Starting phenix.real_space_refine (version: dev) on Sun Feb 19 02:50:15 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oji_12952/02_2023/7oji_12952_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oji_12952/02_2023/7oji_12952.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oji_12952/02_2023/7oji_12952.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oji_12952/02_2023/7oji_12952.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oji_12952/02_2023/7oji_12952_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oji_12952/02_2023/7oji_12952_trim_updated.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.005 sd= 0.040 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 Process input model Symmetric amino acids flipped Residue "A ARG 96": "NH1" <-> "NH2" Residue "A PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 419": "OD1" <-> "OD2" Residue "A ARG 426": "NH1" <-> "NH2" Residue "A PHE 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 507": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 551": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 570": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 605": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 419": "OD1" <-> "OD2" Residue "B ARG 426": "NH1" <-> "NH2" Residue "B PHE 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 507": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 551": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 570": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 605": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 9195 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 572, 4453 Classifications: {'peptide': 572} Link IDs: {'PTRANS': 20, 'TRANS': 551} Chain breaks: 3 Chain: "B" Number of atoms: 4453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 572, 4453 Classifications: {'peptide': 572} Link IDs: {'PTRANS': 20, 'TRANS': 551} Chain breaks: 3 Chain: "A" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 160 Unusual residues: {'ATP': 1, 'CLR': 2, 'PLC': 1, 'TTC': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 1, 'CLR': 2, 'PLC': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 5.59, per 1000 atoms: 0.61 Number of scatterers: 9195 At special positions: 0 Unit cell: (100.98, 91.74, 128.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 58 16.00 P 8 15.00 O 1649 8.00 N 1483 7.00 C 5997 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 592 " - pdb=" SG CYS A 608 " distance=2.03 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS B 603 " distance=2.02 Simple disulfide: pdb=" SG CYS B 592 " - pdb=" SG CYS B 608 " distance=2.03 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: 3.49 Conformation dependent library (CDL) restraints added in 1.3 seconds 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2116 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 48 helices and 4 sheets defined 58.4% alpha, 6.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.32 Creating SS restraints... Processing helix chain 'A' and resid 86 through 93 Processing helix chain 'A' and resid 117 through 119 No H-bonds generated for 'chain 'A' and resid 117 through 119' Processing helix chain 'A' and resid 136 through 147 Processing helix chain 'A' and resid 154 through 168 Processing helix chain 'A' and resid 171 through 173 No H-bonds generated for 'chain 'A' and resid 171 through 173' Processing helix chain 'A' and resid 188 through 202 removed outlier: 3.828A pdb=" N GLU A 199 " --> pdb=" O SER A 195 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N THR A 202 " --> pdb=" O MET A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 234 removed outlier: 4.563A pdb=" N GLN A 234 " --> pdb=" O ARG A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 252 removed outlier: 3.607A pdb=" N LEU A 252 " --> pdb=" O SER A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 280 removed outlier: 4.506A pdb=" N LEU A 274 " --> pdb=" O ALA A 270 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N GLY A 275 " --> pdb=" O GLN A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 298 removed outlier: 3.577A pdb=" N ILE A 298 " --> pdb=" O PHE A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 337 Processing helix chain 'A' and resid 340 through 352 Processing helix chain 'A' and resid 373 through 390 Processing helix chain 'A' and resid 396 through 412 Processing helix chain 'A' and resid 420 through 461 removed outlier: 4.076A pdb=" N ILE A 423 " --> pdb=" O SER A 420 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA A 427 " --> pdb=" O GLN