Starting phenix.real_space_refine on Tue Jun 17 13:50:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6nzu_0560/06_2025/6nzu_0560.cif Found real_map, /net/cci-nas-00/data/ceres_data/6nzu_0560/06_2025/6nzu_0560.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6nzu_0560/06_2025/6nzu_0560.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6nzu_0560/06_2025/6nzu_0560.map" model { file = "/net/cci-nas-00/data/ceres_data/6nzu_0560/06_2025/6nzu_0560.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6nzu_0560/06_2025/6nzu_0560.cif" } resolution = 3.2 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= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 9466 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 4 5.49 5 S 58 5.16 5 C 7908 2.51 5 N 2170 2.21 5 O 2428 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 75 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 12570 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3139 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 402, 3131 Classifications: {'peptide': 402} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 382} Conformer: "B" Number of residues, atoms: 402, 3131 Classifications: {'peptide': 402} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 382} bond proxies already assigned to first conformer: 3180 Chain: "B" Number of atoms: 685 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 81, 678 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} Conformer: "B" Number of residues, atoms: 81, 678 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} bond proxies already assigned to first conformer: 677 Chain: "C" Number of atoms: 547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 547 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 1, 'TRANS': 68} Chain: "D" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 927 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} Chain: "E" Number of atoms: 3139 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 402, 3131 Classifications: {'peptide': 402} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 382} Conformer: "B" Number of residues, atoms: 402, 3131 Classifications: {'peptide': 402} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 382} bond proxies already assigned to first conformer: 3180 Chain: "F" Number of atoms: 685 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 81, 678 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} Conformer: "B" Number of residues, atoms: 81, 678 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} bond proxies already assigned to first conformer: 677 Chain: "G" Number of atoms: 547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 547 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 1, 'TRANS': 68} Chain: "H" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 927 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} Chain: "I" Number of atoms: 937 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 118, 931 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Conformer: "B" Number of residues, atoms: 118, 931 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} bond proxies already assigned to first conformer: 946 Chain: "J" Number of atoms: 937 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 118, 931 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Conformer: "B" Number of residues, atoms: 118, 931 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} bond proxies already assigned to first conformer: 946 Chain: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'PLP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "C" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'8Q1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'PLP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "G" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'8Q1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4837 SG CYS D 95 40.937 34.759 42.193 1.00 28.53 S ATOM 5154 SG CYS D 138 38.986 35.454 38.852 1.00 36.64 S ATOM 10135 SG CYS H 95 106.818 67.369 42.226 1.00 28.88 S ATOM 10452 SG CYS H 138 108.816 66.663 38.916 1.00 37.27 S Time building chain proxies: 12.49, per 1000 atoms: 0.99 Number of scatterers: 12570 At special positions: 0 Unit cell: (148.782, 103.17, 106.428, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 58 16.00 P 4 15.00 O 2428 8.00 N 2170 7.00 C 7908 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 - 3.00 Amino acid : True - 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=5, symmetry=0 Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.00 Conformation dependent library (CDL) restraints added in 3.