Starting phenix.real_space_refine (version: dev) on Thu Feb 23 03:42:48 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fho_31588/02_2023/7fho_31588.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fho_31588/02_2023/7fho_31588.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fho_31588/02_2023/7fho_31588.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fho_31588/02_2023/7fho_31588.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fho_31588/02_2023/7fho_31588.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fho_31588/02_2023/7fho_31588.pdb" } resolution = 2.8 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= -0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 8728 atoms to isotropic. 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 GLU 366": "OE1" <-> "OE2" Residue "A ARG 543": "NH1" <-> "NH2" Residue "C GLU 352": "OE1" <-> "OE2" Residue "C GLU 366": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 10648 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 647, 5321 Classifications: {'peptide': 647} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 626} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 5321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 647, 5321 Classifications: {'peptide': 647} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 626} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 6.15, per 1000 atoms: 0.58 Number of scatterers: 10648 At special positions: 0 Unit cell: (108.498, 120.666, 100.386, 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) Ca 6 19.99 S 44 16.00 O 1866 8.00 N 1630 7.00 C 7102 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 93 " - pdb=" SG CYS A 101 " distance=2.03 Simple disulfide: pdb=" SG CYS C 93 " - pdb=" SG CYS C 101 " 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: 4.38 Conformation dependent library (CDL) restraints added in 1.5 seconds 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2472 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 2 sheets defined 79.3% alpha, 0.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 29 through 43 removed outlier: 3.594A pdb=" N ASP A 43 " --> pdb=" O ASP A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 52 removed outlier: 3.661A pdb=" N ILE A 51 " --> pdb=" O PRO A 48 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU A 52 " --> pdb=" O VAL A 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 48 through 52' Processing helix chain 'A' and resid 57 through 69 removed outlier: 3.738A pdb=" N TYR A 63 " --> pdb=" O GLU A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 83 Processing helix chain 'A' and resid 84 through 88 removed outlier: 3.646A pdb=" N GLU A 88 " --> pdb=" O ASN A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 95 removed outlier: 3.589A pdb=" N GLU A 94 " --> pdb=" O PRO A 90 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LYS A 95 " --> pdb=" O LEU A 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 90 through 95' Processing helix chain 'A' and resid 116 through 137 Processing helix chain 'A' and resid 146 through 149 Processing helix chain 'A' and resid 150 through 174 Processing helix chain 'A' and resid 186 through 198 Processing helix chain 'A' and resid 199 through 238 removed outlier: 4.580A pdb=" N GLY A 214 " --> pdb=" O SER A 210 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N THR A 215 " --> pdb=" O GLY A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 263 removed outlier: 3.843A pdb=" N THR A 263 " --> pdb=" O PHE A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 271 removed outlier: 4.146A pdb=" N TRP A 271 " --> pdb=" O ASN A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 278 Processing helix chain 'A' and resid 281 through 295 removed outlier: 3.665A pdb=" N PHE A 285 " --> pdb=" O SER A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 335 removed outlier: 3.535A pdb=" N ALA A 313 " --> pdb=" O LYS A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 355 removed outlier: 3.770A pdb=" N PHE A 351 " --> pdb=" O CYS A 347 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLU A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLN A 353 " --> pdb=" O LYS A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 376 removed outlier: 3.703A pdb=" N LEU A 370 " --> pdb=" O GLU A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 396 removed outlier: 3.931A pdb=" N ALA A 396 " --> pdb=" O CYS A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 removed outlier: 3.679A pdb=" N GLU A 409 " --> pdb=" O SER A 406 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N HIS A 410 " --> pdb=" O LEU A 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 406 through 410' Processing helix chain 'A' and resid 417 through 429 removed outlier: 3.760A pdb=" N GLN A 422 " --> pdb=" O ALA A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 453 removed outlier: 3.776A pdb=" N TYR A 434 " --> pdb=" O PRO A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 487 removed outlier: 4.183A pdb=" N TRP A 464 " --> pdb=" O ALA A 460 