A 424 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER A 440 " --> pdb=" O GLN A 437 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER A 441 " --> pdb=" O CYS A 438 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N VAL A 442 " --> pdb=" O PHE A 439 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N SER A 443 " --> pdb=" O SER A 440 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL A 445 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N VAL A 450 " --> pdb=" O LEU A 447 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLU A 451 " --> pdb=" O PHE A 448 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N LYS A 453 " --> pdb=" O VAL A 450 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER A 461 " --> pdb=" O GLU A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 476 Processing helix chain 'A' and resid 478 through 497 removed outlier: 3.654A pdb=" N ARG A 482 " --> pdb=" O LEU A 478 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N MET A 483 " --> pdb=" O LEU A 479 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU A 484 " --> pdb=" O PRO A 480 " (cutoff:3.500A) Proline residue: A 485 - end of helix removed outlier: 4.757A pdb=" N PHE A 495 " --> pdb=" O CYS A 491 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N MET A 496 " --> pdb=" O ILE A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 528 Processing helix chain 'A' and resid 534 through 551 removed outlier: 3.976A pdb=" N PHE A 551 " --> pdb=" O PHE A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 571 removed outlier: 3.529A pdb=" N TYR A 570 " --> pdb=" O TRP A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 586 removed outlier: 3.608A pdb=" N ASN A 584 " --> pdb=" O ALA A 580 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU A 585 " --> pdb=" O LEU A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 600 Processing helix chain 'A' and resid 610 through 616 Processing helix chain 'A' and resid 623 through 649 removed outlier: 4.873A pdb=" N LYS A 628 " --> pdb=" O GLY A 625 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 93 Processing helix chain 'B' and resid 117 through 119 No H-bonds generated for 'chain 'B' and resid 117 through 119' Processing helix chain 'B' and resid 136 through 147 Processing helix chain 'B' and resid 154 through 168 Processing helix chain 'B' and resid 171 through 173 No H-bonds generated for 'chain 'B' and resid 171 through 173' Processing helix chain 'B' and resid 188 through 202 removed outlier: 3.829A pdb=" N GLU B 199 " --> pdb=" O SER B 195 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N THR B 202 " --> pdb=" O MET B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 234 removed outlier: 4.564A pdb=" N GLN B 234 " --> pdb=" O ARG B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 252 removed outlier: 3.606A pdb=" N LEU B 252 " --> pdb=" O SER B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 280 removed outlier: 4.506A pdb=" N LEU B 274 " --> pdb=" O ALA B 270 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N GLY B 275 " --> pdb=" O GLN B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 298 removed outlier: 3.576A pdb=" N ILE B 298 " --> pdb=" O PHE B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 337 Processing helix chain 'B' and resid 340 through 352 Processing helix chain 'B' and resid 373 through 390 Processing helix chain 'B' and resid 396 through 412 Processing helix chain 'B' and resid 420 through 461 removed outlier: 4.076A pdb=" N ILE B 423 " --> pdb=" O SER B 420 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA B 427 " --> pdb=" O GLN B 424 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER B 440 " --> pdb=" O GLN B 437 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER B 441 " --> pdb=" O CYS B 438 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N VAL B 442 " --> pdb=" O PHE B 439 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N SER B 443 " --> pdb=" O SER B 440 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL B 445 " --> pdb=" O VAL B 442 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N VAL B 450 " --> pdb=" O LEU B 447 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLU B 451 " --> pdb=" O PHE B 448 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N LYS B 453 " --> pdb=" O VAL B 450 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER B 461 " --> pdb=" O GLU B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 476 Processing helix chain 'B' and resid 478 through 497 removed outlier: 3.653A pdb=" N ARG B 482 " --> pdb=" O LEU