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D 201 " pdb="ZN ZN D 201 " - pdb=" SG CYS D 95 " pdb="ZN ZN D 201 " - pdb=" SG CYS D 138 " pdb=" ZN H 201 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 95 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 138 " 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2980 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 8 sheets defined 47.7% alpha, 9.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.27 Creating SS restraints... Processing helix chain 'A' and resid 70 through 78 removed outlier: 4.264A pdb=" N ALA A 76 " --> pdb=" O ARG A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 83 Processing helix chain 'A' and resid 99 through 115 removed outlier: 3.868A pdb=" N ARG A 107 " --> pdb=" O MET A 103 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLN A 108 " --> pdb=" O GLU A 104 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU A 113 " --> pdb=" O GLN A 109 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ILE A 114 " --> pdb=" O VAL A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 119 No H-bonds generated for 'chain 'A' and resid 117 through 119' Processing helix chain 'A' and resid 126 through 134 Processing helix chain 'A' and resid 135 through 142 Processing helix chain 'A' and resid 156 through 167 removed outlier: 3.919A pdb=" N SER A 162 " --> pdb=" O CYS A 158 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N SER A 165 " --> pdb=" O ASP A 161 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU A 166 " --> pdb=" O SER A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 170 No H-bonds generated for 'chain 'A' and resid 168 through 170' Processing helix chain 'A' and resid 185 through 193 Processing helix chain 'A' and resid 215 through 225 removed outlier: 3.904A pdb=" N ILE A 221 " --> pdb=" O GLU A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 291 Processing helix chain 'A' and resid 297 through 309 removed outlier: 4.088A pdb=" N GLY A 303 " --> pdb=" O PRO A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 314 removed outlier: 4.021A pdb=" N GLN A 313 " --> pdb=" O GLU A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 337 removed outlier: 3.592A pdb=" N HIS A 319 " --> pdb=" O MET A 315 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS A 320 " --> pdb=" O GLU A 316 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LYS A 324 " --> pdb=" O LYS A 320 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLU A 327 " --> pdb=" O SER A 323 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ASN A 332 " --> pdb=" O ARG A 328 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE A 333 " --> pdb=" O LEU A 329 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N SER A 336 " --> pdb=" O ASN A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 368 Processing helix chain 'A' and resid 389 through 395 Processing helix chain 'A' and resid 398 through 402 removed outlier: 3.848A pdb=" N ALA A 402 " --> pdb=" O GLU A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 429 removed outlier: 3.820A pdb=" N VAL A 419 " --> pdb=" O THR A 415 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU A 424 " --> pdb=" O ASP A 420 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE A 427 " --> pdb=" O VAL A 423 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLN A 428 " --> pdb=" O GLU A 424 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N HIS A 429 " --> pdb=" O LYS A 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 21 removed outlier: 3.831A pdb=" N ARG B 14 " --> pdb=" O LEU B 10 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLU B 19 " --> pdb=" O ALA B 15 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LYS B 21 " --> pdb=" O LEU B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 43 removed outlier: 3.567A pdb=" N ARG B 41 " --> pdb=" O ARG B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 76 removed outlier: 3.767A pdb=" N VAL B 65 " --> pdb=" O ARG B 61 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE B 66 " --> pdb=" O ASP B 62 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N HIS B 71 " --> pdb=" O ARG B 67 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ILE B 72 " --> pdb=" O ARG B 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 11 removed outlier: 3.917A pdb=" N LYS C 10 " --> pdb=" O GLU C 6 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ILE C 11 " --> pdb=" O ARG C 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 6 through 11' Processing helix chain 'C' and resid 11 through 16 Processing helix chain 'C' and resid 36 through 50 removed outlier: 3.876A pdb=" N THR C 40 " --> pdb=" O ASP C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 61 removed outlier: 3.954A pdb=" N GLU C 61 " --> pdb=" O GLU C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 74 removed outlier: 3.772A pdb=" N TYR C 72 " --> pdb=" O ALA C 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 45 removed