Starting phenix.real_space_refine on Tue Aug 6 18:51:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8otq_17182/08_2024/8otq_17182.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8otq_17182/08_2024/8otq_17182.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8otq_17182/08_2024/8otq_17182.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8otq_17182/08_2024/8otq_17182.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8otq_17182/08_2024/8otq_17182.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8otq_17182/08_2024/8otq_17182.cif" } resolution = 3.22 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 86 5.16 5 C 10942 2.51 5 N 2754 2.21 5 O 2932 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 337": "OE1" <-> "OE2" Residue "A GLU 346": "OE1" <-> "OE2" Residue "A ARG 500": "NH1" <-> "NH2" Residue "A GLU 531": "OE1" <-> "OE2" Residue "A GLU 616": "OE1" <-> "OE2" Residue "A GLU 782": "OE1" <-> "OE2" Residue "A GLU 849": "OE1" <-> "OE2" Residue "A TYR 1009": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1071": "OE1" <-> "OE2" Residue "B GLU 337": "OE1" <-> "OE2" Residue "B GLU 346": "OE1" <-> "OE2" Residue "B ARG 500": "NH1" <-> "NH2" Residue "B GLU 531": "OE1" <-> "OE2" Residue "B GLU 616": "OE1" <-> "OE2" Residue "B GLU 782": "OE1" <-> "OE2" Residue "B GLU 849": "OE1" <-> "OE2" Residue "B TYR 1009": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1071": "OE1" <-> "OE2" Residue "B GLU 1160": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 16716 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1051, 8297 Classifications: {'peptide': 1051} Link IDs: {'PTRANS': 30, 'TRANS': 1020} Chain breaks: 3 Chain: "B" Number of atoms: 8297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1051, 8297 Classifications: {'peptide': 1051} Link IDs: {'PTRANS': 30, 'TRANS': 1020} Chain breaks: 3 Chain: "A" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 61 Unusual residues: {'CPL': 1, 'PLM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "B" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 61 Unusual residues: {'CPL': 1, 'PLM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Time building chain proxies: 9.94, per 1000 atoms: 0.59 Number of scatterers: 16716 At special positions: 0 Unit cell: (153.107, 105.074, 126.088, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 86 16.00 P 2 15.00 O 2932 8.00 N 2754 7.00 C 10942 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 6.98 Conformation dependent library (CDL) restraints added in 3.2 seconds 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3964 Finding SS restraints... Secondary structure from input PDB file: 86 helices and 9 sheets defined 71.6% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.77 Creating SS restraints... Processing helix chain 'A' and resid 77 through 95 Processing helix chain 'A' and resid 101 through 120 removed outlier: 4.329A pdb=" N VAL A 105 " --> pdb=" O PRO A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.832A pdb=" N HIS A 126 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N ASP A 129 " --> pdb=" O GLU A 125 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N VAL A 130 " --> pdb=" O HIS A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 141 removed outlier: 4.197A pdb=" N LEU A 138 " --> pdb=" O ASP A 134 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU A 139 " --> pdb=" O PRO A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 153 Processing helix chain 'A' and resid 155 through 161 Processing helix chain 'A' and resid 162 through 189 Processing helix chain 'A' and resid 194 through 205 Processing helix chain 'A' and resid 210 through 221 removed outlier: 3.600A pdb=" N VAL A 214 " --> pdb=" O PRO A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 254 removed outlier: 3.586A pdb=" N GLY A 227 " --> pdb=" O SER A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 273 removed outlier: 3.561A pdb=" N LEU A 266 " --> pdb=" O GLY A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 291 removed outlier: 3.525A pdb=" N TRP A 278 " --> pdb=" O ALA A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 317 Processing helix chain 'A' and resid 323 through 337 Processing helix chain 'A' and resid 338 through 341 Processing helix chain 'A' and resid 344 through 379 removed outlier: 3.783A pdb=" N PHE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LEU A 377 " --> pdb=" O THR A 373 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA A 379 " --> pdb=" O LYS A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 406 removed outlier: 4.104A pdb=" N TRP A 385 " --> pdb=" O ASP A 381 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N PHE A 386 " --> pdb=" O LYS A 382 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TYR A 387 " --> pdb=" O MET A 383 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE A 390 " --> pdb=" O PHE A 386 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ARG A 399 " --> pdb=" O ILE A 395 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLY A 400 " --> pdb=" O THR A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 428 Processing helix chain 'A' and resid 432 through 446 removed outlier: 3.813A pdb=" N LEU A 436 " --> pdb=" O GLY A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 481 removed outlier: 3.826A pdb=" N ALA A 471 " --> pdb=" O LEU A 467 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N THR A 472 " --> pdb=" O VAL A 468 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N GLN A 475 " --> pdb=" O ALA A 471 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N THR A 476 " --> pdb=" O THR A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 514 removed outlier: 3.723A pdb=" N SER A 514 " --> pdb=" O ASN A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 529 Processing helix chain 'A' and resid 575 through 601 Processing helix chain 'A' and resid 605 through 621 Processing helix chain 'A' and resid 634 through 