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TRP A 473 " --> pdb=" O PHE A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 494 removed outlier: 4.623A pdb=" N GLU A 494 " --> pdb=" O ASN A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 517 removed outlier: 3.780A pdb=" N ARG A 498 " --> pdb=" O GLU A 494 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY A 510 " --> pdb=" O VAL A 506 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE A 515 " --> pdb=" O GLU A 511 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR A 517 " --> pdb=" O ALA A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 542 removed outlier: 3.566A pdb=" N ILE A 542 " --> pdb=" O MET A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 547 Processing helix chain 'A' and resid 548 through 587 removed outlier: 4.244A pdb=" N PHE A 554 " --> pdb=" O ARG A 550 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE A 562 " --> pdb=" O PHE A 558 " (cutoff:3.500A) Proline residue: A 563 - end of helix Proline residue: A 567 - end of helix Processing helix chain 'A' and resid 601 through 606 Processing helix chain 'A' and resid 615 through 628 removed outlier: 3.668A pdb=" N PHE A 624 " --> pdb=" O MET A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 644 removed outlier: 3.876A pdb=" N MET A 636 " --> pdb=" O TRP A 632 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASP A 641 " --> pdb=" O GLU A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 647 No H-bonds generated for 'chain 'A' and resid 645 through 647' Processing helix chain 'A' and resid 648 through 659 removed outlier: 4.195A pdb=" N PHE A 652 " --> pdb=" O SER A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 684 removed outlier: 3.937A pdb=" N GLU A 682 " --> pdb=" O GLU A 678 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N GLU A 683 " --> pdb=" O LEU A 679 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU A 684 " --> pdb=" O ASP A 680 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 43 removed outlier: 3.599A pdb=" N ASP C 43 " --> pdb=" O ASP C 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 52 removed outlier: 3.630A pdb=" N ILE C 51 " --> pdb=" O PRO C 48 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU C 52 " --> pdb=" O VAL C 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 48 through 52' Processing helix chain 'C' and resid 57 through 69 removed outlier: 3.734A pdb=" N TYR C 63 " --> pdb=" O GLU C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 83 Processing helix chain 'C' and resid 84 through 88 removed outlier: 3.634A pdb=" N GLU C 88 " --> pdb=" O ASN C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 95 removed outlier: 3.577A pdb=" N GLU C 94 " --> pdb=" O PRO C 90 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LYS C 95 " --> pdb=" O LEU C 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 90 through 95' Processing helix chain 'C' and resid 116 through 137 Processing helix chain 'C' and resid 146 through 149 Processing helix chain 'C' and resid 150 through 174 Processing helix chain 'C' and resid 186 through 198 Processing helix chain 'C' and resid 199 through 238 removed outlier: 4.779A pdb=" N GLY C 214 " --> pdb=" O SER C 210 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N THR C 215 " --> pdb=" O GLY C 211 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU C 222 " --> pdb=" O ASN C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 263 Processing helix chain 'C' and resid 266 through 271 removed outlier: 4.199A pdb=" N TRP C 271 " --> pdb=" O ASN C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 278 Processing helix chain 'C' and resid 280 through 335 removed outlier: 4.412A pdb=" N PHE C 284 " --> pdb=" O TRP C 280 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N PHE C 285 " --> pdb=" O SER C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 355 removed outlier: 3.613A pdb=" N CYS C 347 " --> pdb=" O ASP C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 376 removed outlier: 3.513A pdb=" N PHE C 368 " --> pdb=" O SER C 364 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLY C 369 " --> pdb=" O LYS C 365 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASP C 376 " --> pdb=" O PHE C 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 389 Processing helix chain 'C' and resid 390 through 396 removed outlier: 3.546A pdb=" N ALA C 394 " --> pdb=" O ASP C 390 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ALA C 396 " --> pdb=" O CYS C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 removed outlier: 3.710A pdb=" N GLU C 409 " --> pdb=" O SER C 406 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N HIS C 410 " --> pdb=" O LEU C 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 406 through 410' Processing helix chain 'C' and resid 417 through 429 Processing helix chain 'C' and resid 430 through 453 removed outlier: 3.756A pdb=" N TYR C 434 " --> pdb=" O PRO C 430 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU C 453 " --> pdb=" O VAL C 449 " (cutoff:3.500A) Processing helix chain 