Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 21 13:20:05 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yuz_10936/04_2023/6yuz_10936.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yuz_10936/04_2023/6yuz_10936.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/6yuz_10936/04_2023/6yuz_10936.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yuz_10936/04_2023/6yuz_10936.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yuz_10936/04_2023/6yuz_10936.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yuz_10936/04_2023/6yuz_10936.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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 2 9.91 5 S 48 5.16 5 C 6226 2.51 5 N 1640 2.21 5 O 1866 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 191": "OE1" <-> "OE2" Residue "A ASP 235": "OD1" <-> "OD2" Residue "A TYR 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 241": "OD1" <-> "OD2" Residue "A GLU 245": "OE1" <-> "OE2" Residue "A GLU 268": "OE1" <-> "OE2" Residue "A TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 288": "NH1" <-> "NH2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "A ASP 314": "OD1" <-> "OD2" Residue "A ASP 338": "OD1" <-> "OD2" Residue "A GLU 345": "OE1" <-> "OE2" Residue "A ARG 362": "NH1" <-> "NH2" Residue "A TYR 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 384": "OE1" <-> "OE2" Residue "A ASP 391": "OD1" <-> "OD2" Residue "A PHE 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 417": "OD1" <-> "OD2" Residue "A TYR 425": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 437": "OE1" <-> "OE2" Residue "A ASP 449": "OD1" <-> "OD2" Residue "A TYR 480": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 483": "OE1" <-> "OE2" Residue "A ASP 499": "OD1" <-> "OD2" Residue "A PHE 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 532": "OD1" <-> "OD2" Residue "A TYR 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 539": "OD1" <-> "OD2" Residue "A ARG 546": "NH1" <-> "NH2" Residue "A TYR 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 582": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 584": "NH1" <-> "NH2" Residue "A GLU 585": "OE1" <-> "OE2" Residue "A ASP 590": "OD1" <-> "OD2" Residue "A GLU 601": "OE1" <-> "OE2" Residue "A PHE 639": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 641": "OD1" <-> "OD2" Residue "A ARG 665": "NH1" <-> "NH2" Residue "A ARG 671": "NH1" <-> "NH2" Residue "C TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 191": "OE1" <-> "OE2" Residue "C ASP 235": "OD1" <-> "OD2" Residue "C TYR 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 241": "OD1" <-> "OD2" Residue "C GLU 245": "OE1" <-> "OE2" Residue "C GLU 268": "OE1" <-> "OE2" Residue "C TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 288": "NH1" <-> "NH2" Residue "C GLU 298": "OE1" <-> "OE2" Residue "C ASP 314": "OD1" <-> "OD2" Residue "C ASP 338": "OD1" <-> "OD2" Residue "C GLU 345": "OE1" <-> "OE2" Residue "C ARG 362": "NH1" <-> "NH2" Residue "C TYR 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 384": "OE1" <-> "OE2" Residue "C ASP 391": "OD1" <-> "OD2" Residue "C PHE 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 417": "OD1" <-> "OD2" Residue "C TYR 425": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 437": "OE1" <-> "OE2" Residue "C ASP 449": "OD1" <-> "OD2" Residue "C TYR 480": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 483": "OE1" <-> "OE2" Residue "C ASP 499": "OD1" <-> "OD2" Residue "C PHE 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 532": "OD1" <-> "OD2" Residue "C TYR 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 539": "OD1" <-> "OD2" Residue "C ARG 546": "NH1" <-> "NH2" Residue "C TYR 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 582": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 584": "NH1" <-> "NH2" Residue "C GLU 585": "OE1" <-> "OE2" Residue "C ASP 590": "OD1" <-> "OD2" Residue "C GLU 601": "OE1" <-> "OE2" Residue "C PHE 639": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 641": "OD1" <-> "OD2" Residue "C ARG 665": "NH1" <-> "NH2" Residue "C ARG 671": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 9782 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 594, 4834 Classifications: {'peptide': 594} Link IDs: {'PTRANS': 22, 'TRANS': 571} Chain: "C" Number of atoms: 4834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 594, 4834 Classifications: {'peptide': 594} Link IDs: {'PTRANS': 22, 'TRANS': 571} Chain: "A" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 57 Unusual residues: {' CA': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 57 Unusual residues: {' CA': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 5.57, per 1000 atoms: 0.57 Number of scatterers: 9782 At special positions: 0 Unit cell: (133.083, 92.907, 104.625, 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 2 19.99 S 48 16.00 O 1866 8.00 N 1640 7.00 C 6226 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 242 " - pdb=" SG CYS A 273 " distance=2.03 Simple disulfide: pdb=" SG CYS A 571 " - pdb=" SG CYS A 666 " distance=2.08 Simple disulfide: pdb=" SG CYS A 673 " - pdb=" SG CYS A 685 " distance=2.04 Simple disulfide: pdb=" SG CYS C 242 " - pdb=" SG CYS C 273 " distance=2.03 Simple disulfide: pdb=" SG CYS C 571 " - pdb=" SG CYS C 666 " distance=2.04 Simple disulfide: pdb=" SG CYS C 673 " - pdb=" SG CYS C 685 " distance=2.04 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 Links applied NAG-ASN " NAG A 701 " - " ASN A 332 " " NAG A 702 " - " ASN A 513 " " NAG A 703 " - " ASN A 575 " " NAG A 704 " - " ASN A 261 " " NAG C 701 " - " ASN C 332 " " NAG C 702 " - " ASN C 513 " " NAG C 703 " - " ASN C 575 " " NAG C 704 " - " ASN C 261 " Time building additional restraints: 3.53 Conformation dependent library (CDL) restraints added in 1.3 seconds 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2240 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 16 sheets defined 32.0% alpha, 10.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 92 through 111 removed outlier: 4.258A pdb=" N LEU A 98 " --> pdb=" O VAL A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 148 removed outlier: 3.646A pdb=" N ILE A 145 " --> pdb=" O ASP A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 155 removed outlier: 3.578A pdb=" N ILE A 152 " --> pdb=" O LYS A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 203 removed outlier: 3.566A pdb=" N LYS A 203 " --> pdb=" O ALA A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 227 Processing helix chain 'A' and resid 230 through 236 removed outlier: 3.597A pdb=" N TYR A 233 " --> pdb=" O THR A 230 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N THR A 234 " --> pdb=" O GLY A 231 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASP A 235 " --> pdb=" O LYS A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 307 removed outlier: 3.761A pdb=" N LYS A 297 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LYS A 306 " --> pdb=" O PHE A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 369 Processing helix chain 'A' and resid 370 through 372 No H-bonds generated for 'chain 'A' and resid 370 through 372' Processing helix chain 'A' and resid 389 through 394 Processing helix chain 'A' and resid 420 through 435 removed outlier: 3.669A pdb=" N ASN A 434 " --> pdb=" O SER A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 457 Processing helix chain 'A' and resid 458 through 460 No H-bonds generated for 'chain 'A' and resid 458 through 460' Processing helix chain 'A' and resid 461 through 471 Processing helix chain 'A' and resid 503 through 507 removed outlier: 3.984A pdb=" N SER A 507 " --> pdb=" O ARG A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 519 Processing helix chain 'A' and resid 537 through 544 Processing helix chain 'A' and resid 549 through 562 Processing helix chain 'A' and resid 562 through 567 removed outlier: 3.772A pdb=" N ASN A 566 " --> pdb=" O GLU A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 629 Processing helix chain 'A' and resid 655 through 659 Processing helix chain 'C' and resid 93 through 111 removed outlier: 4.258A pdb=" N LEU C 98 " --> pdb=" O VAL C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 148 removed outlier: 3.648A pdb=" N ILE C 145 " --> pdb=" O ASP C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 155 removed outlier: 3.579A pdb=" N ILE C 152 " --> pdb=" O LYS C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 203 removed outlier: 3.566A pdb=" N LYS C 203 " --> pdb=" O ALA C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 227 Processing helix chain 'C' and resid 230 through 236 removed outlier: 3.597A pdb=" N TYR C 233 " --> pdb=" O THR C 230 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N THR C 234 " --> pdb=" O GLY C 231 