639 Processing helix chain 'A' and resid 642 through 654 Processing helix chain 'A' and resid 668 through 677 Processing helix chain 'A' and resid 677 through 703 removed outlier: 4.062A pdb=" N GLU A 681 " --> pdb=" O HIS A 677 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N VAL A 693 " --> pdb=" O VAL A 689 " (cutoff:3.500A) Proline residue: A 694 - end of helix Processing helix chain 'A' and resid 724 through 752 removed outlier: 3.590A pdb=" N ARG A 733 " --> pdb=" O GLU A 729 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE A 734 " --> pdb=" O ASP A 730 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N VAL A 741 " --> pdb=" O TYR A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 761 removed outlier: 3.669A pdb=" N VAL A 760 " --> pdb=" O ARG A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 764 through 777 removed outlier: 3.713A pdb=" N ALA A 768 " --> pdb=" O ASN A 764 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 812 Processing helix chain 'A' and resid 813 through 858 Proline residue: A 819 - end of helix removed outlier: 3.810A pdb=" N ILE A 822 " --> pdb=" O ILE A 818 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU A 823 " --> pdb=" O PRO A 819 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL A 824 " --> pdb=" O LYS A 820 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ARG A 856 " --> pdb=" O LYS A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 861 through 889 removed outlier: 3.530A pdb=" N GLY A 874 " --> pdb=" O ILE A 870 " (cutoff:3.500A) Processing helix chain 'A' and resid 889 through 919 removed outlier: 3.832A pdb=" N ALA A 893 " --> pdb=" O HIS A 889 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL A 894 " --> pdb=" O PRO A 890 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N SER A 895 " --> pdb=" O GLY A 891 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 943 removed outlier: 3.644A pdb=" N ALA A 927 " --> pdb=" O ASP A 923 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASN A 943 " --> pdb=" O LYS A 939 " (cutoff:3.500A) Processing helix chain 'A' and resid 952 through 960 removed outlier: 3.661A pdb=" N VAL A 960 " --> pdb=" O LEU A 956 " (cutoff:3.500A) Processing helix chain 'A' and resid 961 through 964 Processing helix chain 'A' and resid 966 through 976 removed outlier: 3.960A pdb=" N ILE A 970 " --> pdb=" O ASP A 966 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ARG A 976 " --> pdb=" O PHE A 972 " (cutoff:3.500A) Processing helix chain 'A' and resid 1043 through 1050 Processing helix chain 'A' and resid 1069 through 1080 Processing helix chain 'A' and resid 1085 through 1107 Proline residue: A1101 - end of helix removed outlier: 4.231A pdb=" N MET A1104 " --> pdb=" O THR A1100 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLU A1105 " --> pdb=" O PRO A1101 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLN A1106 " --> pdb=" O LEU A1102 " (cutoff:3.500A) Processing helix chain 'A' and resid 1115 through 1124 removed outlier: 3.891A pdb=" N GLY A1124 " --> pdb=" O HIS A1120 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 95 Processing helix chain 'B' and resid 101 through 120 removed outlier: 4.329A pdb=" N VAL B 105 " --> pdb=" O PRO B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 132 removed outlier: 3.833A pdb=" N HIS B 126 " --> pdb=" O LEU B 122 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N ASP B 129 " --> pdb=" O GLU B 125 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N VAL B 130 " --> pdb=" O HIS B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 141 removed outlier: 4.197A pdb=" N LEU B 138 " --> pdb=" O ASP B 134 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU B 139 " --> pdb=" O PRO B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 153 Processing helix chain 'B' and resid 155 through 161 Processing helix chain 'B' and resid 162 through 189 Processing helix chain 'B' and resid 194 through 205 Processing helix chain 'B' and resid 210 through 221 removed outlier: 3.599A pdb=" N VAL B 214 " --> pdb=" O PRO B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 254 removed outlier: 3.587A pdb=" N GLY B 227 " --> pdb=" O SER B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 273 removed outlier: 3.563A pdb=" N LEU B 266 " --> pdb=" O GLY B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 291 removed outlier: 3.526A pdb=" N TRP B 278 " --> pdb=" O ALA B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 317 Processing helix chain 'B' and resid 323 through 337 Processing helix chain 'B' and resid 338 through 341 Processing helix chain 'B' and resid 344 through 379 removed outlier: 3.782A pdb=" N PHE B 348 " --> pdb=" O GLU B 344 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LEU B 377 " --> pdb=" O THR B 373 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA B 379 " --> pdb=" O LYS B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 406 removed outlier: 3.610A pdb=" N TYR B 387 " --> pdb=" O MET B 383 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE B 390 " --> pdb=" O PHE B 386 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ARG B 399 " --> pdb=" O ILE B 395 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLY B 400 " --> pdb=" O THR B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 428 Processing helix chain 'B' and resid 432 through 446 removed outlier: 3.812A pdb=" N LEU B 436 " --> pdb=" O GLY B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 481 removed outlier: 3.826A pdb=" N ALA B 471 " --> pdb=" O LEU B 467 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N THR B 472 " --> pdb=" O VAL B 468 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N GLN B 475 " --> pdb=" O ALA B 471 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N THR B 476 " --> pdb=" O THR B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 514 removed outlier: 3.714A pdb=" N SER B 514 " --> pdb=" O ASN B 