outlier: 4.098A pdb=" N HIS D 42 " --> pdb=" O LYS D 38 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N TYR D 43 " --> pdb=" O VAL D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 109 removed outlier: 3.537A pdb=" N ALA D 100 " --> pdb=" O GLY D 96 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR D 106 " --> pdb=" O SER D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 112 No H-bonds generated for 'chain 'D' and resid 110 through 112' Processing helix chain 'D' and resid 115 through 120 Processing helix chain 'D' and resid 121 through 129 removed outlier: 3.503A pdb=" N ILE D 125 " --> pdb=" O LYS D 121 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS D 127 " --> pdb=" O THR D 123 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU D 128 " --> pdb=" O ASP D 124 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU D 129 " --> pdb=" O ILE D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 135 Processing helix chain 'D' and resid 136 through 153 removed outlier: 4.163A pdb=" N ALA D 142 " --> pdb=" O CYS D 138 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU D 143 " --> pdb=" O SER D 139 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA D 145 " --> pdb=" O LEU D 141 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 78 removed outlier: 3.502A pdb=" N LEU E 74 " --> pdb=" O ASP E 70 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ALA E 76 " --> pdb=" O ARG E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 83 Processing helix chain 'E' and resid 99 through 115 removed outlier: 3.864A pdb=" N ARG E 107 " --> pdb=" O MET E 103 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLN E 108 " --> pdb=" O GLU E 104 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU E 113 " --> pdb=" O GLN E 109 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE E 114 " --> pdb=" O VAL E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 119 No H-bonds generated for 'chain 'E' and resid 117 through 119' Processing helix chain 'E' and resid 126 through 134 Processing helix chain 'E' and resid 135 through 142 Processing helix chain 'E' and resid 156 through 167 removed outlier: 3.915A pdb=" N SER E 162 " --> pdb=" O CYS E 158 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER E 165 " --> pdb=" O ASP E 161 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU E 166 " --> pdb=" O SER E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 170 No H-bonds generated for 'chain 'E' and resid 168 through 170' Processing helix chain 'E' and resid 185 through 193 Processing helix chain 'E' and resid 215 through 225 removed outlier: 3.947A pdb=" N ILE E 221 " --> pdb=" O GLU E 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 291 Processing helix chain 'E' and resid 297 through 309 removed outlier: 4.091A pdb=" N GLY E 303 " --> pdb=" O PRO E 299 " (cutoff:3.500A) Processing helix chain 'E' and resid 309 through 314 removed outlier: 4.047A pdb=" N GLN E 313 " --> pdb=" O GLU E 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 314 through 337 removed outlier: 3.599A pdb=" N HIS E 319 " --> pdb=" O MET E 315 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS E 320 " --> pdb=" O GLU E 316 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LYS E 324 " --> pdb=" O LYS E 320 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLU E 327 " --> pdb=" O SER E 323 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ASN E 332 " --> pdb=" O ARG E 328 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE E 333 " --> pdb=" O LEU E 329 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER E 336 " --> pdb=" O ASN E 332 " (cutoff:3.500A) Processing helix chain 'E' and resid 363 through 368 Processing helix chain 'E' and resid 389 through 395 Processing helix chain 'E' and resid 398 through 402 removed outlier: 3.902A pdb=" N ALA E 402 " --> pdb=" O GLU E 399 " (cutoff:3.500A) Processing helix chain 'E' and resid 415 through 426 removed outlier: 3.792A pdb=" N VAL E 419 " --> pdb=" O THR E 415 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLU E 424 " --> pdb=" O ASP E 420 " (cutoff:3.500A) Processing helix chain 'F' and resid 6 through 21 removed outlier: 3.815A pdb=" N ARG F 14 " --> pdb=" O LEU F 10 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLU F 19 " --> pdb=" O ALA F 15 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER F 20 " --> pdb=" O MET F 16 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LYS F 21 " --> pdb=" O LEU F 17 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 43 removed outlier: 3.574A pdb=" N ARG F 41 " --> pdb=" O ARG F 37 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 76 removed outlier: 3.775A pdb=" N VAL F 65 " --> pdb=" O ARG F 61 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ILE F 66 " --> pdb=" O ASP F 62 