Starting phenix.real_space_refine on Mon Dec 11 22:42:26 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6k_25717/12_2023/7t6k_25717.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6k_25717/12_2023/7t6k_25717.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6k_25717/12_2023/7t6k_25717.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6k_25717/12_2023/7t6k_25717.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6k_25717/12_2023/7t6k_25717.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6k_25717/12_2023/7t6k_25717.pdb" } resolution = 3.0 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= 0.006 sd= 0.066 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 PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 288": "OE1" <-> "OE2" Residue "A ASP 356": "OD1" <-> "OD2" Residue "A GLU 403": "OE1" <-> "OE2" Residue "A TYR 415": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 535": "OE1" <-> "OE2" Residue "A TYR 621": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 288": "OE1" <-> "OE2" Residue "B ASP 356": "OD1" <-> "OD2" Residue "B TYR 415": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 535": "OE1" <-> "OE2" Residue "B ASP 580": "OD1" <-> "OD2" Residue "B TYR 621": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 288": "OE1" <-> "OE2" Residue "C ASP 356": "OD1" <-> "OD2" Residue "C TYR 415": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 535": "OE1" <-> "OE2" Residue "C ASP 580": "OD1" <-> "OD2" Residue "C TYR 621": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 288": "OE1" <-> "OE2" Residue "D ASP 356": "OD1" <-> "OD2" Residue "D TYR 415": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 535": "OE1" <-> "OE2" Residue "D ASP 580": "OD1" <-> "OD2" Residue "D ASP 590": "OD1" <-> "OD2" Residue "D TYR 621": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 10.40, per 1000 atoms: 0.54 Number of scatterers: 19412 At special positions: 0 Unit cell: (130.38, 130.38, 120.84, 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: 7.62 Conformation dependent library (CDL) restraints added in 3.9 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: 120 helices and 8 sheets defined 66.0% alpha, 3.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.96 Creating SS restraints... Processing helix chain 'A' and resid 29 through 46 Processing helix chain 'A' and resid 47 through 56 Processing helix chain 'A' and resid 57 through 66 Processing helix chain 'A' and resid 81 through 89 removed outlier: 3.509A pdb=" N TYR A 89 " --> pdb=" O VAL A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 102 Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.952A pdb=" N ALA A 106 " --> pdb=" O PRO A 103 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS A 107 " --> pdb=" O GLU A 104 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU A 108 " --> pdb=" O LEU A 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 103 through 108' Processing helix chain 'A' and resid 119 through 127 removed outlier: 3.752A pdb=" N ILE A 123 " --> pdb=" O THR A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 139 Processing helix chain 'A' and resid 165 through 174 removed outlier: 3.563A pdb=" N GLY A 174 " --> pdb=" O ALA A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 184 Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 210 through 222 removed outlier: 4.497A pdb=" N GLN A 214 " --> pdb=" O THR A 210 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N TYR A 216 " --> pdb=" O ALA A 212 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASN A 217 " --> pdb=" O CYS A 213 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N TYR A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 250 Processing helix chain 'A' and resid 252 through 260 Processing helix chain 'A' and resid 280 through 285 removed outlier: 4.019A pdb=" N SER A 285 " --> pdb=" O THR A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 298 Processing helix chain 'A' and resid 302 through 310 removed outlier: 3.831A pdb=" N ARG A 305 " --> pdb=" O ARG A 302 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE A 307 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU A 308 " --> pdb=" O ARG A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 324 removed outlier: 3.826A 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: 3.688A pdb=" N LEU A 402 " --> pdb=" O ILE A 398 " (cutoff:3.500A) Proline residue: A 405 - end of helix removed outlier: 3.678A pdb=" N VAL A 410 " --> pdb=" O ASP A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 418 removed outlier: 3.619A pdb=" N PHE A 416 " --> pdb=" O ALA A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 445 Processing helix chain 'A' and resid 450 through 464 Processing helix chain 'A' and resid 465 through 472 removed outlier: 3.641A pdb=" N ARG A 470 " --> pdb=" O TYR A 467 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLY A 471 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 488 Processing helix chain 'A' and resid 488 through 512 removed outlier: 3.961A pdb=" N ARG A 492 " --> pdb=" O GLY A 488 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LEU A 496 " --> pdb=" O ARG A 492 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N VAL A 499 " --> pdb=" O TRP A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 524 removed outlier: 4.468A pdb=" N PHE A 523 " --> pdb=" O LEU A 520 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N