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 529 Processing helix chain 'B' and resid 575 through 601 Processing helix chain 'B' and resid 605 through 621 Processing helix chain 'B' and resid 634 through 639 Processing helix chain 'B' and resid 642 through 654 Processing helix chain 'B' and resid 668 through 677 Processing helix chain 'B' and resid 677 through 703 removed outlier: 4.061A pdb=" N GLU B 681 " --> pdb=" O HIS B 677 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N VAL B 693 " --> pdb=" O VAL B 689 " (cutoff:3.500A) Proline residue: B 694 - end of helix Processing helix chain 'B' and resid 724 through 752 removed outlier: 3.590A pdb=" N ARG B 733 " --> pdb=" O GLU B 729 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE B 734 " --> pdb=" O ASP B 730 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N VAL B 741 " --> pdb=" O TYR B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 756 through 761 removed outlier: 3.669A pdb=" N VAL B 760 " --> pdb=" O ARG B 756 " (cutoff:3.500A) Processing helix chain 'B' and resid 764 through 777 removed outlier: 3.712A pdb=" N ALA B 768 " --> pdb=" O ASN B 764 " (cutoff:3.500A) Processing helix chain 'B' and resid 802 through 812 Processing helix chain 'B' and resid 813 through 858 Proline residue: B 819 - end of helix removed outlier: 3.810A pdb=" N ILE B 822 " --> pdb=" O ILE B 818 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU B 823 " --> pdb=" O PRO B 819 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL B 824 " --> pdb=" O LYS B 820 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ARG B 856 " --> pdb=" O LYS B 852 " (cutoff:3.500A) Processing helix chain 'B' and resid 861 through 889 removed outlier: 3.531A pdb=" N GLY B 874 " --> pdb=" O ILE B 870 " (cutoff:3.500A) Processing helix chain 'B' and resid 889 through 919 removed outlier: 3.833A pdb=" N ALA B 893 " --> pdb=" O HIS B 889 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL B 894 " --> pdb=" O PRO B 890 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N SER B 895 " --> pdb=" O GLY B 891 " (cutoff:3.500A) Processing helix chain 'B' and resid 923 through 943 removed outlier: 3.644A pdb=" N ALA B 927 " --> pdb=" O ASP B 923 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASN B 943 " --> pdb=" O LYS B 939 " (cutoff:3.500A) Processing helix chain 'B' and resid 952 through 960 removed outlier: 3.662A pdb=" N VAL B 960 " --> pdb=" O LEU B 956 " (cutoff:3.500A) Processing helix chain 'B' and resid 961 through 964 Processing helix chain 'B' and resid 966 through 976 removed outlier: 3.960A pdb=" N ILE B 970 " --> pdb=" O ASP B 966 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ARG B 976 " --> pdb=" O PHE B 972 " (cutoff:3.500A) Processing helix chain 'B' and resid 1043 through 1050 Processing helix chain 'B' and resid 1069 through 1080 Processing helix chain 'B' and resid 1085 through 1107 Proline residue: B1101 - end of helix removed outlier: 4.231A pdb=" N MET B1104 " --> pdb=" O THR B1100 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLU B1105 " --> pdb=" O PRO B1101 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLN B1106 " --> pdb=" O LEU B1102 " (cutoff:3.500A) Processing helix chain 'B' and resid 1115 through 1124 removed outlier: 3.889A pdb=" N GLY B1124 " --> pdb=" O HIS B1120 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 978 through 982 removed outlier: 6.662A pdb=" N GLN A1064 " --> pdb=" O VAL A1002 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 987 through 989 removed outlier: 6.899A pdb=" N VAL A1057 " --> pdb=" O ILE A 988 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1125 through 1127 removed outlier: 4.422A pdb=" N LEU A1186 " --> pdb=" O VAL A1127 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ASN A1149 " --> pdb=" O ARG A1185 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N PHE A1187 " --> pdb=" O LEU A1147 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N LEU A1147 " --> pdb=" O PHE A1187 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1135 through 1136 Processing sheet with id=AA5, first strand: chain 'A' and resid 1152 through 1153 Processing sheet with id=AA6, first strand: chain 'B' and resid 978 through 982 removed outlier: 6.662A pdb=" N GLN B1064 " --> pdb=" O VAL B1002 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 987 through 989 removed outlier: 6.898A pdb=" N VAL B1057 " --> pdb=" O ILE B 988 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 1125 through 1127 removed outlier: 4.510A pdb=" N LEU B1186 " --> pdb=" O VAL B1127 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASN B1149 " --> pdb=" O ARG B1185 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N PHE B1187 " --> pdb=" O LEU B1147 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N LEU B1147 " --> pdb=" O PHE B1187 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 1135 through 1137 removed outlier: 3.586A pdb=" N THR B1175 " --> pdb=" O TYR B1153 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N TYR B1153 " --> pdb=" O THR B1175 " (cutoff:3.500A) 1106 hydrogen bonds defined for protein. 3213 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: 5.81 Time building geometry restraints manager: 7.