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N HIS F 71 " --> pdb=" O ARG F 67 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE F 72 " --> pdb=" O ARG F 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 11 removed outlier: 3.918A pdb=" N LYS G 10 " --> pdb=" O GLU G 6 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ILE G 11 " --> pdb=" O ARG G 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 6 through 11' Processing helix chain 'G' and resid 11 through 16 Processing helix chain 'G' and resid 36 through 50 removed outlier: 3.877A pdb=" N THR G 40 " --> pdb=" O ASP G 36 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 61 removed outlier: 3.954A pdb=" N GLU G 61 " --> pdb=" O GLU G 58 " (cutoff:3.500A) Processing helix chain 'G' and resid 66 through 74 removed outlier: 3.772A pdb=" N TYR G 72 " --> pdb=" O ALA G 68 " (cutoff:3.500A) Processing helix chain 'H' and resid 36 through 45 removed outlier: 4.097A pdb=" N HIS H 42 " --> pdb=" O LYS H 38 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N TYR H 43 " --> pdb=" O VAL H 39 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 109 removed outlier: 3.535A pdb=" N ALA H 100 " --> pdb=" O GLY H 96 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR H 106 " --> pdb=" O SER H 102 " (cutoff:3.500A) Processing helix chain 'H' and resid 110 through 112 No H-bonds generated for 'chain 'H' and resid 110 through 112' Processing helix chain 'H' and resid 115 through 120 Processing helix chain 'H' and resid 121 through 129 removed outlier: 3.503A pdb=" N ILE H 125 " --> pdb=" O LYS H 121 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS H 127 " --> pdb=" O THR H 123 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU H 128 " --> pdb=" O ASP H 124 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU H 129 " --> pdb=" O ILE H 125 " (cutoff:3.500A) Processing helix chain 'H' and resid 132 through 135 Processing helix chain 'H' and resid 136 through 153 removed outlier: 4.163A pdb=" N ALA H 142 " --> pdb=" O CYS H 138 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU H 143 " --> pdb=" O SER H 139 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA H 145 " --> pdb=" O LEU H 141 " (cutoff:3.500A) Processing helix chain 'I' and resid 91 through 103 removed outlier: 3.701A pdb=" N GLU I 96 " --> pdb=" O GLU I 92 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ARG I 97 " --> pdb=" O THR I 93 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLU I 100 " --> pdb=" O GLU I 96 " (cutoff:3.500A) Processing helix chain 'I' and resid 103 through 111 removed outlier: 3.955A pdb=" N PHE I 109 " --> pdb=" O SER I 105 " (cutoff:3.500A) Processing helix chain 'I' and resid 112 through 116 removed outlier: 3.908A pdb=" N ASP I 115 " --> pdb=" O ASP I 112 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LYS I 116 " --> pdb=" O LEU I 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 112 through 116' Processing helix chain 'I' and resid 181 through 195 removed outlier: 4.053A pdb=" N ALA I 187 " --> pdb=" O HIS I 183 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA I 188 " --> pdb=" O GLU I 184 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU I 190 " --> pdb=" O LEU I 186 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ALA I 193 " --> pdb=" O GLU I 189 " (cutoff:3.500A) Processing helix chain 'J' and resid 91 through 103 removed outlier: 3.689A pdb=" N GLU J 96 " --> pdb=" O GLU J 92 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ARG J 97 " --> pdb=" O THR J 93 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLU J 100 " --> pdb=" O GLU J 96 " (cutoff:3.500A) Processing helix chain 'J' and resid 103 through 111 removed outlier: 4.005A pdb=" N PHE J 109 " --> pdb=" O SER J 105 " (cutoff:3.500A) Processing helix chain 'J' and resid 112 through 116 removed outlier: 3.900A pdb=" N ASP J 115 " --> pdb=" O ASP J 112 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LYS J 116 " --> pdb=" O LEU J 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 112 through 116' Processing helix chain 'J' and resid 181 through 195 removed outlier: 4.104A pdb=" N ALA J 187 " --> pdb=" O HIS J 183 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA J 188 " --> pdb=" O GLU J 184 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU J 190 " --> pdb=" O LEU J 186 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ALA J 193 " --> pdb=" O GLU J 189 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 121 through 124 removed outlier: 3.555A pdb=" N THR A 124 " --> pdb=" O GLY A 266 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N PHE A 229 " --> pdb=" O LEU A 251 " (cutoff:3.500A) removed outlier: 8.519A pdb=" N SER A 253 " --> pdb=" O PHE A 229 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N THR A 231 " --> pdb=" O