'C' and resid 460 through 487 removed outlier: 4.484A pdb=" N TRP C 464 " --> pdb=" O ALA C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 494 removed outlier: 4.669A pdb=" N GLU C 494 " --> pdb=" O ASN C 490 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 516 removed outlier: 3.714A pdb=" N ARG C 498 " --> pdb=" O GLU C 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 526 through 541 Processing helix chain 'C' and resid 542 through 547 Processing helix chain 'C' and resid 548 through 565 removed outlier: 3.700A pdb=" N PHE C 554 " --> pdb=" O ARG C 550 " (cutoff:3.500A) Proline residue: C 563 - end of helix Processing helix chain 'C' and resid 565 through 587 Processing helix chain 'C' and resid 601 through 606 Processing helix chain 'C' and resid 615 through 628 removed outlier: 3.562A pdb=" N PHE C 624 " --> pdb=" O MET C 620 " (cutoff:3.500A) Processing helix chain 'C' and resid 632 through 644 removed outlier: 3.890A pdb=" N MET C 636 " --> pdb=" O TRP C 632 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS C 640 " --> pdb=" O MET C 636 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP C 641 " --> pdb=" O GLU C 637 " (cutoff:3.500A) Processing helix chain 'C' and resid 645 through 647 No H-bonds generated for 'chain 'C' and resid 645 through 647' Processing helix chain 'C' and resid 648 through 659 removed outlier: 4.119A pdb=" N PHE C 652 " --> pdb=" O SER C 648 " (cutoff:3.500A) Processing helix chain 'C' and resid 662 through 683 Processing sheet with id=AA1, first strand: chain 'A' and resid 341 through 342 removed outlier: 3.532A pdb=" N ILE A 383 " --> pdb=" O ILE A 342 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 341 through 342 686 hydrogen bonds defined for protein. 2025 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.03 Time building geometry restraints manager: 4.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3192 1.34 - 1.46: 2416 1.46 - 1.58: 5254 1.58 - 1.69: 0 1.69 - 1.81: 72 Bond restraints: 10934 Sorted by residual: bond pdb=" C ALA A 187 " pdb=" N PRO A 188 " ideal model delta sigma weight residual 1.334 1.365 -0.031 1.51e-02 4.39e+03 4.08e+00 bond pdb=" C ALA C 187 " pdb=" N PRO C 188 " ideal model delta sigma weight residual 1.335 1.361 -0.026 1.38e-02 5.25e+03 3.48e+00 bond pdb=" CG GLU C 352 " pdb=" CD GLU C 352 " ideal model delta sigma weight residual 1.516 1.486 0.030 2.50e-02 1.60e+03 1.41e+00 bond pdb=" C PHE A 137 " pdb=" N PRO A 138 " ideal model delta sigma weight residual 1.334 1.360 -0.026 2.34e-02 1.83e+03 1.25e+00 bond pdb=" C PHE C 137 " pdb=" N PRO C 138 " ideal model delta sigma weight residual 1.334 1.360 -0.026 2.34e-02 1.83e+03 1.24e+00 ... (remaining 10929 not shown) Histogram of bond angle deviations from ideal: 99.74 - 106.61: 212 106.61 - 113.49: 5830 113.49 - 120.36: 4262 120.36 - 127.24: 4462 127.24 - 134.11: 110 Bond angle restraints: 14876 Sorted by residual: angle pdb=" C GLU C 111 " pdb=" N LEU C 112 " pdb=" CA LEU C 112 " ideal model delta sigma weight residual 122.21 113.43 8.78 2.87e+00 1.21e-01 9.35e+00 angle pdb=" C GLU A 111 " pdb=" N LEU A 112 " pdb=" CA LEU A 112 " ideal model delta sigma weight residual 122.21 113.51 8.70 2.87e+00 1.21e-01 9.19e+00 angle pdb=" N GLY A 110 " pdb=" CA GLY A 110 " pdb=" C GLY A 110 " ideal model delta sigma weight residual 113.18 120.35 -7.17 2.37e+00 1.78e-01 9.16e+00 angle pdb=" N GLY C 110 " pdb=" CA GLY C 110 " pdb=" C GLY C 110 " ideal model delta sigma weight residual 113.18 120.34 -7.16 2.37e+00 1.78e-01 9.12e+00 angle pdb=" C ILE C 186 " pdb=" N ALA C 187 " pdb=" CA ALA C 187 " ideal model delta sigma weight residual 120.58 124.36 -3.78 1.32e+00 5.74e-01 8.19e+00 ... (remaining 14871 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.90: 5691 16.90 - 33.79: 518 33.79 - 50.69: 79 50.69 - 67.58: 21 67.58 - 84.48: 3 Dihedral angle restraints: 6312 sinusoidal: 2484 harmonic: 3828 Sorted by residual: dihedral pdb=" CB CYS C 93 " pdb=" SG CYS C 93 " pdb=" SG CYS C 101 " pdb=" CB CYS C 101 " ideal model delta sinusoidal sigma weight residual 93.00 148.41 -55.41 1 1.00e+01 1.00e-02 4.15e+01 dihedral pdb=" CB CYS A 93 " pdb=" SG CYS A 93 " pdb=" SG CYS A 101 " pdb=" CB CYS A 101 " ideal model delta sinusoidal sigma weight residual 93.00 147.57 -54.57 1 1.00e+01 1.00e-02 4.04e+01 dihedral pdb=" CA GLY A 110 " pdb=" C GLY A 110 " pdb=" N GLU A 111 " pdb=" CA GLU A 111 " ideal model delta harmonic sigma weight residual 180.00 158.54 21.46 0 5.00e+00 4.00e-02 1.84e+01 ... (remaining 6309 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1107 0.032 - 0.064: 443 0.064 - 0.096: 105 0.096 - 0.128: 28 0.128 - 0.159: 3 Chirality restraints: 1686 Sorted by residual: chirality pdb=" CA GLU C 111 " pdb=" N GLU C 111 " pdb=" C GLU C 111 " pdb=" CB GLU C 111 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.35e-01 chirality pdb=" CA GLU A 111 " pdb=" N GLU A 111 " pdb=" C GLU A 111 " pdb=" CB GLU A 111 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.34e-01 chirality pdb=" CA ILE C 542 " pdb=" N ILE C 542 " pdb=" C ILE C 542 " pdb=" CB