Starting phenix.real_space_refine on Mon Mar 18 00:08:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6l_25718/03_2024/7t6l_25718.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6l_25718/03_2024/7t6l_25718.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6l_25718/03_2024/7t6l_25718.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6l_25718/03_2024/7t6l_25718.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6l_25718/03_2024/7t6l_25718.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6l_25718/03_2024/7t6l_25718.pdb" } resolution = 3.7 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= 0.002 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 140 5.16 5 C 12548 2.51 5 N 3284 2.21 5 O 3440 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 250": "OE1" <-> "OE2" Residue "A ASP 279": "OD1" <-> "OD2" Residue "A GLU 315": "OE1" <-> "OE2" Residue "A TYR 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 478": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 515": "OE1" <-> "OE2" Residue "A GLU 522": "OE1" <-> "OE2" Residue "A PHE 553": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 590": "OD1" <-> "OD2" Residue "A TYR 621": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 100": "OE1" <-> "OE2" Residue "B TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 250": "OE1" <-> "OE2" Residue "B ASP 279": "OD1" <-> "OD2" Residue "B GLU 315": "OE1" <-> "OE2" Residue "B TYR 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 478": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 493": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 553": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 611": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 621": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 250": "OE1" <-> "OE2" Residue "C ASP 279": "OD1" <-> "OD2" Residue "C GLU 315": "OE1" <-> "OE2" Residue "C TYR 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 478": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 493": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 515": "OE1" <-> "OE2" Residue "C GLU 522": "OE1" <-> "OE2" Residue "C PHE 553": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 611": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 621": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 279": "OD1" <-> "OD2" Residue "D GLU 315": "OE1" <-> "OE2" Residue "D TYR 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 415": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 478": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 493": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 515": "OE1" <-> "OE2" Residue "D GLU 522": "OE1" <-> "OE2" Residue "D PHE 553": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 590": "OD1" <-> "OD2" Residue "D PHE 611": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 621": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 19412 Number of models: 1 Model: "" Number of chains: 4 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 Time building chain proxies: 10.34, per 1000 atoms: 0.53 Number of scatterers: 19412 At special positions: 0 Unit cell: (141.93, 141.93, 121.18, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 140 16.00 O 3440 8.00 N 3284 7.00 C 12548 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.80 Conformation dependent library (CDL) restraints added in 3.7 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... Secondary structure from input PDB file: 109 helices and 8 sheets defined 64.7% alpha, 2.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.04 Creating SS restraints... Processing helix chain 'A' and resid 29 through 47 removed outlier: 3.720A pdb=" N SER A 47 " --> pdb=" O ARG A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 56 removed outlier: 3.587A pdb=" N GLN A 51 " --> pdb=" O SER A 47 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN A 56 " --> pdb=" O ALA A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 67 removed outlier: 3.679A pdb=" N ASN A 67 " --> pdb=" O ILE A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 89 removed outlier: 3.731A pdb=" N TYR A 89 " --> pdb=" O VAL A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 102 removed outlier: 3.610A pdb=" N ALA A 95 " --> pdb=" O ASN A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 107 removed outlier: 3.989A pdb=" N ALA A 106 " --> pdb=" O PRO A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 127 removed outlier: 3.737A pdb=" N ILE A 123 " --> pdb=" O THR A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 140 Processing helix chain 'A' and resid 165 through 174 Processing helix chain 'A' and resid 175 through 184 Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 213 through 222 Processing helix chain 'A' and resid 242 through 250 Processing helix chain 'A' and resid 252 through 264 removed outlier: 4.078A pdb=" N LYS A 262 " --> pdb=" O HIS A 258 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARG A 263 " --> pdb=" O LEU A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 298 Processing helix chain 'A' and resid 303 through 308 removed outlier: 3.895A pdb=" N ILE A 307 " --> pdb=" O GLU A 303 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 303 through 308' Processing helix chain 'A' and resid 310 through 324 removed outlier: 3.918A pdb=" N GLU A 315 " --> pdb=" O THR A 311 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LEU A 316 " --> pdb=" O PRO A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 