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASP C 235 " --> pdb=" O LYS C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 307 removed outlier: 3.761A pdb=" N LYS C 297 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS C 306 " --> pdb=" O PHE C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 369 Processing helix chain 'C' and resid 370 through 372 No H-bonds generated for 'chain 'C' and resid 370 through 372' Processing helix chain 'C' and resid 389 through 394 Processing helix chain 'C' and resid 420 through 435 removed outlier: 3.671A pdb=" N ASN C 434 " --> pdb=" O SER C 430 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 457 Processing helix chain 'C' and resid 458 through 460 No H-bonds generated for 'chain 'C' and resid 458 through 460' Processing helix chain 'C' and resid 461 through 471 Processing helix chain 'C' and resid 503 through 507 removed outlier: 3.981A pdb=" N SER C 507 " --> pdb=" O ARG C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 514 through 519 Processing helix chain 'C' and resid 537 through 544 Processing helix chain 'C' and resid 549 through 562 Processing helix chain 'C' and resid 562 through 567 removed outlier: 3.772A pdb=" N ASN C 566 " --> pdb=" O GLU C 562 " (cutoff:3.500A) Processing helix chain 'C' and resid 655 through 659 Processing sheet with id=AA1, first strand: chain 'A' and resid 123 through 125 removed outlier: 6.296A pdb=" N MET A 123 " --> pdb=" O THR A 478 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N TRP A 443 " --> pdb=" O ILE A 477 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N TYR A 479 " --> pdb=" O TRP A 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 167 through 170 removed outlier: 7.284A pdb=" N LYS A 167 " --> pdb=" O GLU A 178 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N SER A 169 " --> pdb=" O GLY A 176 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N GLY A 176 " --> pdb=" O SER A 169 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 209 through 211 removed outlier: 3.587A pdb=" N GLY A 382 " --> pdb=" O PHE A 311 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 239 through 240 Processing sheet with id=AA5, first strand: chain 'A' and resid 398 through 399 Processing sheet with id=AA6, first strand: chain 'A' and resid 632 through 634 removed outlier: 5.127A pdb=" N ARG A 619 " --> pdb=" O GLU A 649 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLU A 649 " --> pdb=" O ARG A 619 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILE A 647 " --> pdb=" O ARG A 621 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N SER A 623 " --> pdb=" O GLY A 645 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N GLY A 645 " --> pdb=" O SER A 623 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 604 through 606 Processing sheet with id=AA8, first strand: chain 'A' and resid 673 through 674 Processing sheet with id=AA9, first strand: chain 'C' and resid 123 through 125 removed outlier: 6.294A pdb=" N MET C 123 " --> pdb=" O THR C 478 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N TRP C 443 " --> pdb=" O ILE C 477 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N TYR C 479 " --> pdb=" O TRP C 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 167 through 170 removed outlier: 7.285A pdb=" N LYS C 167 " --> pdb=" O GLU C 178 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N SER C 169 " --> pdb=" O GLY C 176 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N GLY C 176 " --> pdb=" O SER C 169 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 209 through 211 removed outlier: 3.587A pdb=" N GLY C 382 " --> pdb=" O PHE C 311 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 239 through 240 Processing sheet with id=AB4, first strand: chain 'C' and resid 398 through 399 Processing sheet with id=AB5, first strand: chain 'C' and resid 632 through 634 removed outlier: 5.087A pdb=" N ARG C 619 " --> pdb=" O GLU C 649 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLU C 649 " --> pdb=" O ARG C 619 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ILE C 647 " --> pdb=" O ARG C 621 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N SER C 623 " --> pdb=" O GLY C 645 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N GLY C 645 " --> pdb=" O SER C 623 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 604 through 606 Processing sheet with id=AB7, first strand: chain 'C' and resid 673 through 674 275 hydrogen bonds defined for protein. 