Starting phenix.real_space_refine on Mon Mar 18 01:37:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6m_25719/03_2024/7t6m_25719_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6m_25719/03_2024/7t6m_25719.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6m_25719/03_2024/7t6m_25719_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6m_25719/03_2024/7t6m_25719_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6m_25719/03_2024/7t6m_25719_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6m_25719/03_2024/7t6m_25719.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6m_25719/03_2024/7t6m_25719.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6m_25719/03_2024/7t6m_25719_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6m_25719/03_2024/7t6m_25719_updated.pdb" } resolution = 2.8 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= 0.007 sd= 0.081 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 12 5.49 5 S 140 5.16 5 C 12648 2.51 5 N 3284 2.21 5 O 3516 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 108": "OE1" <-> "OE2" Residue "A PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 289": "OE1" <-> "OE2" Residue "A GLU 303": "OE1" <-> "OE2" Residue "A TYR 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 406": "OD1" <-> "OD2" Residue "A ASP 525": "OD1" <-> "OD2" Residue "A PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 621": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 108": "OE1" <-> "OE2" Residue "B PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 289": "OE1" <-> "OE2" Residue "B GLU 303": "OE1" <-> "OE2" Residue "B TYR 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 406": "OD1" <-> "OD2" Residue "B ASP 525": "OD1" <-> "OD2" Residue "B PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 30": "OE1" <-> "OE2" Residue "C ASP 46": "OD1" <-> "OD2" Residue "C GLU 104": "OE1" <-> "OE2" Residue "C GLU 108": "OE1" <-> "OE2" Residue "C PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 289": "OE1" <-> "OE2" Residue "C TYR 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 406": "OD1" <-> "OD2" Residue "C PHE 408": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 525": "OD1" <-> "OD2" Residue "C PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 627": "OD1" <-> "OD2" Residue "D GLU 104": "OE1" <-> "OE2" Residue "D GLU 108": "OE1" <-> "OE2" Residue "D PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 289": "OE1" <-> "OE2" Residue "D GLU 303": "OE1" <-> "OE2" Residue "D TYR 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 406": "OD1" <-> "OD2" Residue "D ASP 525": "OD1" <-> "OD2" Residue "D PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 627": "OD1" <-> "OD2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 19600 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4853 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 24, 'TRANS': 581} Chain breaks: 1 Chain: "B" Number of atoms: 4853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4853 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 24, 'TRANS': 581} Chain breaks: 1 Chain: "C" Number of atoms: 4853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4853 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 24, 'TRANS': 581} Chain breaks: 1 Chain: "D" Number of atoms: 4853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4853 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 24, 'TRANS': 581} Chain breaks: 1 Chain: "A" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 47 Unusual residues: {'PIO': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 47 Unusual residues: {'PIO': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 47 Unusual residues: {'PIO': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 47 Unusual residues: {'PIO': 1} Classifications: {'undetermined': 1} Time building chain proxies: 10.17, per 1000 atoms: 0.52 Number of scatterers: 19600 At special positions: 0 Unit cell: (120.84, 119.78, 120.84, 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 140 16.00 P 12 15.00 O 3516 8.00 N 3284 7.00 C 12648 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 8.01 Conformation dependent library (CDL) restraints added in 2.8 seconds 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4576 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 116 helices and 8 sheets defined 57.2% alpha, 3.