SER A 524 " --> pdb=" O GLY A 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 520 through 524' Processing helix chain 'A' and resid 525 through 538 Processing helix chain 'A' and resid 552 through 566 removed outlier: 3.575A pdb=" N CYS A 556 " --> pdb=" O PRO A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 605 removed outlier: 4.710A pdb=" N GLN A 587 " --> pdb=" O TRP A 583 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N GLU A 588 " --> pdb=" O ARG A 584 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ASP A 590 " --> pdb=" O ALA A 586 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLU A 591 " --> pdb=" O GLN A 587 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ARG A 594 " --> pdb=" O ASP A 590 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N VAL A 598 " --> pdb=" O ARG A 594 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA A 599 " --> pdb=" O ALA A 595 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 46 Processing helix chain 'B' and resid 47 through 56 Processing helix chain 'B' and resid 57 through 66 Processing helix chain 'B' and resid 81 through 89 removed outlier: 3.508A pdb=" N VAL B 85 " --> pdb=" O THR B 81 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR B 89 " --> pdb=" O VAL B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 102 Processing helix chain 'B' and resid 103 through 108 removed outlier: 3.958A pdb=" N ALA B 106 " --> pdb=" O PRO B 103 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS B 107 " --> pdb=" O GLU B 104 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU B 108 " --> pdb=" O LEU B 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 103 through 108' Processing helix chain 'B' and resid 119 through 127 removed outlier: 3.742A pdb=" N ILE B 123 " --> pdb=" O THR B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 139 Processing helix chain 'B' and resid 165 through 174 removed outlier: 3.545A pdb=" N GLY B 174 " --> pdb=" O ALA B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 184 Processing helix chain 'B' and resid 198 through 205 Processing helix chain 'B' and resid 210 through 222 removed outlier: 4.494A pdb=" N GLN B 214 " --> pdb=" O THR B 210 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N TYR B 216 " --> pdb=" O ALA B 212 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASN B 217 " --> pdb=" O CYS B 213 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N TYR B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 250 Processing helix chain 'B' and resid 252 through 260 Processing helix chain 'B' and resid 280 through 285 removed outlier: 4.026A pdb=" N SER B 285 " --> pdb=" O THR B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 298 Processing helix chain 'B' and resid 302 through 310 removed outlier: 3.832A pdb=" N ARG B 305 " --> pdb=" O ARG B 302 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE B 307 " --> pdb=" O ALA B 304 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU B 308 " --> pdb=" O ARG B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 324 removed outlier: 3.907A 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: 3.688A pdb=" N LEU B 402 " --> pdb=" O ILE B 398 " (cutoff:3.500A) Proline residue: B 405 - end of helix removed outlier: 3.666A pdb=" N VAL B 410 " --> pdb=" O ASP B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 418 removed outlier: 3.611A pdb=" N PHE B 416 " --> pdb=" O ALA B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 445 Processing helix chain 'B' and resid 450 through 464 Processing helix chain 'B' and resid 465 through 472 removed outlier: 3.594A pdb=" N ARG B 470 " --> pdb=" O TYR B 467 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLY B 471 " --> pdb=" O PHE B 468 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE B 472 " --> pdb=" O ALA B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 488 Processing helix chain 'B' and resid 489 through 512 removed outlier: 4.125A pdb=" N LEU B 496 " --> pdb=" O ARG B 492 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N VAL B 499 " --> pdb=" O TRP B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 524 removed outlier: 4.468A pdb=" N PHE B 523 " --> pdb=" O LEU B 520 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N SER B 524 " --> pdb=" O GLY B 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 520 through 524' Processing helix chain 'B' and resid 525 through 538 Processing helix chain 'B' and resid 552 through 566 removed outlier: 3.579A pdb=" N CYS B 556 " --> pdb=" O PRO B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 605 removed outlier: 4.810A pdb=" N GLN B 587 " --> pdb=" O TRP B 583 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N GLU B 588 " --> pdb=" O ARG B 584 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASP B 590 " --> pdb=" O ALA B 586 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLU B 591 " --> pdb=" O GLN B 587 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ARG B 594 " --> pdb=" O ASP B 590 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N VAL B 598 " --> pdb=" O ARG B 594 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA B 599 " --> pdb=" O ALA B 595 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 46 Processing helix chain 'C' and resid 47 through 56 Processing helix chain 'C' and resid 57 through 66 Processing helix chain 'C' and resid 81 through 89 removed outlier: 3.507A