (mp10) REVERT: A 811 LYS cc_start: 0.6917 (OUTLIER) cc_final: 0.6189 (tmtt) REVERT: A 957 GLN cc_start: 0.6047 (tp-100) cc_final: 0.5781 (tt0) REVERT: A 1002 GLN cc_start: 0.6404 (tt0) cc_final: 0.6026 (tp40) REVERT: A 1003 SER cc_start: 0.7089 (t) cc_final: 0.6796 (p) REVERT: A 1045 LYS cc_start: 0.7444 (ttpp) cc_final: 0.7054 (mmmt) REVERT: A 1073 LYS cc_start: 0.6502 (tttt) cc_final: 0.6281 (ttmm) REVERT: A 1107 ARG cc_start: 0.7734 (mtm-85) cc_final: 0.7107 (mtt180) REVERT: B 118 LEU cc_start: 0.6766 (tp) cc_final: 0.6378 (mm) REVERT: B 140 PHE cc_start: 0.7499 (p90) cc_final: 0.7170 (p90) REVERT: B 198 ASP cc_start: 0.7261 (m-30) cc_final: 0.6991 (p0) REVERT: B 200 TYR cc_start: 0.6945 (m-80) cc_final: 0.6600 (m-80) REVERT: B 228 ASP cc_start: 0.5537 (t0) cc_final: 0.5304 (t0) REVERT: B 241 LEU cc_start: 0.5736 (mt) cc_final: 0.5424 (mp) REVERT: B 271 GLN cc_start: 0.6327 (OUTLIER) cc_final: 0.6034 (mp10) REVERT: B 307 THR cc_start: 0.8409 (m) cc_final: 0.7952 (t) REVERT: B 309 GLU cc_start: 0.5996 (mp0) cc_final: 0.5750 (mp0) REVERT: B 400 PHE cc_start: 0.7156 (p90) cc_final: 0.6883 (p90) REVERT: B 528 LYS cc_start: 0.8070 (tppp) cc_final: 0.7829 (mmmm) REVERT: B 661 GLU cc_start: 0.7614 (mt-10) cc_final: 0.7301 (mm-30) REVERT: B 721 SER cc_start: 0.6856 (m) cc_final: 0.6104 (p) REVERT: B 776 LYS cc_start: 0.6579 (tttt) cc_final: 0.6232 (ttpt) REVERT: B 786 LYS cc_start: 0.8319 (pttt) cc_final: 0.8086 (pttm) REVERT: B 950 ASP cc_start: 0.6662 (t70) cc_final: 0.6290 (m-30) REVERT: B 1003 SER cc_start: 0.6970 (t) cc_final: 0.6525 (m) REVERT: B 1045 LYS cc_start: 0.8110 (ttpp) cc_final: 0.7634 (tttm) REVERT: B 1072 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.7463 (mp0) REVERT: B 1092 GLU cc_start: 0.8047 (mm-30) cc_final: 0.7778 (mt-10) REVERT: B 1114 ILE cc_start: 0.8225 (mm) cc_final: 0.7933 (tt) REVERT: C 32 PHE cc_start: 0.6245 (m-80) cc_final: 0.5880 (m-80) REVERT: C 63 THR cc_start: 0.7208 (m) cc_final: 0.7003 (p) REVERT: C 133 PHE cc_start: 0.5815 (m-80) cc_final: 0.5376 (t80) REVERT: C 269 TYR cc_start: 0.8012 (m-80) cc_final: 0.7425 (m-10) REVERT: C 281 GLU cc_start: 0.6738 (pm20) cc_final: 0.6360 (pm20) REVERT: C 316 SER cc_start: 0.7536 (t) cc_final: 0.7251 (p) REVERT: C 335 LEU cc_start: 0.7750 (mt) cc_final: 0.7167 (tt) REVERT: C 353 TRP cc_start: 0.5010 (p-90) cc_final: 0.4218 (p-90) REVERT: C 427 ASP cc_start: 0.7232 (m-30) cc_final: 0.6919 (t0) REVERT: C 558 LYS cc_start: 0.7831 (tttt) cc_final: 0.7533 (mmmt) REVERT: C 614 ASP cc_start: 0.7699 (t0) cc_final: 0.7451 (m-30) REVERT: C 661 GLU cc_start: 0.7604 (mt-10) cc_final: 0.7357 (tt0) REVERT: C 786 LYS cc_start: 0.8479 (pttt) cc_final: 0.7932 (ptpp) REVERT: C 902 MET cc_start: 0.7230 (mmm) cc_final: 0.6561 (tpt) REVERT: C 990 GLU cc_start: 0.6415 (mt-10) cc_final: 0.5988 (tm-30) outliers start: 52 outliers final: 28 residues processed: 262 average time/residue: 0.3353 time to fit residues: 140.6407 Evaluate side-chains 235 residues out of total 2581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 204 time to evaluate : 2.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 811 LYS Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 830 ASP Chi-restraints excluded: chain C residue 854 LYS Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 95 optimal weight: 4.9990 chunk 255 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 166 optimal weight: 4.9990 chunk 70 optimal weight: 0.9980 chunk 284 optimal weight: 0.9980 chunk 236 optimal weight: 0.3980 chunk 131 optimal weight: 6.9990 chunk 23 optimal weight: 7.9990 chunk 94 optimal weight: 2.9990 chunk 149 optimal weight: 0.9980 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 GLN B 506 GLN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5996 moved from start: 0.3102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 23565 Z= 0.222 Angle : 0.514 8.560 32059 Z= 0.268 Chirality : 0.044 0.150 3671 Planarity : 0.004 0.062 4144 Dihedral : 4.857 57.634 3139 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.05 % Allowed : 10.73 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.15), residues: 2878 helix: 1.81 (0.20), residues: 688 sheet: 0.09 (0.18), residues: 662 loop : -0.75 (0.15), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 436 HIS 0.003 0.001 HIS A 519 PHE 0.017 0.001 PHE B 400 TYR 0.020 0.001 TYR B 351 ARG 0.006 0.000 ARG B 190 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 211 time to evaluate : 2.