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.78 Creating SS restraints... Processing helix chain 'A' and resid 30 through 46 Processing helix chain 'A' and resid 48 through 55 Processing helix chain 'A' and resid 82 through 88 Processing helix chain 'A' and resid 92 through 101 Processing helix chain 'A' and resid 103 through 105 No H-bonds generated for 'chain 'A' and resid 103 through 105' Processing helix chain 'A' and resid 113 through 115 No H-bonds generated for 'chain 'A' and resid 113 through 115' Processing helix chain 'A' and resid 120 through 127 Processing helix chain 'A' and resid 130 through 138 Processing helix chain 'A' and resid 166 through 173 Processing helix chain 'A' and resid 176 through 184 Processing helix chain 'A' and resid 199 through 205 Processing helix chain 'A' and resid 210 through 221 removed outlier: 4.263A pdb=" N GLN A 214 " --> pdb=" O THR A 210 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N MET A 215 " --> pdb=" O PHE A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 249 Processing helix chain 'A' and resid 253 through 261 Processing helix chain 'A' and resid 281 through 284 No H-bonds generated for 'chain 'A' and resid 281 through 284' Processing helix chain 'A' and resid 292 through 297 Processing helix chain 'A' and resid 302 through 309 Processing helix chain 'A' and resid 311 through 323 Processing helix chain 'A' and resid 325 through 348 Processing helix chain 'A' and resid 380 through 408 Proline residue: A 405 - end of helix removed outlier: 3.547A pdb=" N PHE A 408 " --> pdb=" O ILE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 417 removed outlier: 3.791A pdb=" N PHE A 416 " --> pdb=" O ALA A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 444 Processing helix chain 'A' and resid 451 through 471 removed outlier: 3.678A pdb=" N VAL A 465 " --> pdb=" O GLY A 461 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N MET A 466 " --> pdb=" O TRP A 462 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N TYR A 467 " --> pdb=" O CYS A 463 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N PHE A 468 " --> pdb=" O SER A 464 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ALA A 469 " --> pdb=" O VAL A 465 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ARG A 470 " --> pdb=" O MET A 466 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N GLY A 471 " --> pdb=" O TYR A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 486 Proline residue: A 477 - end of helix removed outlier: 4.009A pdb=" N ILE A 480 " --> pdb=" O GLY A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 510 removed outlier: 4.923A pdb=" N TRP A 495 " --> pdb=" O MET A 491 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N LEU A 496 " --> pdb=" O ARG A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 537 Processing helix chain 'A' and resid 553 through 565 Processing helix chain 'A' and resid 570 through 587 Processing helix chain 'A' and resid 589 through 607 Processing helix chain 'B' and resid 30 through 46 Processing helix chain 'B' and resid 48 through 55 Processing helix chain 'B' and resid 82 through 88 Processing helix chain 'B' and resid 92 through 101 Processing helix chain 'B' and resid 103 through 105 No H-bonds generated for 'chain 'B' and resid 103 through 105' Processing helix chain 'B' and resid 113 through 115 No H-bonds generated for 'chain 'B' and resid 113 through 115' Processing helix chain 'B' and resid 120 through 127 Processing helix chain 'B' and resid 130 through 138 Processing helix chain 'B' and resid 166 through 173 Processing helix chain 'B' and resid 176 through 184 Processing helix chain 'B' and resid 199 through 205 Processing helix chain 'B' and resid 210 through 221 removed outlier: 4.172A pdb=" N GLN B 214 " --> pdb=" O THR B 210 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N MET B 215 " --> pdb=" O PHE B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 249 Processing helix chain 'B' and resid 253 through 261 Processing helix chain 'B' and resid 281 through 284 No H-bonds generated for 'chain 'B' and resid 281 through 284' Processing helix chain 'B' and resid 292 through 297 Processing helix chain 'B' and resid 302 through 309 Processing helix chain 'B' and resid 311 through 323 Processing helix chain 'B' and resid 325 through 348 Processing helix chain 'B' and resid 380 through 408 Proline residue: B 405 - end of helix removed outlier: 3.548A pdb=" N PHE B 408 " --> pdb=" O ILE B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 417 removed outlier: 3.790A pdb=" N PHE B 416 " --> pdb=" O ALA B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 444 Processing helix chain 'B' and resid 451 through 471 removed outlier: 