SER A 253 " (cutoff:3.500A) removed outlier: 9.210A pdb=" N SER A 255 " --> pdb=" O THR A 231 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N HIS A 230 " --> pdb=" O SER A 198 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N VAL A 200 " --> pdb=" O HIS A 230 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N ASP A 232 " --> pdb=" O VAL A 200 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N HIS A 148 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 8.762A pdb=" N SER A 201 " --> pdb=" O HIS A 148 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ILE A 150 " --> pdb=" O SER A 201 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N LEU A 149 " --> pdb=" O THR A 174 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N LEU A 176 " --> pdb=" O LEU A 149 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N THR A 151 " --> pdb=" O LEU A 176 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 340 through 342 Processing sheet with id=AA3, first strand: chain 'D' and resid 62 through 66 removed outlier: 3.771A pdb=" N ASP D 71 " --> pdb=" O ALA D 66 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N LYS D 74 " --> pdb=" O PHE D 90 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N PHE D 90 " --> pdb=" O LYS D 74 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N GLN D 76 " --> pdb=" O ALA D 88 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ALA D 88 " --> pdb=" O GLN D 76 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N GLN D 78 " --> pdb=" O VAL D 86 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 121 through 124 removed outlier: 3.557A pdb=" N THR E 124 " --> pdb=" O GLY E 266 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N PHE E 229 " --> pdb=" O LEU E 251 " (cutoff:3.500A) removed outlier: 8.507A pdb=" N SER E 253 " --> pdb=" O PHE E 229 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N THR E 231 " --> pdb=" O SER E 253 " (cutoff:3.500A) removed outlier: 9.196A pdb=" N SER E 255 " --> pdb=" O THR E 231 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N HIS E 230 " --> pdb=" O SER E 198 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N VAL E 200 " --> pdb=" O HIS E 230 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N ASP E 232 " --> pdb=" O VAL E 200 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N HIS E 148 " --> pdb=" O LEU E 199 " (cutoff:3.500A) removed outlier: 8.765A pdb=" N SER E 201 " --> pdb=" O HIS E 148 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ILE E 150 " --> pdb=" O SER E 201 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N LEU E 149 " --> pdb=" O THR E 174 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N LEU E 176 " --> pdb=" O LEU E 149 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N THR E 151 " --> pdb=" O LEU E 176 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 340 through 342 Processing sheet with id=AA6, first strand: chain 'H' and resid 62 through 66 removed outlier: 3.770A pdb=" N ASP H 71 " --> pdb=" O ALA H 66 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N LYS H 74 " --> pdb=" O PHE H 90 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N PHE H 90 " --> pdb=" O LYS H 74 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N GLN H 76 " --> pdb=" O ALA H 88 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ALA H 88 " --> pdb=" O GLN H 76 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N GLN H 78 " --> pdb=" O VAL H 86 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'I' and resid 131 through 135 removed outlier: 3.527A pdb=" N VAL I 144 " --> pdb=" O SER I 157 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'J' and resid 131 through 132 removed outlier: 3.543A pdb=" N VAL J 144 " --> pdb=" O SER J 157 " (cutoff:3.500A) 430 hydrogen bonds defined for protein. 1222 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: 3.37 Time building geometry restraints manager: 4.00 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: 2999 1.33 - 1.45: 2540 1.45 - 1.57: 7145 1.57 - 1.69: 4 1.69 - 1.81: 94 Bond restraints: 12782 Sorted by residual: bond pdb=" O27 8Q1 G 101 " pdb=" P24 8Q1 G 101 " ideal model delta sigma weight residual 1.678 1.609 0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" O27 8Q1 C 101 " pdb=" P24 8Q1 C 101 " ideal model delta sigma weight residual 1.678 1.609 0.069 2.00e-02 2.50e+03 1.19e+01 bond pdb=" C2 PLP A 501 " pdb=" N1 PLP A 501 " ideal model delta sigma weight residual 1.380 1.328 0.052 2.00e-02 2.50e+03 6.81e+00 bond pdb=" C2 PLP E 501 " pdb=" N1 PLP E 501 " ideal model delta sigma weight residual 1.380 1.328 0.052 2.00e-02 2.50e+03 6.81e+00 bond pdb=" CG1 ILE A 268 " pdb=" CD1 ILE A 268 " ideal model delta sigma weight residual 1.513 1.411 0.102 3.90e-02 6.57e+02 6.78e+00 ... (remaining 12777 