349 Processing helix chain 'A' and resid 379 through 410 removed outlier: 3.629A pdb=" N GLY A 388 " --> pdb=" O ILE A 384 " (cutoff:3.500A) Proline residue: A 405 - end of helix Processing helix chain 'A' and resid 411 through 418 removed outlier: 3.640A pdb=" N GLN A 418 " --> pdb=" O ARG A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 445 Processing helix chain 'A' and resid 450 through 464 removed outlier: 3.942A pdb=" N PHE A 456 " --> pdb=" O VAL A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 470 removed outlier: 4.098A pdb=" N ARG A 470 " --> pdb=" O TYR A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 513 removed outlier: 3.641A pdb=" N LEU A 490 " --> pdb=" O ILE A 486 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N MET A 491 " --> pdb=" O PHE A 487 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N ARG A 492 " --> pdb=" O GLY A 488 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N PHE A 493 " --> pdb=" O ASP A 489 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N VAL A 499 " --> pdb=" O TRP A 495 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N VAL A 500 " --> pdb=" O LEU A 496 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N GLY A 503 " --> pdb=" O VAL A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 538 removed outlier: 3.518A pdb=" N LEU A 538 " --> pdb=" O PHE A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 566 removed outlier: 3.725A pdb=" N CYS A 556 " --> pdb=" O PRO A 552 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE A 557 " --> pdb=" O PHE A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 605 removed outlier: 3.940A pdb=" N ASN A 572 " --> pdb=" O LEU A 568 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N GLN A 587 " --> pdb=" O TRP A 583 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N GLU A 588 " --> pdb=" O ARG A 584 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLU A 591 " --> pdb=" O GLN A 587 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N VAL A 598 " --> pdb=" O ARG A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 613 Processing helix chain 'B' and resid 30 through 47 removed outlier: 3.717A pdb=" N SER B 47 " --> pdb=" O ARG B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 56 removed outlier: 3.586A pdb=" N GLN B 51 " --> pdb=" O SER B 47 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN B 56 " --> pdb=" O ALA B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 67 removed outlier: 3.679A pdb=" N ASN B 67 " --> pdb=" O ILE B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 89 removed outlier: 3.735A pdb=" N TYR B 89 " --> pdb=" O VAL B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 102 removed outlier: 3.612A pdb=" N ALA B 95 " --> pdb=" O ASN B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 107 removed outlier: 3.991A pdb=" N ALA B 106 " --> pdb=" O PRO B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 127 removed outlier: 3.733A pdb=" N ILE B 123 " --> pdb=" O THR B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 140 Processing helix chain 'B' and resid 165 through 174 Processing helix chain 'B' and resid 175 through 184 Processing helix chain 'B' and resid 198 through 205 Processing helix chain 'B' and resid 213 through 222 Processing helix chain 'B' and resid 242 through 251 removed outlier: 3.708A pdb=" N GLY B 251 " --> pdb=" O ALA B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 264 removed outlier: 4.078A pdb=" N LYS B 262 " --> pdb=" O HIS B 258 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG B 263 " --> pdb=" O LEU B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 298 Processing helix chain 'B' and resid 303 through 308 removed outlier: 3.857A pdb=" N ILE B 307 " --> pdb=" O GLU B 303 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU B 308 " --> pdb=" O ALA B 304 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 303 through 308' Processing helix chain 'B' and resid 310 through 324 removed outlier: 3.908A pdb=" N GLU B 315 " --> pdb=" O THR B 311 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N LEU B 316 " --> pdb=" O PRO B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 349 Processing helix chain 'B' and resid 379 through 410 removed outlier: 3.613A pdb=" N GLY B 388 " --> pdb=" O ILE B 384 " (cutoff:3.500A) Proline residue: B 405 - end of helix Processing helix chain 'B' and resid 411 through 418 removed outlier: 3.631A pdb=" N GLN B 418 " --> pdb=" O ARG B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 445 Processing helix chain 'B' and resid 450 through 464 removed outlier: 3.992A pdb=" N PHE B 456 " --> pdb=" O VAL B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 470 removed outlier: 3.787A pdb=" N ARG B 470 " --> pdb=" O TYR B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 513 removed outlier: 3.641A pdb=" N LEU B 490 " --> pdb=" O ILE B 486 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N MET B 491 " --> pdb=" O PHE B 487 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N ARG B 492 " --> pdb=" O GLY B 488 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N PHE B 493 " --> pdb=" O ASP B 489 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU B 496 " --> pdb=" O ARG B 492 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N VAL B 499 " --> pdb=" O TRP B 495 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N VAL B 500 " --> pdb=" O LEU B 496 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N