3.672A pdb=" N VAL B 465 " --> pdb=" O GLY B 461 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N MET B 466 " --> pdb=" O TRP B 462 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N TYR B 467 " --> pdb=" O CYS B 463 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N PHE B 468 " --> pdb=" O SER B 464 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ALA B 469 " --> pdb=" O VAL B 465 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ARG B 470 " --> pdb=" O MET B 466 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N GLY B 471 " --> pdb=" O TYR B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 486 Proline residue: B 477 - end of helix removed outlier: 4.013A pdb=" N ILE B 480 " --> pdb=" O GLY B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 490 through 510 removed outlier: 4.925A pdb=" N TRP B 495 " --> pdb=" O MET B 491 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N LEU B 496 " --> pdb=" O ARG B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 537 Processing helix chain 'B' and resid 553 through 565 Processing helix chain 'B' and resid 570 through 587 Processing helix chain 'B' and resid 589 through 607 Processing helix chain 'C' and resid 30 through 46 Processing helix chain 'C' and resid 48 through 55 Processing helix chain 'C' and resid 82 through 88 Processing helix chain 'C' and resid 92 through 101 Processing helix chain 'C' and resid 103 through 105 No H-bonds generated for 'chain 'C' and resid 103 through 105' Processing helix chain 'C' and resid 113 through 115 No H-bonds generated for 'chain 'C' and resid 113 through 115' Processing helix chain 'C' and resid 120 through 127 Processing helix chain 'C' and resid 130 through 138 Processing helix chain 'C' and resid 166 through 173 Processing helix chain 'C' and resid 176 through 184 Processing helix chain 'C' and resid 199 through 205 Processing helix chain 'C' and resid 210 through 221 removed outlier: 4.447A pdb=" N GLN C 214 " --> pdb=" O THR C 210 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N MET C 215 " --> pdb=" O PHE C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 249 Processing helix chain 'C' and resid 253 through 261 Processing helix chain 'C' and resid 281 through 284 No H-bonds generated for 'chain 'C' and resid 281 through 284' Processing helix chain 'C' and resid 292 through 297 Processing helix chain 'C' and resid 303 through 309 Processing helix chain 'C' and resid 311 through 323 Processing helix chain 'C' and resid 325 through 348 Processing helix chain 'C' and resid 380 through 408 Proline residue: C 405 - end of helix removed outlier: 3.543A pdb=" N PHE C 408 " --> pdb=" O ILE C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 417 removed outlier: 3.803A pdb=" N PHE C 416 " --> pdb=" O ALA C 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 423 through 444 Processing helix chain 'C' and resid 451 through 471 removed outlier: 3.673A pdb=" N VAL C 465 " --> pdb=" O GLY C 461 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N MET C 466 " --> pdb=" O TRP C 462 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N TYR C 467 " --> pdb=" O CYS C 463 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N PHE C 468 " --> pdb=" O SER C 464 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ALA C 469 " --> pdb=" O VAL C 465 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ARG C 470 " --> pdb=" O MET C 466 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N GLY C 471 " --> pdb=" O TYR C 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 486 Proline residue: C 477 - end of helix removed outlier: 4.008A pdb=" N ILE C 480 " --> pdb=" O GLY C 476 " (cutoff:3.500A) Processing helix chain 'C' and resid 490 through 510 removed outlier: 4.936A pdb=" N TRP C 495 " --> pdb=" O MET C 491 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N LEU C 496 " --> pdb=" O ARG C 492 " (cutoff:3.500A) Processing helix chain 'C' and resid 526 through 537 Processing helix chain 'C' and resid 553 through 565 Processing helix chain 'C' and resid 570 through 587 Processing helix chain 'C' and resid 589 through 607 Processing helix chain 'D' and resid 30 through 46 Processing helix chain 'D' and resid 48 through 55 Processing helix chain 'D' and resid 82 through 88 Processing helix chain 'D' and resid 92 through 101 Processing helix chain 'D' and resid 103 through 105 No H-bonds generated for 'chain 'D' and resid 103 through 105' Processing helix chain 'D' and resid 113 through 115 No H-bonds generated for 'chain 'D' and resid 113 