Starting phenix.real_space_refine on Tue Mar 19 02:06:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tld_25988/03_2024/7tld_25988.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tld_25988/03_2024/7tld_25988.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tld_25988/03_2024/7tld_25988.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tld_25988/03_2024/7tld_25988.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tld_25988/03_2024/7tld_25988.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tld_25988/03_2024/7tld_25988.pdb" } resolution = 2.89 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 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 14586 2.51 5 N 3786 2.21 5 O 4335 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 191": "OE1" <-> "OE2" Residue "A PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "A PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 427": "OD1" <-> "OD2" Residue "A TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 619": "OE1" <-> "OE2" Residue "A TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 661": "OE1" <-> "OE2" Residue "A TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 773": "OE1" <-> "OE2" Residue "A PHE 898": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 927": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1072": "OE1" <-> "OE2" Residue "A GLU 1092": "OE1" <-> "OE2" Residue "A GLU 1111": "OE1" <-> "OE2" Residue "A PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 224": "OE1" <-> "OE2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 309": "OE1" <-> "OE2" Residue "B TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 465": "OE1" <-> "OE2" Residue "B PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 619": "OE1" <-> "OE2" Residue "B GLU 661": "OE1" <-> "OE2" Residue "B TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 702": "OE1" <-> "OE2" Residue "B TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 773": "OE1" <-> "OE2" Residue "B PHE 898": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1072": "OE1" <-> "OE2" Residue "B ASP 1084": "OD1" <-> "OD2" Residue "B PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1146": "OD1" <-> "OD2" Residue "C TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 38": "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 PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 169": "OE1" <-> "OE2" Residue "C TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 465": "OE1" <-> "OE2" Residue "C PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 583": "OE1" <-> "OE2" Residue "C PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 773": "OE1" <-> "OE2" Residue "C PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 898": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 918": "OE1" <-> "OE2" Residue "C TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1111": "OE1" <-> "OE2" Residue "C PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 22812 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 972, 7604 Classifications: {'peptide': 972} Link IDs: {'PTRANS': 52, 'TRANS': 919} Chain breaks: 11 Chain: "B" Number of atoms: 7604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 972, 7604 Classifications: {'peptide': 972} Link IDs: {'PTRANS': 52, 'TRANS': 919} Chain breaks: 11 Chain: "C" Number of atoms: 7604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 972, 7604 Classifications: {'peptide': 972} Link IDs: {'PTRANS': 52, 'TRANS': 919} Chain breaks: 11 Time building chain proxies: 12.04, per 1000 atoms: 0.53 Number of scatterers: 22812 At special positions: 0 Unit cell: (139.656, 126.96, 170.338, 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 4335 8.00 N 3786 7.00 C 14586 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=2.01 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.02 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=2.04 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=2.04 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=2.00 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=2.03 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=2.01 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 383 " - pdb=" SG CYS C 985 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.01 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.05 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.00 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.01 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=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.04 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.00 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.20 Conformation dependent library (CDL) restraints added in 4.5 seconds 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5484 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 47 sheets defined 27.5% alpha, 27.