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: 0.8325 (p0) cc_final: 0.7680 (p0) REVERT: A 237 ARG cc_start: 0.6629 (mtt90) cc_final: 0.6130 (mtm-85) REVERT: A 239 GLN cc_start: 0.6273 (tt0) cc_final: 0.5839 (tt0) REVERT: A 269 TYR cc_start: 0.7402 (m-80) cc_final: 0.6954 (m-10) REVERT: A 529 LYS cc_start: 0.8416 (mttt) cc_final: 0.7649 (mmtt) REVERT: A 558 LYS cc_start: 0.8025 (tttt) cc_final: 0.7255 (mmmt) REVERT: A 786 LYS cc_start: 0.7725 (pttt) cc_final: 0.7324 (pttm) REVERT: A 790 LYS cc_start: 0.7795 (pttt) cc_final: 0.7244 (pttp) REVERT: A 804 GLN cc_start: 0.7302 (mm-40) cc_final: 0.6507 (mp10) REVERT: A 912 THR cc_start: 0.7383 (OUTLIER) cc_final: 0.7052 (p) REVERT: A 957 GLN cc_start: 0.6068 (tp-100) cc_final: 0.5789 (tt0) REVERT: A 1002 GLN cc_start: 0.6392 (tt0) cc_final: 0.6041 (tp40) REVERT: A 1003 SER cc_start: 0.7087 (t) cc_final: 0.6777 (p) REVERT: A 1045 LYS cc_start: 0.7401 (ttpp) cc_final: 0.6982 (mmmt) REVERT: A 1073 LYS cc_start: 0.6624 (tttt) cc_final: 0.6379 (ttmm) REVERT: A 1107 ARG cc_start: 0.7767 (mtm-85) cc_final: 0.7119 (mtt180) REVERT: B 118 LEU cc_start: 0.6708 (tp) cc_final: 0.6276 (mm) REVERT: B 200 TYR cc_start: 0.6944 (m-80) cc_final: 0.6504 (m-80) REVERT: B 241 LEU cc_start: 0.5717 (mt) cc_final: 0.5454 (mp) REVERT: B 271 GLN cc_start: 0.6441 (OUTLIER) cc_final: 0.6155 (mp10) REVERT: B 307 THR cc_start: 0.8446 (m) cc_final: 0.7982 (t) REVERT: B 309 GLU cc_start: 0.6036 (mp0) cc_final: 0.5791 (mp0) REVERT: B 364 ASP cc_start: 0.8047 (t0) cc_final: 0.7673 (t0) REVERT: B 400 PHE cc_start: 0.7188 (p90) cc_final: 0.6881 (p90) REVERT: B 440 ASN cc_start: 0.8313 (OUTLIER) cc_final: 0.8112 (p0) REVERT: B 568 ASP cc_start: 0.6959 (OUTLIER) cc_final: 0.6592 (m-30) REVERT: B 661 GLU cc_start: 0.7644 (mt-10) cc_final: 0.7334 (mm-30) REVERT: B 776 LYS cc_start: 0.6505 (tttt) cc_final: 0.6153 (ttpt) REVERT: B 786 LYS cc_start: 0.8323 (pttt) cc_final: 0.8092 (pttm) REVERT: B 950 ASP cc_start: 0.6656 (t70) cc_final: 0.6165 (m-30) REVERT: B 1003 SER cc_start: 0.6965 (t) cc_final: 0.6506 (m) REVERT: B 1045 LYS cc_start: 0.8118 (ttpp) cc_final: 0.7652 (tttm) REVERT: B 1072 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.7463 (mp0) REVERT: B 1114 ILE cc_start: 0.8244 (mm) cc_final: 0.7943 (tt) REVERT: C 32 PHE cc_start: 0.6248 (m-80) cc_final: 0.5891 (m-80) REVERT: C 63 THR cc_start: 0.7210 (m) cc_final: 0.6995 (p) REVERT: C 117 LEU cc_start: 0.6891 (tp) cc_final: 0.6514 (mm) REVERT: C 132 GLU cc_start: 0.7869 (mt-10) cc_final: 0.7370 (mt-10) REVERT: C 133 PHE cc_start: 0.5830 (m-80) cc_final: 0.5362 (t80) REVERT: C 205 SER cc_start: 0.7814 (p) cc_final: 0.7313 (t) REVERT: C 239 GLN cc_start: 0.7377 (tt0) cc_final: 0.7156 (tt0) REVERT: C 269 TYR cc_start: 0.8037 (m-80) cc_final: 0.7463 (m-10) REVERT: C 281 GLU cc_start: 0.6752 (pm20) cc_final: 0.6400 (pm20) REVERT: C 305 SER cc_start: 0.7972 (t) cc_final: 0.7656 (p) REVERT: C 316 SER cc_start: 0.7567 (t) cc_final: 0.7281 (p) REVERT: C 335 LEU cc_start: 0.7717 (mt) cc_final: 0.7152 (tt) REVERT: C 353 TRP cc_start: 0.4938 (p-90) cc_final: 0.4183 (p-90) REVERT: C 427 ASP cc_start: 0.7265 (m-30) cc_final: 0.6955 (t0) REVERT: C 558 LYS cc_start: 0.7798 (tttt) cc_final: 0.7502 (mmmt) REVERT: C 614 ASP cc_start: 0.7686 (t0) cc_final: 0.7433 (m-30) REVERT: C 661 GLU cc_start: 0.7553 (mt-10) cc_final: 0.7330 (tt0) REVERT: C 786 LYS cc_start: 0.8485 (pttt) cc_final: 0.7873 (ptpp) REVERT: C 902 MET cc_start: 0.7322 (mmm) cc_final: 0.6773 (tpt) REVERT: C 990 GLU cc_start: 0.6400 (mt-10) cc_final: 0.5958 (tm-30) REVERT: C 1029 MET cc_start: 0.6873 (tpp) cc_final: 0.6529 (tpp) REVERT: C 1072 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7392 (mp0) outliers start: 53 outliers final: 38 residues processed: 247 average time/residue: 0.3237 time to fit residues: 129.1826 Evaluate side-chains 244 residues out of total 2581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 200 time to evaluate : 2.