GLY B 503 " --> pdb=" O VAL B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 538 removed outlier: 3.520A pdb=" N LEU B 538 " --> pdb=" O PHE B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 566 removed outlier: 3.767A pdb=" N CYS B 556 " --> pdb=" O PRO B 552 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE B 557 " --> pdb=" O PHE B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 605 removed outlier: 3.914A pdb=" N ASN B 572 " --> pdb=" O LEU B 568 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N GLN B 587 " --> pdb=" O TRP B 583 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N GLU B 588 " --> pdb=" O ARG B 584 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLU B 591 " --> pdb=" O GLN B 587 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N VAL B 598 " --> pdb=" O ARG B 594 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 47 removed outlier: 3.715A pdb=" N SER C 47 " --> pdb=" O ARG C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 56 removed outlier: 3.590A pdb=" N GLN C 51 " --> pdb=" O SER C 47 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASN C 56 " --> pdb=" O ALA C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 67 removed outlier: 3.680A pdb=" N ASN C 67 " --> pdb=" O ILE C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 removed outlier: 3.732A pdb=" N TYR C 89 " --> pdb=" O VAL C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 102 removed outlier: 3.610A pdb=" N ALA C 95 " --> pdb=" O ASN C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 107 removed outlier: 3.990A pdb=" N ALA C 106 " --> pdb=" O PRO C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 127 removed outlier: 3.732A pdb=" N ILE C 123 " --> pdb=" O THR C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 140 Processing helix chain 'C' and resid 165 through 174 Processing helix chain 'C' and resid 175 through 184 Processing helix chain 'C' and resid 198 through 205 Processing helix chain 'C' and resid 213 through 222 Processing helix chain 'C' and resid 242 through 250 Processing helix chain 'C' and resid 252 through 264 removed outlier: 4.082A pdb=" N LYS C 262 " --> pdb=" O HIS C 258 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG C 263 " --> pdb=" O LEU C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 298 Processing helix chain 'C' and resid 303 through 308 removed outlier: 3.895A pdb=" N ILE C 307 " --> pdb=" O GLU C 303 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU C 308 " --> pdb=" O ALA C 304 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 303 through 308' Processing helix chain 'C' and resid 310 through 324 removed outlier: 3.912A pdb=" N GLU C 315 " --> pdb=" O THR C 311 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N LEU C 316 " --> pdb=" O PRO C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 349 Processing helix chain 'C' and resid 379 through 410 removed outlier: 3.615A pdb=" N GLY C 388 " --> pdb=" O ILE C 384 " (cutoff:3.500A) Proline residue: C 405 - end of helix Processing helix chain 'C' and resid 411 through 418 removed outlier: 3.630A pdb=" N GLN C 418 " --> pdb=" O ARG C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 445 Processing helix chain 'C' and resid 450 through 464 removed outlier: 4.343A pdb=" N PHE C 456 " --> pdb=" O VAL C 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 470 removed outlier: 3.847A pdb=" N ARG C 470 " --> pdb=" O TYR C 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 513 removed outlier: 3.697A pdb=" N LEU C 490 " --> pdb=" O ILE C 486 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N MET C 491 " --> pdb=" O PHE C 487 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N ARG C 492 " --> pdb=" O GLY C 488 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N PHE C 493 " --> pdb=" O ASP C 489 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N VAL C 499 " --> pdb=" O TRP C 495 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N VAL C 500 " --> pdb=" O LEU C 496 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N GLY C 503 " --> pdb=" O VAL C 499 " (cutoff:3.500A) Processing helix chain 'C' and resid 525 through 538 removed outlier: 3.504A pdb=" N LEU C 538 " --> pdb=" O PHE C 534 " (cutoff:3.500A) Processing helix chain 'C' and resid 552 through 566 removed outlier: 3.688A pdb=" N CYS C 556 " --> pdb=" O PRO C 552 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE C 557 " --> pdb=" O PHE C 553 " (cutoff:3.500A) Processing helix chain 'C' and resid 568 through 605 removed outlier: 3.917A pdb=" N ASN C 572 " --> pdb=" O LEU C 568 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N GLN C 587 " --> pdb=" O TRP C 583 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N GLU C 588 " --> pdb=" O ARG C 584 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLU C 591 " --> pdb=" O GLN C 587 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N VAL C 598 " --> pdb=" O ARG C 594 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 47 removed outlier: 3.715A pdb=" N SER D 47 " --> pdb=" O ARG D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 56 removed outlier: 3.586A pdb=" N GLN D 51 " --> pdb=" O SER D 47 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASN D 56 " --> pdb=" O ALA D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 59 through 67 removed outlier: 3.680A pdb=" N ASN D 67 " --> pdb=" O ILE D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 89 removed outlier: 3.722A