pdb=" N TYR C 89 " --> pdb=" O VAL C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 102 Processing helix chain 'C' and resid 103 through 108 removed outlier: 3.950A pdb=" N ALA C 106 " --> pdb=" O PRO C 103 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS C 107 " --> pdb=" O GLU C 104 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU C 108 " --> pdb=" O LEU C 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 103 through 108' Processing helix chain 'C' and resid 119 through 127 removed outlier: 3.768A pdb=" N ILE C 123 " --> pdb=" O THR C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 139 Processing helix chain 'C' and resid 165 through 174 removed outlier: 3.610A pdb=" N GLY C 174 " --> pdb=" O ALA C 170 " (cutoff:3.500A) 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 220 removed outlier: 3.502A pdb=" N ASN C 217 " --> pdb=" O CYS C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 250 Processing helix chain 'C' and resid 252 through 260 Processing helix chain 'C' and resid 280 through 285 removed outlier: 4.027A pdb=" N SER C 285 " --> pdb=" O THR C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 298 Processing helix chain 'C' and resid 302 through 310 removed outlier: 3.830A pdb=" N ARG C 305 " --> pdb=" O ARG C 302 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE C 307 " --> pdb=" O ALA C 304 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU C 308 " --> pdb=" O ARG C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 324 removed outlier: 3.909A 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: 3.686A pdb=" N LEU C 402 " --> pdb=" O ILE C 398 " (cutoff:3.500A) Proline residue: C 405 - end of helix removed outlier: 3.661A pdb=" N VAL C 410 " --> pdb=" O ASP C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 418 removed outlier: 3.613A pdb=" N PHE C 416 " --> pdb=" O ALA C 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 445 Processing helix chain 'C' and resid 450 through 464 Processing helix chain 'C' and resid 465 through 472 removed outlier: 3.563A pdb=" N ARG C 470 " --> pdb=" O TYR C 467 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLY C 471 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 488 Processing helix chain 'C' and resid 488 through 512 removed outlier: 3.978A pdb=" N ARG C 492 " --> pdb=" O GLY C 488 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N LEU C 496 " --> pdb=" O ARG C 492 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N VAL C 499 " --> pdb=" O TRP C 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 524 removed outlier: 4.465A pdb=" N PHE C 523 " --> pdb=" O LEU C 520 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N SER C 524 " --> pdb=" O GLY C 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 520 through 524' Processing helix chain 'C' and resid 525 through 538 Processing helix chain 'C' and resid 552 through 566 removed outlier: 3.576A pdb=" N CYS C 556 " --> pdb=" O PRO C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 605 removed outlier: 4.844A pdb=" N GLN C 587 " --> pdb=" O TRP C 583 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N GLU C 588 " --> pdb=" O ARG C 584 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASP C 590 " --> pdb=" O ALA C 586 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLU C 591 " --> pdb=" O GLN C 587 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG C 594 " --> pdb=" O ASP C 590 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL C 598 " --> pdb=" O ARG C 594 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA C 599 " --> pdb=" O ALA C 595 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 46 Processing helix chain 'D' and resid 47 through 56 Processing helix chain 'D' and resid 57 through 66 Processing helix chain 'D' and resid 81 through 89 Processing helix chain 'D' and resid 91 through 102 Processing helix chain 'D' and resid 103 through 108 removed outlier: 3.951A pdb=" N ALA D 106 " --> pdb=" O PRO D 103 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS D 107 " --> pdb=" O GLU D 104 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU D 108 " --> pdb=" O LEU D 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 103 through 108' Processing helix chain 'D' and resid 119 through 127 removed outlier: 3.767A pdb=" N ILE D 123 " --> pdb=" O THR D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 139 Processing helix chain 'D' and resid 165 through 174 removed outlier: 3.616A pdb=" N GLY D 174 " --> pdb=" O ALA D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 184 Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 210 through 220 removed outlier: 4.507A pdb=" N GLN D 214 " --> pdb=" O THR D 210 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N TYR D 216 " --> pdb=" O ALA D 212 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASN D 217 " --> pdb=" O CYS D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 250 Processing helix chain 'D' and resid 252 through 260 Processing helix chain 'D' and resid 280 through 285 removed outlier: 4.026A pdb=" N SER D 285 " --> pdb=" O THR D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 298 Processing helix chain 'D' and resid 302 through 310 removed outlier: 3.834A pdb=" N ARG D 305 " --> pdb=" O ARG D 302 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE D 307 " --> pdb=" O ALA D 304 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU D 308 " --> pdb=" O