through 115' Processing helix chain 'D' and resid 120 through 127 Processing helix chain 'D' and resid 130 through 138 Processing helix chain 'D' and resid 166 through 173 Processing helix chain 'D' and resid 176 through 184 Processing helix chain 'D' and resid 199 through 205 Processing helix chain 'D' and resid 210 through 221 removed outlier: 4.263A pdb=" N GLN D 214 " --> pdb=" O THR D 210 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N MET D 215 " --> pdb=" O PHE D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 249 Processing helix chain 'D' and resid 253 through 261 Processing helix chain 'D' and resid 281 through 284 No H-bonds generated for 'chain 'D' and resid 281 through 284' Processing helix chain 'D' and resid 292 through 297 Processing helix chain 'D' and resid 302 through 309 Processing helix chain 'D' and resid 311 through 323 Processing helix chain 'D' and resid 325 through 348 Processing helix chain 'D' and resid 380 through 408 Proline residue: D 405 - end of helix removed outlier: 3.548A pdb=" N PHE D 408 " --> pdb=" O ILE D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 412 through 417 removed outlier: 3.787A pdb=" N PHE D 416 " --> pdb=" O ALA D 412 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 444 Processing helix chain 'D' and resid 451 through 471 removed outlier: 3.671A pdb=" N VAL D 465 " --> pdb=" O GLY D 461 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N MET D 466 " --> pdb=" O TRP D 462 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N TYR D 467 " --> pdb=" O CYS D 463 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N PHE D 468 " --> pdb=" O SER D 464 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ALA D 469 " --> pdb=" O VAL D 465 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ARG D 470 " --> pdb=" O MET D 466 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N GLY D 471 " --> pdb=" O TYR D 467 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 486 Proline residue: D 477 - end of helix removed outlier: 4.014A pdb=" N ILE D 480 " --> pdb=" O GLY D 476 " (cutoff:3.500A) Processing helix chain 'D' and resid 490 through 510 removed outlier: 4.925A pdb=" N TRP D 495 " --> pdb=" O MET D 491 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N LEU D 496 " --> pdb=" O ARG D 492 " (cutoff:3.500A) Processing helix chain 'D' and resid 526 through 537 Processing helix chain 'D' and resid 553 through 565 Processing helix chain 'D' and resid 570 through 587 Processing helix chain 'D' and resid 589 through 607 Processing sheet with id= A, first strand: chain 'A' and resid 630 through 636 removed outlier: 6.175A pdb=" N LEU A 277 " --> pdb=" O VAL A 266 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N VAL A 266 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ASP A 279 " --> pdb=" O LYS A 264 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LYS A 264 " --> pdb=" O ASP A 279 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 352 through 354 Processing sheet with id= C, first strand: chain 'B' and resid 630 through 636 removed outlier: 6.179A pdb=" N LEU B 277 " --> pdb=" O VAL B 266 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N VAL B 266 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ASP B 279 " --> pdb=" O LYS B 264 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LYS B 264 " --> pdb=" O ASP B 279 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 352 through 354 Processing sheet with id= E, first strand: chain 'C' and resid 630 through 636 removed outlier: 6.173A pdb=" N LEU C 277 " --> pdb=" O VAL C 266 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N VAL C 266 " --> pdb=" O LEU C 277 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASP C 279 " --> pdb=" O LYS C 264 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LYS C 264 " --> pdb=" O ASP C 279 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 352 through 354 Processing sheet with id= G, first strand: chain 'D' and resid 630 through 636 removed outlier: 6.177A pdb=" N LEU D 277 " --> pdb=" O VAL D 266 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N VAL D 266 " --> pdb=" O LEU D 277 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ASP D 279 " --> pdb=" O LYS D 264 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LYS D 264 " --> pdb=" O ASP D 279 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 352 through 354 903 hydrogen bonds defined for protein. 2640 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: 5.96 Time building geometry restraints manager: 8.