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 2659 1.31 - 1.44: 4279 1.44 - 1.57: 9932 1.57 - 1.70: 6 1.70 - 1.82: 158 Bond restraints: 17034 Sorted by residual: bond pdb=" C LEU B1086 " pdb=" N GLU B1087 " ideal model delta sigma weight residual 1.334 1.436 -0.102 1.27e-02 6.20e+03 6.45e+01 bond pdb=" C GLU B 847 " pdb=" N GLU B 848 " ideal model delta sigma weight residual 1.334 1.255 0.079 1.27e-02 6.20e+03 3.87e+01 bond pdb=" C GLU A 847 " pdb=" N GLU A 848 " ideal model delta sigma weight residual 1.334 1.256 0.078 1.27e-02 6.20e+03 3.78e+01 bond pdb=" C ARG A 499 " pdb=" N ARG A 500 " ideal model delta sigma weight residual 1.334 1.399 -0.065 1.27e-02 6.20e+03 2.61e+01 bond pdb=" C ARG B 499 " pdb=" N ARG B 500 " ideal model delta sigma weight residual 1.334 1.399 -0.065 1.27e-02 6.20e+03 2.61e+01 ... (remaining 17029 not shown) Histogram of bond angle deviations from ideal: 99.28 - 110.03: 2278 110.03 - 120.78: 15879 120.78 - 131.53: 4879 131.53 - 142.28: 32 142.28 - 153.02: 2 Bond angle restraints: 23070 Sorted by residual: angle pdb=" C39 CPL A1401 " pdb=" C40 CPL A1401 " pdb=" C41 CPL A1401 " ideal model delta sigma weight residual 127.51 153.02 -25.51 3.00e+00 1.11e-01 7.23e+01 angle pdb=" C39 CPL B1401 " pdb=" C40 CPL B1401 " pdb=" C41 CPL B1401 " ideal model delta sigma weight residual 127.51 152.99 -25.48 3.00e+00 1.11e-01 7.21e+01 angle pdb=" O LEU B1086 " pdb=" C LEU B1086 " pdb=" N GLU B1087 " ideal model delta sigma weight residual 122.12 128.95 -6.83 1.06e+00 8.90e-01 4.15e+01 angle pdb=" O GLU B1087 " pdb=" C GLU B1087 " pdb=" N TYR B1088 " ideal model delta sigma weight residual 122.07 128.45 -6.38 1.03e+00 9.43e-01 3.84e+01 angle pdb=" CA LEU B1086 " pdb=" C LEU B1086 " pdb=" N GLU B1087 " ideal model delta sigma weight residual 117.30 110.42 6.88 1.16e+00 7.43e-01 3.52e+01 ... (remaining 23065 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.72: 9521 30.72 - 61.45: 654 61.45 - 92.17: 37 92.17 - 122.89: 0 122.89 - 153.61: 6 Dihedral angle restraints: 10218 sinusoidal: 4100 harmonic: 6118 Sorted by residual: dihedral pdb=" C33 CPL B1401 " pdb=" C31 CPL B1401 " pdb=" C32 CPL B1401 " pdb=" O2 CPL B1401 " ideal model delta sinusoidal sigma weight residual 171.65 -34.74 -153.61 1 3.00e+01 1.11e-03 2.02e+01 dihedral pdb=" C33 CPL A1401 " pdb=" C31 CPL A1401 " pdb=" C32 CPL A1401 " pdb=" O2 CPL A1401 " ideal model delta sinusoidal sigma weight residual 171.65 -34.74 -153.61 1 3.00e+01 1.11e-03 2.02e+01 dihedral pdb=" C3 CPL B1401 " pdb=" C1 CPL B1401 " pdb=" C2 CPL B1401 " pdb=" O3P CPL B1401 " ideal model delta sinusoidal sigma weight residual 72.09 -73.31 145.40 1 3.00e+01 1.11e-03 1.94e+01 ... (remaining 10215 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 2053 0.048 - 0.096: 506 0.096 - 0.144: 148 0.144 - 0.192: 43 0.192 - 0.240: 12 Chirality restraints: 2762 Sorted by residual: chirality pdb=" C2 CPL B1401 " pdb=" C1 CPL B1401 " pdb=" C3 CPL B1401 " pdb=" O2 CPL B1401 " both_signs ideal model delta sigma weight residual False -2.32 -2.55 0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" C2 CPL A1401 " pdb=" C1 CPL A1401 " pdb=" C3 CPL A1401 " pdb=" O2 CPL A1401 " both_signs ideal model delta sigma weight residual False -2.32 -2.55 0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CA ILE A 734 " pdb=" N ILE A 734 " pdb=" C ILE A 734 " pdb=" CB ILE A 734 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.23 2.00e-01 2.50e+01 1.28e+00 ... (remaining 2759 not shown) Planarity restraints: 2828 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR B 641 " -0.059 5.00e-02 4.00e+02 8.92e-02 1.27e+01 pdb=" N PRO B 642 " 0.154 5.00e-02 4.00e+02 pdb=" CA PRO B 642 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO B 642 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 641 " 0.059 5.00e-02 4.00e+02 8.91e-02 1.27e+01 pdb=" N PRO A 642 " -0.154 5.00e-02 4.00e+02 pdb=" CA PRO A 642 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO A 642 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 732 " -0.014 2.00e-02 2.50e+03 2.88e-02 8.28e+00 pdb=" C LEU B 732 " 0.050 2.00e-02 2.50e+03 pdb=" O LEU B 732 " -0.019 2.00e-02 2.50e+03 pdb=" N ARG B 733 " -0.017 2.00e-02 2.50e+03 ... (remaining 2825 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 503 2.71 - 3.25: 17619 3.25 - 3.80: 26965 3.80 - 4.35: 30677 4.35 - 4.90: 52772 Nonbonded interactions: 128536 Sorted by model distance: nonbonded pdb=" N GLU A1071 " pdb=" OE1 GLU A1071 " model vdw 2.157 3.120 nonbonded pdb=" N GLU B1071 " pdb=" OE1 GLU B1071 " model vdw 2.158 3.120 nonbonded pdb=" N GLU A 346 " pdb=" OE1 GLU A 346 " model vdw 2.227 3.120 nonbonded pdb=" N GLU B 346 " pdb=" OE1 GLU B 346 " model vdw 2.227 3.120 nonbonded pdb=" N GLU A 531 " pdb=" OE1 GLU A 531 " model vdw 2.233 3.120 ... (remaining 128531 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 2.100 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: 0.610 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 47.950 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 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 : 0.006 0.123 17034 Z= 0.350 Angle : 0.902 25.515 23070 Z= 0.507 Chirality : 0.050 0.240 2762 Planarity : 0.005 0.089 2828 Dihedral : 19.192 153.613 6254 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.80 % Favored : 94.10 % Rotamer: Outliers : 2.99 % Allowed : 33.96 % Favored : 63.05 % 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: 1.04 (0.19), residues: 2086 helix: 1.84 (0.14), residues: 1354 sheet: 1.45 (0.64), residues: 54 loop : -1.87 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 643 HIS 0.006 0.001 HIS B1172 PHE 0.014 0.001 PHE A 598 TYR 0.029 0.001 TYR B 758 ARG 0.004 0.000 ARG B 585 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 220 time to evaluate : 1.979 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 678 MET cc_start: 0.7124 (pmm) cc_final: 0.6851 (pmm) REVERT: A 758 TYR cc_start: 0.8985 (t80) cc_final: 0.8773 (t80) REVERT: A 900 GLN cc_start: 0.8408 (OUTLIER) cc_final: 0.8191 (mt0) REVERT: A 967 MET cc_start: 0.8986 (mmm) cc_final: 0.8483 (mpp) REVERT: A 986 GLU cc_start: 0.7840 (mm-30) cc_final: 0.7546 (mt-10) REVERT: A 1109 PHE cc_start: 0.8651 (m-80) cc_final: 0.7919 (m-80) REVERT: A 1172 HIS cc_start: 0.6138 (OUTLIER) cc_final: 0.5791 (m-70) REVERT: B 205 MET cc_start: 0.8712 (mtm) cc_final: 0.8504 (mtm) REVERT: B 477 LEU cc_start: 0.9464 (tp) cc_final: 0.9261 (tp) REVERT: B 967 MET cc_start: 0.8807 (mmm) cc_final: 0.8600 (mmm) REVERT: B 1109 PHE cc_start: 0.8616 (m-80) cc_final: 0.8117 (m-80) outliers start: 54 outliers final: 11 residues processed: 257 average time/residue: 0.3039 time to fit residues: 116.0710 Evaluate side-chains 188 residues out of total 1808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 175 time to evaluate : 1.