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 811 LYS Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 568 ASP Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 830 ASP Chi-restraints excluded: chain C residue 854 LYS Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 274 optimal weight: 3.9990 chunk 32 optimal weight: 9.9990 chunk 162 optimal weight: 0.5980 chunk 207 optimal weight: 20.0000 chunk 160 optimal weight: 3.9990 chunk 239 optimal weight: 5.9990 chunk 158 optimal weight: 1.9990 chunk 283 optimal weight: 1.9990 chunk 177 optimal weight: 0.5980 chunk 172 optimal weight: 0.5980 chunk 130 optimal weight: 20.0000 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 580 GLN B1088 HIS C 564 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5995 moved from start: 0.3228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23565 Z= 0.201 Angle : 0.502 9.966 32059 Z= 0.261 Chirality : 0.044 0.223 3671 Planarity : 0.004 0.054 4144 Dihedral : 4.747 57.775 3139 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.09 % Allowed : 10.85 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.15), residues: 2878 helix: 1.88 (0.20), residues: 688 sheet: 0.12 (0.18), residues: 661 loop : -0.74 (0.15), residues: 1529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 436 HIS 0.003 0.001 HIS B 49 PHE 0.017 0.001 PHE B 400 TYR 0.020 0.001 TYR B 351 ARG 0.008 0.000 ARG B 190 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 211 time to evaluate : 2.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: 0.8331 (p0) cc_final: 0.7709 (p0) REVERT: A 237 ARG cc_start: 0.6630 (mtt90) cc_final: 0.6131 (mtm-85) REVERT: A 239 GLN cc_start: 0.6324 (tt0) cc_final: 0.5704 (tt0) REVERT: A 269 TYR cc_start: 0.7426 (m-80) cc_final: 0.6939 (m-10) REVERT: A 529 LYS cc_start: 0.8379 (mttt) cc_final: 0.7610 (mmtt) REVERT: A 558 LYS cc_start: 0.8044 (tttt) cc_final: 0.7252 (mmmt) REVERT: A 661 GLU cc_start: 0.7397 (mt-10) cc_final: 0.6854 (mm-30) REVERT: A 780 GLU cc_start: 0.6811 (mt-10) cc_final: 0.6386 (mm-30) REVERT: A 786 LYS cc_start: 0.7742 (pttt) cc_final: 0.7405 (pttm) REVERT: A 790 LYS cc_start: 0.7809 (pttt) cc_final: 0.7203 (pttp) REVERT: A 804 GLN cc_start: 0.7334 (mm-40) cc_final: 0.6583 (mp10) REVERT: A 912 THR cc_start: 0.7454 (OUTLIER) cc_final: 0.7087 (p) REVERT: A 957 GLN cc_start: 0.6090 (tp-100) cc_final: 0.5793 (tt0) REVERT: A 1002 GLN cc_start: 0.6393 (tt0) cc_final: 0.6025 (tp40) REVERT: A 1003 SER cc_start: 0.7091 (t) cc_final: 0.6782 (p) REVERT: A 1045 LYS cc_start: 0.7403 (ttpp) cc_final: 0.7020 (mmmt) REVERT: A 1073 LYS cc_start: 0.6649 (tttt) cc_final: 0.6397 (ttmm) REVERT: A 1107 ARG cc_start: 0.7774 (mtm-85) cc_final: 0.7127 (mtt180) REVERT: B 118 LEU cc_start: 0.6690 (tp) cc_final: 0.6275 (mm) REVERT: B 200 TYR cc_start: 0.7102 (m-80) cc_final: 0.6586 (m-80) REVERT: B 241 LEU cc_start: 0.5662 (mt) cc_final: 0.5441 (mp) REVERT: B 271 GLN cc_start: 0.6458 (OUTLIER) cc_final: 0.6145 (mp10) REVERT: B 307 THR cc_start: 0.8356 (m) cc_final: 0.7861 (t) REVERT: B 309 GLU cc_start: 0.6007 (mp0) cc_final: 0.5756 (mp0) REVERT: B 364 ASP cc_start: 0.8048 (t0) cc_final: 0.7699 (t0) REVERT: B 400 PHE cc_start: 0.7161 (p90) cc_final: 0.6865 (p90) REVERT: B 440 ASN cc_start: 0.8437 (OUTLIER) cc_final: 0.8199 (p0) REVERT: B 568 ASP cc_start: 0.6865 (m-30) cc_final: 0.6563 (m-30) REVERT: B 661 GLU cc_start: 0.7656 (mt-10) cc_final: 0.7321 (mm-30) REVERT: B 776 LYS cc_start: 0.6488 (tttt) cc_final: 0.6132 (ttpt) REVERT: B 786 LYS cc_start: 0.8373 (pttt) cc_final: 0.8131 (pttm) REVERT: B 950 ASP cc_start: 0.6648 (t70) cc_final: 0.6168 (m-30) REVERT: B 1003 SER cc_start: 0.6967 (t) cc_final: 0.6507 (m) REVERT: B 1045 LYS cc_start: 0.8112 (ttpp) cc_final: 0.7701 (ttpp) REVERT: B 1072 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7460 (mp0) REVERT: B 1092 GLU cc_start: 0.8075 (mm-30) cc_final: 0.7821 (mt-10) REVERT: B 1114 ILE cc_start: 0.8229 (mm) cc_final: 0.7934 (tt) REVERT: C 32 PHE cc_start: 0.6174 (m-80) cc_final: 0.5846 (m-80) REVERT: C 63 THR cc_start: 0.7220 (m) cc_final: 0.7014 (p) REVERT: C 117 LEU cc_start: 0.6881 (tp) cc_final: 0.6509 (mm) REVERT: C 133 PHE cc_start: 0.5784 (m-80) cc_final: 0.5328 (t80) REVERT: C 205 SER cc_start: 0.7810 (p) cc_final: 0.7378 (t) REVERT: C 231 ILE cc_start: 0.8522 (OUTLIER) cc_final: 0.8233 (pt) REVERT: C 269 TYR cc_start: 0.8048 (m-80) cc_final: 0.7397 (m-10) REVERT: C 281 GLU cc_start: 0.6805 (pm20) cc_final: 0.6461 (pm20) REVERT: C 305 SER cc_start: 0.7988 (t) cc_final: 0.7679 (p) REVERT: C 316 SER cc_start: 0.7572 (t) cc_final: 0.7304 (p) REVERT: C 335 LEU cc_start: 0.7776 (mt) cc_final: 0.7131 (tt) REVERT: C 353 TRP cc_start: 0.4785 (p-90) cc_final: 0.4181 (p-90) REVERT: C 427 ASP cc_start: 0.7273 (m-30) cc_final: 0.6970 (t0) REVERT: C 558 LYS cc_start: 0.7803 (tttt) cc_final: 0.7500 (mmmt) REVERT: C 614 ASP cc_start: 0.7719 (t0) cc_final: 0.7472 (m-30) REVERT: C 661 GLU cc_start: 0.7575 (mt-10) cc_final: 0.7351 (tt0) REVERT: C 702 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7606 (tp30) REVERT: C 786 LYS cc_start: 0.8485 (pttt) cc_final: 0.7869 (ptpp) REVERT: C 902 MET cc_start: 0.7304 (mmm) cc_final: 0.6801 (tpt) REVERT: C 990 GLU cc_start: 0.6397 (mt-10) cc_final: 0.5958 (tm-30) REVERT: C 1029 MET cc_start: 0.6859 (tpp) cc_final: 0.6524 (tpp) REVERT: C 1072 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.7287 (mp0) outliers start: 54 outliers final: 39 residues processed: 249 average time/residue: 0.3195 time to fit residues: 129.1897 Evaluate side-chains 245 residues out of total 2581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 199 time to evaluate : 2.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 811 LYS Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 564 GLN Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 702 GLU Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 830 ASP Chi-restraints excluded: chain C residue 854 LYS Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 175 optimal weight: 0.8980 chunk 113 optimal weight: 6.9990 chunk 169 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 54 optimal weight: 0.5980 chunk 180 optimal weight: 0.6980 chunk 193 optimal weight: 0.9990 chunk 140 optimal weight: 10.0000 chunk 26 optimal weight: 10.0000 chunk 222 optimal weight: 10.0000 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 564 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5994 moved from start: 0.3318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 23565 Z= 0.188 Angle : 0.498 9.407 32059 Z= 0.259 Chirality : 0.043 0.191 3671 Planarity : 0.004 0.053 4144 Dihedral : 4.656 57.996 3139 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.94 % Allowed : 11.04 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.15), residues: 2878 helix: 1.97 (0.20), residues: 687 sheet: 0.16 (0.18), residues: 661 loop : -0.73 (0.15), residues: 1530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP C 436 HIS 0.004 0.001 HIS C 207 PHE 0.016 0.001 PHE B 400 TYR 0.021 0.001 TYR B 351 ARG 0.005 0.000 ARG B 190 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 206 time to evaluate : 2.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: 0.8338 (p0) cc_final: 0.7720 (p0) REVERT: A 237 ARG cc_start: 0.6585 (mtt90) cc_final: 0.6066 (mtm-85) REVERT: A 239 GLN cc_start: 0.6202 (tt0) cc_final: 0.5771 (tt0) REVERT: A 269 TYR cc_start: 0.7427 (m-80) cc_final: 0.6946 (m-10) REVERT: A 529 LYS cc_start: 0.8380 (mttt) cc_final: 0.7619 (mmtt) REVERT: A 558 LYS cc_start: 0.8028 (tttt) cc_final: 0.7146 (mmmt) REVERT: A 661 GLU cc_start: 0.7400 (mt-10) cc_final: 0.6855 (mm-30) REVERT: A 780 GLU cc_start: 0.6811 (mt-10) cc_final: 0.6382 (mm-30) REVERT: A 786 LYS cc_start: 0.7746 (pttt) cc_final: 0.7443 (pttm) REVERT: A 790 LYS cc_start: 0.7862 (pttt) cc_final: 0.7234 (pttp) REVERT: A 804 GLN cc_start: 0.7201 (mm-40) cc_final: 0.6567 (mp10) REVERT: A 912 THR cc_start: 0.7457 (OUTLIER) cc_final: 