pdb=" N TYR D 89 " --> pdb=" O VAL D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 102 removed outlier: 3.622A pdb=" N ALA D 95 " --> pdb=" O ASN D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 107 removed outlier: 3.990A pdb=" N ALA D 106 " --> pdb=" O PRO D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 127 removed outlier: 3.750A pdb=" N ILE D 123 " --> pdb=" O THR D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 140 Processing helix chain 'D' and resid 165 through 174 Processing helix chain 'D' and resid 175 through 184 Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 213 through 222 Processing helix chain 'D' and resid 242 through 251 removed outlier: 3.743A pdb=" N GLY D 251 " --> pdb=" O ALA D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 264 removed outlier: 4.080A pdb=" N LYS D 262 " --> pdb=" O HIS D 258 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG D 263 " --> pdb=" O LEU D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 298 Processing helix chain 'D' and resid 303 through 308 removed outlier: 3.865A pdb=" N ILE D 307 " --> pdb=" O GLU D 303 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU D 308 " --> pdb=" O ALA D 304 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 303 through 308' Processing helix chain 'D' and resid 310 through 324 removed outlier: 3.907A pdb=" N GLU D 315 " --> pdb=" O THR D 311 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N LEU D 316 " --> pdb=" O PRO D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 349 Processing helix chain 'D' and resid 379 through 410 removed outlier: 3.615A pdb=" N GLY D 388 " --> pdb=" O ILE D 384 " (cutoff:3.500A) Proline residue: D 405 - end of helix Processing helix chain 'D' and resid 411 through 418 removed outlier: 3.614A pdb=" N GLN D 418 " --> pdb=" O ARG D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 445 Processing helix chain 'D' and resid 450 through 464 removed outlier: 4.344A pdb=" N PHE D 456 " --> pdb=" O VAL D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 465 through 470 removed outlier: 3.780A pdb=" N ARG D 470 " --> pdb=" O TYR D 467 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 513 removed outlier: 3.604A pdb=" N LEU D 490 " --> pdb=" O ILE D 486 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N MET D 491 " --> pdb=" O PHE D 487 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N ARG D 492 " --> pdb=" O GLY D 488 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N PHE D 493 " --> pdb=" O ASP D 489 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU D 496 " --> pdb=" O ARG D 492 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N VAL D 499 " --> pdb=" O TRP D 495 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N VAL D 500 " --> pdb=" O LEU D 496 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLY D 503 " --> pdb=" O VAL D 499 " (cutoff:3.500A) Processing helix chain 'D' and resid 525 through 538 removed outlier: 3.518A pdb=" N LEU D 538 " --> pdb=" O PHE D 534 " (cutoff:3.500A) Processing helix chain 'D' and resid 552 through 566 removed outlier: 3.742A pdb=" N CYS D 556 " --> pdb=" O PRO D 552 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE D 557 " --> pdb=" O PHE D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 568 through 605 removed outlier: 3.861A pdb=" N ASN D 572 " --> pdb=" O LEU D 568 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N GLN D 587 " --> pdb=" O TRP D 583 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N GLU D 588 " --> pdb=" O ARG D 584 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLU D 591 " --> pdb=" O GLN D 587 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N VAL D 598 " --> pdb=" O ARG D 594 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 273 through 279 Processing sheet with id=AA2, first strand: chain 'A' and resid 352 through 354 Processing sheet with id=AA3, first strand: chain 'B' and resid 273 through 279 Processing sheet with id=AA4, first strand: chain 'B' and resid 352 through 354 Processing sheet with id=AA5, first strand: chain 'C' and resid 273 through 279 Processing sheet with id=AA6, first strand: chain 'C' and resid 352 through 354 Processing sheet with id=AA7, first strand: chain 'D' and resid 273 through 279 Processing sheet with id=AA8, first strand: chain 'D' and resid 352 through 354 1025 hydrogen bonds defined for protein. 3033 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: 5.68 Time building geometry restraints manager: 7.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5942 1.34 - 1.46: 3808 1.46 - 1.58: 9882 1.58 - 1.70: 0 1.70 - 1.82: 228 Bond restraints: 19860 Sorted by residual: bond pdb=" CB PHE D 574 " pdb=" CG PHE D 574 " ideal model delta sigma weight residual 1.502 1.409 0.093 2.30e-02 1.89e+03 1.65e+01 bond pdb=" CB PHE B 574 " pdb=" CG PHE B 574 " ideal model delta sigma weight residual 1.502 1.410 0.092 2.30e-02 1.89e+03 1.58e+01 bond pdb=" CB PHE C 574 " pdb=" CG PHE C 574 " ideal model delta sigma weight residual 1.502 1.416 0.086 2.30e-02 1.89e+03 1.41e+01 bond pdb=" CB PHE A 574 " pdb=" CG PHE A 574 " ideal model delta sigma weight residual 1.502 1.417 0.085 2.30e-02 1.89e+03 1.37e+01 bond pdb=" CD2 PHE A 574 " pdb=" CE2 PHE A 574 " ideal model delta sigma weight residual 1.382 1.287 0.095 3.00e-02 1.11e+03 1.00e+01 ... (remaining 19855 not shown) Histogram of bond angle deviations from ideal: 95.66 - 103.37: 211 103.37 - 111.08: 6934 111.08 - 118.79: 8853 