B 478 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N MET B 483 " --> pdb=" O LEU B 479 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU B 484 " --> pdb=" O PRO B 480 " (cutoff:3.500A) Proline residue: B 485 - end of helix removed outlier: 4.757A pdb=" N PHE B 495 " --> pdb=" O CYS B 491 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N MET B 496 " --> pdb=" O ILE B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 528 Processing helix chain 'B' and resid 534 through 551 removed outlier: 3.976A pdb=" N PHE B 551 " --> pdb=" O PHE B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 566 through 571 removed outlier: 3.528A pdb=" N TYR B 570 " --> pdb=" O TRP B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 586 removed outlier: 3.607A pdb=" N ASN B 584 " --> pdb=" O ALA B 580 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU B 585 " --> pdb=" O LEU B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 595 through 600 Processing helix chain 'B' and resid 610 through 616 Processing helix chain 'B' and resid 623 through 649 removed outlier: 4.874A pdb=" N LYS B 628 " --> pdb=" O GLY B 625 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 69 through 71 removed outlier: 3.557A pdb=" N GLY A 69 " --> pdb=" O PHE A 39 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASP A 105 " --> pdb=" O HIS A 40 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 263 through 268 removed outlier: 6.918A pdb=" N LEU A 258 " --> pdb=" O MET A 265 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N HIS A 267 " --> pdb=" O LEU A 256 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N LEU A 256 " --> pdb=" O HIS A 267 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ILE A 242 " --> pdb=" O ILE A 78 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N GLY A 80 " --> pdb=" O ILE A 242 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 69 through 71 removed outlier: 3.557A pdb=" N GLY B 69 " --> pdb=" O PHE B 39 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASP B 105 " --> pdb=" O HIS B 40 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 263 through 268 removed outlier: 6.917A pdb=" N LEU B 258 " --> pdb=" O MET B 265 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N HIS B 267 " --> pdb=" O LEU B 256 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N LEU B 256 " --> pdb=" O HIS B 267 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ILE B 242 " --> pdb=" O ILE B 78 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N GLY B 80 " --> pdb=" O ILE B 242 " (cutoff:3.500A) 474 hydrogen bonds defined for protein. 1086 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: 2.28 Time building geometry restraints manager: 3.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1414 1.31 - 1.44: 2486 1.44 - 1.57: 5370 1.57 - 1.69: 37 1.69 - 1.82: 94 Bond restraints: 9401 Sorted by residual: bond pdb=" C5 ATP A 705 " pdb=" N7 ATP A 705 " ideal model delta sigma weight residual 1.387 1.524 -0.137 1.00e-02 1.00e+04 1.88e+02 bond pdb=" C5 ATP B 704 " pdb=" N7 ATP B 704 " ideal model delta sigma weight residual 1.387 1.524 -0.137 1.00e-02 1.00e+04 1.86e+02 bond pdb=" C6 ATP B 704 " pdb=" N6 ATP B 704 " ideal model delta sigma weight residual 1.337 1.451 -0.114 1.10e-02 8.26e+03 1.06e+02 bond pdb=" C6 ATP A 705 " pdb=" N6 ATP A 705 " ideal model delta sigma weight residual 1.337 1.449 -0.112 1.10e-02 8.26e+03 1.04e+02 bond pdb=" C4 ATP B 704 " pdb=" N9 ATP B 704 " ideal model delta sigma weight residual 1.374 1.272 0.102 1.00e-02 1.00e+04 1.04e+02 ... (remaining 9396 not shown) Histogram of bond angle deviations from ideal: 98.26 - 106.53: 276 106.53 - 114.80: 5760 114.80 - 123.07: 6307 123.07 - 131.34: 393 131.34 - 139.61: 17 Bond angle restraints: 12753 Sorted by residual: angle pdb=" PB ATP B 704 " pdb=" O3B ATP B 704 " pdb=" PG ATP B 704 " ideal model delta sigma weight residual 139.87 121.04 18.83 1.00e+00 1.00e+00 3.55e+02 angle pdb=" PB ATP A 705 " pdb=" O3B ATP A 705 " pdb=" PG ATP A 705 " ideal model delta sigma weight residual 139.87 122.31 17.56 1.00e+00 1.00e+00 3.08e+02 angle pdb=" C4 ATP B 704 " pdb=" N9 ATP B 704 " pdb=" C8 ATP B 704 " ideal model delta sigma weight residual 105.72 121.81 -16.09 1.00e+00 1.00e+00 2.59e+02 angle pdb=" C4 ATP A 705 " pdb=" N9 ATP A 705 " pdb=" C8 ATP A 705 " ideal model delta sigma weight residual 105.72 121.70 -15.98 1.00e+00 1.00e+00 2.55e+02 angle pdb=" PA ATP B 704 " pdb=" O3A ATP B 704 " pdb=" PB ATP B 704 " ideal model delta sigma weight residual 136.83 121.22 15.61 1.00e+00 1.00e+00 2.44e+02 ... (remaining 