0.7089 (p) REVERT: A 957 GLN cc_start: 0.6109 (tp-100) cc_final: 0.5821 (tt0) REVERT: A 1002 GLN cc_start: 0.6396 (tt0) cc_final: 0.6017 (tp40) REVERT: A 1003 SER cc_start: 0.7055 (t) cc_final: 0.6740 (p) REVERT: A 1045 LYS cc_start: 0.7405 (ttpp) cc_final: 0.7019 (mmmt) REVERT: A 1073 LYS cc_start: 0.6654 (tttt) cc_final: 0.6398 (ttmm) REVERT: A 1107 ARG cc_start: 0.7774 (mtm-85) cc_final: 0.7134 (mtt180) REVERT: B 118 LEU cc_start: 0.6677 (tp) cc_final: 0.6262 (mm) REVERT: B 200 TYR cc_start: 0.7108 (m-80) cc_final: 0.6583 (m-80) REVERT: B 271 GLN cc_start: 0.6467 (OUTLIER) cc_final: 0.6171 (mp10) REVERT: B 307 THR cc_start: 0.8350 (m) cc_final: 0.7852 (t) REVERT: B 309 GLU cc_start: 0.6016 (mp0) cc_final: 0.5762 (mp0) REVERT: B 364 ASP cc_start: 0.8022 (t0) cc_final: 0.7672 (t0) REVERT: B 400 PHE cc_start: 0.7155 (p90) cc_final: 0.6817 (p90) REVERT: B 568 ASP cc_start: 0.6900 (m-30) cc_final: 0.6601 (m-30) REVERT: B 661 GLU cc_start: 0.7675 (mt-10) cc_final: 0.7331 (mm-30) REVERT: B 776 LYS cc_start: 0.6471 (tttt) cc_final: 0.6119 (ttpt) REVERT: B 786 LYS cc_start: 0.8374 (pttt) cc_final: 0.8131 (pttm) REVERT: B 950 ASP cc_start: 0.6645 (t70) cc_final: 0.6212 (m-30) REVERT: B 1003 SER cc_start: 0.6967 (t) cc_final: 0.6503 (m) REVERT: B 1045 LYS cc_start: 0.8110 (ttpp) cc_final: 0.7646 (tttm) REVERT: B 1072 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.7449 (mp0) REVERT: B 1092 GLU cc_start: 0.8053 (mm-30) cc_final: 0.7819 (mt-10) REVERT: B 1114 ILE cc_start: 0.8216 (mm) cc_final: 0.7919 (tt) REVERT: C 32 PHE cc_start: 0.6155 (m-80) cc_final: 0.5844 (m-80) REVERT: C 81 ASN cc_start: 0.7064 (p0) cc_final: 0.6626 (p0) REVERT: C 117 LEU cc_start: 0.6884 (tp) cc_final: 0.6504 (mt) REVERT: C 133 PHE cc_start: 0.5912 (m-80) cc_final: 0.5440 (t80) REVERT: C 205 SER cc_start: 0.7787 (p) cc_final: 0.7383 (t) REVERT: C 231 ILE cc_start: 0.8515 (OUTLIER) cc_final: 0.8315 (mt) REVERT: C 239 GLN cc_start: 0.7454 (tt0) cc_final: 0.6819 (tt0) REVERT: C 269 TYR cc_start: 0.8057 (m-80) cc_final: 0.7420 (m-10) REVERT: C 281 GLU cc_start: 0.6801 (pm20) cc_final: 0.6464 (pm20) REVERT: C 305 SER cc_start: 0.7963 (t) cc_final: 0.7706 (p) REVERT: C 316 SER cc_start: 0.7620 (t) cc_final: 0.7367 (p) REVERT: C 335 LEU cc_start: 0.7772 (mt) cc_final: 0.7244 (tt) REVERT: C 353 TRP cc_start: 0.4758 (p-90) cc_final: 0.4218 (p-90) REVERT: C 427 ASP cc_start: 0.7254 (m-30) cc_final: 0.6972 (t0) REVERT: C 558 LYS cc_start: 0.7793 (tttt) cc_final: 0.7511 (mmmt) REVERT: C 614 ASP cc_start: 0.7712 (t0) cc_final: 0.7453 (m-30) REVERT: C 661 GLU cc_start: 0.7615 (mt-10) cc_final: 0.7313 (tt0) REVERT: C 690 GLN cc_start: 0.7472 (mt0) cc_final: 0.6836 (mm-40) REVERT: C 702 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7623 (tp30) REVERT: C 786 LYS cc_start: 0.8487 (pttt) cc_final: 0.7868 (ptpp) REVERT: C 902 MET cc_start: 0.7316 (mmm) cc_final: 0.6678 (tpt) REVERT: C 990 GLU cc_start: 0.6382 (mt-10) cc_final: 0.5981 (tm-30) REVERT: C 1029 MET cc_start: 0.6855 (tpp) cc_final: 0.6534 (tpp) REVERT: C 1072 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7302 (mp0) outliers start: 50 outliers final: 40 residues processed: 241 average time/residue: 0.3271 time to fit residues: 126.1161 Evaluate side-chains 242 residues out of total 2581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 196 time to evaluate : 2.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 811 LYS Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 564 GLN Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 702 GLU Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 854 LYS Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 257 optimal weight: 0.7980 chunk 271 optimal weight: 0.7980 chunk 247 optimal weight: 5.9990 chunk 264 optimal weight: 0.9980 chunk 158 optimal weight: 0.8980 chunk 115 optimal weight: 3.9990 chunk 207 optimal weight: 20.0000 chunk 81 optimal weight: 1.9990 chunk 238 optimal weight: 4.9990 chunk 249 optimal weight: 3.9990 chunk 263 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 564 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5995 