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3116 1.31 - 1.43: 5435 1.43 - 1.56: 11244 1.56 - 1.68: 25 1.68 - 1.81: 228 Bond restraints: 20048 Sorted by residual: bond pdb=" CB VAL B 598 " pdb=" CG2 VAL B 598 " ideal model delta sigma weight residual 1.521 1.428 0.093 3.30e-02 9.18e+02 8.00e+00 bond pdb=" CB VAL D 598 " pdb=" CG2 VAL D 598 " ideal model delta sigma weight residual 1.521 1.431 0.090 3.30e-02 9.18e+02 7.46e+00 bond pdb=" CB VAL A 598 " pdb=" CG2 VAL A 598 " ideal model delta sigma weight residual 1.521 1.431 0.090 3.30e-02 9.18e+02 7.44e+00 bond pdb=" CB VAL C 598 " pdb=" CG2 VAL C 598 " ideal model delta sigma weight residual 1.521 1.432 0.089 3.30e-02 9.18e+02 7.30e+00 bond pdb=" C THR B 311 " pdb=" N PRO B 312 " ideal model delta sigma weight residual 1.336 1.366 -0.030 1.25e-02 6.40e+03 5.64e+00 ... (remaining 20043 not shown) Histogram of bond angle deviations from ideal: 96.93 - 104.36: 334 104.36 - 111.79: 8783 111.79 - 119.21: 7721 119.21 - 126.64: 10049 126.64 - 134.07: 337 Bond angle restraints: 27224 Sorted by residual: angle pdb=" CA LEU B 61 " pdb=" CB LEU B 61 " pdb=" CG LEU B 61 " ideal model delta sigma weight residual 116.30 133.62 -17.32 3.50e+00 8.16e-02 2.45e+01 angle pdb=" CA LEU D 61 " pdb=" CB LEU D 61 " pdb=" CG LEU D 61 " ideal model delta sigma weight residual 116.30 133.60 -17.30 3.50e+00 8.16e-02 2.44e+01 angle pdb=" CA LEU A 61 " pdb=" CB LEU A 61 " pdb=" CG LEU A 61 " ideal model delta sigma weight residual 116.30 133.54 -17.24 3.50e+00 8.16e-02 2.43e+01 angle pdb=" C GLY A 626 " pdb=" N ASP A 627 " pdb=" CA ASP A 627 " ideal model delta sigma weight residual 122.07 128.79 -6.72 1.43e+00 4.89e-01 2.21e+01 angle pdb=" CA ASP A 627 " pdb=" CB ASP A 627 " pdb=" CG ASP A 627 " ideal model delta sigma weight residual 112.60 116.74 -4.14 1.00e+00 1.00e+00 1.71e+01 ... (remaining 27219 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.30: 10920 20.30 - 40.60: 824 40.60 - 60.90: 114 60.90 - 81.20: 49 81.20 - 101.50: 13 Dihedral angle restraints: 11920 sinusoidal: 4840 harmonic: 7080 Sorted by residual: dihedral pdb=" CA TRP B 29 " pdb=" C TRP B 29 " pdb=" N GLU B 30 " pdb=" CA GLU B 30 " ideal model delta harmonic sigma weight residual -180.00 -150.13 -29.87 0 5.00e+00 4.00e-02 3.57e+01 dihedral pdb=" CA TRP A 29 " pdb=" C TRP A 29 " pdb=" N GLU A 30 " pdb=" CA GLU A 30 " ideal model delta harmonic sigma weight residual -180.00 -150.15 -29.85 0 5.00e+00 4.00e-02 3.57e+01 dihedral pdb=" CA TRP D 29 " pdb=" C TRP D 29 " pdb=" N GLU D 30 " pdb=" CA GLU D 30 " ideal model delta harmonic sigma weight residual -180.00 -150.19 -29.81 0 5.00e+00 4.00e-02 3.55e+01 ... (remaining 11917 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.119: 2922 0.119 - 0.237: 150 0.237 - 0.356: 20 0.356 - 0.475: 4 0.475 - 0.593: 4 Chirality restraints: 3100 Sorted by residual: chirality pdb=" CG LEU C 308 " pdb=" CB LEU C 308 " pdb=" CD1 LEU C 308 " pdb=" CD2 LEU C 308 " both_signs ideal model delta sigma weight residual False -2.59 -2.00 -0.59 2.00e-01 2.50e+01 8.80e+00 chirality pdb=" CG LEU A 308 " pdb=" CB LEU A 308 " pdb=" CD1 LEU A 308 " pdb=" CD2 LEU A 308 " both_signs ideal model delta sigma weight residual False -2.59 -2.03 -0.56 2.00e-01 2.50e+01 7.92e+00 chirality pdb=" CG LEU D 308 " pdb=" CB LEU D 308 " pdb=" CD1 LEU D 308 " pdb=" CD2 LEU D 308 " both_signs ideal model delta sigma weight residual False -2.59 -2.03 -0.56 2.00e-01 2.50e+01 7.77e+00 ... (remaining 3097 not shown) Planarity restraints: 3424 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 29 " 0.023 2.00e-02 2.50e+03 2.05e-02 1.05e+01 pdb=" CG TRP B 29 " -0.055 2.00e-02 2.50e+03 pdb=" CD1 TRP B 29 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP B 29 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 29 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 29 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 29 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 29 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 29 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP B 29 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 29 " 0.023 2.00e-02 2.50e+03 2.05e-02 1.05e+01 pdb=" CG TRP A 29 " -0.055 2.00e-02 2.50e+03 pdb=" CD1 TRP A 29 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP A 29 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 29 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 29 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 29 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 29 