118.79 - 126.50: 10632 126.50 - 134.21: 334 Bond angle restraints: 26964 Sorted by residual: angle pdb=" N ILE D 367 " pdb=" CA ILE D 367 " pdb=" C ILE D 367 " ideal model delta sigma weight residual 113.53 108.25 5.28 9.80e-01 1.04e+00 2.90e+01 angle pdb=" CA LEU C 98 " pdb=" CB LEU C 98 " pdb=" CG LEU C 98 " ideal model delta sigma weight residual 116.30 133.84 -17.54 3.50e+00 8.16e-02 2.51e+01 angle pdb=" C ASP A 223 " pdb=" N GLU A 224 " pdb=" CA GLU A 224 " ideal model delta sigma weight residual 121.54 131.08 -9.54 1.91e+00 2.74e-01 2.49e+01 angle pdb=" CA LEU A 98 " pdb=" CB LEU A 98 " pdb=" CG LEU A 98 " ideal model delta sigma weight residual 116.30 133.78 -17.48 3.50e+00 8.16e-02 2.49e+01 angle pdb=" C ASP D 223 " pdb=" N GLU D 224 " pdb=" CA GLU D 224 " ideal model delta sigma weight residual 121.54 131.05 -9.51 1.91e+00 2.74e-01 2.48e+01 ... (remaining 26959 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.60: 10323 16.60 - 33.21: 1198 33.21 - 49.81: 212 49.81 - 66.41: 48 66.41 - 83.02: 31 Dihedral angle restraints: 11812 sinusoidal: 4732 harmonic: 7080 Sorted by residual: dihedral pdb=" CA PHE D 493 " pdb=" C PHE D 493 " pdb=" N CYS D 494 " pdb=" CA CYS D 494 " ideal model delta harmonic sigma weight residual 180.00 148.24 31.76 0 5.00e+00 4.00e-02 4.03e+01 dihedral pdb=" CA PHE C 493 " pdb=" C PHE C 493 " pdb=" N CYS C 494 " pdb=" CA CYS C 494 " ideal model delta harmonic sigma weight residual 180.00 148.63 31.37 0 5.00e+00 4.00e-02 3.94e+01 dihedral pdb=" CA PHE B 493 " pdb=" C PHE B 493 " pdb=" N CYS B 494 " pdb=" CA CYS B 494 " ideal model delta harmonic sigma weight residual 180.00 149.54 30.46 0 5.00e+00 4.00e-02 3.71e+01 ... (remaining 11809 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 2773 0.106 - 0.211: 261 0.211 - 0.317: 34 0.317 - 0.422: 0 0.422 - 0.528: 4 Chirality restraints: 3072 Sorted by residual: chirality pdb=" CB ILE A 575 " pdb=" CA ILE A 575 " pdb=" CG1 ILE A 575 " pdb=" CG2 ILE A 575 " both_signs ideal model delta sigma weight residual False 2.64 2.12 0.53 2.00e-01 2.50e+01 6.96e+00 chirality pdb=" CB ILE D 575 " pdb=" CA ILE D 575 " pdb=" CG1 ILE D 575 " pdb=" CG2 ILE D 575 " both_signs ideal model delta sigma weight residual False 2.64 2.17 0.47 2.00e-01 2.50e+01 5.61e+00 chirality pdb=" CB ILE C 575 " pdb=" CA ILE C 575 " pdb=" CG1 ILE C 575 " pdb=" CG2 ILE C 575 " both_signs ideal model delta sigma weight residual False 2.64 2.17 0.47 2.00e-01 2.50e+01 5.56e+00 ... (remaining 3069 not shown) Planarity restraints: 3416 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 493 " -0.054 2.00e-02 2.50e+03 5.06e-02 4.49e+01 pdb=" CG PHE C 493 " 0.116 2.00e-02 2.50e+03 pdb=" CD1 PHE C 493 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE C 493 " -0.034 2.00e-02 2.50e+03 pdb=" CE1 PHE C 493 " -0.020 2.00e-02 2.50e+03 pdb=" CE2 PHE C 493 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE C 493 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 493 " -0.057 2.00e-02 2.50e+03 5.01e-02 4.40e+01 pdb=" CG PHE A 493 " 0.114 2.00e-02 2.50e+03 pdb=" CD1 PHE A 493 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 PHE A 493 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 493 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 493 " -0.022 2.00e-02 2.50e+03 pdb=" CZ PHE A 493 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 493 " 0.053 2.00e-02 2.50e+03 4.94e-02 4.27e+01 pdb=" CG PHE D 493 " -0.112 2.00e-02 2.50e+03 pdb=" CD1 PHE D 493 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE D 493 " 0.034 2.00e-02 2.50e+03 pdb=" CE1 PHE D 493 " 0.023 2.00e-02 2.50e+03 pdb=" CE2 PHE D 493 " -0.006 2.00e-02 2.50e+03 pdb=" CZ PHE D 493 " 0.006 2.00e-02 2.50e+03 ... (remaining 3413 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.78: 3971 2.78 - 3.31: 17949 3.31 - 3.84: 32596 3.84 - 4.37: 36435 4.37 - 4.90: 62630 Nonbonded interactions: 153581 Sorted by model distance: nonbonded pdb=" OE2 GLU B 522 " pdb=" OG SER B 532 " model vdw 2.245 2.440 nonbonded pdb=" OE1 GLN C 267 " pdb=" OG SER C 275 " model vdw 2.313 2.440 nonbonded pdb=" OE1 GLN B 267 " pdb=" OG SER B 275 " model vdw 2.314 2.440 nonbonded pdb=" OE1 GLN A 267 " pdb=" OG SER A 275 " model vdw 2.314 2.440 nonbonded pdb=" OE1 GLN D 267 " pdb=" OG SER D 275 " model vdw 2.314 2.440 ... (remaining 153576 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 12.650 Check model and map are aligned: 0.280 Set scattering table: 0.180 Process input model: 50.650 Find NCS groups from input model: 1.540 Set up NCS constraints: 0.130 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 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 : 0.007 0.095 19860 Z= 0.427 Angle : 1.179 17.544 26964 Z= 0.613 Chirality : 0.066 0.528 3072 Planarity : 0.009 0.092 3416 Dihedral : 15.114 83.018 7236 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -4.03 (0.12), residues: 2408 helix: -2.53 (0.10), residues: 1460 sheet: -3.06 (0.46), residues: 76 loop : -2.60 (0.16), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 613 HIS 0.006 0.001 HIS C 258 PHE 0.116 0.005 PHE C 493 TYR 0.030 0.002 TYR A 467 ARG 0.016 0.001 ARG B 154 *********************** 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 342 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 342 time to evaluate : 2.356 Fit side-chains revert: symmetry clash REVERT: A 315 GLU cc_start: 0.8302 (tp30) cc_final: 0.8045 (tp30) REVERT: A 447 MET cc_start: 0.6885 (ppp) cc_final: 0.6550 (ppp) REVERT: A 472 PHE cc_start: 