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.36 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 4.095A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.077A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.455A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.818A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.874A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.771A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) 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: 3.737A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.556A pdb=" N LEU A 821 " --> pdb=" O PRO A 817 " (cutoff:3.500A) removed outlier: 3.702A 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 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 removed outlier: 3.539A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) 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 removed outlier: 3.837A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.652A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.770A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.298A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.985A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 389 removed outlier: 4.004A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.666A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) 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: 3.841A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.752A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.539A pdb=" N ASN B 919 " --> pdb=" O VAL B 915 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 939 removed outlier: 3.504A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.535A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.265A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 3.992A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 351 through 353 No H-bonds generated for 'chain 'C' and resid 351 through 353' Processing helix chain 'C' and resid 364 through 370 removed outlier: 4.153A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 389 Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.075A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.715A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.766A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 825 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.626A 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 removed outlier: 3.506A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.756A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) 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: 3.508A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.447A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.069A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.365A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.043A 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: 6.206A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) 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 47 through 55 removed outlier: 3.809A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.695A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.321A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.099A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.099A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AB1, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.738A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.557A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 704 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.591A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 718 through 728 removed outlier: 7.165A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.355A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 790 removed outlier: 5.808A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.564A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.631A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR B 95 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.691A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.205A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.296A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.384A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.949A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.890A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AD1, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.430A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 701 through 704 Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.530A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 718 through 728 removed outlier: 5.751A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.489A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.497A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.465A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 47 through 52 removed outlier: 7.280A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 83 through 85 Processing sheet with id=AE1, first strand: chain 'C' and resid 83 through 85 removed outlier: 6.175A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.034A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 348 through 349 removed outlier: 7.047A pdb=" N ALA C 348 " --> pdb=" O VAL C 401 " (cutoff:3.500A) removed outlier: 9.373A pdb=" N