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 801 LEU Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 849 GLU Chi-restraints excluded: chain A residue 900 GLN Chi-restraints excluded: chain A residue 915 GLU Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain A residue 1172 HIS Chi-restraints excluded: chain B residue 801 LEU Chi-restraints excluded: chain B residue 808 LEU Chi-restraints excluded: chain B residue 915 GLU Chi-restraints excluded: chain B residue 1119 LEU Chi-restraints excluded: chain B residue 1188 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 0.7980 chunk 159 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 107 optimal weight: 0.8980 chunk 85 optimal weight: 5.9990 chunk 164 optimal weight: 6.9990 chunk 63 optimal weight: 8.9990 chunk 100 optimal weight: 2.9990 chunk 122 optimal weight: 0.5980 chunk 190 optimal weight: 5.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 HIS A 677 HIS A 685 ASN A 691 ASN A 736 ASN A1120 HIS B 136 HIS B 677 HIS B 691 ASN B 736 ASN B 764 ASN B1120 HIS ** B1172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.1489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 17034 Z= 0.247 Angle : 0.606 8.084 23070 Z= 0.306 Chirality : 0.039 0.189 2762 Planarity : 0.005 0.085 2828 Dihedral : 11.168 144.205 2371 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 3.76 % Allowed : 31.64 % Favored : 64.60 % 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: 1.62 (0.19), residues: 2086 helix: 2.18 (0.14), residues: 1376 sheet: 1.16 (0.64), residues: 58 loop : -1.45 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 643 HIS 0.003 0.001 HIS B1172 PHE 0.013 0.001 PHE B 625 TYR 0.034 0.001 TYR B 758 ARG 0.008 0.001 ARG A 585 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 174 time to evaluate : 2.003 Fit side-chains revert: symmetry clash REVERT: A 94 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8955 (tt) REVERT: A 382 LYS cc_start: 0.7019 (OUTLIER) cc_final: 0.6269 (ptpp) REVERT: A 579 MET cc_start: 0.8024 (mmm) cc_final: 0.7762 (mmp) REVERT: A 662 MET cc_start: 0.7230 (mpp) cc_final: 0.6969 (tpt) REVERT: A 925 MET cc_start: 0.8527 (ppp) cc_final: 0.7982 (ppp) REVERT: A 967 MET cc_start: 0.8922 (mmm) cc_final: 0.8438 (mpp) REVERT: B 382 LYS cc_start: 0.7090 (OUTLIER) cc_final: 0.6335 (ptpp) REVERT: B 925 MET cc_start: 0.8468 (ppp) cc_final: 0.8036 (ppp) REVERT: B 967 MET cc_start: 0.8789 (mmm) cc_final: 0.8558 (mmm) outliers start: 68 outliers final: 32 residues processed: 223 average time/residue: 0.2538 time to fit residues: 91.1959 Evaluate side-chains 191 residues out of total 1808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 156 time to evaluate : 1.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 382 LYS Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 909 SER Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 1057 VAL Chi-restraints excluded: chain A residue 1148 ILE Chi-restraints excluded: chain A residue 1178 TYR Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 382 LYS Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 850 VAL Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 867 LEU Chi-restraints excluded: chain B residue 909 SER Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 1057 VAL Chi-restraints excluded: chain B residue 1176 PHE Chi-restraints excluded: chain B residue 1188 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 105 optimal weight: 3.9990 chunk 59 optimal weight: 6.9990 chunk 158 optimal weight: 7.9990 chunk 129 optimal weight: 0.9980 chunk 52 optimal weight: 0.6980 chunk 191 optimal weight: 0.9980 chunk 206 optimal weight: 20.0000 chunk 170 optimal weight: 0.5980 chunk 189 optimal weight: 0.6980 chunk 65 optimal weight: 5.9990 chunk 153 optimal weight: 7.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 702 GLN A 764 ASN ** A1172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 685 ASN B 702 GLN ** B1172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17034 Z= 0.169 Angle : 0.542 6.722 23070 Z= 0.276 Chirality : 0.038 0.171 2762 Planarity : 0.004 0.084 2828 Dihedral : 10.335 143.781 2345 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 3.04 % Allowed : 31.47 % Favored : 65.49 % 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: 1.90 (0.19), residues: 2086 helix: 2.46 (0.14), residues: 1368 sheet: 1.29 (0.65), residues: 58 loop : -1.46 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 635 HIS 0.004 0.001 HIS B 677 PHE 0.014 0.001 PHE A 769 TYR 0.019 0.001 TYR A 758 ARG 0.004 0.000 ARG A 585 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 166 time to evaluate : 2.048 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8968 (tt) REVERT: A 205 MET cc_start: 0.8814 (OUTLIER) cc_final: 0.8590 (mtm) REVERT: A 382 LYS cc_start: 0.6879 (OUTLIER) cc_final: 0.6154 (ptpp) REVERT: A 578 MET cc_start: 0.8181 (mpp) cc_final: 0.7928 (mpp) REVERT: A 662 MET cc_start: 0.7206 (mpp) cc_final: 0.6922 (tpt) REVERT: A 857 MET cc_start: 0.8452 (tmm) cc_final: 0.8105 (tmm) REVERT: A 967 MET cc_start: 0.8864 (mmm) cc_final: 0.8395 (mpp) REVERT: B 578 MET cc_start: 0.8092 (mpp) cc_final: 0.7795 (mpp) REVERT: B 579 MET cc_start: 0.8087 (OUTLIER) cc_final: 0.7703 (mmp) REVERT: B 925 MET cc_start: 0.8511 (ppp) cc_final: 0.8151 (ppp) REVERT: B 967 MET cc_start: 0.8744 (mmm) cc_final: 0.8527 (mmm) REVERT: B 1107 MET cc_start: 0.6697 (tmm) cc_final: 0.6404 (tmm) outliers start: 55 outliers final: 19 residues processed: 212 average time/residue: 0.2366 time to fit residues: 81.9084 Evaluate side-chains 179 residues out of total 1808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 156 time to evaluate : 1.