ARG D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 312 through 324 removed outlier: 3.911A 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: 3.744A pdb=" N LEU D 402 " --> pdb=" O ILE D 398 " (cutoff:3.500A) Proline residue: D 405 - end of helix removed outlier: 3.651A pdb=" N VAL D 410 " --> pdb=" O ASP D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 418 removed outlier: 3.664A pdb=" N PHE D 416 " --> pdb=" O ALA D 412 " (cutoff:3.500A) removed outlier: 3.719A 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 Processing helix chain 'D' and resid 465 through 472 removed outlier: 3.601A pdb=" N ARG D 470 " --> pdb=" O TYR D 467 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLY D 471 " --> pdb=" O PHE D 468 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE D 472 " --> pdb=" O ALA D 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 488 Processing helix chain 'D' and resid 489 through 512 removed outlier: 4.154A pdb=" N LEU D 496 " --> pdb=" O ARG D 492 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N VAL D 499 " --> pdb=" O TRP D 495 " (cutoff:3.500A) Processing helix chain 'D' and resid 520 through 524 removed outlier: 4.468A pdb=" N PHE D 523 " --> pdb=" O LEU D 520 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N SER D 524 " --> pdb=" O GLY D 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 520 through 524' Processing helix chain 'D' and resid 525 through 538 Processing helix chain 'D' and resid 552 through 566 removed outlier: 3.578A pdb=" N CYS D 556 " --> pdb=" O PRO D 552 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 605 removed outlier: 4.827A pdb=" N GLN D 587 " --> pdb=" O TRP D 583 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N GLU D 588 " --> pdb=" O ARG D 584 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ASP D 590 " --> pdb=" O ALA D 586 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N GLU D 591 " --> pdb=" O GLN D 587 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ARG D 594 " --> pdb=" O ASP D 590 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N VAL D 598 " --> pdb=" O ARG D 594 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA D 599 " --> pdb=" O ALA D 595 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 264 through 269 removed outlier: 7.006A pdb=" N SER A 275 " --> pdb=" O GLN A 267 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N THR A 269 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N LEU A 273 " --> pdb=" O THR A 269 " (cutoff:3.500A) 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 264 through 269 removed outlier: 7.005A pdb=" N SER B 275 " --> pdb=" O GLN B 267 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N THR B 269 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N LEU B 273 " --> pdb=" O THR B 269 " (cutoff:3.500A) 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 264 through 269 removed outlier: 7.005A pdb=" N SER C 275 " --> pdb=" O GLN C 267 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N THR C 269 " --> pdb=" O LEU C 273 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N LEU C 273 " --> pdb=" O THR C 269 " (cutoff:3.500A) 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 264 through 269 removed outlier: 7.008A pdb=" N SER D 275 " --> pdb=" O GLN D 267 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N THR D 269 " --> pdb=" O LEU D 273 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N LEU D 273 " --> pdb=" O THR D 269 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 352 through 354 1047 hydrogen bonds defined for protein. 3063 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: 6.16 Time building geometry restraints manager: 8.23 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: 5960 1.34 - 1.46: 3688 1.46 - 1.58: 9984 1.58 - 1.70: 0 1.70 - 1.82: 228 Bond restraints: 19860 Sorted by residual: bond pdb=" C ARG D 326 " pdb=" N PRO D 327 " ideal model delta sigma weight residual 1.336 1.365 -0.029 1.20e-02 6.94e+03 5.74e+00 bond pdb=" C ARG A 326 " pdb=" N PRO A 327 " ideal model delta sigma weight residual 1.336 1.365 -0.029 1.20e-02 6.94e+03 5.69e+00 bond pdb=" C ARG C 326 " pdb=" N PRO C 327 " ideal model delta sigma weight residual 1.336 1.365 -0.029 1.20e-02 6.94e+03 5.69e+00 bond pdb=" C ARG B 326 " pdb=" N PRO B 327 " ideal model delta sigma weight residual 1.336 1.364 -0.028 1.20e-02 6.94e+03 5.49e+00 bond pdb=" C THR C 311 " pdb=" N PRO C 312 " ideal model delta sigma weight residual 1.334 1.388 -0.054 2.34e-02 1.83e+03 5.38e+00 ... (remaining 19855 not shown) Histogram of bond angle deviations from ideal: 98.07 - 105.50: 390 105.50 - 112.93: 10224 112.93 - 120.36: 8490 120.36 - 127.79: 7658 127.79 - 135.22: 202 Bond angle restraints: 26964 Sorted by residual: angle pdb=" C ASP D 223 " pdb=" N GLU D 224 " pdb=" CA GLU D 224 " ideal model delta sigma weight residual 121.54 131.33 -9.79 1.91e+00 2.74e-01 2.63e+01 angle pdb=" C ASP C 223 " pdb=" N GLU C 224 " pdb=" CA GLU C 224 " ideal model delta sigma weight residual 121.54 131.28 -9.74 1.91e+00 2.74e-01 2.60e+01 angle pdb=" C ASP A 223 " pdb=" N GLU A 224 " pdb=" CA GLU A 224 " ideal model delta sigma weight residual 121.54 131.25 -9.71 1.91e+00 2.74e-01 2.58e+01 angle pdb=" C ASP B 223 " pdb=" N GLU B 224 " pdb=" CA GLU B 224 " ideal model delta sigma weight residual 121.54 131.21 -9.67 1.91e+00 2.74e-01 2.56e+01 angle pdb=" C GLU A 605 " pdb=" N ARG A 606 " pdb=" CA ARG A 606 " ideal model delta sigma weight residual 123.91 131.48 -7.57 1.66e+00 3.63e-01 2.08e+01 ... (remaining 26959 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 10631 17.85 - 35.69: 953 35.69 - 53.54: 183 53.54 - 71.38: 36 71.38 - 89.23: 9 Dihedral angle restraints: 11812 sinusoidal: 4732 harmonic: 7080 Sorted by residual: dihedral pdb=" CA MET D 485 " pdb=" C MET D 485 " pdb=" N ILE D 486 " pdb=" CA ILE D 486 " ideal model delta harmonic sigma weight residual 180.00 152.59 27.41 0 5.00e+00 4.00e-02 3.01e+01 dihedral pdb=" CA MET B 485 " pdb=" C MET B 485 " pdb=" N ILE B 486 " pdb=" CA ILE B 486 " ideal model delta harmonic sigma weight residual 180.00 152.86 27.14 0 5.00e+00 4.00e-02 2.95e+01 dihedral pdb=" CA MET A 485 " pdb=" C MET A 485 " pdb=" N ILE A 486 " pdb=" CA ILE A 486 " ideal model delta harmonic sigma weight residual 180.00 158.01 21.99 0 5.00e+00 4.00e-02 1.93e+01 ... (remaining 11809 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 2894 0.112 - 0.225: 164 0.225 - 0.337: 11 0.337 - 0.450: 0 0.450 - 0.562: 3 Chirality restraints: 3072 Sorted by residual: chirality pdb=" CB VAL B 585 " pdb=" CA VAL B 585 " pdb=" CG1 VAL B 585 " pdb=" CG2 VAL B 585 " both_signs ideal model delta sigma weight residual False -2.63 -2.07 -0.56 2.00e-01 2.50e+01 7.89e+00 chirality pdb=" CB VAL D 585 " pdb=" CA VAL D 585 " pdb=" CG1 VAL D 585 " pdb=" CG2 VAL D 585 " both_signs ideal model delta sigma weight residual False -2.63 -2.07 -0.56 2.00e-01 2.50e+01 7.71e+00 chirality pdb=" CB VAL C 585 " pdb=" CA VAL C 585 " pdb=" CG1 VAL C 585 " pdb=" CG2 VAL C 585 " both_signs ideal model delta sigma weight residual False -2.63 -2.08 -0.55 2.00e-01 2.50e+01 7.67e+00 ... (remaining 3069 not shown) Planarity restraints: 3416 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 456 " -0.026 2.00e-02 2.50e+03 1.98e-02 6.89e+00 pdb=" CG PHE C 456 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 PHE C 456 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE C 456 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE C 456 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE C 456 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE C 456 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 456 " -0.026 2.00e-02 2.50e+03 1.96e-02 6.70e+00 pdb=" CG PHE B 456 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 PHE B 456 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE B 456 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE B 456 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 456 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE B 456 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 456 " -0.026 2.00e-02 2.50e+03 1.95e-02 6.69e+00 pdb=" CG PHE D 456 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 PHE D 456 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE D 456 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE D 456 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE D 456 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE D 456 " -0.011 2.00e-02 2.50e+03 ... (remaining 3413 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 5830 2.83 - 3.35: 17302 3.35 - 3.87: 32794 3.87 - 4.38: 37888 4.38 - 4.90: 65135 Nonbonded interactions: 158949 Sorted by model distance: nonbonded pdb=" OD1 ASP B 525 " pdb=" OG1 THR B 528 " model vdw 2.313 2.440 nonbonded pdb=" OD1 ASP C 525 " pdb=" OG1 THR C 528 " model vdw 2.313 2.440 nonbonded pdb=" OD1 ASP D 525 " pdb=" OG1 THR D 528 " model vdw 2.313 2.440 nonbonded pdb=" OD1 ASP A 525 " pdb=" OG1 THR A 528 " model vdw 2.313 2.440 nonbonded pdb=" O THR A 479 " pdb=" NE2 GLN A 483 " model vdw 2.338 2.520 ... (remaining 158944 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: 1.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.830 Check model and map are aligned: 0.320 Set scattering table: 0.200 Process input model: 51.650 Find NCS groups from input model: 1.320 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:12.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 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 : 0.005 0.062 19860 Z= 0.329 Angle : 1.050 10.300 26964 Z= 0.560 Chirality : 0.060 0.562 3072 Planarity : 0.008 0.062 3416 Dihedral : 14.248 89.227 7236 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.05 % Allowed : 0.43 % Favored : 99.52 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.51 (0.13), residues: 2408 helix: -2.28 (0.10), residues: 1452 sheet: -1.59 (0.49), residues: 88 loop : -2.20 (0.17), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 593 HIS 0.009 0.001 HIS B 201 PHE 0.044 0.003 PHE C 456 TYR 0.024 0.002 TYR A 339 ARG 0.003 0.000 ARG C 606 *********************** 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 357 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 356 time to evaluate : 2.284 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 357 average time/residue: 1.2046 time to fit residues: 488.2737 Evaluate side-chains 230 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 230 time to evaluate : 2.098 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.8400 ------------------------------------------------------------------------------- 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: 4.9990 chunk 100 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 188 optimal weight: 0.0070 chunk 72 optimal weight: 9.9990 chunk 114 optimal weight: 0.9990 chunk 140 optimal weight: 2.9990 chunk 217 optimal weight: 5.9990 overall best weight: 1.