ARG C 403 " --> pdb=" O ALA C 348 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 348 through 349 removed outlier: 7.047A pdb=" N ALA C 348 " --> pdb=" O VAL C 401 " (cutoff:3.500A) removed outlier: 9.373A pdb=" N ARG C 403 " --> pdb=" O ALA C 348 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.891A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AE7, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.500A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.621A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 718 through 728 removed outlier: 7.215A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF2, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.551A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1031 hydrogen bonds defined for protein. 2826 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: 10.62 Time building geometry restraints manager: 10.02 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: 5963 1.33 - 1.46: 4425 1.46 - 1.58: 12808 1.58 - 1.70: 0 1.70 - 1.82: 129 Bond restraints: 23325 Sorted by residual: bond pdb=" CA HIS A1083 " pdb=" C HIS A1083 " ideal model delta sigma weight residual 1.519 1.543 -0.024 5.30e-03 3.56e+04 2.07e+01 bond pdb=" CA PRO B 862 " pdb=" C PRO B 862 " ideal model delta sigma weight residual 1.517 1.544 -0.027 6.70e-03 2.23e+04 1.68e+01 bond pdb=" CZ ARG A 905 " pdb=" NH2 ARG A 905 " ideal model delta sigma weight residual 1.330 1.290 0.040 1.30e-02 5.92e+03 9.63e+00 bond pdb=" CA PRO A 862 " pdb=" C PRO A 862 " ideal model delta sigma weight residual 1.517 1.538 -0.021 6.70e-03 2.23e+04 9.59e+00 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 9.57e+00 ... (remaining 23320 not shown) Histogram of bond angle deviations from ideal: 96.70 - 104.48: 367 104.48 - 112.25: 9955 112.25 - 120.03: 11116 120.03 - 127.80: 10186 127.80 - 135.58: 116 Bond angle restraints: 31740 Sorted by residual: angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 119.23 -8.53 1.22e+00 6.72e-01 4.89e+01 angle pdb=" N PRO C 986 " pdb=" CA PRO C 986 " pdb=" C PRO C 986 " ideal model delta sigma weight residual 110.70 118.44 -7.74 1.22e+00 6.72e-01 4.03e+01 angle pdb=" N PRO B 986 " pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 110.70 117.94 -7.24 1.22e+00 6.72e-01 3.52e+01 angle pdb=" N PRO C 862 " pdb=" CA PRO C 862 " pdb=" CB PRO C 862 " ideal model delta sigma weight residual 103.22 106.14 -2.92 5.20e-01 3.70e+00 3.16e+01 angle pdb=" CA HIS B 207 " pdb=" CB HIS B 207 " pdb=" CG HIS B 207 " ideal model delta sigma weight residual 113.80 119.42 -5.62 1.00e+00 1.00e+00 3.15e+01 ... (remaining 31735 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 12953 17.93 - 35.86: 771 35.86 - 53.79: 136 53.79 - 71.73: 50 71.73 - 89.66: 31 Dihedral angle restraints: 13941 sinusoidal: 5451 harmonic: 8490 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 -162.94 76.94 1 1.00e+01 1.00e-02 7.43e+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 -150.22 64.22 1 1.00e+01 1.00e-02 5.43e+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 93.00 152.19 -59.19 1 1.00e+01 1.00e-02 4.68e+01 ... (remaining 13938 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 2099 0.076 - 0.152: 1223 0.152 - 0.228: 256 0.228 - 0.305: 45 0.305 - 0.381: 10 Chirality restraints: 3633 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 2.34 0.38 2.00e-01 2.50e+01 3.62e+00 chirality pdb=" CA PRO A 986 " pdb=" N PRO A 986 " pdb=" C PRO A 986 " pdb=" CB PRO A 986 " both_signs ideal model delta sigma weight residual False 2.72 2.35 0.37 2.00e-01 2.50e+01 3.41e+00 chirality pdb=" CA PRO B 986 " pdb=" N PRO B 986 " pdb=" C PRO B 986 " pdb=" CB PRO B 986 " both_signs ideal model delta sigma weight residual False 2.72 2.36 0.36 2.00e-01 2.50e+01 3.18e+00 ... (remaining 3630 not shown) Planarity restraints: 4107 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 279 " -0.149 2.00e-02 2.50e+03 8.14e-02 1.33e+02 pdb=" CG TYR B 279 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 TYR B 279 " 0.061 2.00e-02 2.50e+03 pdb=" CD2 TYR B 279 " 0.071 2.00e-02 2.50e+03 pdb=" CE1 TYR B 279 " 0.048 2.00e-02 2.50e+03 pdb=" CE2 TYR B 279 " 0.041 2.00e-02 2.50e+03 pdb=" CZ TYR B 279 " 0.007 2.00e-02 2.50e+03 pdb=" OH TYR B 279 " -0.126 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 269 " 0.144 2.00e-02 2.50e+03 7.42e-02 1.10e+02 pdb=" CG TYR C 269 " -0.062 2.00e-02 2.50e+03 pdb=" CD1 TYR C 269 " -0.071 2.00e-02 2.50e+03 pdb=" CD2 TYR C 269 " -0.063 2.00e-02 2.50e+03 pdb=" CE1 TYR C 269 " -0.022 2.00e-02 2.50e+03 pdb=" CE2 TYR C 269 " -0.030 2.00e-02 2.50e+03 pdb=" CZ TYR C 269 " 0.009 2.00e-02 2.50e+03 pdb=" OH TYR C 269 " 0.094 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 279 " 0.121 2.00e-02 2.50e+03 6.74e-02 9.07e+01 pdb=" CG TYR A 279 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 TYR A 279 " -0.049 2.00e-02 2.50e+03 pdb=" CD2 TYR A 279 " -0.057 2.00e-02 2.50e+03 pdb=" CE1 TYR A 279 " -0.042 2.00e-02 2.50e+03 pdb=" CE2 TYR A 279 " -0.037 2.00e-02 2.50e+03 pdb=" CZ TYR A 279 " -0.009 2.00e-02 2.50e+03 pdb=" OH TYR A 279 " 0.108 2.00e-02 2.50e+03 ... (remaining 4104 not shown) Histogram