0.7893 (m-80) cc_final: 0.7682 (m-10) REVERT: A 570 MET cc_start: 0.8428 (mmm) cc_final: 0.8207 (mmm) REVERT: B 447 MET cc_start: 0.6883 (ppp) cc_final: 0.6515 (ppp) REVERT: B 481 MET cc_start: 0.7975 (mmm) cc_final: 0.7713 (tpt) REVERT: B 553 PHE cc_start: 0.8179 (t80) cc_final: 0.7673 (p90) REVERT: B 570 MET cc_start: 0.8425 (mmm) cc_final: 0.8014 (mmm) REVERT: C 447 MET cc_start: 0.6894 (ppp) cc_final: 0.6532 (ppp) REVERT: C 570 MET cc_start: 0.8326 (mmm) cc_final: 0.7992 (mmm) REVERT: D 447 MET cc_start: 0.6900 (ppp) cc_final: 0.6529 (ppp) REVERT: D 481 MET cc_start: 0.7907 (mmm) cc_final: 0.7564 (tpt) REVERT: D 570 MET cc_start: 0.8315 (mmm) cc_final: 0.8035 (mmm) outliers start: 0 outliers final: 0 residues processed: 342 average time/residue: 0.2570 time to fit residues: 142.8330 Evaluate side-chains 254 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 254 time to evaluate : 2.253 ------------------------------------------------------------------------------- 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: 0.9990 chunk 181 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 122 optimal weight: 0.0670 chunk 97 optimal weight: 4.9990 chunk 188 optimal weight: 5.9990 chunk 72 optimal weight: 7.9990 chunk 114 optimal weight: 0.6980 chunk 140 optimal weight: 3.9990 chunk 217 optimal weight: 0.9980 overall best weight: 0.7320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 ASN A 208 ASN A 306 GLN A 582 HIS B 37 ASN B 208 ASN C 37 ASN C 91 ASN C 208 ASN C 306 GLN D 37 ASN D 208 ASN ** D 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19860 Z= 0.192 Angle : 0.589 7.038 26964 Z= 0.300 Chirality : 0.038 0.197 3072 Planarity : 0.005 0.041 3416 Dihedral : 4.769 27.522 2644 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.57 % Allowed : 9.83 % Favored : 88.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.16), residues: 2408 helix: -0.46 (0.13), residues: 1460 sheet: -2.42 (0.47), residues: 84 loop : -2.25 (0.18), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 495 HIS 0.011 0.001 HIS A 582 PHE 0.040 0.001 PHE A 493 TYR 0.012 0.001 TYR C 467 ARG 0.003 0.000 ARG B 584 *********************** 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 325 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 292 time to evaluate : 2.063 Fit side-chains REVERT: A 447 MET cc_start: 0.6924 (ppp) cc_final: 0.6422 (ppp) REVERT: A 472 PHE cc_start: 0.7979 (m-80) cc_final: 0.7740 (m-10) REVERT: B 447 MET cc_start: 0.6955 (ppp) cc_final: 0.6445 (ppp) REVERT: B 570 MET cc_start: 0.8353 (mmm) cc_final: 0.8127 (mmm) REVERT: C 447 MET cc_start: 0.6942 (ppp) cc_final: 0.6468 (ppp) REVERT: C 493 PHE cc_start: 0.4594 (t80) cc_final: 0.4044 (t80) REVERT: C 554 MET cc_start: 0.7741 (tpp) cc_final: 0.7525 (tpp) REVERT: D 306 GLN cc_start: 0.8396 (OUTLIER) cc_final: 0.8193 (mp10) REVERT: D 340 MET cc_start: 0.9379 (mmt) cc_final: 0.9020 (mmt) REVERT: D 447 MET cc_start: 0.6957 (ppp) cc_final: 0.6474 (ppp) outliers start: 33 outliers final: 25 residues processed: 311 average time/residue: 0.2478 time to fit residues: 126.8143 Evaluate side-chains 289 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 263 time to evaluate : 2.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 601 THR Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 306 GLN Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain D residue 567 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 121 optimal weight: 0.9990 chunk 67 optimal weight: 4.9990 chunk 181 optimal weight: 0.8980 chunk 148 optimal weight: 2.9990 chunk 60 optimal weight: 7.9990 chunk 218 optimal weight: 6.9990 chunk 235 optimal weight: 4.9990 chunk 194 optimal weight: 1.9990 chunk 216 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 chunk 175 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 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 582 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 19860 Z= 0.253 Angle : 0.602 6.595 26964 Z= 0.303 Chirality : 0.039 0.161 3072 Planarity : 0.004 0.036 3416 Dihedral : 4.415 17.737 2644 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.62 % Allowed : 13.55 % Favored : 84.83 % 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: -0.86 (0.17), residues: 2408 helix: 0.31 (0.14), residues: 1456 sheet: -2.15 (0.50), residues: 84 loop : -1.86 (0.19), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 495 HIS 0.009 0.001 HIS A 582 PHE 0.035 0.001 PHE A 493 TYR 0.015 0.001 TYR C 467 ARG 0.004 0.000 ARG A 584 *********************** 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 306 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 272 time to evaluate : 2.326 Fit side-chains REVERT: A 447 MET cc_start: 0.6999 (ppp) cc_final: 0.6549 (ppp) REVERT: A 472 PHE cc_start: 0.8207 (m-80) cc_final: 0.8004 (m-10) REVERT: B 447 MET cc_start: 0.7014 (ppp) cc_final: 0.6545 (ppp) REVERT: B 554 MET cc_start: 0.6960 (tpp) cc_final: 0.6654 (tpp) REVERT: B 570 MET cc_start: 0.8470 (mmm) cc_final: 0.8165 (mmm) REVERT: C 447 MET cc_start: 0.6986 (ppp) cc_final: 0.6549 (ppp) REVERT: D 306 GLN cc_start: 0.8408 (OUTLIER) cc_final: 0.8181 (mp10) REVERT: D 447 MET cc_start: 0.7009 (ppp) cc_final: 0.6550 (ppp) outliers start: 34 outliers final: 27 residues processed: 299 average time/residue: 0.2508 time to fit residues: 123.5576 Evaluate side-chains 267 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 239 time to evaluate : 2.