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 ASN A 230 GLN A 369 GLN ** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 636 HIS B 230 GLN B 369 GLN B 636 HIS C 230 GLN C 369 GLN C 636 HIS D 230 GLN D 369 GLN D 636 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 19860 Z= 0.281 Angle : 0.633 9.332 26964 Z= 0.319 Chirality : 0.042 0.157 3072 Planarity : 0.005 0.036 3416 Dihedral : 4.608 21.013 2644 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.62 % Allowed : 9.97 % Favored : 87.40 % 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: -1.27 (0.16), residues: 2408 helix: -0.30 (0.13), residues: 1468 sheet: -1.97 (0.49), residues: 96 loop : -1.48 (0.19), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 462 HIS 0.005 0.001 HIS A 201 PHE 0.020 0.002 PHE D 456 TYR 0.013 0.001 TYR B 222 ARG 0.004 0.000 ARG C 589 *********************** 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 301 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 246 time to evaluate : 2.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 55 outliers final: 24 residues processed: 275 average time/residue: 1.3024 time to fit residues: 407.0949 Evaluate side-chains 232 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 208 time to evaluate : 2.026 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 16 residues processed: 8 average time/residue: 0.6356 time to fit residues: 9.1329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 121 optimal weight: 7.9990 chunk 67 optimal weight: 9.9990 chunk 181 optimal weight: 7.9990 chunk 148 optimal weight: 1.9990 chunk 60 optimal weight: 7.9990 chunk 218 optimal weight: 6.9990 chunk 235 optimal weight: 5.9990 chunk 194 optimal weight: 2.9990 chunk 216 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 175 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 374 GLN B 37 ASN B 230 GLN C 31 GLN C 37 ASN C 230 GLN D 37 ASN D 230 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.2429 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= 0.346 Angle : 0.635 6.282 26964 Z= 0.323 Chirality : 0.044 0.151 3072 Planarity : 0.004 0.043 3416 Dihedral : 4.537 22.956 2644 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 4.91 % Allowed : 12.40 % Favored : 82.68 % 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: -0.62 (0.16), residues: 2408 helix: 0.25 (0.13), residues: 1468 sheet: -1.51 (0.49), residues: 88 loop : -1.35 (0.20), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 462 HIS 0.006 0.001 HIS B 201 PHE 0.012 0.002 PHE A 72 TYR 0.010 0.001 TYR A 547 ARG 0.005 0.000 ARG C 589 *********************** 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 308 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 205 time to evaluate : 2.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 103 outliers final: 39 residues processed: 275 average time/residue: 1.3010 time to fit residues: 405.0850 Evaluate side-chains 233 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 194 time to evaluate : 2.265 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 31 residues processed: 8 average time/residue: 1.4966 time to fit residues: 16.2750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 215 optimal weight: 5.9990 chunk 164 optimal weight: 0.9990 chunk 113 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 104 optimal weight: 0.6980 chunk 146 optimal weight: 3.9990 chunk 219 optimal weight: 0.8980 chunk 231 optimal weight: 0.9990 chunk 114 optimal weight: 0.8980 chunk 207 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 GLN B 31 GLN C 31 GLN D 31 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19860 Z= 0.184 Angle : 0.553 7.608 26964 Z= 0.281 Chirality : 0.040 0.257 3072 Planarity : 0.004 0.043 3416 Dihedral : 4.220 18.633 2644 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 4.06 % Allowed : 14.27 % Favored : 81.68 % 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: 0.78 (0.14), residues: 1468 sheet: -0.89 (0.52), residues: 88 loop : -1.10 (0.20), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 462 HIS 0.004 0.001 HIS B 201 PHE 0.011 0.001 PHE D 456 TYR 0.010 0.001 TYR B 222 ARG 0.006 0.000 ARG D 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 300 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 215 time to evaluate : 2.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 85 outliers final: 32 residues processed: 268 average time/residue: 1.2417 time to fit residues: 378.2483 Evaluate side-chains 227 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 195 time to evaluate : 2.204 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 21 residues processed: 11 average time/residue: 1.0796 time to fit residues: 16.6861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 8.9990 chunk 3 optimal weight: 2.9990 chunk 172 optimal weight: 0.8980 chunk 95 optimal weight: 5.9990 chunk 197 optimal weight: 2.9990 chunk 160 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 118 optimal weight: 6.9990 chunk 208 optimal weight: 0.1980 chunk 58 optimal weight: 4.