moved from start: 0.3378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 23565 Z= 0.196 Angle : 0.498 9.339 32059 Z= 0.259 Chirality : 0.044 0.198 3671 Planarity : 0.004 0.053 4144 Dihedral : 4.560 58.077 3138 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.05 % Allowed : 11.04 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.15), residues: 2878 helix: 2.02 (0.20), residues: 685 sheet: 0.15 (0.18), residues: 661 loop : -0.71 (0.15), residues: 1532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP C 436 HIS 0.003 0.001 HIS C 207 PHE 0.016 0.001 PHE B 400 TYR 0.020 0.001 TYR B 351 ARG 0.004 0.000 ARG B 190 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 203 time to evaluate : 2.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: 0.8346 (p0) cc_final: 0.7782 (m-40) REVERT: A 237 ARG cc_start: 0.6695 (mtt90) cc_final: 0.6171 (mtm-85) REVERT: A 239 GLN cc_start: 0.6246 (tt0) cc_final: 0.6006 (tt0) REVERT: A 269 TYR cc_start: 0.7459 (m-80) cc_final: 0.6994 (m-10) REVERT: A 529 LYS cc_start: 0.8383 (mttt) cc_final: 0.7641 (mmtt) REVERT: A 558 LYS cc_start: 0.8033 (tttt) cc_final: 0.7144 (mmmt) REVERT: A 661 GLU cc_start: 0.7409 (mt-10) cc_final: 0.6861 (mm-30) REVERT: A 780 GLU cc_start: 0.6817 (mt-10) cc_final: 0.6384 (mm-30) REVERT: A 786 LYS cc_start: 0.7739 (pttt) cc_final: 0.7428 (pttm) REVERT: A 790 LYS cc_start: 0.7881 (pttt) cc_final: 0.7255 (pttp) REVERT: A 804 GLN cc_start: 0.7233 (mm-40) cc_final: 0.6579 (mp10) REVERT: A 912 THR cc_start: 0.7452 (OUTLIER) cc_final: 0.7079 (p) REVERT: A 957 GLN cc_start: 0.6113 (tp-100) cc_final: 0.5822 (tt0) REVERT: A 1002 GLN cc_start: 0.6398 (tt0) cc_final: 0.6018 (tp40) REVERT: A 1003 SER cc_start: 0.7044 (t) cc_final: 0.6743 (p) REVERT: A 1045 LYS cc_start: 0.7409 (ttpp) cc_final: 0.7019 (mmmt) REVERT: A 1073 LYS cc_start: 0.6675 (tttt) cc_final: 0.6407 (ttmm) REVERT: A 1107 ARG cc_start: 0.7776 (mtm-85) cc_final: 0.7140 (mtt180) REVERT: B 118 LEU cc_start: 0.6672 (tp) cc_final: 0.6263 (mm) REVERT: B 200 TYR cc_start: 0.7122 (m-80) cc_final: 0.6720 (m-80) REVERT: B 271 GLN cc_start: 0.6468 (OUTLIER) cc_final: 0.6172 (mp10) REVERT: B 307 THR cc_start: 0.8336 (m) cc_final: 0.7853 (t) REVERT: B 309 GLU cc_start: 0.6023 (mp0) cc_final: 0.5768 (mp0) REVERT: B 351 TYR cc_start: 0.7651 (p90) cc_final: 0.7289 (p90) REVERT: B 364 ASP cc_start: 0.8007 (t0) cc_final: 0.7732 (t0) REVERT: B 400 PHE cc_start: 0.7155 (p90) cc_final: 0.6816 (p90) REVERT: B 440 ASN cc_start: 0.8417 (OUTLIER) cc_final: 0.8182 (p0) REVERT: B 568 ASP cc_start: 0.6863 (m-30) cc_final: 0.6557 (m-30) REVERT: B 661 GLU cc_start: 0.7677 (mt-10) cc_final: 0.7332 (mm-30) REVERT: B 776 LYS cc_start: 0.6471 (tttt) cc_final: 0.6121 (ttpt) REVERT: B 786 LYS cc_start: 0.8374 (pttt) cc_final: 0.8130 (pttm) REVERT: B 950 ASP cc_start: 0.6645 (t70) cc_final: 0.6214 (m-30) REVERT: B 1003 SER cc_start: 0.6969 (t) cc_final: 0.6501 (m) REVERT: B 1045 LYS cc_start: 0.8147 (ttpp) cc_final: 0.7674 (tttm) REVERT: B 1072 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.7458 (mp0) REVERT: B 1092 GLU cc_start: 0.8062 (mm-30) cc_final: 0.7805 (mt-10) REVERT: B 1114 ILE cc_start: 0.8223 (mm) cc_final: 0.7928 (tt) REVERT: C 32 PHE cc_start: 0.6099 (m-80) cc_final: 0.5804 (m-80) REVERT: C 81 ASN cc_start: 0.7081 (p0) cc_final: 0.6644 (p0) REVERT: C 117 LEU cc_start: 0.6874 (tp) cc_final: 0.6527 (mp) REVERT: C 132 GLU cc_start: 0.7782 (mt-10) cc_final: 0.7301 (mt-10) REVERT: C 133 PHE cc_start: 0.5626 (m-80) cc_final: 0.5414 (t80) REVERT: C 205 SER cc_start: 0.7704 (p) cc_final: 0.7331 (t) REVERT: C 231 ILE cc_start: 0.8371 (OUTLIER) cc_final: 0.8157 (mt) REVERT: C 239 GLN cc_start: 0.7441 (tt0) cc_final: 0.6813 (tt0) REVERT: C 269 TYR cc_start: 0.7945 (m-80) cc_final: 0.7338 (m-10) REVERT: C 281 GLU cc_start: 0.6742 (pm20) cc_final: 0.6405 (pm20) REVERT: C 305 SER cc_start: 0.8015 (t) cc_final: 0.7726 (p) REVERT: C 316 SER cc_start: 0.7626 (t) cc_final: 0.7331 (p) REVERT: C 335 LEU cc_start: 0.7767 (mt) cc_final: 0.7241 (tt) REVERT: C 353 TRP cc_start: 0.4804 (p-90) cc_final: 