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 582 HIS Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 306 GLN Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 567 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 215 optimal weight: 2.9990 chunk 164 optimal weight: 0.8980 chunk 113 optimal weight: 0.9990 chunk 24 optimal weight: 4.9990 chunk 104 optimal weight: 0.8980 chunk 146 optimal weight: 1.9990 chunk 219 optimal weight: 0.7980 chunk 231 optimal weight: 5.9990 chunk 114 optimal weight: 0.9980 chunk 207 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 ASN ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 ASN ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 582 HIS D 37 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19860 Z= 0.181 Angle : 0.556 7.931 26964 Z= 0.277 Chirality : 0.038 0.156 3072 Planarity : 0.004 0.034 3416 Dihedral : 4.233 18.256 2644 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.67 % Allowed : 14.55 % Favored : 82.78 % 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: -0.42 (0.17), residues: 2408 helix: 0.65 (0.14), residues: 1460 sheet: -1.84 (0.53), residues: 84 loop : -1.69 (0.20), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 495 HIS 0.013 0.001 HIS C 582 PHE 0.018 0.001 PHE A 493 TYR 0.010 0.001 TYR C 467 ARG 0.003 0.000 ARG B 584 *********************** 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 309 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 253 time to evaluate : 2.400 Fit side-chains REVERT: A 250 GLU cc_start: 0.8235 (tp30) cc_final: 0.8025 (tp30) REVERT: A 447 MET cc_start: 0.7138 (ppp) cc_final: 0.6618 (ppp) REVERT: A 472 PHE cc_start: 0.8184 (m-80) cc_final: 0.7918 (m-10) REVERT: A 554 MET cc_start: 0.7154 (tpp) cc_final: 0.6852 (tpp) REVERT: B 37 ASN cc_start: 0.8550 (OUTLIER) cc_final: 0.7793 (t0) REVERT: B 447 MET cc_start: 0.7135 (ppp) cc_final: 0.6624 (ppp) REVERT: B 554 MET cc_start: 0.6917 (tpp) cc_final: 0.6674 (tpp) REVERT: B 570 MET cc_start: 0.8455 (mmm) cc_final: 0.8119 (mmm) REVERT: C 37 ASN cc_start: 0.8536 (OUTLIER) cc_final: 0.7784 (t0) REVERT: C 250 GLU cc_start: 0.8281 (tp30) cc_final: 0.8066 (tp30) REVERT: C 447 MET cc_start: 0.7121 (ppp) cc_final: 0.6624 (ppp) REVERT: C 554 MET cc_start: 0.7451 (tpp) cc_final: 0.7185 (tpp) REVERT: D 37 ASN cc_start: 0.8570 (OUTLIER) cc_final: 0.7762 (t0) REVERT: D 306 GLN cc_start: 0.8395 (OUTLIER) cc_final: 0.8180 (mp10) REVERT: D 447 MET cc_start: 0.7112 (ppp) cc_final: 0.6612 (ppp) outliers start: 56 outliers final: 28 residues processed: 296 average time/residue: 0.2514 time to fit residues: 123.1966 Evaluate side-chains 275 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 243 time to evaluate : 1.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain B residue 37 ASN Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain C residue 37 ASN Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 384 ILE Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 577 MET Chi-restraints excluded: chain D residue 37 ASN Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 215 MET Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 306 GLN Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 384 ILE Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 567 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 193 optimal weight: 4.9990 chunk 131 optimal weight: 10.0000 chunk 3 optimal weight: 6.9990 chunk 172 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 197 optimal weight: 4.9990 chunk 160 optimal weight: 0.6980 chunk 0 optimal weight: 7.9990 chunk 118 optimal weight: 10.0000 chunk 208 optimal weight: 0.8980 chunk 58 optimal weight: 7.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 19860 Z= 0.302 Angle : 0.628 7.793 26964 Z= 0.314 Chirality : 0.041 0.176 3072 Planarity : 0.004 0.031 3416 Dihedral : 4.264 17.858 2644 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.91 % Allowed : 16.03 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.17), residues: 2408 helix: 0.78 (0.14), residues: 1448 sheet: -1.73 (0.56), residues: 84 loop : -1.46 (0.21), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 495 HIS 0.008 0.001 HIS C 582 PHE 0.030 0.002 PHE C 574 TYR 0.014 0.001 TYR B 467 ARG 0.003 0.000 ARG B 584 *********************** 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 293 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 232 time to evaluate : 2.098 Fit side-chains revert: symmetry clash REVERT: A 447 MET cc_start: 0.7272 (ppp) cc_final: 0.6770 (ppp) REVERT: A 472 PHE cc_start: 0.8445 (m-80) cc_final: 0.8113 (m-10) REVERT: A 554 MET cc_start: 0.7123 (tpp) cc_final: 0.6728 (tpp) REVERT: A 584 ARG cc_start: 0.7701 (mtm180) cc_final: 0.7477 (mtm110) REVERT: B 205 LEU cc_start: 0.8215 (OUTLIER) cc_final: 0.7914 (mp) REVERT: B 447 MET cc_start: 0.7263 (ppp) cc_final: 0.6762 (ppp) REVERT: B 554 MET cc_start: 0.6971 (tpp) cc_final: 0.6662 (tpp) REVERT: C 447 MET cc_start: 0.7250 (ppp) cc_final: 0.6739 (ppp) REVERT: C 584 ARG cc_start: 0.7542 (mtm180) cc_final: 0.7341 (mtm110) REVERT: D 306 GLN cc_start: 0.8463 (OUTLIER) cc_final: 0.8251 (mp10) REVERT: D 447 MET cc_start: 0.7276 (ppp) cc_final: 0.6770 (ppp) outliers start: 61 outliers final: 47 residues processed: 278 average time/residue: 0.2572 time to fit residues: 117.3269 Evaluate side-chains 264 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 215 time to evaluate : 1.