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 GLN B 206 GLN B 230 GLN C 206 GLN C 230 GLN D 206 GLN D 230 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 19860 Z= 0.346 Angle : 0.614 7.346 26964 Z= 0.313 Chirality : 0.044 0.158 3072 Planarity : 0.004 0.044 3416 Dihedral : 4.365 21.173 2644 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 4.44 % Allowed : 14.60 % Favored : 80.96 % 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: 0.02 (0.17), residues: 2408 helix: 0.75 (0.14), residues: 1468 sheet: -1.01 (0.50), residues: 88 loop : -1.09 (0.20), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 593 HIS 0.007 0.001 HIS D 201 PHE 0.011 0.002 PHE B 425 TYR 0.011 0.001 TYR D 547 ARG 0.006 0.000 ARG C 180 *********************** 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 290 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 197 time to evaluate : 2.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 93 outliers final: 38 residues processed: 269 average time/residue: 1.2176 time to fit residues: 372.4289 Evaluate side-chains 227 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 189 time to evaluate : 2.260 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 32 residues processed: 6 average time/residue: 1.5615 time to fit residues: 13.4115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 78 optimal weight: 7.9990 chunk 208 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 136 optimal weight: 6.9990 chunk 57 optimal weight: 0.9990 chunk 232 optimal weight: 0.1980 chunk 192 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 76 optimal weight: 4.9990 chunk 121 optimal weight: 1.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 GLN B 74 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19860 Z= 0.180 Angle : 0.546 7.473 26964 Z= 0.279 Chirality : 0.040 0.301 3072 Planarity : 0.004 0.043 3416 Dihedral : 4.133 16.903 2644 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 3.58 % Allowed : 16.56 % Favored : 79.87 % 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: 0.39 (0.17), residues: 2408 helix: 1.05 (0.14), residues: 1468 sheet: -0.80 (0.50), residues: 88 loop : -0.95 (0.21), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 593 HIS 0.004 0.001 HIS C 201 PHE 0.008 0.001 PHE B 534 TYR 0.009 0.001 TYR C 216 ARG 0.010 0.000 ARG A 180 *********************** 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 280 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 205 time to evaluate : 2.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 75 outliers final: 36 residues processed: 270 average time/residue: 1.1514 time to fit residues: 357.1055 Evaluate side-chains 229 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 193 time to evaluate : 2.426 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 32 residues processed: 4 average time/residue: 1.8598 time to fit residues: 11.2992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 223 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 132 optimal weight: 2.9990 chunk 169 optimal weight: 0.9990 chunk 131 optimal weight: 20.0000 chunk 195 optimal weight: 0.9990 chunk 129 optimal weight: 0.0570 chunk 231 optimal weight: 0.7980 chunk 144 optimal weight: 5.9990 chunk 141 optimal weight: 0.8980 chunk 106 optimal weight: 0.7980 overall best weight: 0.7100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 GLN C 230 GLN D 230 GLN D 483 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 19860 Z= 0.170 Angle : 0.541 7.779 26964 Z= 0.275 Chirality : 0.039 0.162 3072 Planarity : 0.004 0.041 3416 Dihedral : 4.015 16.100 2644 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.67 % Allowed : 16.60 % Favored : 79.72 % 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: 0.56 (0.17), residues: 2408 helix: 1.17 (0.14), residues: 1468 sheet: -0.86 (0.50), residues: 88 loop : -0.84 (0.21), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 495 HIS 0.003 0.000 HIS B 201 PHE 0.013 0.001 PHE A 456 TYR 0.008 0.001 TYR C 216 ARG 0.008 0.000 ARG A 180 *********************** REFINEMENT MACRO_CYCLE 7 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 273 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 196 time to evaluate : 2.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 77 outliers final: 43 residues processed: 259 average time/residue: 1.2405 time to fit residues: 367.4572 Evaluate side-chains 234 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 191 time to evaluate : 2.522 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 39 residues processed: 4 average time/residue: 1.9032 time to fit residues: 11.3629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 143 optimal weight: 5.9990 chunk 92 optimal weight: 7.9990 chunk 138 optimal weight: 8.9990 chunk 69 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 147 optimal weight: 0.7980 chunk 157 optimal weight: 0.8980 chunk 114 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 181 optimal weight: 7.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 230 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.2769 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= 0.210 Angle : 0.564 9.085 26964 Z= 0.286 Chirality : 0.040 0.182 3072 Planarity : 0.004 0.039 3416 Dihedral : 4.016 16.040 2644 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.20 % Allowed : 17.56 % Favored : 79.25 % 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: 0.59 (0.17), residues: 2408 helix: 1.20 (0.14), residues: 1468 sheet: -0.89 (0.49), residues: 88 loop : -0.83 (0.21), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 495 HIS 0.004 0.001 HIS B 201 PHE 0.011 0.001 PHE A 456 TYR 0.007 0.001 TYR C 216 ARG 0.007 0.000 ARG A 180 *********************** REFINEMENT MACRO_CYCLE 8 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 263 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 196 time to evaluate : 2.