12748 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.35: 4975 14.35 - 28.70: 393 28.70 - 43.06: 99 43.06 - 57.41: 13 57.41 - 71.76: 11 Dihedral angle restraints: 5491 sinusoidal: 2195 harmonic: 3296 Sorted by residual: dihedral pdb=" CA HIS B 283 " pdb=" C HIS B 283 " pdb=" N CYS B 284 " pdb=" CA CYS B 284 " ideal model delta harmonic sigma weight residual -180.00 -146.86 -33.14 0 5.00e+00 4.00e-02 4.39e+01 dihedral pdb=" CA HIS A 283 " pdb=" C HIS A 283 " pdb=" N CYS A 284 " pdb=" CA CYS A 284 " ideal model delta harmonic sigma weight residual -180.00 -146.92 -33.08 0 5.00e+00 4.00e-02 4.38e+01 dihedral pdb=" CA VAL B 493 " pdb=" C VAL B 493 " pdb=" N TYR B 494 " pdb=" CA TYR B 494 " ideal model delta harmonic sigma weight residual -180.00 -159.59 -20.41 0 5.00e+00 4.00e-02 1.67e+01 ... (remaining 5488 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.323: 1461 0.323 - 0.647: 4 0.647 - 0.970: 0 0.970 - 1.294: 0 1.294 - 1.617: 2 Chirality restraints: 1467 Sorted by residual: chirality pdb=" CG LEU B 595 " pdb=" CB LEU B 595 " pdb=" CD1 LEU B 595 " pdb=" CD2 LEU B 595 " both_signs ideal model delta sigma weight residual False -2.59 -0.97 -1.62 2.00e-01 2.50e+01 6.54e+01 chirality pdb=" CG LEU A 595 " pdb=" CB LEU A 595 " pdb=" CD1 LEU A 595 " pdb=" CD2 LEU A 595 " both_signs ideal model delta sigma weight residual False -2.59 -0.97 -1.62 2.00e-01 2.50e+01 6.52e+01 chirality pdb=" C21 TTC A 701 " pdb=" C16 TTC A 701 " pdb=" C20 TTC A 701 " pdb=" O24 TTC A 701 " both_signs ideal model delta sigma weight residual False -2.50 -2.98 0.47 2.00e-01 2.50e+01 5.63e+00 ... (remaining 1464 not shown) Planarity restraints: 1542 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 TTC A 701 " 0.009 2.00e-02 2.50e+03 1.08e-02 6.46e+00 pdb=" C11 TTC A 701 " 0.001 2.00e-02 2.50e+03 pdb=" C13 TTC A 701 " 0.009 2.00e-02 2.50e+03 pdb=" C14 TTC A 701 " 0.008 2.00e-02 2.50e+03 pdb=" C15 TTC A 701 " 0.004 2.00e-02 2.50e+03 pdb=" C16 TTC A 701 " 0.019 2.00e-02 2.50e+03 pdb=" C17 TTC A 701 " 0.007 2.00e-02 2.50e+03 pdb=" C19 TTC A 701 " -0.007 2.00e-02 2.50e+03 pdb=" C2 TTC A 701 " 0.004 2.00e-02 2.50e+03 pdb=" C21 TTC A 701 " -0.033 2.00e-02 2.50e+03 pdb=" C27 TTC A 701 " -0.022 2.00e-02 2.50e+03 pdb=" C3 TTC A 701 " 0.010 2.00e-02 2.50e+03 pdb=" C4 TTC A 701 " 0.001 2.00e-02 2.50e+03 pdb=" C5 TTC A 701 " 0.001 2.00e-02 2.50e+03 pdb=" C6 TTC A 701 " 0.004 2.00e-02 2.50e+03 pdb=" C7 TTC A 701 " -0.005 2.00e-02 2.50e+03 pdb=" C8 TTC A 701 " 0.001 2.00e-02 2.50e+03 pdb=" C9 TTC A 701 " -0.002 2.00e-02 2.50e+03 pdb=" N10 TTC A 701 " -0.007 2.00e-02 2.50e+03 pdb=" N12 TTC A 701 " 0.006 2.00e-02 2.50e+03 pdb=" O18 TTC A 701 " -0.001 2.00e-02 2.50e+03 pdb=" O26 TTC A 701 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A 211 " 0.024 5.00e-02 4.00e+02 3.66e-02 2.15e+00 pdb=" N PRO A 212 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 212 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 212 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 211 " -0.024 5.00e-02 4.00e+02 3.65e-02 2.13e+00 pdb=" N PRO B 212 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO B 212 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 212 " -0.020 5.00e-02 4.00e+02 ... (remaining 1539 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1829 2.77 - 3.30: 9251 3.30 - 3.83: 14408 3.83 - 4.37: 17239 4.37 - 4.90: 30144 Nonbonded interactions: 72871 Sorted by model distance: nonbonded pdb=" O GLY B 594 " pdb=" OG1 THR B 598 " model vdw 2.231 2.440 nonbonded pdb=" O GLY A 594 " pdb=" OG1 THR A 598 " model vdw 2.232 2.440 nonbonded pdb=" OD1 ASP B 91 " pdb=" OH TYR B 123 " model vdw 2.297 2.440 nonbonded pdb=" OD1 ASP A 91 " pdb=" OH TYR A 123 " model vdw 2.298 2.440 nonbonded pdb=" O TYR B 336 " pdb=" OG SER B 339 " model vdw 2.312 2.440 ... (remaining 72866 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' and (resid 34 through 654 or resid 702 through 703)) selection = (chain 'B' and (resid 34 through 654 or resid 702 through 703)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 58 5.16 5 C 5997 2.51 5 N 1483 2.21 5 O 1649 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 3.800 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: 12.050 Check model and map are aligned: 0.150 Process input model: 26.400 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.090 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:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 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 : 0.012 0.195 9401 Z= 0.826 Angle : 1.079 18.833 12753 Z= 0.646 Chirality : 0.080 1.617 1467 Planarity : 0.004 0.037 1542 Dihedral : 11.462 71.759 3366 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.79 % Favored : 95.04 % Rotamer Outliers : 0.