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 382 LYS Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 1057 VAL Chi-restraints excluded: chain A residue 1178 TYR Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 579 MET Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 867 LEU Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 1057 VAL Chi-restraints excluded: chain B residue 1176 PHE Chi-restraints excluded: chain B residue 1188 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 188 optimal weight: 0.4980 chunk 143 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 91 optimal weight: 9.9990 chunk 128 optimal weight: 0.8980 chunk 191 optimal weight: 0.6980 chunk 202 optimal weight: 0.0980 chunk 100 optimal weight: 9.9990 chunk 181 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 685 ASN ** B1172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 17034 Z= 0.148 Angle : 0.513 8.287 23070 Z= 0.260 Chirality : 0.037 0.136 2762 Planarity : 0.004 0.083 2828 Dihedral : 10.042 142.432 2345 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.65 % Allowed : 31.75 % Favored : 65.60 % 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: 2.11 (0.19), residues: 2086 helix: 2.59 (0.14), residues: 1366 sheet: 1.47 (0.63), residues: 58 loop : -1.30 (0.25), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 635 HIS 0.003 0.000 HIS A 600 PHE 0.017 0.001 PHE A 769 TYR 0.010 0.001 TYR B 312 ARG 0.003 0.000 ARG A 903 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 167 time to evaluate : 1.908 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8976 (tt) REVERT: A 205 MET cc_start: 0.8694 (OUTLIER) cc_final: 0.8486 (mtm) REVERT: A 578 MET cc_start: 0.8012 (mpp) cc_final: 0.7784 (mpp) REVERT: A 662 MET cc_start: 0.7151 (mpp) cc_final: 0.6915 (tpt) REVERT: A 737 TYR cc_start: 0.7409 (OUTLIER) cc_final: 0.7108 (m-10) REVERT: A 857 MET cc_start: 0.8491 (tmm) cc_final: 0.7771 (tmm) REVERT: A 967 MET cc_start: 0.8833 (mmm) cc_final: 0.8571 (mmm) REVERT: B 578 MET cc_start: 0.7968 (mpp) cc_final: 0.7741 (mpp) REVERT: B 685 ASN cc_start: 0.8090 (m110) cc_final: 0.7659 (p0) REVERT: B 967 MET cc_start: 0.8705 (mmm) cc_final: 0.8340 (mmm) outliers start: 48 outliers final: 27 residues processed: 205 average time/residue: 0.2443 time to fit residues: 80.6516 Evaluate side-chains 188 residues out of total 1808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 158 time to evaluate : 1.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 737 TYR Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 1057 VAL Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1178 TYR Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 833 LEU Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 867 LEU Chi-restraints excluded: chain B residue 892 ILE Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 1057 VAL Chi-restraints excluded: chain B residue 1161 ILE Chi-restraints excluded: chain B residue 1176 PHE Chi-restraints excluded: chain B residue 1188 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 169 optimal weight: 10.0000 chunk 115 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 151 optimal weight: 0.0040 chunk 83 optimal weight: 0.0020 chunk 173 optimal weight: 10.0000 chunk 140 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 103 optimal weight: 5.9990 chunk 182 optimal weight: 3.9990 chunk 51 optimal weight: 9.9990 overall best weight: 2.2006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 17034 Z= 0.288 Angle : 0.578 7.468 23070 Z= 0.294 Chirality : 0.039 0.136 2762 Planarity : 0.004 0.089 2828 Dihedral : 9.906 142.735 2345 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 3.60 % Allowed : 30.42 % Favored : 65.98 % 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: 2.01 (0.19), residues: 2086 helix: 2.48 (0.14), residues: 1370 sheet: 1.33 (0.62), residues: 58 loop : -1.27 (0.25), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 635 HIS 0.005 0.001 HIS A 600 PHE 0.018 0.001 PHE A 769 TYR 0.015 0.001 TYR B 312 ARG 0.003 0.000 ARG A 903 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 160 time to evaluate : 1.941 Fit side-chains REVERT: A 205 MET cc_start: 0.8990 (OUTLIER) cc_final: 0.8766 (mtm) REVERT: A 578 MET cc_start: 0.8017 (mpp) cc_final: 0.7760 (mpp) REVERT: A 670 LEU cc_start: 0.6659 (OUTLIER) cc_final: 0.6390 (mp) REVERT: A 737 TYR cc_start: 0.7377 (OUTLIER) cc_final: 0.7161 (m-10) REVERT: A 857 MET cc_start: 0.8488 (tmm) cc_final: 0.8031 (tmm) REVERT: A 967 MET cc_start: 0.8805 (mmm) cc_final: 0.8569 (mmm) REVERT: A 1172 HIS cc_start: 0.6773 (OUTLIER) cc_final: 0.6465 (m-70) REVERT: B 578 MET cc_start: 0.7990 (mpp) cc_final: 0.7674 (mpp) REVERT: B 685 ASN cc_start: 0.8106 (m110) cc_final: 0.7699 (p0) REVERT: B 737 TYR cc_start: 0.7091 (OUTLIER) cc_final: 0.6830 (m-80) REVERT: B 967 MET cc_start: 0.8743 (mmm) cc_final: 0.8359 (mmm) REVERT: B 1107 MET cc_start: 0.6785 (tmm) cc_final: 0.6539 (tmm) REVERT: B 1169 ARG cc_start: 0.6730 (ttt180) cc_final: 0.6506 (ttt180) outliers start: 65 outliers final: 38 residues processed: 214 average time/residue: 0.2440 time to fit residues: 84.1520 Evaluate side-chains 196 residues out of total 1808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 153 time to evaluate : 2.