ILE C 542 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.91e-01 ... (remaining 1683 not shown) Planarity restraints: 1832 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 562 " 0.032 5.00e-02 4.00e+02 4.88e-02 3.81e+00 pdb=" N PRO A 563 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 563 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 563 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 562 " 0.031 5.00e-02 4.00e+02 4.71e-02 3.55e+00 pdb=" N PRO C 563 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO C 563 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 563 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 293 " 0.009 2.00e-02 2.50e+03 1.75e-02 3.06e+00 pdb=" C VAL C 293 " -0.030 2.00e-02 2.50e+03 pdb=" O VAL C 293 " 0.011 2.00e-02 2.50e+03 pdb=" N TYR C 294 " 0.010 2.00e-02 2.50e+03 ... (remaining 1829 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 366 2.72 - 3.27: 11324 3.27 - 3.81: 17529 3.81 - 4.36: 21125 4.36 - 4.90: 35713 Nonbonded interactions: 86057 Sorted by model distance: nonbonded pdb=" OG SER C 265 " pdb=" OE1 GLN C 633 " model vdw 2.179 2.440 nonbonded pdb=" OG SER A 265 " pdb=" OE1 GLN A 633 " model vdw 2.181 2.440 nonbonded pdb=" OH TYR C 114 " pdb=" OD1 ASP C 615 " model vdw 2.198 2.440 nonbonded pdb=" OH TYR A 114 " pdb=" OD1 ASP A 615 " model vdw 2.211 2.440 nonbonded pdb=" OH TYR C 216 " pdb=" O VAL C 657 " model vdw 2.236 2.440 ... (remaining 86052 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 'C' } 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 Ca 6 9.91 5 S 44 5.16 5 C 7102 2.51 5 N 1630 2.21 5 O 1866 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.010 Extract box with map and model: 3.950 Check model and map are aligned: 0.170 Process input model: 29.790 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.100 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 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 : 0.002 0.031 10934 Z= 0.153 Angle : 0.572 8.776 14876 Z= 0.329 Chirality : 0.036 0.159 1686 Planarity : 0.004 0.049 1832 Dihedral : 12.957 84.477 3834 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer Outliers : 0.17 % 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: 1.34 (0.24), residues: 1282 helix: 1.43 (0.17), residues: 948 sheet: None (None), residues: 0 loop : -0.59 (0.37), residues: 334 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 160 time to evaluate : 1.216 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 161 average time/residue: 1.1507 time to fit residues: 200.6376 Evaluate side-chains 103 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 102 time to evaluate : 1.131 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 1.6411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 108 optimal weight: 1.9990 chunk 97 optimal weight: 6.9990 chunk 53 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 chunk 116 optimal weight: 0.0770 overall best weight: 1.7944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 ASN A 497 ASN C 547 ASN C 585 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 10934 Z= 0.287 Angle : 0.579 7.793 14876 Z= 0.299 Chirality : 0.040 0.177 1686 Planarity : 0.004 0.044 1832 Dihedral : 3.897 22.976 1406 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer Outliers : 1.21 % 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: 1.86 (0.24), residues: 1282 helix: 1.80 (0.17), residues: 950 sheet: None (None), residues: 0 loop : -0.37 (0.37), residues: 332 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 119 time to evaluate : 1.373 Fit side-chains outliers start: 14 outliers final: 6 residues processed: 128 average time/residue: 0.9844 time to fit residues: 138.7500 Evaluate side-chains 110 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 104 time to evaluate : 1.300 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 4 residues processed: 2 average time/residue: 0.6501 time to fit residues: 3.2439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 64 optimal weight: 8.9990 chunk 36 optimal weight: 8.9990 chunk 96 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 116 optimal weight: 3.9990 chunk 125 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 39 optimal weight: 7.9990 chunk 93 optimal weight: 6.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 ASN C 585 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.046 10934 Z= 0.346 Angle : 0.603 8.236 14876 Z= 0.311 Chirality : 0.041 0.216 1686 Planarity : 0.004 0.044 1832 Dihedral : 4.014 24.307 1406 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer Outliers : 2.08 % 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: 1.77 (0.24), residues: 1282 helix: 1.80 (0.16), residues: 948 sheet: None (None), residues: 0 loop : -0.59 (0.36), residues: 334 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 119 time to evaluate : 0.947 Fit side-chains outliers start: 24 outliers final: 9 residues processed: 135 average time/residue: 0.9930 time to fit residues: 147.6054 Evaluate side-chains 114 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 