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -0.15 (0.24), residues: 1128 helix: 1.03 (0.19), residues: 672 sheet: -1.28 (0.50), residues: 82 loop : -1.91 (0.31), residues: 374 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 178 time to evaluate : 1.094 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 182 average time/residue: 0.2503 time to fit residues: 61.0114 Evaluate side-chains 92 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 89 time to evaluate : 1.006 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1006 time to fit residues: 1.9131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 29 optimal weight: 5.9990 chunk 58 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 89 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 54 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 GLN B 162 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 9401 Z= 0.182 Angle : 0.559 11.615 12753 Z= 0.291 Chirality : 0.040 0.161 1467 Planarity : 0.005 0.032 1542 Dihedral : 6.607 78.628 1312 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.55 % Favored : 96.28 % Rotamer Outliers : 1.64 % 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 (0.25), residues: 1128 helix: 1.04 (0.20), residues: 676 sheet: -0.82 (0.50), residues: 76 loop : -1.68 (0.31), residues: 376 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 92 time to evaluate : 1.086 Fit side-chains outliers start: 16 outliers final: 8 residues processed: 102 average time/residue: 0.2016 time to fit residues: 30.1092 Evaluate side-chains 86 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 78 time to evaluate : 1.064 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0945 time to fit residues: 2.8192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 7.9990 chunk 32 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 chunk 70 optimal weight: 10.0000 chunk 28 optimal weight: 8.9990 chunk 103 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 102 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 83 optimal weight: 8.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 ASN B 271 GLN B 457 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.3226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.041 9401 Z= 0.460 Angle : 0.706 13.717 12753 Z= 0.359 Chirality : 0.047 0.191 1467 Planarity : 0.006 0.042 1542 Dihedral : 7.134 80.264 1312 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer Outliers : 1.95 % 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: -0.54 (0.24), residues: 1128 helix: 0.58 (0.20), residues: 670 sheet: -0.50 (0.52), residues: 76 loop : -1.99 (0.29), residues: 382 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 89 time to evaluate : 1.119 Fit side-chains outliers start: 19 outliers final: 5 residues processed: 101 average time/residue: 0.1928 time to fit residues: 29.0389 Evaluate side-chains 83 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 78 time to evaluate : 1.105 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0950 time to fit residues: 2.2966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 4.9990 chunk 77 optimal weight: 10.0000 chunk 53 optimal weight: 0.9990 chunk 11 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 104 optimal weight: 0.6980 chunk 110 optimal weight: 0.8980 chunk 54 optimal weight: 0.7980 chunk 98 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 HIS B 375 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.3360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 9401 Z= 0.159 Angle : 0.496 10.374 12753 Z= 0.259 Chirality : 0.038 0.155 1467 Planarity : 0.004 0.034 1542 Dihedral : 6.437 66.605 1312 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer Outliers : 1.64 % 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 (0.25), residues: 1128 helix: 0.90 (0.20), residues: 682 sheet: -0.16 (0.54), residues: 76 loop : -1.68 (0.31), residues: 370 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 90 time to evaluate : 1.099 Fit side-chains outliers start: 16 outliers final: 4 residues processed: 101 average time/residue: 0.1899 time to fit residues: 28.5658 Evaluate side-chains 86 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 82 time to evaluate : 1.093 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0886 time to fit residues: 2.1194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 2.9990 chunk 62 optimal weight: 