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 67 outliers final: 50 residues processed: 251 average time/residue: 1.2049 time to fit residues: 346.6297 Evaluate side-chains 237 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 187 time to evaluate : 2.452 Switching outliers to nearest non-outliers outliers start: 50 outliers final: 46 residues processed: 4 average time/residue: 1.7421 time to fit residues: 10.5528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 210 optimal weight: 3.9990 chunk 221 optimal weight: 0.8980 chunk 202 optimal weight: 0.9980 chunk 215 optimal weight: 2.9990 chunk 129 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 169 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 194 optimal weight: 4.9990 chunk 203 optimal weight: 0.9990 chunk 214 optimal weight: 5.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 19860 Z= 0.198 Angle : 0.564 7.663 26964 Z= 0.284 Chirality : 0.040 0.202 3072 Planarity : 0.004 0.039 3416 Dihedral : 4.001 17.360 2644 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.20 % Allowed : 17.65 % Favored : 79.15 % 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: 0.63 (0.17), residues: 2408 helix: 1.24 (0.14), residues: 1468 sheet: -0.92 (0.49), residues: 88 loop : -0.81 (0.21), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 495 HIS 0.004 0.001 HIS A 201 PHE 0.012 0.001 PHE A 456 TYR 0.008 0.001 TYR C 216 ARG 0.006 0.000 ARG A 180 *********************** REFINEMENT MACRO_CYCLE 9 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 254 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 187 time to evaluate : 2.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 67 outliers final: 52 residues processed: 246 average time/residue: 1.2723 time to fit residues: 361.2247 Evaluate side-chains 240 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 188 time to evaluate : 2.194 Switching outliers to nearest non-outliers outliers start: 52 outliers final: 48 residues processed: 4 average time/residue: 1.8842 time to fit residues: 11.3355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 141 optimal weight: 1.9990 chunk 227 optimal weight: 0.9990 chunk 139 optimal weight: 7.9990 chunk 108 optimal weight: 0.8980 chunk 158 optimal weight: 4.9990 chunk 239 optimal weight: 0.9990 chunk 220 optimal weight: 2.9990 chunk 190 optimal weight: 0.0370 chunk 19 optimal weight: 0.9990 chunk 147 optimal weight: 0.6980 chunk 116 optimal weight: 0.9990 overall best weight: 0.7262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 230 GLN D 230 GLN ** D 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 19860 Z= 0.173 Angle : 0.552 10.008 26964 Z= 0.276 Chirality : 0.039 0.202 3072 Planarity : 0.004 0.038 3416 Dihedral : 3.903 17.577 2644 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.01 % Allowed : 17.84 % Favored : 79.15 % 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: 0.76 (0.17), residues: 2408 helix: 1.33 (0.14), residues: 1472 sheet: -0.84 (0.48), residues: 88 loop : -0.76 (0.21), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 495 HIS 0.004 0.001 HIS B 201 PHE 0.015 0.001 PHE A 456 TYR 0.008 0.001 TYR C 216 ARG 0.007 0.000 ARG A 180 ********************** REFINEMENT MACRO_CYCLE 10 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 263 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 200 time to evaluate : 2.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 63 outliers final: 49 residues processed: 255 average time/residue: 1.2014 time to fit residues: 349.7797 Evaluate side-chains 242 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 193 time to evaluate : 1.734 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 45 residues processed: 4 average time/residue: 1.5019 time to fit residues: 8.9732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 151 optimal weight: 0.9990 chunk 202 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 175 optimal weight: 6.9990 chunk 28 optimal weight: 0.5980 chunk 52 optimal weight: 0.5980 chunk 190 optimal weight: 6.9990 chunk 79 optimal weight: 0.6980 chunk 195 optimal weight: 0.9980 chunk 24 optimal weight: 0.5980 chunk 35 optimal weight: 5.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 483 GLN ** D 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.140132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.111461 restraints weight = 24625.235| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 1.80 r_work: 0.3137 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 19860 Z= 0.176 Angle : 0.555 7.352 26964 Z= 0.281 Chirality : 0.039 0.203 3072 Planarity : 0.004 0.037 3416 Dihedral : 3.881 18.332 2644 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.96 % Allowed : 18.18 % Favored : 78.86 % 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: 0.83 (0.17), residues: 2408 helix: 1.36 (0.14), residues: 1480 sheet: -0.78 (0.48), residues: 88 loop : -0.68 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 495 HIS 0.004 0.001 HIS B 201 PHE 0.023 0.001 PHE A 456 TYR 0.008 0.001 TYR C 216 ARG 0.007 0.000 ARG A 180 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6425.03 seconds wall clock time: 117 minutes 48.34 seconds (7068.34 seconds total)