105 time to evaluate : 1.158 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 5 residues processed: 4 average time/residue: 0.1075 time to fit residues: 2.4060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 115 optimal weight: 1.9990 chunk 87 optimal weight: 0.0270 chunk 60 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 78 optimal weight: 7.9990 chunk 116 optimal weight: 1.9990 chunk 123 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 110 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 overall best weight: 0.9642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 ASN C 96 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 10934 Z= 0.184 Angle : 0.513 7.235 14876 Z= 0.266 Chirality : 0.038 0.243 1686 Planarity : 0.004 0.044 1832 Dihedral : 3.788 23.850 1406 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer Outliers : 1.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.13 (0.24), residues: 1282 helix: 2.03 (0.17), residues: 950 sheet: None (None), residues: 0 loop : -0.39 (0.37), residues: 332 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 128 time to evaluate : 1.257 Fit side-chains outliers start: 13 outliers final: 5 residues processed: 139 average time/residue: 0.9181 time to fit residues: 141.3073 Evaluate side-chains 115 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 110 time to evaluate : 1.227 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 5 residues processed: 0 time to fit residues: 1.7903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 103 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 1 optimal weight: 0.5980 chunk 92 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 chunk 0 optimal weight: 0.7980 chunk 63 optimal weight: 0.9980 chunk 111 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 ASN C 96 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 10934 Z= 0.176 Angle : 0.511 7.748 14876 Z= 0.262 Chirality : 0.038 0.265 1686 Planarity : 0.004 0.043 1832 Dihedral : 3.680 22.522 1406 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer Outliers : 0.87 % 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: 2.27 (0.24), residues: 1282 helix: 2.12 (0.17), residues: 952 sheet: None (None), residues: 0 loop : -0.31 (0.37), residues: 330 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 112 time to evaluate : 1.189 Fit side-chains outliers start: 10 outliers final: 5 residues processed: 122 average time/residue: 0.9903 time to fit residues: 132.9636 Evaluate side-chains 114 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 109 time to evaluate : 1.176 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 5 residues processed: 0 time to fit residues: 1.6358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 41 optimal weight: 0.0370 chunk 111 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 72 optimal weight: 0.4980 chunk 30 optimal weight: 0.2980 chunk 123 optimal weight: 3.9990 chunk 102 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 65 optimal weight: 6.9990 overall best weight: 0.7460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 ASN C 96 ASN C 218 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 10934 Z= 0.162 Angle : 0.500 8.285 14876 Z= 0.254 Chirality : 0.038 0.270 1686 Planarity : 0.004 0.043 1832 Dihedral : 3.597 21.712 1406 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer Outliers : 1.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.53 (0.24), residues: 1282 helix: 2.28 (0.17), residues: 954 sheet: None (None), residues: 0 loop : -0.11 (0.38), residues: 328 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 119 time to evaluate : 1.296 Fit side-chains outliers start: 15 outliers final: 7 residues processed: 131 average time/residue: 1.0846 time to fit residues: 155.4869 Evaluate side-chains 112 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 105 time to evaluate : 1.269 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 5 residues processed: 2 average time/residue: 1.9880 time to fit residues: 5.8913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 119 optimal weight: 3.9990 chunk 13 optimal weight: 0.3980 chunk 70 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 123 optimal weight: 0.4980 chunk 77 optimal weight: 0.9980 chunk 75 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 chunk 76 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 ASN C 96 ASN C 585 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 10934 Z= 0.162 Angle : 0.499 8.576 14876 Z= 0.253 Chirality : 0.038 0.240 1686 Planarity : 0.004 0.045 1832 Dihedral : 3.553 22.098 1406 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer Outliers : 1.