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 737 TYR Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 909 SER Chi-restraints excluded: chain A residue 956 LEU Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 1057 VAL Chi-restraints excluded: chain A residue 1148 ILE Chi-restraints excluded: chain A residue 1172 HIS Chi-restraints excluded: chain A residue 1178 TYR Chi-restraints excluded: chain A residue 1188 VAL Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 737 TYR Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 867 LEU Chi-restraints excluded: chain B residue 909 SER Chi-restraints excluded: chain B residue 956 LEU Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 1057 VAL Chi-restraints excluded: chain B residue 1117 VAL Chi-restraints excluded: chain B residue 1148 ILE Chi-restraints excluded: chain B residue 1167 ILE Chi-restraints excluded: chain B residue 1176 PHE Chi-restraints excluded: chain B residue 1188 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 68 optimal weight: 10.0000 chunk 182 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 119 optimal weight: 0.5980 chunk 50 optimal weight: 2.9990 chunk 203 optimal weight: 0.9990 chunk 168 optimal weight: 7.9990 chunk 94 optimal weight: 6.9990 chunk 16 optimal weight: 0.9980 chunk 67 optimal weight: 0.6980 chunk 106 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 736 ASN ** B 736 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17034 Z= 0.164 Angle : 0.538 15.579 23070 Z= 0.269 Chirality : 0.037 0.149 2762 Planarity : 0.004 0.094 2828 Dihedral : 9.777 142.833 2345 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 3.65 % Allowed : 30.31 % Favored : 66.04 % 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: 2.20 (0.19), residues: 2086 helix: 2.62 (0.14), residues: 1374 sheet: 1.53 (0.64), residues: 58 loop : -1.24 (0.25), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 635 HIS 0.003 0.000 HIS A 600 PHE 0.015 0.001 PHE A 769 TYR 0.029 0.001 TYR A 641 ARG 0.003 0.000 ARG B1158 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 159 time to evaluate : 2.015 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 205 MET cc_start: 0.8803 (OUTLIER) cc_final: 0.8583 (mtm) REVERT: A 346 GLU cc_start: 0.8943 (pm20) cc_final: 0.8665 (pm20) REVERT: A 578 MET cc_start: 0.7967 (mpp) cc_final: 0.7617 (mpp) REVERT: A 737 TYR cc_start: 0.7449 (OUTLIER) cc_final: 0.7236 (m-80) REVERT: A 857 MET cc_start: 0.8485 (tmm) cc_final: 0.8035 (tmm) REVERT: A 967 MET cc_start: 0.8797 (mmm) cc_final: 0.8565 (mmm) REVERT: A 1107 MET cc_start: 0.7011 (tmm) cc_final: 0.6740 (ppp) REVERT: A 1172 HIS cc_start: 0.6810 (OUTLIER) cc_final: 0.6479 (m-70) REVERT: B 346 GLU cc_start: 0.8942 (pm20) cc_final: 0.8666 (pm20) REVERT: B 578 MET cc_start: 0.7978 (mpp) cc_final: 0.7656 (mpp) REVERT: B 670 LEU cc_start: 0.6737 (OUTLIER) cc_final: 0.6489 (mp) REVERT: B 685 ASN cc_start: 0.8153 (m110) cc_final: 0.7765 (p0) REVERT: B 967 MET cc_start: 0.8698 (mmm) cc_final: 0.8307 (mmm) REVERT: B 1107 MET cc_start: 0.6816 (tmm) cc_final: 0.6509 (tmm) outliers start: 66 outliers final: 36 residues processed: 214 average time/residue: 0.2526 time to fit residues: 88.1308 Evaluate side-chains 197 residues out of total 1808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 157 time to evaluate : 1.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 737 TYR Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 909 SER Chi-restraints excluded: chain A residue 956 LEU Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 1057 VAL Chi-restraints excluded: chain A residue 1172 HIS Chi-restraints excluded: chain A residue 1178 TYR Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain B residue 833 LEU Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 867 LEU Chi-restraints excluded: chain B residue 909 SER Chi-restraints excluded: chain B residue 956 LEU Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 1057 VAL Chi-restraints excluded: chain B residue 1161 ILE Chi-restraints excluded: chain B residue 1176 PHE Chi-restraints excluded: chain B residue 1188 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 195 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 115 optimal weight: 4.9990 chunk 148 optimal weight: 2.9990 chunk 114 optimal weight: 0.9980 chunk 171 optimal weight: 30.0000 chunk 113 optimal weight: 0.8980 chunk 202 optimal weight: 3.9990 chunk 126 optimal weight: 0.9980 chunk 123 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 736 ASN ** B1172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17034 Z= 0.184 Angle : 0.540 11.777 23070 Z= 0.270 Chirality : 0.038 0.170 2762 Planarity : 0.004 0.094 2828 Dihedral : 9.674 142.189 2345 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.77 % Allowed : 30.97 % Favored : 66.26 % 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: 2.20 (0.19), residues: 2086 helix: 2.64 (0.14), residues: 1374 sheet: 1.60 (0.64), residues: 58 loop : -1.28 (0.25), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 635 HIS 0.004 0.000 HIS A 600 PHE 0.014 0.001 PHE A 769 TYR 0.018 0.001 TYR A 641 ARG 0.003 0.000 ARG B 856 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 157 time to evaluate : 1.920 Fit side-chains revert: symmetry clash REVERT: A 205 MET cc_start: 0.8874 (OUTLIER) cc_final: 0.8646 (mtm) REVERT: A 346 GLU cc_start: 0.8921 (pm20) cc_final: 0.8657 (pm20) REVERT: A 578 MET cc_start: 0.8027 (mpp) cc_final: 0.7670 (mpp) REVERT: A 857 MET cc_start: 0.8474 (tmm) cc_final: 0.8008 (tmm) REVERT: A 967 MET cc_start: 0.8788 (mmm) cc_final: 0.8360 (mmm) REVERT: A 1107 MET cc_start: 0.6950 (tmm) cc_final: 0.6683 (ppp) REVERT: A 1172 HIS cc_start: 0.6837 (OUTLIER) cc_final: 0.6484 (m-70) REVERT: B 346 GLU cc_start: 0.8964 (pm20) cc_final: 0.8691 (pm20) REVERT: B 578 MET cc_start: 0.7966 (mpp) cc_final: 0.7661 (mpp) REVERT: B 967 MET cc_start: 0.8715 (mmm) cc_final: 0.8331 (mmm) REVERT: B 1107 MET cc_start: 0.6885 (tmm) cc_final: 0.6582 (tmm) outliers start: 50 outliers final: 32 residues processed: 199 average time/residue: 0.2470 time to fit residues: 79.6828 Evaluate side-chains 190 residues out of total 1808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 156 time to evaluate : 1.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 909 SER Chi-restraints excluded: chain A residue 956 LEU Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 1057 VAL Chi-restraints excluded: chain A residue 1172 HIS Chi-restraints excluded: chain A residue 1178 TYR Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 909 SER Chi-restraints excluded: chain B residue 956 LEU Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 1057 VAL Chi-restraints excluded: chain B residue 1161 ILE Chi-restraints excluded: chain B residue 1176 PHE Chi-restraints excluded: chain B residue 1188 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 125 optimal weight: 3.9990 chunk 80 optimal weight: 0.9990 chunk 120 optimal weight: 0.8980 chunk 60 optimal weight: 10.0000 chunk 39 optimal weight: 1.9990 chunk 128 optimal weight: 0.9990 chunk 137 optimal weight: 0.9980 chunk 100 optimal weight: 8.9990 chunk 18 optimal weight: 3.9990 chunk 159 optimal weight: 6.9990 chunk 184 optimal weight: 3.