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 29 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP A 29 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 29 " 0.023 2.00e-02 2.50e+03 2.03e-02 1.03e+01 pdb=" CG TRP D 29 " -0.055 2.00e-02 2.50e+03 pdb=" CD1 TRP D 29 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP D 29 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP D 29 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP D 29 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 29 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 29 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 29 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP D 29 " 0.002 2.00e-02 2.50e+03 ... (remaining 3421 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 5593 2.82 - 3.34: 18070 3.34 - 3.86: 34180 3.86 - 4.38: 40350 4.38 - 4.90: 68084 Nonbonded interactions: 166277 Sorted by model distance: nonbonded pdb=" O PRO B 544 " pdb=" OH TYR B 555 " model vdw 2.300 2.440 nonbonded pdb=" O PRO C 544 " pdb=" OH TYR C 555 " model vdw 2.300 2.440 nonbonded pdb=" O PRO D 544 " pdb=" OH TYR D 555 " model vdw 2.300 2.440 nonbonded pdb=" O PRO A 544 " pdb=" OH TYR A 555 " model vdw 2.300 2.440 nonbonded pdb=" OG1 THR D 379 " pdb=" OD2 ASP D 382 " model vdw 2.303 2.440 ... (remaining 166272 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 0.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 7.560 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 50.740 Find NCS groups from input model: 1.230 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 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 0.093 20048 Z= 0.412 Angle : 1.073 17.321 27224 Z= 0.561 Chirality : 0.066 0.593 3100 Planarity : 0.008 0.073 3424 Dihedral : 15.210 101.498 7344 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % 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: -2.68 (0.14), residues: 2408 helix: -1.95 (0.10), residues: 1436 sheet: 0.06 (0.49), residues: 92 loop : -1.35 (0.18), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.003 TRP B 29 HIS 0.007 0.002 HIS C 201 PHE 0.034 0.003 PHE B 456 TYR 0.034 0.003 TYR A 621 ARG 0.006 0.001 ARG A 134 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 327 time to evaluate : 1.857 Fit side-chains REVERT: A 51 GLN cc_start: 0.8319 (tp40) cc_final: 0.8039 (mm-40) REVERT: A 260 MET cc_start: 0.8295 (mmm) cc_final: 0.7977 (mmm) REVERT: B 51 GLN cc_start: 0.8293 (tp40) cc_final: 0.8058 (mm-40) REVERT: B 260 MET cc_start: 0.8266 (mmm) cc_final: 0.7949 (mmm) REVERT: C 51 GLN cc_start: 0.8255 (tp40) cc_final: 0.8001 (mm-40) REVERT: C 260 MET cc_start: 0.8274 (mmm) cc_final: 0.7961 (mmm) REVERT: D 51 GLN cc_start: 0.8319 (tp40) cc_final: 0.8061 (mm-40) REVERT: D 260 MET cc_start: 0.8289 (mmm) cc_final: 0.7978 (mmm) outliers start: 0 outliers final: 0 residues processed: 327 average time/residue: 1.3992 time to fit residues: 511.0934 Evaluate side-chains 225 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 225 time to evaluate : 2.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 2.9990 chunk 181 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 62 optimal weight: 4.9990 chunk 122 optimal weight: 0.9990 chunk 97 optimal weight: 6.9990 chunk 188 optimal weight: 10.0000 chunk 72 optimal weight: 4.9990 chunk 114 optimal weight: 2.9990 chunk 140 optimal weight: 0.8980 chunk 217 optimal weight: 4.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 ASN A 261 GLN A 306 GLN A 587 GLN B 129 ASN B 201 HIS B 261 GLN B 306 GLN C 129 ASN C 261 GLN C 306 GLN D 261 GLN D 306 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 20048 Z= 0.248 Angle : 0.577 6.567 27224 Z= 0.293 Chirality : 0.042 0.177 3100 Planarity : 0.005 0.054 3424 Dihedral : 8.881 98.195 2752 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.77 % Allowed : 9.26 % Favored : 88.98 % 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: -0.70 (0.16), residues: 2408 helix: -0.17 (0.13), residues: 1400 sheet: 0.07 (0.51), residues: 92 loop : -0.78 (0.19), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 29 HIS 0.004 0.001 HIS B 201 PHE 0.012 0.001 PHE B 456 TYR 0.013 0.002 TYR A 432 ARG 0.003 0.000 ARG C 75 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 245 time to evaluate : 2.