7.9990 chunk 1 optimal weight: 8.9990 chunk 82 optimal weight: 7.9990 chunk 45 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 76 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 56 optimal weight: 0.7980 chunk 98 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 HIS B 243 HIS ** B 600 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.3693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.047 9401 Z= 0.425 Angle : 0.630 10.091 12753 Z= 0.323 Chirality : 0.043 0.221 1467 Planarity : 0.005 0.036 1542 Dihedral : 6.680 76.125 1312 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer Outliers : 1.95 % 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: -0.25 (0.25), residues: 1128 helix: 0.81 (0.20), residues: 674 sheet: -0.20 (0.55), residues: 76 loop : -1.93 (0.30), residues: 378 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 82 time to evaluate : 1.145 Fit side-chains outliers start: 19 outliers final: 10 residues processed: 94 average time/residue: 0.1992 time to fit residues: 27.7376 Evaluate side-chains 89 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 79 time to evaluate : 1.101 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0967 time to fit residues: 3.2227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 64 optimal weight: 0.0020 chunk 27 optimal weight: 5.9990 chunk 110 optimal weight: 0.9980 chunk 91 optimal weight: 0.7980 chunk 51 optimal weight: 7.9990 chunk 9 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 57 optimal weight: 6.9990 overall best weight: 0.9592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 155 HIS ** B 600 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.3782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 9401 Z= 0.179 Angle : 0.500 11.656 12753 Z= 0.259 Chirality : 0.038 0.144 1467 Planarity : 0.004 0.033 1542 Dihedral : 6.186 71.270 1312 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer Outliers : 1.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.26), residues: 1128 helix: 1.00 (0.21), residues: 674 sheet: -0.01 (0.57), residues: 76 loop : -1.77 (0.31), residues: 378 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 80 time to evaluate : 1.075 Fit side-chains outliers start: 10 outliers final: 3 residues processed: 85 average time/residue: 0.1861 time to fit residues: 24.1563 Evaluate side-chains 83 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 80 time to evaluate : 1.003 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1950 time to fit residues: 2.2472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 2.9990 chunk 12 optimal weight: 6.9990 chunk 62 optimal weight: 3.9990 chunk 80 optimal weight: 7.9990 chunk 92 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 109 optimal weight: 6.9990 chunk 68 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 HIS A 283 HIS B 299 ASN ** B 600 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.3969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.038 9401 Z= 0.365 Angle : 0.599 11.605 12753 Z= 0.305 Chirality : 0.042 0.165 1467 Planarity : 0.005 0.034 1542 Dihedral : 6.420 74.392 1312 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer Outliers : 1.43 % 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: -0.15 (0.25), residues: 1128 helix: 0.86 (0.20), residues: 674 sheet: 0.13 (0.58), residues: 76 loop : -1.91 (0.30), residues: 378 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 81 time to evaluate : 1.166 Fit side-chains outliers start: 14 outliers final: 4 residues processed: 88 average time/residue: 0.1798 time to fit residues: 24.5542 Evaluate side-chains 80 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 76 time to evaluate : 1.099 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0905 time to fit residues: 2.1330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 0.7980 chunk 65 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 21 optimal weight: 6.9990 chunk 69 optimal weight: 7.9990 chunk 74 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 86 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 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 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 600 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.4022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 9401 Z= 0.184 Angle : 0.509 12.106 12753 Z= 0.259 Chirality : 0.038 0.143 1467 Planarity : 0.004 0.033 1542 Dihedral : 6.047 69.932 1312 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer Outliers : 0.41 % 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: 