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.63 (0.24), residues: 1282 helix: 2.35 (0.17), residues: 954 sheet: None (None), residues: 0 loop : -0.06 (0.38), residues: 328 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 110 time to evaluate : 1.247 Fit side-chains outliers start: 12 outliers final: 4 residues processed: 119 average time/residue: 1.0017 time to fit residues: 131.4157 Evaluate side-chains 107 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 103 time to evaluate : 1.151 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 0 time to fit residues: 1.6096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 49 optimal weight: 7.9990 chunk 73 optimal weight: 0.7980 chunk 37 optimal weight: 20.0000 chunk 24 optimal weight: 0.7980 chunk 23 optimal weight: 0.5980 chunk 78 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 96 optimal weight: 5.9990 chunk 112 optimal weight: 0.3980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 ASN C 153 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 10934 Z= 0.161 Angle : 0.516 8.912 14876 Z= 0.260 Chirality : 0.038 0.285 1686 Planarity : 0.004 0.044 1832 Dihedral : 3.516 21.829 1406 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer Outliers : 0.87 % 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: 2.71 (0.24), residues: 1282 helix: 2.42 (0.17), residues: 940 sheet: None (None), residues: 0 loop : 0.05 (0.37), residues: 342 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 112 time to evaluate : 1.327 Fit side-chains outliers start: 10 outliers final: 5 residues processed: 121 average time/residue: 0.9267 time to fit residues: 124.9424 Evaluate side-chains 107 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 102 time to evaluate : 1.272 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 5 residues processed: 0 time to fit residues: 1.7734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 118 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 103 optimal weight: 0.0970 chunk 108 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 121 optimal weight: 0.3980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 298 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 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 : 0.002 0.039 10934 Z= 0.159 Angle : 0.516 9.208 14876 Z= 0.261 Chirality : 0.038 0.256 1686 Planarity : 0.004 0.045 1832 Dihedral : 3.490 21.589 1406 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer Outliers : 0.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.74 (0.24), residues: 1282 helix: 2.44 (0.17), residues: 940 sheet: None (None), residues: 0 loop : 0.07 (0.37), residues: 342 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 110 time to evaluate : 1.278 Fit side-chains outliers start: 9 outliers final: 5 residues processed: 119 average time/residue: 0.8872 time to fit residues: 117.7924 Evaluate side-chains 111 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 106 time to evaluate : 1.247 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 5 residues processed: 0 time to fit residues: 1.7192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 74 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 chunk 127 optimal weight: 0.5980 chunk 117 optimal weight: 0.5980 chunk 101 optimal weight: 20.0000 chunk 10 optimal weight: 0.8980 chunk 78 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 80 optimal weight: 0.8980 chunk 108 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 497 ASN C 298 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 10934 Z= 0.169 Angle : 0.527 9.543 14876 Z= 0.265 Chirality : 0.039 0.271 1686 Planarity : 0.004 0.046 1832 Dihedral : 3.516 21.373 1406 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % 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: 2.85 (0.24), residues: 1282 helix: 2.51 (0.17), residues: 938 sheet: None (None), residues: 0 loop : 0.16 (0.37), residues: 344 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 104 time to evaluate : 1.328 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 109 average time/residue: 0.9008 time to fit residues: 109.8591 Evaluate side-chains 108 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 102 time to evaluate : 1.231 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 5 residues processed: 1 average time/residue: 0.2113 time to fit residues: 1.9078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 31 optimal weight: 3.9990 chunk 93 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 chunk 101 optimal weight: 20.0000 chunk 42 optimal weight: 4.9990 chunk 104 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.166900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.108322 restraints weight = 12888.257| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 1.90 r_work: 0.3103 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 10934 Z= 0.191 Angle : 0.536 9.791 14876 Z= 0.270 Chirality : 0.039 0.282 1686 Planarity : 0.004 0.044 1832 Dihedral : 3.570 21.564 1406 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % 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: 2.83 (0.24), residues: 1282 helix: 2.49 (0.17), residues: 940 sheet: None (None), residues: 0 loop : 0.15 (0.37), residues: 342 =============================================================================== Job complete usr+sys time: 3131.30 seconds wall clock time: 56 minutes 19.47 seconds (3379.47 seconds total)