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 GLN cc_start: 0.8067 (mt0) cc_final: 0.7611 (mt0) REVERT: A 466 MET cc_start: 0.8824 (OUTLIER) cc_final: 0.8513 (mtt) REVERT: B 128 GLN cc_start: 0.7993 (mt0) cc_final: 0.7541 (mt0) REVERT: B 309 GLU cc_start: 0.7142 (mt-10) cc_final: 0.6854 (mt-10) REVERT: C 128 GLN cc_start: 0.8006 (mt0) cc_final: 0.7560 (mt0) REVERT: C 222 TYR cc_start: 0.8261 (m-80) cc_final: 0.8009 (m-80) outliers start: 37 outliers final: 15 residues processed: 258 average time/residue: 1.5069 time to fit residues: 429.8490 Evaluate side-chains 227 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 211 time to evaluate : 2.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 MET Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 466 MET Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain B residue 340 MET Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain C residue 340 MET Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain D residue 340 MET Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 581 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 121 optimal weight: 2.9990 chunk 67 optimal weight: 8.9990 chunk 181 optimal weight: 0.9980 chunk 148 optimal weight: 0.9990 chunk 60 optimal weight: 10.0000 chunk 218 optimal weight: 6.9990 chunk 235 optimal weight: 2.9990 chunk 194 optimal weight: 6.9990 chunk 216 optimal weight: 0.7980 chunk 74 optimal weight: 0.9980 chunk 175 optimal weight: 6.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 31 GLN D 267 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 20048 Z= 0.224 Angle : 0.536 6.420 27224 Z= 0.273 Chirality : 0.040 0.176 3100 Planarity : 0.005 0.049 3424 Dihedral : 8.576 99.565 2752 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.10 % Allowed : 11.64 % Favored : 86.26 % 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: 0.23 (0.16), residues: 2408 helix: 0.58 (0.13), residues: 1420 sheet: 1.52 (0.53), residues: 72 loop : -0.51 (0.20), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 29 HIS 0.004 0.001 HIS A 201 PHE 0.009 0.001 PHE D 537 TYR 0.010 0.001 TYR C 222 ARG 0.006 0.000 ARG D 180 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 239 time to evaluate : 2.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 GLN cc_start: 0.8012 (mt0) cc_final: 0.7608 (mt0) REVERT: A 466 MET cc_start: 0.8817 (OUTLIER) cc_final: 0.8509 (mtt) REVERT: B 128 GLN cc_start: 0.7923 (mt0) cc_final: 0.7526 (mt0) REVERT: B 309 GLU cc_start: 0.7189 (mt-10) cc_final: 0.6917 (mt-10) REVERT: C 128 GLN cc_start: 0.7949 (mt0) cc_final: 0.7559 (mt0) REVERT: D 128 GLN cc_start: 0.8073 (mt0) cc_final: 0.7687 (mt0) outliers start: 44 outliers final: 19 residues processed: 262 average time/residue: 1.6248 time to fit residues: 470.0730 Evaluate side-chains 242 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 222 time to evaluate : 2.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 466 MET Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 581 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 215 optimal weight: 1.9990 chunk 164 optimal weight: 4.9990 chunk 113 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 146 optimal weight: 2.9990 chunk 219 optimal weight: 0.8980 chunk 231 optimal weight: 0.4980 chunk 114 optimal weight: 0.8980 chunk 207 optimal weight: 0.6980 chunk 62 optimal weight: 5.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 ASN B 131 ASN C 131 ASN C 261 GLN D 131 ASN D 261 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20048 Z= 0.182 Angle : 0.500 5.793 27224 Z= 0.256 Chirality : 0.039 0.166 3100 Planarity : 0.004 0.048 3424 Dihedral : 8.424 100.365 2752 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.05 % Allowed : 13.93 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.17), residues: 2408 helix: 1.01 (0.14), residues: 1420 sheet: 1.66 (0.53), residues: 72 loop : -0.37 (0.20), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 29 HIS 0.003 0.001 HIS A 201 PHE 0.008 0.001 PHE D 537 TYR 0.010 0.001 TYR A 555 ARG 0.007 0.000 ARG B 180 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 233 time to evaluate : 2.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 GLN cc_start: 0.7812 (mt0) cc_final: 0.7447 (mt0) REVERT: A 466 MET cc_start: 0.8776 (OUTLIER) cc_final: 0.8434 (mtt) REVERT: B 128 GLN cc_start: 0.7724 (mt0) cc_final: 0.7355 (mt0) REVERT: B 177 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7393 (tp30) REVERT: B 309 GLU cc_start: 0.7257 (mt-10) cc_final: 0.6991 (mt-10) REVERT: C 128 GLN cc_start: 0.7741 (mt0) cc_final: 0.7335 (mt0) REVERT: D 128 GLN cc_start: 0.7890 (mt0) cc_final: 0.7505 (mt0) outliers start: 43 outliers final: 17 residues processed: 254 average time/residue: 1.5571 time to fit residues: 438.8407 Evaluate side-chains 236 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 217 time to evaluate : 2.