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.29: 15605 1.29 - 2.58: 1323 2.58 - 3.87: 232 3.87 - 5.15: 85 5.15 - 6.44: 27 Bond angle restraints: 17272 Sorted by residual: angle pdb=" C TYR B 28 " pdb=" N ARG B 29 " pdb=" CA ARG B 29 " ideal model delta sigma weight residual 120.54 125.19 -4.65 1.35e+00 5.49e-01 1.19e+01 angle pdb=" N LEU E 449 " pdb=" CA LEU E 449 " pdb=" CB LEU E 449 " ideal model delta sigma weight residual 113.65 108.75 4.90 1.47e+00 4.63e-01 1.11e+01 angle pdb=" C THR E 382 " pdb=" N SER E 383 " pdb=" CA SER E 383 " ideal model delta sigma weight residual 121.54 127.70 -6.16 1.91e+00 2.74e-01 1.04e+01 angle pdb=" CA ARG B 29 " pdb=" C ARG B 29 " pdb=" O ARG B 29 " ideal model delta sigma weight residual 120.90 117.97 2.93 1.07e+00 8.73e-01 7.47e+00 angle pdb=" C GLU A 362 " pdb=" N GLY A 363 " pdb=" CA GLY A 363 " ideal model delta sigma weight residual 121.41 126.66 -5.25 1.96e+00 2.60e-01 7.16e+00 ... (remaining 17267 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.11: 7531 28.11 - 56.22: 272 56.22 - 84.32: 23 84.32 - 112.43: 2 112.43 - 140.54: 10 Dihedral angle restraints: 7838 sinusoidal: 3206 harmonic: 4632 Sorted by residual: dihedral pdb=" C5A PLP E 501 " pdb=" O4P PLP E 501 " pdb=" P PLP E 501 " pdb=" O1P PLP E 501 " ideal model delta sinusoidal sigma weight residual 76.43 -62.74 139.17 1 2.00e+01 2.50e-03 4.22e+01 dihedral pdb=" C5A PLP A 501 " pdb=" O4P PLP A 501 " pdb=" P PLP A 501 " pdb=" O1P PLP A 501 " ideal model delta sinusoidal sigma weight residual 76.43 -61.11 137.54 1 2.00e+01 2.50e-03 4.17e+01 dihedral pdb=" CA ALA J 204 " pdb=" C ALA J 204 " pdb=" N TYR J 205 " pdb=" CA TYR J 205 " ideal model delta harmonic sigma weight residual 180.00 -150.70 -29.30 0 5.00e+00 4.00e-02 3.43e+01 ... (remaining 7835 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1218 0.049 - 0.098: 547 0.098 - 0.147: 170 0.147 - 0.196: 12 0.196 - 0.246: 3 Chirality restraints: 1950 Sorted by residual: chirality pdb=" CG LEU E 251 " pdb=" CB LEU E 251 " pdb=" CD1 LEU E 251 " pdb=" CD2 LEU E 251 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" CG LEU A 251 " pdb=" CB LEU A 251 " pdb=" CD1 LEU A 251 " pdb=" CD2 LEU A 251 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CB VAL A 265 " pdb=" CA VAL A 265 " pdb=" CG1 VAL A 265 " pdb=" CG2 VAL A 265 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 9.82e-01 ... (remaining 1947 not shown) Planarity restraints: 2216 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C38 8Q1 C 101 " 0.048 2.00e-02 2.50e+03 5.10e-02 3.25e+01 pdb=" C39 8Q1 C 101 " -0.021 2.00e-02 2.50e+03 pdb=" C42 8Q1 C 101 " 0.062 2.00e-02 2.50e+03 pdb=" N41 8Q1 C 101 " -0.080 2.00e-02 2.50e+03 pdb=" O40 8Q1 C 101 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C38 8Q1 G 101 " 0.047 2.00e-02 2.50e+03 5.09e-02 3.24e+01 pdb=" C39 8Q1 G 101 " -0.021 2.00e-02 2.50e+03 pdb=" C42 8Q1 G 101 " 0.061 2.00e-02 2.50e+03 pdb=" N41 8Q1 G 101 " -0.080 2.00e-02 2.50e+03 pdb=" O40 8Q1 G 101 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG E 273 " -0.043 5.00e-02 4.00e+02 6.48e-02 6.71e+00 pdb=" N PRO E 274 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO E 274 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO E 274 " -0.037 5.00e-02 4.00e+02 ... (remaining 2213 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 129 2.63 - 3.19: 11105 3.19 - 3.76: 17423 3.76 - 4.33: 26542 4.33 - 4.90: 44845 Nonbonded interactions: 100044 Sorted by model distance: nonbonded pdb=" O LEU H 52 " pdb=" OD1 ASP H 53 " model vdw 2.057 3.040 nonbonded pdb=" O LEU D 52 " pdb=" OD1 ASP D 53 " model vdw 2.057 3.040 nonbonded pdb=" O VAL H 72 " pdb=" OG1 THR H 92 " model vdw 2.196 3.040 nonbonded pdb=" O PRO H 133 " pdb=" OG SER J 157 " model vdw 2.197 3.040 nonbonded pdb=" O VAL D 72 " pdb=" OG1 THR D 92 " model vdw 2.201 3.040 ... (remaining 100039 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: 0.04 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 56 through 104 or resid 106 through 457 or resid 501)) selection = (chain 'E' and (resid 56 through 104 or resid 106 through 457 or resid 501)) } ncs_group { reference = (chain 'B' and (resid 5 through 70 or resid 72 through 85)) selection = (chain 'F' and (resid 5 through 70 or resid 72 through 85)) } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = (chain 'I' and (resid 90 through 134 or resid 136 through 207)) selection = (chain 'J' and (resid 90 through 134 or resid 136 through 207)) } 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=0.50 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: 14.