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 736 ASN ** B1172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.2648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17034 Z= 0.187 Angle : 0.549 10.256 23070 Z= 0.273 Chirality : 0.038 0.204 2762 Planarity : 0.004 0.093 2828 Dihedral : 9.594 141.993 2345 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.71 % Allowed : 30.64 % Favored : 66.65 % 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: 2.21 (0.19), residues: 2086 helix: 2.66 (0.14), residues: 1376 sheet: 1.30 (0.63), residues: 62 loop : -1.29 (0.25), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 635 HIS 0.004 0.001 HIS A 600 PHE 0.020 0.001 PHE B 769 TYR 0.013 0.001 TYR A 641 ARG 0.002 0.000 ARG B 856 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 161 time to evaluate : 1.848 Fit side-chains REVERT: A 205 MET cc_start: 0.8834 (OUTLIER) cc_final: 0.8614 (mtm) REVERT: A 346 GLU cc_start: 0.8855 (pm20) cc_final: 0.8574 (pm20) REVERT: A 578 MET cc_start: 0.8003 (mpp) cc_final: 0.7604 (mpp) REVERT: A 857 MET cc_start: 0.8474 (tmm) cc_final: 0.7988 (tmm) REVERT: A 967 MET cc_start: 0.8769 (mmm) cc_final: 0.8339 (mmm) REVERT: A 1104 MET cc_start: 0.8657 (mmp) cc_final: 0.8280 (mmp) REVERT: A 1107 MET cc_start: 0.6982 (tmm) cc_final: 0.6657 (ppp) REVERT: A 1172 HIS cc_start: 0.6806 (OUTLIER) cc_final: 0.6450 (m-70) REVERT: B 346 GLU cc_start: 0.8930 (pm20) cc_final: 0.8637 (pm20) REVERT: B 578 MET cc_start: 0.7944 (mpp) cc_final: 0.7579 (mpp) REVERT: B 670 LEU cc_start: 0.6691 (OUTLIER) cc_final: 0.6403 (mp) REVERT: B 967 MET cc_start: 0.8713 (mmm) cc_final: 0.8330 (mmm) REVERT: B 1073 MET cc_start: 0.8999 (mmp) cc_final: 0.8617 (mmp) REVERT: B 1107 MET cc_start: 0.6867 (tmm) cc_final: 0.6560 (tmm) outliers start: 49 outliers final: 36 residues processed: 202 average time/residue: 0.2454 time to fit residues: 79.1969 Evaluate side-chains 194 residues out of total 1808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 155 time to evaluate : 1.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 909 SER Chi-restraints excluded: chain A residue 956 LEU Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 1057 VAL Chi-restraints excluded: chain A residue 1172 HIS Chi-restraints excluded: chain A residue 1176 PHE Chi-restraints excluded: chain A residue 1178 TYR Chi-restraints excluded: chain A residue 1188 VAL Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain B residue 677 HIS Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 909 SER Chi-restraints excluded: chain B residue 956 LEU Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 1057 VAL Chi-restraints excluded: chain B residue 1161 ILE Chi-restraints excluded: chain B residue 1176 PHE Chi-restraints excluded: chain B residue 1188 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/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-5409/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-5409/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-5409/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-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/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-5409/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-5409/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: 64.7107 > 50: distance: 16 - 21: 22.625 distance: 21 - 22: 15.686 distance: 21 - 27: 32.586 distance: 22 - 23: 40.201 distance: 22 - 25: 36.011 distance: 23 - 24: 3.275 distance: 23 - 28: 30.573 distance: 24 - 52: 31.350 distance: 25 - 26: 10.182 distance: 26 - 27: 9.538 distance: 28 - 29: 28.380 distance: 28 - 34: 28.945 distance: 29 - 30: 40.318 distance: 29 - 32: 32.388 distance: 30 - 31: 32.209 distance: 30 - 35: 53.302 distance: 31 - 60: 14.858 distance: 32 - 33: 27.801 distance: 33 - 34: 44.529 distance: 35 - 36: 11.703 distance: 36 - 37: 40.664 distance: 36 - 39: 57.684 distance: 37 - 38: 39.591 distance: 37 - 44: 19.409 distance: 38 - 68: 13.554 distance: 39 - 40: 10.461 distance: 40 - 41: 11.647 distance: 41 - 43: 58.286 distance: 44 - 45: 7.989 distance: 45 - 46: 10.674 distance: 45 - 48: 11.693 distance: 46 - 47: 23.708 distance: 46 - 52: 15.273 distance: 47 - 77: 20.708 distance: 48 - 49: 27.277 distance: 49 - 50: 31.592 distance: 49 - 51: 22.377 distance: 52 - 53: 42.026 distance: 53 - 54: 36.110 distance: 53 - 56: 17.824 distance: 54 - 55: 8.659 distance: 54 - 60: 39.050 distance: 56 - 57: 42.315 distance: 57 - 58: 18.311 distance: 57 - 59: 17.947 distance: 60 - 61: 49.711 distance: 61 - 62: 29.336 distance: 61 - 64: 41.597 distance: 62 - 63: 39.368 distance: 62 - 68: 25.350 distance: 64 - 65: 12.282 distance: 65 - 66: 34.105 distance: 65 - 67: 42.315 distance: 68 - 69: 24.565 distance: 69 - 70: 10.691 distance: 69 - 72: 30.820 distance: 70 - 71: 7.399 distance: 70 - 77: 34.578 distance: 72 - 73: 38.195 distance: 73 - 74: 20.851 distance: 74 - 75: 6.609 distance: 75 - 76: 16.104 distance: 77 - 78: 31.121 distance: 78 - 79: 36.243 distance: 78 - 81: 36.158 distance: 79 - 80: 40.983 distance: 79 - 85: 47.141 distance: 81 - 82: 24.960 distance: 82 - 83: 32.842 distance: 82 - 84: 35.992 distance: 85 - 86: 14.986 distance: 86 - 87: 20.977 distance: 86 - 89: 41.968 distance: 87 - 88: 14.288 distance: 87 - 92: 51.796 distance: 89 - 90: 19.696 distance: 89 - 91: 30.844 distance: 92 - 93: 37.492 distance: 93 - 94: 22.474 distance: 93 - 96: 30.244 distance: 94 - 95: 14.643 distance: 94 - 98: 20.910 distance: 95 - 119: 27.960 distance: 96 - 97: 47.667