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 466 MET Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 177 GLU Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 581 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 193 optimal weight: 10.0000 chunk 131 optimal weight: 5.9990 chunk 3 optimal weight: 7.9990 chunk 172 optimal weight: 0.7980 chunk 95 optimal weight: 1.9990 chunk 197 optimal weight: 1.9990 chunk 160 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 118 optimal weight: 0.0370 chunk 208 optimal weight: 0.6980 chunk 58 optimal weight: 5.9990 overall best weight: 0.9060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN B 56 ASN B 131 ASN C 261 GLN D 261 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20048 Z= 0.171 Angle : 0.494 5.678 27224 Z= 0.254 Chirality : 0.039 0.161 3100 Planarity : 0.004 0.046 3424 Dihedral : 8.288 100.300 2752 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.00 % Allowed : 14.22 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.17), residues: 2408 helix: 1.22 (0.14), residues: 1420 sheet: 1.70 (0.54), residues: 72 loop : -0.27 (0.20), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 29 HIS 0.003 0.001 HIS D 201 PHE 0.008 0.001 PHE C 537 TYR 0.009 0.001 TYR B 555 ARG 0.006 0.000 ARG B 33 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 247 time to evaluate : 2.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 GLN cc_start: 0.7672 (mt0) cc_final: 0.7236 (mt0) REVERT: A 466 MET cc_start: 0.8765 (OUTLIER) cc_final: 0.8405 (mtt) REVERT: B 128 GLN cc_start: 0.7642 (mt0) cc_final: 0.7227 (mt0) REVERT: B 177 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7375 (tp30) REVERT: B 309 GLU cc_start: 0.7266 (mt-10) cc_final: 0.6995 (mt-10) REVERT: C 128 GLN cc_start: 0.7615 (mt0) cc_final: 0.7198 (mt0) REVERT: C 554 MET cc_start: 0.8927 (mmp) cc_final: 0.8537 (tpt) REVERT: D 128 GLN cc_start: 0.7682 (mt0) cc_final: 0.7264 (mt0) REVERT: D 554 MET cc_start: 0.8938 (mmp) cc_final: 0.8523 (tpt) outliers start: 42 outliers final: 14 residues processed: 266 average time/residue: 1.5660 time to fit residues: 460.1876 Evaluate side-chains 235 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 219 time to evaluate : 2.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 466 MET Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 177 GLU Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 581 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 53.887 > 50: distance: 42 - 45: 17.703 distance: 45 - 46: 15.524 distance: 46 - 47: 16.580 distance: 46 - 49: 15.502 distance: 47 - 48: 21.802 distance: 47 - 53: 21.594 distance: 49 - 50: 13.041 distance: 50 - 51: 11.841 distance: 50 - 52: 30.523 distance: 53 - 54: 13.067 distance: 54 - 55: 15.990 distance: 54 - 57: 13.255 distance: 55 - 56: 40.777 distance: 55 - 61: 16.846 distance: 57 - 58: 24.793 distance: 57 - 59: 15.548 distance: 58 - 60: 40.704 distance: 61 - 62: 23.097 distance: 62 - 63: 10.818 distance: 62 - 65: 9.593 distance: 63 - 64: 10.151 distance: 63 - 72: 18.454 distance: 65 - 66: 34.554 distance: 66 - 67: 28.856 distance: 67 - 68: 23.526 distance: 68 - 69: 7.133 distance: 69 - 70: 15.836 distance: 69 - 71: 11.619 distance: 72 - 73: 20.254 distance: 73 - 74: 5.600 distance: 73 - 76: 10.826 distance: 74 - 75: 33.783 distance: 74 - 77: 17.558 distance: 77 - 78: 8.017 distance: 78 - 79: 40.883 distance: 78 - 81: 7.196 distance: 79 - 80: 16.704 distance: 79 - 86: 14.835 distance: 81 - 82: 11.118 distance: 82 - 83: 30.953 distance: 83 - 84: 13.724 distance: 83 - 85: 18.182 distance: 86 - 87: 11.552 distance: 87 - 88: 20.468 distance: 87 - 90: 21.092 distance: 88 - 89: 34.291 distance: 88 - 94: 20.886 distance: 90 - 91: 16.451 distance: 91 - 92: 8.244 distance: 91 - 93: 25.372 distance: 94 - 95: 5.909 distance: 95 - 96: 9.019 distance: 95 - 98: 24.998 distance: 96 - 97: 22.722 distance: 96 - 100: 15.190 distance: 98 - 99: 12.662 distance: 100 - 101: 10.962 distance: 101 - 102: 18.644 distance: 101 - 104: 11.951 distance: 102 - 103: 16.793 distance: 102 - 108: 23.677 distance: 104 - 105: 18.030 distance: 105 - 106: 11.483 distance: 105 - 107: 24.292 distance: 108 - 109: 12.128 distance: 109 - 110: 29.751 distance: 110 - 111: 16.964 distance: 110 - 112: 12.932 distance: 112 - 113: 19.534 distance: 113 - 114: 23.814 distance: 113 - 116: 12.573 distance: 114 - 115: 20.029 distance: 114 - 120: 22.350 distance: 116 - 117: 14.316 distance: 117 - 118: 12.223 distance: 117 - 119: 13.219