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.120 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 39.740 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.070 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 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 : 0.018 0.901 12791 Z= 0.990 Angle : 0.857 6.443 17272 Z= 0.437 Chirality : 0.057 0.246 1950 Planarity : 0.005 0.065 2216 Dihedral : 15.220 140.538 4858 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 2.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % 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: -5.92 (0.15), residues: 1574 helix: -4.61 (0.09), residues: 682 sheet: -3.15 (0.31), residues: 220 loop : -3.24 (0.19), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP I 173 HIS 0.006 0.001 HIS E 230 PHE 0.020 0.002 PHE B 23 TYR 0.015 0.002 TYR D 35 ARG 0.005 0.001 ARG F 14 Details of bonding type rmsd hydrogen bonds : bond 0.33122 ( 430) hydrogen bonds : angle 11.05944 ( 1222) metal coordination : bond 0.53484 ( 4) covalent geometry : bond 0.01311 (12782) covalent geometry : angle 0.85711 (17272) Misc. bond : bond 0.40479 ( 5) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 2.440 Fit side-chains REVERT: A 119 ARG cc_start: 0.8225 (mtm180) cc_final: 0.7802 (mtm180) REVERT: A 223 SER cc_start: 0.8549 (t) cc_final: 0.8321 (p) REVERT: D 57 LYS cc_start: 0.7620 (tttt) cc_final: 0.7359 (tppt) REVERT: E 119 ARG cc_start: 0.8237 (mtm180) cc_final: 0.7775 (mtm180) REVERT: E 385 SER cc_start: 0.9094 (t) cc_final: 0.8814 (p) REVERT: H 115 GLU cc_start: 0.7184 (pt0) cc_final: 0.6884 (mp0) REVERT: I 198 LEU cc_start: 0.8068 (mm) cc_final: 0.7683 (mt) outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 0.4027 time to fit residues: 89.3769 Evaluate side-chains 116 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 1.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 5.9990 chunk 118 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 79 optimal weight: 0.8980 chunk 63 optimal weight: 4.9990 chunk 122 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 91 optimal weight: 0.0050 chunk 141 optimal weight: 5.9990 overall best weight: 1.1398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 HIS A 429 HIS A 456 GLN D 48 ASN E 156 HIS E 429 HIS I 153 GLN J 153 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.146093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.112741 restraints weight = 33935.979| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 4.79 r_work: 0.2661 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2640 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2640 r_free = 0.2640 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2640 r_free = 0.2640 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2640 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12791 Z= 0.130 Angle : 0.586 8.079 17272 Z= 0.298 Chirality : 0.044 0.135 1950 Planarity : 0.005 0.052 2216 Dihedral : 9.786 136.117 1800 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 0.81 % Allowed : 8.06 % Favored : 91.13 % 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: -4.25 (0.17), residues: 1574 helix: -2.90 (0.15), residues: 702 sheet: -2.57 (0.30), residues: 240 loop : -2.58 (0.21), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP I 173 HIS 0.003 0.001 HIS H 42 PHE 0.012 0.001 PHE D 93 TYR 0.013 0.001 TYR F 28 ARG 0.003 0.001 ARG A 393 Details of bonding type rmsd hydrogen bonds : bond 0.04350 ( 430) hydrogen bonds : angle 5.14274 ( 1222) metal coordination : bond 0.00661 ( 4) covalent geometry : bond 0.00288 (12782) covalent geometry : angle 0.58553 (17272) Misc. bond : bond 0.00086 ( 5) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 149 time to evaluate : 1.294 Fit side-chains REVERT: A 119 ARG cc_start: 0.8834 (mtm180) cc_final: 0.8453 (mtm180) REVERT: A 155 GLU cc_start: 0.8888 (mm-30) cc_final: 0.8639 (tp30) REVERT: A 364 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.6805 (mm-30) REVERT: D 57 LYS cc_start: 0.7798 (tttt) cc_final: 0.7387 (tptt) REVERT: E 119 ARG cc_start: 0.8819 (mtm180) cc_final: 0.8444 (mtm180) REVERT: E 145 ARG cc_start: 0.8163 (ptp90) cc_final: 0.7928 (ptp90) REVERT: E 155 GLU cc_start: 0.8906 (mm-30) cc_final: 0.8654 (tp30) REVERT: E 364 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.6838 (mm-30) REVERT: E 385 SER cc_start: 0.9173 (t) cc_final: 0.8684 (p) REVERT: I 198 LEU cc_start: 0.8115 (mm) cc_final: 0.7712 (mt) REVERT: J 152 LYS cc_start: 0.8432 (mmtm) cc_final: 0.8144 (mmtt) outliers start: 11 outliers final: 2 residues processed: 155 average time/residue: 0.3408 time to fit residues: 70.4173 Evaluate side-chains 130 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 126 time to evaluate : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 364 GLU Chi-restraints excluded: chain I residue 142 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 92 optimal weight: 4.9990 chunk 47 optimal weight: 0.0670 chunk 120 optimal weight: 20.0000 chunk 42 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 