of nonbonded interaction distances: 2.52 - 3.00: 11105 3.00 - 3.47: 21932 3.47 - 3.95: 38444 3.95 - 4.42: 43176 4.42 - 4.90: 73564 Nonbonded interactions: 188221 Sorted by model distance: nonbonded pdb=" OG SER A1123 " pdb=" OE2 GLU B 918 " model vdw 2.524 2.440 nonbonded pdb=" OE2 GLU A 918 " pdb=" OG SER C1123 " model vdw 2.527 2.440 nonbonded pdb=" OG SER B 591 " pdb=" OE1 GLU B 619 " model vdw 2.529 2.440 nonbonded pdb=" OG SER B1123 " pdb=" OE2 GLU C 918 " model vdw 2.535 2.440 nonbonded pdb=" OG1 THR A 109 " pdb=" OD1 ASP A 111 " model vdw 2.554 2.440 ... (remaining 188216 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' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.270 Check model and map are aligned: 0.380 Set scattering table: 0.240 Process input model: 64.000 Find NCS groups from input model: 1.360 Set up NCS constraints: 0.110 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:13.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 89.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4541 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 : 0.013 0.045 23325 Z= 0.812 Angle : 1.803 10.763 31740 Z= 1.231 Chirality : 0.093 0.381 3633 Planarity : 0.014 0.203 4107 Dihedral : 13.313 89.656 8340 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 0.07 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.24 % Favored : 94.59 % Rotamer: Outliers : 0.94 % Allowed : 2.42 % Favored : 96.65 % 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: -1.25 (0.14), residues: 2844 helix: -1.11 (0.16), residues: 669 sheet: -0.11 (0.20), residues: 588 loop : -0.93 (0.14), residues: 1587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.103 0.023 TRP B 104 HIS 0.011 0.003 HIS C 207 PHE 0.088 0.012 PHE B 718 TYR 0.149 0.020 TYR B 279 ARG 0.009 0.001 ARG A1019 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 372 time to evaluate : 2.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 224 GLU cc_start: 0.3665 (pt0) cc_final: 0.3266 (mt-10) REVERT: A 305 SER cc_start: 0.7088 (t) cc_final: 0.6679 (t) REVERT: A 307 THR cc_start: 0.6899 (m) cc_final: 0.6502 (p) REVERT: A 309 GLU cc_start: 0.5304 (mp0) cc_final: 0.5101 (pt0) REVERT: A 314 GLN cc_start: 0.5945 (tt0) cc_final: 0.5222 (tp40) REVERT: A 558 LYS cc_start: 0.6950 (tttt) cc_final: 0.6413 (mttp) REVERT: A 584 ILE cc_start: 0.6067 (mm) cc_final: 0.5864 (mp) REVERT: A 661 GLU cc_start: 0.6597 (mt-10) cc_final: 0.5644 (mm-30) REVERT: A 702 GLU cc_start: 0.7202 (tt0) cc_final: 0.6373 (mm-30) REVERT: A 704 SER cc_start: 0.7259 (p) cc_final: 0.7022 (t) REVERT: A 779 GLN cc_start: 0.5003 (tp40) cc_final: 0.4460 (tp40) REVERT: A 780 GLU cc_start: 0.5789 (mt-10) cc_final: 0.4920 (mm-30) REVERT: A 814 LYS cc_start: 0.5978 (mttp) cc_final: 0.5697 (mtpm) REVERT: A 854 LYS cc_start: 0.2788 (mttp) cc_final: 0.2310 (ptmt) REVERT: A 985 CYS cc_start: 0.5578 (p) cc_final: 0.4310 (p) REVERT: A 988 GLU cc_start: 0.4866 (tp30) cc_final: 0.4457 (pm20) REVERT: A 1050 MET cc_start: 0.7242 (ptp) cc_final: 0.7025 (ptm) REVERT: A 1107 ARG cc_start: 0.6447 (mtm180) cc_final: 0.5589 (mtt180) REVERT: B 237 ARG cc_start: 0.5234 (mtt90) cc_final: 0.4884 (mtp-110) REVERT: B 269 TYR cc_start: 0.6625 (m-80) cc_final: 0.6302 (m-80) REVERT: B 271 GLN cc_start: 0.4384 (mt0) cc_final: 0.4055 (mp10) REVERT: B 278 LYS cc_start: 0.3679 (tttt) cc_final: 0.3451 (tttt) REVERT: B 314 GLN cc_start: 0.6883 (tt0) cc_final: 0.6352 (tt0) REVERT: B 317 ASN cc_start: 0.7021 (m-40) cc_final: 0.6544 (m110) REVERT: B 319 ARG cc_start: 0.6135 (mtm180) cc_final: 0.5877 (mtt-85) REVERT: B 355 ARG cc_start: 0.6221 (ttt90) cc_final: 0.6018 (ttm-80) REVERT: B 389 ASP cc_start: 0.6291 (t0) cc_final: 0.5852 (m-30) REVERT: B 554 GLU cc_start: 0.6194 (mt-10) cc_final: 0.5860 (mm-30) REVERT: B 569 ILE cc_start: 0.5819 (mm) cc_final: 0.5590 (tt) REVERT: B 646 ARG cc_start: 0.6353 (ttm170) cc_final: 0.5287 (tpt170) REVERT: B 661 GLU cc_start: 0.7061 (mt-10) cc_final: 0.6631 (mt-10) REVERT: B 697 MET cc_start: 0.6917 (ptm) cc_final: 0.6571 (ptp) REVERT: B 702 GLU cc_start: 0.7074 (tt0) cc_final: 0.6842 (tt0) REVERT: B 735 SER cc_start: 0.6481 (t) cc_final: 0.5727 (p) REVERT: B 750 SER cc_start: 0.5494 (t) cc_final: 0.5088 (m) REVERT: B 790 LYS cc_start: 0.6958 (pttt) cc_final: 0.6096 (ptmm) REVERT: B 814 LYS cc_start: 0.6289 (mttt) cc_final: 0.5238 (mmmt) REVERT: B 912 THR cc_start: 0.6574 (m) cc_final: 0.6149 (p) REVERT: B 947 LYS cc_start: 0.6290 (mttt) cc_final: 0.5962 (mtpt) REVERT: B 957 GLN cc_start: 0.4909 (tp-100) cc_final: 0.4551 (tt0) REVERT: B 988 GLU cc_start: 0.4714 (tp30) cc_final: 0.3986 (mp0) REVERT: B 990 GLU cc_start: 0.4664 (mt-10) cc_final: 0.4310 (tt0) REVERT: B 1010 GLN cc_start: 0.4676 (mm-40) cc_final: 0.3762 (pt0) REVERT: B 1045 LYS cc_start: 0.6746 (ttpp) cc_final: 0.5969 (mptp) REVERT: B 1050 MET cc_start: 0.6648 (ptt) cc_final: 0.6366 (ptm) REVERT: B 1073 LYS cc_start: 0.5907 (mttt) cc_final: 0.5628 (mtpt) REVERT: B 1108 ASN cc_start: 0.7436 (m-40) cc_final: 0.7195 (m110) REVERT: B 1113 GLN cc_start: 0.6013 (mt0) cc_final: 0.5105 (mt0) REVERT: B 1118 ASP cc_start: 0.6314 (m-30) cc_final: 0.6058 (t0) REVERT: B 1119 ASN cc_start: 0.5381 (m-40) cc_final: 0.4732 (m110) REVERT: C 200 TYR cc_start: 0.5649 (m-80) cc_final: 0.5368 (m-80) REVERT: C 273 ARG cc_start: 0.4136 (mmt90) cc_final: 0.3719 (mmt-90) REVERT: C 309 GLU cc_start: 0.5082 (tp30) cc_final: 0.4552 (tt0) REVERT: C 340 GLU cc_start: 0.7200 (mt-10) cc_final: 0.6947 (mp0) REVERT: C 383 CYS cc_start: 0.4851 (t) cc_final: 0.3918 (t) REVERT: C 528 LYS cc_start: 0.6116 (tttt) cc_final: 0.5303 (ttmm) REVERT: C 586 ASP cc_start: 0.5612 (m-30) cc_final: 0.5242 (m-30) REVERT: C 646 ARG cc_start: 0.6741 (mtm110) cc_final: 0.6056 (tmm160) REVERT: C 661 GLU cc_start: 0.5645 (mm-30) cc_final: 0.5410 (tp30) REVERT: C 663 ASP cc_start: 0.6843 (t0) cc_final: 0.6627 (t0) REVERT: C 675 GLN cc_start: 0.5041 (mt0) cc_final: 0.4623 (mt0) REVERT: C 702 GLU cc_start: 0.7371 (tt0) cc_final: 0.6778 (tp30) REVERT: C 776 LYS cc_start: 0.5327 (tttt) cc_final: 0.5112 (ttpp) REVERT: C 814 LYS cc_start: 0.5887 (mttt) cc_final: 0.5308 (mtpt) REVERT: C 823 PHE cc_start: 0.5832 (m-80) cc_final: 0.5616 (m-80) REVERT: C 902 MET cc_start: 0.6698 (mmm) cc_final: 0.6205 (tpt) REVERT: C 907 ASN cc_start: 0.6306 (OUTLIER) cc_final: 0.6056 (m110) REVERT: C 990 GLU cc_start: 0.4628 (mt-10) cc_final: 0.4021 (mp0) REVERT: C 1010 GLN cc_start: 0.4773 (mm-40) cc_final: 0.4049 (mt0) REVERT: C 1045 LYS cc_start: 0.6168 (ttpp) cc_final: 0.5933 (tmtp) outliers start: 24 outliers final: 6 residues processed: 392 average time/residue: 1.0862 time to fit residues: 502.0498 Evaluate side-chains 275 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 268 time to evaluate : 2.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 907 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 245 optimal weight: 0.9990 chunk 220 optimal weight: 1.9990 chunk 122 optimal weight: 6.9990 chunk 75 optimal weight: 2.9990 chunk 148 optimal weight: 0.8980 chunk 117 optimal weight: 0.8980 chunk 228 optimal weight: 1.9990 chunk 88 optimal weight: 0.6980 chunk 138 optimal weight: 3.9990 chunk 169 optimal weight: 0.6980 chunk 264 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 ASN A 914 ASN A1088 HIS B 30 ASN B 207 HIS B 606 ASN B 914 ASN B 955 ASN B1101 HIS C 196 ASN C 207 HIS C 394 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 616 ASN C 764 ASN C1119 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4501 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 23325 Z= 0.206 Angle : 0.618 9.753 31740 Z= 0.331 Chirality : 0.047 0.206 3633 Planarity : 0.004 0.036 4107 Dihedral : 5.875 53.187 3107 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.64 % Favored : 97.33 % Rotamer: Outliers : 1.64 % Allowed : 7.13 % Favored : 91.23 % 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: 2844 helix: 1.15 (0.20), residues: 680 sheet: -0.25 (0.19), residues: 659 loop : -0.63 (0.15), residues: 1505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 64 HIS 0.003 0.001 HIS C 207 PHE 0.028 0.002 PHE B 168 TYR 0.022 0.002 TYR B 170 ARG 0.003 0.000 ARG C 567 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 299 time to evaluate : 2.690 Fit side-chains revert: symmetry clash REVERT: A 239 GLN cc_start: 0.5201 (tt0) cc_final: 0.4802 (tt0) REVERT: A 305 SER cc_start: 0.7143 (t) cc_final: 0.6839 (t) REVERT: A 307 THR cc_start: 0.6892 (m) cc_final: 0.6469 (p) REVERT: A 314 GLN cc_start: 0.5757 (tt0) cc_final: 0.5085 (tp-100) REVERT: A 532 ASN cc_start: 0.6827 (t0) cc_final: 0.6615 (m-40) REVERT: A 558 LYS cc_start: 0.7078 (tttt) cc_final: 0.6529 (mptp) REVERT: A 603 ASN cc_start: 0.6981 (t0) cc_final: 0.6469 (m110) REVERT: A 661 GLU cc_start: 0.6751 (mt-10) cc_final: 0.5810 (mm-30) REVERT: A 674 TYR cc_start: 0.7361 (t80) cc_final: 0.6939 (t80) REVERT: A 702 GLU cc_start: 0.7198 (tt0) cc_final: 0.6669 (tp30) REVERT: A 779 GLN cc_start: 0.4892 (tp40) cc_final: 0.4476 (tp40) REVERT: A 814 LYS cc_start: 0.6103 (mttp) cc_final: 0.5669 (mtpp) REVERT: A 854 LYS cc_start: 0.2400 (mttp) cc_final: 0.1886 (ptmt) REVERT: A 988 GLU cc_start: 0.5082 (tp30) cc_final: 0.4518 (mp0) REVERT: A 1010 GLN cc_start: 0.4458 (mt0) cc_final: 0.4031 (mm-40) REVERT: A 1092 GLU cc_start: 0.5299 (mp0) cc_final: 0.5046 (mt-10) REVERT: A 1107 ARG cc_start: 0.6550 (mtm180) cc_final: 0.5658 (mtt180) REVERT: B 271 GLN cc_start: 0.4658 (mt0) cc_final: 0.4263 (mp10) REVERT: B 314 GLN cc_start: 0.6666 (tt0) cc_final: 0.5941 (tt0) REVERT: B 319 ARG cc_start: 0.5877 (mtm180) cc_final: 0.5628 (ttm110) REVERT: B 389 ASP cc_start: 0.5837 (t0) cc_final: 0.5382 (m-30) REVERT: B 569 ILE cc_start: 0.6157 (mm) cc_final: 0.5850 (tt) REVERT: B 612 TYR cc_start: 0.5741 (m-80) cc_final: 0.5477 (m-80) REVERT: B 646 ARG cc_start: 0.6327 (ttm170) cc_final: 0.5241 (tpt170) REVERT: B 661 GLU cc_start: 0.6962 (mt-10) cc_final: 0.6675 (mt-10) REVERT: B 697 MET cc_start: 0.6800 (ptm) cc_final: 0.6420 (ptp) REVERT: B 702 GLU cc_start: 0.7118 (tt0) cc_final: 0.6832 (tp30) REVERT: B 735 SER cc_start: 0.6430 (t) cc_final: 0.5732 (p) REVERT: B 790 LYS cc_start: 0.6800 (pttt) cc_final: 0.5913 (ptmm) REVERT: B 814 LYS cc_start: 0.6471 (mttt) cc_final: 0.5483 (mmmt) REVERT: B 988 GLU cc_start: 0.4961 (tp30) cc_final: 0.4382 (mp0) REVERT: B 1010 GLN cc_start: 0.4631 (mm-40) cc_final: 0.3667 (pt0) REVERT: B 1045 LYS cc_start: 0.6726 (ttpp) cc_final: 0.5980 (mptt) REVERT: B 1073 LYS cc_start: 0.5480 (mttt) cc_final: 0.5246 (mtpp) REVERT: B 1113 GLN cc_start: 0.5917 (mt0) cc_final: 0.4948 (mt0) REVERT: B 1119 ASN cc_start: 0.5323 (m-40) cc_final: 0.4895 (m-40) REVERT: C 273 ARG cc_start: 0.3417 (mmt90) cc_final: 0.3172 (mmt-90) REVERT: C 305 SER cc_start: 0.6585 (t) cc_final: 0.5990 (p) REVERT: C 317 ASN cc_start: 0.7010 (t0) cc_final: 0.6711 (t0) REVERT: C 340 GLU cc_start: 0.7375 (mt-10) cc_final: 0.7054 (mp0) REVERT: C 383 CYS cc_start: 0.5056 (t) cc_final: 0.4608 (t) REVERT: C 424 LYS cc_start: 0.4151 (tptp) cc_final: 0.3747 (tptp) REVERT: C 528 LYS cc_start: 0.6049 (tttt) cc_final: 0.5269 (ttmm) REVERT: C 675 GLN cc_start: 0.5258 (mt0) cc_final: 0.4960 (mt0) REVERT: C 702 GLU cc_start: 0.7428 (tt0) cc_final: 0.6761 (tp30) REVERT: C 776 LYS cc_start: 0.5343 (tttt) cc_final: 0.5092 (ttmp) REVERT: C 814 LYS cc_start: 0.5952 (mttt) cc_final: 0.5315 (mtpt) REVERT: C 823 PHE cc_start: 0.6163 (m-80) cc_final: 0.5882 (m-80) REVERT: C 907 ASN cc_start: 0.6389 (OUTLIER) cc_final: 0.6173 (m-40) REVERT: C 990 GLU cc_start: 0.3837 (mt-10) cc_final: 0.3247 (mp0) REVERT: C 1010 GLN cc_start: 0.5179 (mm-40) cc_final: 0.4420 (tt0) outliers start: 42 outliers final: 16 residues processed: 325 average time/residue: 0.9252 time to fit residues: 361.9352 Evaluate side-chains 259 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 242 time to evaluate : 2.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain C residue 536 ASN Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1133 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 146 optimal weight: 0.5980 chunk 82 optimal weight: 3.9990 chunk 219 optimal weight: 0.5980 chunk 179 optimal weight: 4.9990 chunk 72 optimal weight: 0.7980 chunk 264 optimal weight: 4.9990 chunk 285 optimal weight: 4.9990 chunk 235 optimal weight: 2.9990 chunk 262 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 212 optimal weight: 5.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 ASN A 613 GLN A 914 ASN A 919 ASN B 334 ASN B 394 ASN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1088 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4528 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 23325 Z= 0.256 Angle : 0.581 10.470 31740 Z= 0.307 Chirality : 0.046 0.180 3633 Planarity : 0.004 0.038 4107 Dihedral : 5.246 47.836 3104 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.65 % Allowed : 8.50 % Favored : 88.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.15), residues: 2844 helix: 1.45 (0.20), residues: 679 sheet: -0.27 (0.19), residues: 673 loop : -0.61 (0.15), residues: 1492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 64 HIS 0.005 0.001 HIS C1064 PHE 0.027 0.002 PHE B 168 TYR 0.022 0.002 TYR C1067 ARG 0.004 0.000 ARG C 357 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 264 time to evaluate : 2.177 Fit side-chains revert: symmetry clash REVERT: A 47 VAL cc_start: 0.5855 (OUTLIER) cc_final: 0.5555 (p) REVERT: A 88 ASP cc_start: 0.6499 (OUTLIER) cc_final: 0.5724 (t0) REVERT: A 228 ASP cc_start: 0.4357 (t0) cc_final: 0.3791 (t0) REVERT: A 239 GLN cc_start: 0.5235 (tt0) cc_final: 0.4839 (tt0) REVERT: A 305 SER cc_start: 0.7093 (t) cc_final: 0.6617 (p) REVERT: A 314 GLN cc_start: 0.5967 (tt0) cc_final: 0.5308 (tp-100) REVERT: A 378 LYS cc_start: 0.4347 (pttm) cc_final: 0.4106 (pttm) REVERT: A 558 LYS cc_start: 0.7101 (tttt) cc_final: 0.6531 (mptp) REVERT: A 603 ASN cc_start: 0.6868 (t0) cc_final: 0.6360 (m-40) REVERT: A 661 GLU cc_start: 0.6702 (mt-10) cc_final: 0.5759 (mm-30) REVERT: A 674 TYR cc_start: 0.7496 (t80) cc_final: 0.7102 (t80) REVERT: A 702 GLU cc_start: 0.7224 (tt0) cc_final: 0.6701 (tp30) REVERT: A 779 GLN cc_start: 0.4904 (tp40) cc_final: 0.4438 (tp40) REVERT: A 814 LYS cc_start: 0.6101 (mttp) cc_final: 0.5528 (mtpp) REVERT: A 854 LYS cc_start: 0.2536 (mttp) cc_final: 0.2070 (ptpt) REVERT: A 988 GLU cc_start: 0.5061 (tp30) cc_final: 0.4574 (mp0) REVERT: A 1010 GLN cc_start: 0.4384 (mt0) cc_final: 0.4082 (mm-40) REVERT: A 1092 GLU cc_start: 0.5474 (mp0) cc_final: 0.5243 (mt-10) REVERT: A 1107 ARG cc_start: 0.6642 (mtm180) cc_final: 0.5687 (mtt180) REVERT: B 271 GLN cc_start: 0.4461 (mt0) cc_final: 0.3951 (mp10) REVERT: B 314 GLN cc_start: 0.6984 (tt0) cc_final: 0.6346 (tt0) REVERT: B 319 ARG cc_start: 0.6013 (mtm180) cc_final: 0.5780 (ttm110) REVERT: B 528 LYS cc_start: 0.6743 (tttt) cc_final: 0.6444 (ttmp) REVERT: B 549 THR cc_start: 0.6501 (OUTLIER) cc_final: 0.6301 (t) REVERT: B 564 GLN cc_start: 0.4391 (OUTLIER) cc_final: 0.3746 (mm-40) REVERT: B 569 ILE cc_start: 0.6262 (mm) cc_final: 0.5996 (tt) REVERT: B 612 TYR cc_start: 0.5977 (m-80) cc_final: 0.5707 (m-80) REVERT: B 646 ARG cc_start: 0.6333 (ttm170) cc_final: 0.5230 (tpt170) REVERT: B 661 GLU cc_start: 0.6933 (mt-10) cc_final: 0.6639 (mt-10) REVERT: B 702 GLU cc_start: 0.7061 (tt0) cc_final: 0.6797 (tp30) REVERT: B 735 SER cc_start: 0.6600 (t) cc_final: 0.5783 (p) REVERT: B 790 LYS cc_start: 0.6745 (pttt) cc_final: 0.6164 (ptmm) REVERT: B 814 LYS cc_start: 0.6476 (mttt) cc_final: 0.5477 (mmmt) REVERT: B 988 GLU cc_start: 0.4972 (tp30) cc_final: 0.4442 (mp0) REVERT: B 1010 GLN cc_start: 0.4797 (mm-40) cc_final: 0.3835 (pt0) REVERT: B 1045 LYS cc_start: 0.6778 (ttpp) cc_final: 0.5962 (mptp) REVERT: B 1113 GLN cc_start: 0.5938 (mt0) cc_final: 0.4875 (mt0) REVERT: B 1119 ASN cc_start: 0.5439 (m-40) cc_final: 0.5239 (m-40) REVERT: C 84 LEU cc_start: 0.3444 (OUTLIER) cc_final: 0.3208 (mt) REVERT: C 273 ARG cc_start: 0.3538 (mmt90) cc_final: 0.3237 (mmt-90) REVERT: C 305 SER cc_start: 0.6704 (t) cc_final: 0.6156 (p) REVERT: C 317 ASN cc_start: 0.7299 (t0) cc_final: 0.7043 (t0) REVERT: C 340 GLU cc_start: 0.7379 (mt-10) cc_final: 0.7046 (mp0) REVERT: C 383 CYS cc_start: 0.5008 (t) cc_final: 0.4523 (t) REVERT: C 396 TYR cc_start: 0.4579 (m-80) cc_final: 0.4153 (m-80) REVERT: C 424 LYS cc_start: 0.4163 (tptp) cc_final: 0.3827 (tptp) REVERT: C 516 GLU cc_start: 0.5243 (tp30) cc_final: 0.4692 (mt-10) REVERT: C 528 LYS cc_start: 0.5829 (tttt) cc_final: 0.5156 (tppt) REVERT: C 564 GLN cc_start: 0.5645 (tp40) cc_final: 0.5344 (mp-120) REVERT: C 574 ASP cc_start: 0.5857 (t0) cc_final: 0.5639 (t0) REVERT: C 675 GLN cc_start: 0.5430 (mt0) cc_final: 0.4973 (mt0) REVERT: C 702 GLU cc_start: 0.7394 (tt0) cc_final: 0.6892 (tp30) REVERT: C 776 LYS cc_start: 0.5333 (tttt) cc_final: 0.5077 (ttmp) REVERT: C 814 LYS cc_start: 0.5778 (mttt) cc_final: 0.5105 (mtpt) REVERT: C 823 PHE cc_start: 0.6261 (m-80) cc_final: 0.6057 (m-80) REVERT: C 990 GLU cc_start: 0.3762 (mt-10) cc_final: 0.3271 (mp0) REVERT: C 1010 GLN cc_start: 0.5130 (mm-40) cc_final: 0.4283 (pt0) outliers start: 68 outliers final: 34 residues processed: 311 average time/residue: 0.9261 time to fit residues: 346.5254 Evaluate side-chains 271 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 232 time to evaluate : 2.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 704 SER Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 985 CYS Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 536 ASN Chi-restraints excluded: chain C residue 673 SER Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 261 optimal weight: 1.9990 chunk 199 optimal weight: 0.1980 chunk 137 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 126 optimal weight: 0.9980 chunk 177 optimal weight: 0.9980 chunk 265 optimal weight: 0.8980 chunk 281 optimal weight: 0.8980 chunk 138 optimal weight: 8.9990 chunk 251 optimal weight: 0.6980 chunk 75 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN B 125 ASN B 394 ASN B 957 GLN C 196 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN C1002 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4513 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23325 Z= 0.168 Angle : 0.513 6.990 31740 Z= 0.271 Chirality : 0.044 0.171 3633 Planarity : 0.004 0.044 4107 Dihedral : 4.745 32.626 3102 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.38 % Allowed : 10.41 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 2844 helix: 1.88 (0.20), residues: 673 sheet: -0.23 (0.19), residues: 658 loop : -0.53 (0.15), residues: 1513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 64 HIS 0.002 0.001 HIS A1088 PHE 0.031 0.001 PHE B 168 TYR 0.025 0.001 TYR B 170 ARG 0.009 0.000 ARG A 328 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 263 time to evaluate : 2.600 Fit side-chains REVERT: A 47 VAL cc_start: 0.5896 (t) cc_final: 0.5535 (p) REVERT: A 200 TYR cc_start: 0.4530 (OUTLIER) cc_final: 0.3694 (t80) REVERT: A 228 ASP cc_start: 0.4010 (t0) cc_final: 0.3334 (t0) REVERT: A 239 GLN cc_start: 0.5093 (tt0) cc_final: 0.4710 (tt0) REVERT: A 305 SER cc_start: 0.7249 (t) cc_final: 0.6804 (p) REVERT: A 314 GLN cc_start: 0.5988 (tt0) cc_final: 0.5291 (tp-100) REVERT: A 340 GLU cc_start: 0.5539 (mp0) cc_final: 0.5260 (mp0) REVERT: A 378 LYS cc_start: 0.4537 (pttm) cc_final: 0.4316 (pttm) REVERT: A 558 LYS cc_start: 0.7082 (tttt) cc_final: 0.6509 (mptp) REVERT: A 578 ASP cc_start: 0.4781 (t0) cc_final: 0.4501 (t0) REVERT: A 603 ASN cc_start: 0.6819 (t0) cc_final: 0.6353 (m110) REVERT: A 661 GLU cc_start: 0.6809 (mt-10) cc_final: 0.5997 (mm-30) REVERT: A 674 TYR cc_start: 0.7365 (t80) cc_final: 0.7010 (t80) REVERT: A 702 GLU cc_start: 0.7232 (tt0) cc_final: 0.6710 (tp30) REVERT: A 740 MET cc_start: 0.5797 (ttt) cc_final: 0.5535 (ttt) REVERT: A 779 GLN cc_start: 0.4880 (tp40) cc_final: 0.4462 (tp40) REVERT: A 814 LYS cc_start: 0.6427 (mttp) cc_final: 0.5999 (mtpp) REVERT: A 854 LYS cc_start: 0.2498 (mttp) cc_final: 0.2041 (ptpt) REVERT: A 988 GLU cc_start: 0.5023 (tp30) cc_final: 0.4614 (mp0) REVERT: A 1010 GLN cc_start: 0.4538 (mt0) cc_final: 0.4222 (mm-40) REVERT: A 1092 GLU cc_start: 0.5499 (mp0) cc_final: 0.5276 (mt-10) REVERT: A 1107 ARG cc_start: 0.6465 (mtm180) cc_final: 0.5555 (mtt180) REVERT: B 271 GLN cc_start: 0.4556 (mt0) cc_final: 0.4044 (mp10) REVERT: B 314 GLN cc_start: 0.7122 (tt0) cc_final: 0.6446 (tp40) REVERT: B 319 ARG cc_start: 0.5922 (mtm180) cc_final: 0.5719 (ttm110) REVERT: B 324 GLU cc_start: 0.3906 (pt0) cc_final: 0.3301 (pm20) REVERT: B 534 VAL cc_start: 0.7191 (t) cc_final: 0.6669 (m) REVERT: B 549 THR cc_start: 0.6472 (OUTLIER) cc_final: 0.6264 (t) REVERT: B 564 GLN cc_start: 0.4485 (OUTLIER) cc_final: 0.3853 (mm-40) REVERT: B 569 ILE cc_start: 0.6250 (mm) cc_final: 0.5978 (tt) REVERT: B 613 GLN cc_start: 0.6778 (mt0) cc_final: 0.6421 (mt0) REVERT: B 646 ARG cc_start: 0.6323 (ttm170) cc_final: 0.5321 (tpt170) REVERT: B 661 GLU cc_start: 0.6905 (mt-10) cc_final: 0.6604 (mt-10) REVERT: B 702 GLU cc_start: 0.7013 (tt0) cc_final: 0.6748 (tp30) REVERT: B 735 SER cc_start: 0.6727 (t) cc_final: 0.5912 (p) REVERT: B 779 GLN cc_start: 0.4548 (tp40) cc_final: 0.4001 (tt0) REVERT: B 790 LYS cc_start: 0.6719 (pttt) cc_final: 0.6216 (ptmm) REVERT: B 814 LYS cc_start: 0.6497 (mttt) cc_final: 0.5483 (mmmt) REVERT: B 988 GLU cc_start: 0.4922 (tp30) cc_final: 0.4452 (mp0) REVERT: B 1010 GLN cc_start: 0.4792 (mm-40) cc_final: 0.3839 (pt0) REVERT: B 1045 LYS cc_start: 0.6771 (ttpp) cc_final: 0.5958 (mptt) REVERT: B 1113 GLN cc_start: 0.6024 (mt0) cc_final: 0.4918 (mt0) REVERT: C 237 ARG cc_start: 0.4407 (mtm-85) cc_final: 0.4187 (mtm-85) REVERT: C 273 ARG cc_start: 0.3606 (mmt90) cc_final: 0.3255 (mmt-90) REVERT: C 290 ASP cc_start: 0.6064 (t0) cc_final: 0.5350 (t0) REVERT: C 305 SER cc_start: 0.6891 (t) cc_final: 0.6425 (p) REVERT: C 317 ASN cc_start: 0.7306 (t0) cc_final: 0.7067 (t0) REVERT: C 340 GLU cc_start: 0.7362 (mt-10) cc_final: 0.7018 (mp0) REVERT: C 359 SER cc_start: 0.6817 (p) cc_final: 0.6450 (m) REVERT: C 378 LYS cc_start: 0.5885 (OUTLIER) cc_final: 0.5466 (ttmt) REVERT: C 383 CYS cc_start: 0.5108 (t) cc_final: 0.4800 (t) REVERT: C 396 TYR cc_start: 0.4600 (m-80) cc_final: 0.4136 (m-80) REVERT: C 424 LYS cc_start: 0.4229 (tptp) cc_final: 0.3889 (tptp) REVERT: C 528 LYS cc_start: 0.6064 (tttt) cc_final: 0.5348 (tppt) REVERT: C 564 GLN cc_start: 0.5704 (tp40) cc_final: 0.5415 (mp-120) REVERT: C 569 ILE cc_start: 0.6399 (mm) cc_final: 0.6047 (tp) REVERT: C 574 ASP cc_start: 0.5944 (t0) cc_final: 0.5731 (t0) REVERT: C 643 PHE cc_start: 0.3584 (t80) cc_final: 0.3289 (t80) REVERT: C 675 GLN cc_start: 0.5422 (mt0) cc_final: 0.4957 (mt0) REVERT: C 702 GLU cc_start: 0.7425 (tt0) cc_final: 0.6839 (tp30) REVERT: C 776 LYS cc_start: 0.5162 (tttt) cc_final: 0.4892 (ttmp) REVERT: C 814 LYS cc_start: 0.5964 (mttt) cc_final: 0.5225 (mtpt) REVERT: C 823 PHE cc_start: 0.6209 (m-80) cc_final: 0.5986 (m-80) REVERT: C 990 GLU cc_start: 0.3712 (mt-10) cc_final: 0.3229 (mp0) REVERT: C 1010 GLN cc_start: 0.5133 (mm-40) cc_final: 0.4244 (pt0) outliers start: 61 outliers final: 32 residues processed: 306 average time/residue: 0.9462 time to fit residues: 348.1298 Evaluate side-chains 277 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 241 time to evaluate : 2.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 704 SER Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 985 CYS Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 536 ASN Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1127 ASP Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 63.3663 > 50: distance: 11 - 19: 26.315 distance: 19 - 20: 10.577 distance: 20 - 21: 20.755 distance: 20 - 23: 12.136 distance: 21 - 22: 38.604 distance: 21 - 29: 12.111 distance: 23 - 24: 29.395 distance: 24 - 25: 9.439 distance: 24 - 26: 9.125 distance: 25 - 27: 22.314 distance: 26 - 28: 20.657 distance: 27 - 28: 10.242 distance: 29 - 30: 23.202 distance: 30 - 31: 8.193 distance: 30 - 33: 42.642 distance: 31 - 32: 12.761 distance: 31 - 34: 41.286 distance: 34 - 35: 23.355 distance: 35 - 36: 10.298 distance: 36 - 42: 41.279 distance: 38 - 39: 39.074 distance: 38 - 40: 12.503 distance: 39 - 41: 39.881 distance: 42 - 43: 15.081 distance: 43 - 44: 52.278 distance: 43 - 46: 44.069 distance: 44 - 45: 31.350 distance: 46 - 47: 13.307 distance: 47 - 48: 17.819 distance: 47 - 49: 5.459 distance: 49 - 51: 4.898 distance: 50 - 51: 6.888 distance: 52 - 53: 7.063 distance: 53 - 54: 23.899 distance: 53 - 56: 17.613 distance: 54 - 55: 14.128 distance: 54 - 60: 40.860 distance: 56 - 57: 4.750 distance: 57 - 58: 6.432 distance: 57 - 59: 15.146 distance: 60 - 61: 26.174 distance: 61 - 62: 47.942 distance: 61 - 64: 10.239 distance: 62 - 63: 9.364 distance: 62 - 68: 19.371 distance: 64 - 65: 7.781 distance: 65 - 66: 26.106 distance: 65 - 67: 28.692 distance: 68 - 69: 17.849 distance: 68 - 74: 49.162 distance: 69 - 70: 12.617 distance: 69 - 72: 37.085 distance: 70 - 71: 15.692 distance: 70 - 75: 5.565 distance: 72 - 73: 29.264 distance: 73 - 74: 18.898 distance: 75 - 76: 21.541 distance: 76 - 77: 33.503 distance: 76 - 79: 49.953 distance: 77 - 78: 51.322 distance: 77 - 82: 27.858 distance: 79 - 80: 44.967 distance: 79 - 81: 10.152 distance: 82 - 83: 21.756 distance: 82 - 131: 30.482 distance: 83 - 84: 34.415 distance: 83 - 86: 55.051 distance: 84 - 85: 21.266 distance: 84 - 90: 24.301 distance: 85 - 128: 33.571 distance: 86 - 87: 20.973 distance: 87 - 88: 42.486 distance: 87 - 89: 41.576 distance: 90 - 91: 15.879 distance: 90 - 96: 6.538 distance: 91 - 92: 12.871 distance: 91 - 94: 28.667 distance: 92 - 93: 18.018 distance: 92 - 97: 25.090 distance: 94 - 95: 47.093 distance: 95 - 96: 44.337