0.11 (0.26), residues: 1128 helix: 1.03 (0.21), residues: 674 sheet: 0.34 (0.59), residues: 76 loop : -1.75 (0.32), residues: 378 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 79 time to evaluate : 1.138 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 82 average time/residue: 0.1905 time to fit residues: 24.2725 Evaluate side-chains 78 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 77 time to evaluate : 1.064 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0873 time to fit residues: 1.5731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.0980 chunk 102 optimal weight: 6.9990 chunk 105 optimal weight: 4.9990 chunk 61 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 80 optimal weight: 7.9990 chunk 31 optimal weight: 0.0770 chunk 92 optimal weight: 3.9990 chunk 67 optimal weight: 7.9990 chunk 108 optimal weight: 0.0970 chunk 66 optimal weight: 0.9980 overall best weight: 1.0538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A 155 HIS A 283 HIS ** B 600 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.4117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 9401 Z= 0.177 Angle : 0.517 12.863 12753 Z= 0.257 Chirality : 0.038 0.140 1467 Planarity : 0.004 0.032 1542 Dihedral : 5.846 69.837 1312 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer Outliers : 0.20 % 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: 0.29 (0.26), residues: 1128 helix: 1.21 (0.21), residues: 666 sheet: 0.49 (0.59), residues: 76 loop : -1.71 (0.31), residues: 386 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 80 time to evaluate : 1.110 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 81 average time/residue: 0.1950 time to fit residues: 23.9912 Evaluate side-chains 77 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 76 time to evaluate : 1.038 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0974 time to fit residues: 1.4942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 9.9990 chunk 75 optimal weight: 0.8980 chunk 113 optimal weight: 0.7980 chunk 104 optimal weight: 0.9980 chunk 90 optimal weight: 0.0370 chunk 9 optimal weight: 3.9990 chunk 69 optimal weight: 0.8980 chunk 55 optimal weight: 0.6980 chunk 71 optimal weight: 9.9990 chunk 96 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 HIS ** B 600 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.4197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.025 9401 Z= 0.139 Angle : 0.492 12.608 12753 Z= 0.245 Chirality : 0.037 0.140 1467 Planarity : 0.004 0.032 1542 Dihedral : 5.591 67.257 1312 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer Outliers : 0.20 % 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: 0.46 (0.26), residues: 1128 helix: 1.32 (0.21), residues: 666 sheet: 0.66 (0.59), residues: 76 loop : -1.60 (0.32), residues: 386 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 77 time to evaluate : 0.953 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 78 average time/residue: 0.1803 time to fit residues: 21.6243 Evaluate side-chains 75 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 1.052 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 6.9990 chunk 13 optimal weight: 0.0870 chunk 25 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 93 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 0.1980 chunk 79 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 HIS A 283 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.110327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.093972 restraints weight = 16731.878| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 1.93 r_work: 0.3142 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3512 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3512 r_free = 0.3512 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3506 r_free = 0.3506 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3506 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.4240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.026 9401 Z= 0.136 Angle : 0.490 12.754 12753 Z= 0.244 Chirality : 0.037 0.154 1467 Planarity : 0.004 0.031 1542 Dihedral : 5.511 67.634 1312 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer Outliers : 0.61 % 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: 0.57 (0.26), residues: 1128 helix: 1.39 (0.21), residues: 668 sheet: 0.75 (0.59), residues: 76 loop : -1.55 (0.32), residues: 384 =============================================================================== Job complete usr+sys time: 2024.59 seconds wall clock time: 38 minutes 16.55 seconds (2296.55 seconds total)