0.4262 (p-90) REVERT: C 558 LYS cc_start: 0.7786 (tttt) cc_final: 0.7489 (mmmt) REVERT: C 614 ASP cc_start: 0.7753 (t0) cc_final: 0.7464 (m-30) REVERT: C 661 GLU cc_start: 0.7610 (mt-10) cc_final: 0.7351 (tt0) REVERT: C 690 GLN cc_start: 0.7423 (mt0) cc_final: 0.6849 (mm-40) REVERT: C 702 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7645 (tp30) REVERT: C 786 LYS cc_start: 0.8486 (pttt) cc_final: 0.7868 (ptpp) REVERT: C 902 MET cc_start: 0.7324 (mmm) cc_final: 0.6836 (tpt) REVERT: C 990 GLU cc_start: 0.6359 (mt-10) cc_final: 0.5951 (tm-30) REVERT: C 1029 MET cc_start: 0.6857 (tpp) cc_final: 0.6551 (tpp) REVERT: C 1072 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7266 (mp0) outliers start: 53 outliers final: 42 residues processed: 240 average time/residue: 0.3191 time to fit residues: 123.1869 Evaluate side-chains 248 residues out of total 2581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 199 time to evaluate : 2.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 811 LYS Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 564 GLN Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 702 GLU Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 830 ASP Chi-restraints excluded: chain C residue 854 LYS Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 173 optimal weight: 1.9990 chunk 279 optimal weight: 0.6980 chunk 170 optimal weight: 0.7980 chunk 132 optimal weight: 20.0000 chunk 194 optimal weight: 4.9990 chunk 292 optimal weight: 0.5980 chunk 269 optimal weight: 0.7980 chunk 233 optimal weight: 20.0000 chunk 24 optimal weight: 1.9990 chunk 180 optimal weight: 4.9990 chunk 143 optimal weight: 0.3980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 564 GLN C1083 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5987 moved from start: 0.3487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 23565 Z= 0.151 Angle : 0.491 10.590 32059 Z= 0.253 Chirality : 0.043 0.184 3671 Planarity : 0.004 0.052 4144 Dihedral : 4.450 58.663 3138 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.63 % Allowed : 11.51 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.15), residues: 2878 helix: 2.15 (0.20), residues: 683 sheet: 0.21 (0.19), residues: 641 loop : -0.67 (0.15), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP C 436 HIS 0.003 0.001 HIS C 207 PHE 0.016 0.001 PHE B 400 TYR 0.020 0.001 TYR A 170 ARG 0.004 0.000 ARG B 190 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 214 time to evaluate : 2.658 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: 0.8259 (p0) cc_final: 0.7786 (m-40) REVERT: A 237 ARG cc_start: 0.6628 (mtt90) cc_final: 0.6076 (mtm-85) REVERT: A 269 TYR cc_start: 0.7453 (m-80) cc_final: 0.6926 (m-10) REVERT: A 529 LYS cc_start: 0.8273 (mttt) cc_final: 0.7564 (mmtt) REVERT: A 558 LYS cc_start: 0.8028 (tttt) cc_final: 0.7144 (mmmt) REVERT: A 661 GLU cc_start: 0.7444 (mt-10) cc_final: 0.6873 (mm-30) REVERT: A 780 GLU cc_start: 0.6813 (mt-10) cc_final: 0.6385 (mm-30) REVERT: A 786 LYS cc_start: 0.7741 (pttt) cc_final: 0.7439 (pttm) REVERT: A 790 LYS cc_start: 0.7897 (pttt) cc_final: 0.7275 (pttp) REVERT: A 804 GLN cc_start: 0.7252 (mm-40) cc_final: 0.6567 (mp10) REVERT: A 912 THR cc_start: 0.7464 (OUTLIER) cc_final: 0.7099 (p) REVERT: A 957 GLN cc_start: 0.6104 (tp-100) cc_final: 0.5820 (tt0) REVERT: A 1002 GLN cc_start: 0.6400 (tt0) cc_final: 0.6013 (tp40) REVERT: A 1003 SER cc_start: 0.7086 (t) cc_final: 0.6793 (p) REVERT: A 1045 LYS cc_start: 0.7418 (ttpp) cc_final: 0.7022 (mmmt) REVERT: A 1073 LYS cc_start: 0.6673 (tttt) cc_final: 0.6405 (ttmm) REVERT: A 1107 ARG cc_start: 0.7782 (mtm-85) cc_final: 0.7077 (mtt90) REVERT: B 118 LEU cc_start: 0.6677 (tp) cc_final: 0.6269 (mm) REVERT: B 200 TYR cc_start: 0.7111 (m-80) cc_final: 0.6765 (m-80) REVERT: B 271 GLN cc_start: 0.6465 (OUTLIER) cc_final: 0.6202 (mp10) REVERT: B 307 THR cc_start: 0.8328 (m) cc_final: 0.7851 (t) REVERT: B 309 GLU cc_start: 0.5998 (mp0) cc_final: 0.5730 (mp0) REVERT: B 351 TYR cc_start: 0.7733 (p90) cc_final: 0.7432 (p90) REVERT: B 364 ASP cc_start: 0.8050 (t0) cc_final: 0.7810 (t0) REVERT: B 400 PHE cc_start: 0.7154 (p90) cc_final: 0.6819 (p90) REVERT: B 440 ASN cc_start: 0.8371 (OUTLIER) cc_final: 0.8124 (p0) REVERT: B 568 ASP cc_start: 0.6845 (m-30) cc_final: 0.6575 (m-30) REVERT: B 661 GLU cc_start: 0.7672 (mt-10) cc_final: 0.7328 (mm-30) REVERT: B 776 LYS cc_start: 0.6566 (tttt) cc_final: 0.6215 (ttpt) REVERT: B 786 LYS cc_start: 0.8393 (pttt) cc_final: 0.8157 (pttm) REVERT: B 950 ASP cc_start: 0.6633 (t70) cc_final: 0.6161 (m-30) REVERT: B 1003 SER cc_start: 0.6978 (t) cc_final: 0.6503 (m) REVERT: B 1045 LYS cc_start: 0.8143 (ttpp) cc_final: 0.7709 (ttpp) REVERT: B 1072 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.7426 (mp0) REVERT: B 1081 ILE cc_start: 0.7477 (mm) cc_final: 0.7266 (mm) REVERT: B 1092 GLU cc_start: 0.7995 (mm-30) cc_final: 0.7702 (mt-10) REVERT: B 1114 ILE cc_start: 0.8219 (mm) cc_final: 0.7924 (tt) REVERT: C 32 PHE cc_start: 0.5967 (m-80) cc_final: 0.5712 (m-80) REVERT: C 81 ASN cc_start: 0.7053 (p0) cc_final: 0.6745 (p0) REVERT: C 117 LEU cc_start: 0.6864 (tp) cc_final: 0.6490 (mp) REVERT: C 205 SER cc_start: 0.7652 (p) cc_final: 0.7269 (t) REVERT: C 239 GLN cc_start: 0.7399 (tt0) cc_final: 0.6864 (tt0) REVERT: C 269 TYR cc_start: 0.7970 (m-80) cc_final: 0.7375 (m-10) REVERT: C 281 GLU cc_start: 0.6735 (pm20) cc_final: 0.6394 (pm20) REVERT: C 305 SER cc_start: 0.8047 (t) cc_final: 0.7785 (p) REVERT: C 316 SER cc_start: 0.7561 (t) cc_final: 0.7291 (p) REVERT: C 335 LEU cc_start: 0.7687 (mt) cc_final: 0.7162 (tt) REVERT: C 353 TRP cc_start: 0.4768 (p-90) cc_final: 0.4082 (p-90) REVERT: C 398 ASP cc_start: 0.8263 (m-30) cc_final: 0.7223 (m-30) REVERT: C 558 LYS cc_start: 0.7788 (tttt) cc_final: 0.7466 (mmmt) REVERT: C 614 ASP cc_start: 0.7777 (t0) cc_final: 0.7474 (m-30) REVERT: C 661 GLU cc_start: 0.7577 (mt-10) cc_final: 0.7272 (tt0) REVERT: C 690 GLN cc_start: 0.7429 (mt0) cc_final: 0.6846 (mm-40) REVERT: C 786 LYS cc_start: 0.8437 (pttt) cc_final: 0.7796 (ptpp) REVERT: C 902 MET cc_start: 0.7289 (mmm) cc_final: 0.6828 (tpt) REVERT: C 990 GLU cc_start: 0.6330 (mt-10) cc_final: 0.5933 (tm-30) REVERT: C 1029 MET cc_start: 0.6831 (tpp) cc_final: 0.6556 (tpp) outliers start: 42 outliers final: 36 residues processed: 243 average time/residue: 0.3442 time to fit residues: 134.3788 Evaluate side-chains 240 residues out of total 2581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 200 time to evaluate : 2.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 811 LYS Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 830 ASP Chi-restraints excluded: chain C residue 854 LYS Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 185 optimal weight: 0.5980 chunk 248 optimal weight: 4.9990 chunk 71 optimal weight: 6.9990 chunk 215 optimal weight: 7.9990 chunk 34 optimal weight: 5.9990 chunk 64 optimal weight: 0.7980 chunk 233 optimal weight: 20.0000 chunk 97 optimal weight: 10.0000 chunk 239 optimal weight: 5.9990 chunk 29 optimal weight: 0.7980 chunk 43 optimal weight: 9.9990 overall best weight: 2.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 655 HIS ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.145784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.102410 restraints weight = 33336.067| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 2.22 r_work: 0.3028 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.3437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 23565 Z= 0.393 Angle : 0.569 8.580 32059 Z= 0.295 Chirality : 0.046 0.173 3671 Planarity : 0.004 0.056 4144 Dihedral : 4.735 57.097 3138 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.90 % Allowed : 11.39 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.15), residues: 2878 helix: 1.81 (0.20), residues: 684 sheet: -0.01 (0.18), residues: 691 loop : -0.81 (0.16), residues: 1503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 436 HIS 0.005 0.001 HIS A 519 PHE 0.015 0.002 PHE C 817 TYR 0.021 0.002 TYR C1067 ARG 0.005 0.000 ARG B 190 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4727.64 seconds wall clock time: 86 minutes 32.88 seconds (5192.88 seconds total)