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 525 ASP Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 577 MET Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 255 MET Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 525 ASP Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 525 ASP Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 215 MET Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 306 GLN Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 525 ASP Chi-restraints excluded: chain D residue 564 ILE Chi-restraints excluded: chain D residue 567 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 78 optimal weight: 0.4980 chunk 208 optimal weight: 0.3980 chunk 45 optimal weight: 0.9990 chunk 136 optimal weight: 6.9990 chunk 57 optimal weight: 3.9990 chunk 232 optimal weight: 1.9990 chunk 192 optimal weight: 6.9990 chunk 107 optimal weight: 0.9990 chunk 19 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 582 HIS ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19860 Z= 0.192 Angle : 0.574 10.075 26964 Z= 0.283 Chirality : 0.039 0.186 3072 Planarity : 0.004 0.031 3416 Dihedral : 4.179 17.421 2644 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.67 % Allowed : 17.99 % Favored : 79.34 % 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: 0.05 (0.17), residues: 2408 helix: 0.96 (0.14), residues: 1448 sheet: -1.44 (0.58), residues: 84 loop : -1.35 (0.21), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 495 HIS 0.009 0.001 HIS B 185 PHE 0.025 0.001 PHE A 553 TYR 0.009 0.001 TYR A 467 ARG 0.002 0.000 ARG D 584 *********************** REFINEMENT MACRO_CYCLE 6 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 298 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 242 time to evaluate : 2.261 Fit side-chains revert: symmetry clash REVERT: A 447 MET cc_start: 0.7224 (ppp) cc_final: 0.6680 (ppp) REVERT: A 472 PHE cc_start: 0.8387 (m-80) cc_final: 0.8056 (m-10) REVERT: A 554 MET cc_start: 0.7106 (tpp) cc_final: 0.6709 (tpp) REVERT: B 205 LEU cc_start: 0.8135 (OUTLIER) cc_final: 0.7533 (mp) REVERT: B 447 MET cc_start: 0.7212 (ppp) cc_final: 0.6692 (ppp) REVERT: B 554 MET cc_start: 0.6936 (tpp) cc_final: 0.6660 (tpp) REVERT: C 402 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8626 (tt) REVERT: C 447 MET cc_start: 0.7210 (ppp) cc_final: 0.6689 (ppp) REVERT: C 553 PHE cc_start: 0.7652 (p90) cc_final: 0.7451 (p90) REVERT: C 554 MET cc_start: 0.7307 (tpp) cc_final: 0.7054 (tpp) REVERT: C 574 PHE cc_start: 0.7688 (m-10) cc_final: 0.7196 (m-10) REVERT: D 306 GLN cc_start: 0.8395 (OUTLIER) cc_final: 0.8129 (mp10) REVERT: D 447 MET cc_start: 0.7230 (ppp) cc_final: 0.6697 (ppp) REVERT: D 474 MET cc_start: 0.7806 (OUTLIER) cc_final: 0.7563 (ttp) outliers start: 56 outliers final: 37 residues processed: 288 average time/residue: 0.2488 time to fit residues: 118.0269 Evaluate side-chains 272 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 231 time to evaluate : 2.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 525 ASP Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 577 MET Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 255 MET Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 525 ASP Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain B residue 582 HIS Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain C residue 525 ASP Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 215 MET Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 255 MET Chi-restraints excluded: chain D residue 306 GLN Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 525 ASP Chi-restraints excluded: chain D residue 564 ILE Chi-restraints excluded: chain D residue 567 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 58.2427 > 50: distance: 78 - 84: 16.630 distance: 84 - 85: 29.123 distance: 85 - 86: 3.493 distance: 86 - 87: 21.679 distance: 88 - 89: 16.387 distance: 89 - 90: 48.333 distance: 92 - 93: 25.506 distance: 93 - 94: 12.910 distance: 94 - 95: 35.933 distance: 94 - 96: 20.390 distance: 96 - 97: 16.444 distance: 96 - 102: 5.505 distance: 97 - 98: 15.700 distance: 97 - 100: 45.743 distance: 98 - 99: 6.243 distance: 98 - 103: 41.117 distance: 100 - 101: 40.719 distance: 101 - 102: 32.809 distance: 104 - 105: 39.601 distance: 105 - 106: 22.841 distance: 108 - 109: 3.480 distance: 109 - 110: 13.385 distance: 109 - 112: 29.402 distance: 110 - 111: 33.190 distance: 110 - 116: 9.356 distance: 112 - 113: 8.755 distance: 113 - 115: 37.162 distance: 116 - 117: 4.025 distance: 117 - 118: 21.445 distance: 117 - 120: 13.989 distance: 118 - 119: 39.684 distance: 120 - 121: 11.044 distance: 121 - 122: 6.537 distance: 121 - 123: 8.734 distance: 122 - 124: 7.552 distance: 123 - 125: 8.809 distance: 124 - 126: 9.274 distance: 125 - 126: 12.990 distance: 126 - 127: 13.192 distance: 128 - 129: 9.582 distance: 129 - 130: 23.417 distance: 129 - 132: 28.113 distance: 130 - 131: 11.575 distance: 130 - 134: 17.547 distance: 132 - 133: 14.587 distance: 134 - 135: 25.358 distance: 135 - 136: 13.418 distance: 135 - 138: 23.997 distance: 136 - 137: 9.246 distance: 136 - 141: 20.882 distance: 138 - 139: 12.592 distance: 138 - 140: 24.143 distance: 141 - 142: 12.252 distance: 142 - 143: 21.128 distance: 142 - 145: 14.889 distance: 143 - 144: 15.372 distance: 143 - 149: 33.712 distance: 145 - 146: 39.506 distance: 146 - 147: 4.767 distance: 149 - 150: 19.158 distance: 150 - 151: 19.740 distance: 150 - 153: 22.263 distance: 151 - 152: 24.743 distance: 151 - 157: 7.464 distance: 153 - 154: 39.984 distance: 154 - 155: 6.946 distance: 154 - 156: 45.696