114 optimal weight: 0.3980 chunk 51 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 70 optimal weight: 5.9990 chunk 86 optimal weight: 5.9990 overall best weight: 0.6922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 456 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.145258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.113286 restraints weight = 32487.428| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 4.12 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3166 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3166 r_free = 0.3166 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3166 r_free = 0.3166 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3166 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 12791 Z= 0.096 Angle : 0.504 6.822 17272 Z= 0.254 Chirality : 0.042 0.131 1950 Planarity : 0.004 0.054 2216 Dihedral : 7.864 138.039 1800 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 0.88 % Allowed : 10.41 % Favored : 88.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.04 (0.19), residues: 1574 helix: -1.70 (0.18), residues: 706 sheet: -2.12 (0.31), residues: 240 loop : -2.14 (0.21), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP I 168 HIS 0.002 0.001 HIS H 42 PHE 0.006 0.001 PHE D 93 TYR 0.012 0.001 TYR D 43 ARG 0.002 0.000 ARG B 37 Details of bonding type rmsd hydrogen bonds : bond 0.03592 ( 430) hydrogen bonds : angle 4.43795 ( 1222) metal coordination : bond 0.00560 ( 4) covalent geometry : bond 0.00206 (12782) covalent geometry : angle 0.50429 (17272) Misc. bond : bond 0.00038 ( 5) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 140 time to evaluate : 1.344 Fit side-chains REVERT: A 119 ARG cc_start: 0.8236 (mtm180) cc_final: 0.8000 (mtm180) REVERT: A 364 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.6962 (mm-30) REVERT: A 385 SER cc_start: 0.8967 (t) cc_final: 0.8713 (p) REVERT: C 39 ASP cc_start: 0.8001 (OUTLIER) cc_final: 0.7792 (m-30) REVERT: D 57 LYS cc_start: 0.7672 (tttt) cc_final: 0.7466 (tptt) REVERT: E 119 ARG cc_start: 0.8211 (mtm180) cc_final: 0.7981 (mtm180) REVERT: E 364 GLU cc_start: 0.7542 (OUTLIER) cc_final: 0.6799 (mm-30) REVERT: E 436 MET cc_start: 0.8241 (ttm) cc_final: 0.8000 (ttm) REVERT: G 39 ASP cc_start: 0.8062 (OUTLIER) cc_final: 0.7790 (m-30) outliers start: 12 outliers final: 3 residues processed: 147 average time/residue: 0.3363 time to fit residues: 66.6281 Evaluate side-chains 132 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 125 time to evaluate : 1.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 LYS Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain E residue 364 GLU Chi-restraints excluded: chain G residue 39 ASP Chi-restraints excluded: chain H residue 59 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/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-5710/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-5710/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-5710/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-5710/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-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/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-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 60.2854 > 50: distance: 28 - 31: 14.660 distance: 31 - 32: 11.679 distance: 32 - 33: 12.712 distance: 32 - 35: 7.386 distance: 33 - 34: 14.419 distance: 33 - 39: 10.185 distance: 35 - 36: 32.816 distance: 36 - 37: 25.134 distance: 36 - 38: 17.868 distance: 39 - 40: 14.036 distance: 40 - 41: 24.144 distance: 40 - 43: 8.978 distance: 41 - 42: 21.278 distance: 41 - 45: 17.518 distance: 43 - 44: 23.274 distance: 45 - 46: 9.884 distance: 46 - 47: 39.664 distance: 46 - 49: 12.837 distance: 47 - 48: 13.553 distance: 47 - 51: 25.238 distance: 49 - 50: 19.321 distance: 51 - 52: 48.203 distance: 52 - 53: 17.907 distance: 53 - 54: 50.074 distance: 53 - 55: 38.649 distance: 55 - 56: 37.372 distance: 56 - 57: 44.733 distance: 56 - 59: 26.602 distance: 57 - 58: 41.136 distance: 57 - 61: 43.621 distance: 59 - 60: 33.017 distance: 61 - 62: 15.017 distance: 62 - 63: 10.062 distance: 62 - 65: 21.304 distance: 63 - 64: 18.228 distance: 63 - 66: 30.853 distance: 66 - 67: 25.476 distance: 67 - 68: 58.428 distance: 67 - 70: 16.035 distance: 68 - 72: 46.165 distance: 70 - 71: 22.101 distance: 72 - 73: 20.866 distance: 73 - 74: 15.280 distance: 73 - 76: 16.603 distance: 74 - 75: 30.673 distance: 74 - 79: 13.708 distance: 76 - 77: 12.839 distance: 76 - 78: 17.146 distance: 79 - 80: 12.352 distance: 80 - 81: 15.623 distance: 80 - 83: 16.734 distance: 81 - 82: 27.539 distance: 81 - 85: 24.074 distance: 83 - 84: 21.132 distance: 85 - 86: 20.597 distance: 86 - 87: 10.048 distance: 86 - 89: 14.193 distance: 87 - 88: 6.887 distance: 87 - 90: 8.028