741 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: 2.83 Time building geometry restraints manager: 3.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1604 1.31 - 1.44: 2882 1.44 - 1.56: 5462 1.56 - 1.69: 0 1.69 - 1.81: 82 Bond restraints: 10030 Sorted by residual: bond pdb=" C7 NAG C 704 " pdb=" N2 NAG C 704 " ideal model delta sigma weight residual 1.346 1.465 -0.119 2.00e-02 2.50e+03 3.52e+01 bond pdb=" C7 NAG A 704 " pdb=" N2 NAG A 704 " ideal model delta sigma weight residual 1.346 1.463 -0.117 2.00e-02 2.50e+03 3.45e+01 bond pdb=" C7 NAG C 702 " pdb=" N2 NAG C 702 " ideal model delta sigma weight residual 1.346 1.463 -0.117 2.00e-02 2.50e+03 3.43e+01 bond pdb=" C7 NAG A 702 " pdb=" N2 NAG A 702 " ideal model delta sigma weight residual 1.346 1.463 -0.117 2.00e-02 2.50e+03 3.41e+01 bond pdb=" C7 NAG C 701 " pdb=" N2 NAG C 701 " ideal model delta sigma weight residual 1.346 1.462 -0.116 2.00e-02 2.50e+03 3.39e+01 ... (remaining 10025 not shown) Histogram of bond angle deviations from ideal: 100.47 - 107.18: 299 107.18 - 113.89: 5578 113.89 - 120.60: 3931 120.60 - 127.31: 3689 127.31 - 134.02: 123 Bond angle restraints: 13620 Sorted by residual: angle pdb=" CA LEU C 573 " pdb=" C LEU C 573 " pdb=" O LEU C 573 " ideal model delta sigma weight residual 120.84 116.79 4.05 1.08e+00 8.57e-01 1.40e+01 angle pdb=" N THR A 624 " pdb=" CA THR A 624 " pdb=" C THR A 624 " ideal model delta sigma weight residual 111.36 107.61 3.75 1.09e+00 8.42e-01 1.19e+01 angle pdb=" CA LEU A 573 " pdb=" C LEU A 573 " pdb=" O LEU A 573 " ideal model delta sigma weight residual 120.70 117.21 3.49 1.14e+00 7.69e-01 9.39e+00 angle pdb=" CA ASN C 575 " pdb=" CB ASN C 575 " pdb=" CG ASN C 575 " ideal model delta sigma weight residual 112.60 115.65 -3.05 1.00e+00 1.00e+00 9.32e+00 angle pdb=" CA ASN A 625 " pdb=" C ASN A 625 " pdb=" O ASN A 625 " ideal model delta sigma weight residual 120.54 117.42 3.12 1.04e+00 9.25e-01 8.99e+00 ... (remaining 13615 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 5354 17.74 - 35.48: 395 35.48 - 53.22: 77 53.22 - 70.97: 26 70.97 - 88.71: 6 Dihedral angle restraints: 5858 sinusoidal: 2374 harmonic: 3484 Sorted by residual: dihedral pdb=" CB CYS A 673 " pdb=" SG CYS A 673 " pdb=" SG CYS A 685 " pdb=" CB CYS A 685 " ideal model delta sinusoidal sigma weight residual -86.00 -26.50 -59.50 1 1.00e+01 1.00e-02 4.73e+01 dihedral pdb=" CB CYS C 673 " pdb=" SG CYS C 673 " pdb=" SG CYS C 685 " pdb=" CB CYS C 685 " ideal model delta sinusoidal sigma weight residual -86.00 -26.52 -59.48 1 1.00e+01 1.00e-02 4.72e+01 dihedral pdb=" CA ASN A 261 " pdb=" C ASN A 261 " pdb=" N SER A 262 " pdb=" CA SER A 262 " ideal model delta harmonic sigma weight residual 180.00 152.18 27.82 0 5.00e+00 4.00e-02 3.09e+01 ... (remaining 5855 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1353 0.071 - 0.142: 124 0.142 - 0.213: 14 0.213 - 0.284: 1 0.284 - 0.355: 2 Chirality restraints: 1494 Sorted by residual: chirality pdb=" CA ARG A 574 " pdb=" N ARG A 574 " pdb=" C ARG A 574 " pdb=" CB ARG A 574 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.16e+00 chirality pdb=" CA ARG C 574 " pdb=" N ARG C 574 " pdb=" C ARG C 574 " pdb=" CB ARG C 574 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.46e+00 chirality pdb=" CA ILE A 620 " pdb=" N ILE A 620 " pdb=" C ILE A 620 " pdb=" CB ILE A 620 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.25 2.00e-01 2.50e+01 1.57e+00 ... (remaining 1491 not shown) Planarity restraints: 1748 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS A 572 " -0.012 2.00e-02 2.50e+03 2.45e-02 5.98e+00 pdb=" C HIS A 572 " 0.042 2.00e-02 2.50e+03 pdb=" O HIS A 572 " -0.016 2.00e-02 2.50e+03 pdb=" N LEU A 573 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 336 " 0.029 5.00e-02 4.00e+02 4.35e-02 3.02e+00 pdb=" N PRO A 337 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 337 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 337 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 336 " 0.029 5.00e-02 4.00e+02 4.32e-02 2.99e+00 pdb=" N PRO C 337 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO C 337 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 337 " 0.024 5.00e-02 4.00e+02 ... (remaining 1745 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1791 2.77 - 3.30: 9088 3.30 - 3.83: 16306 3.83 - 4.37: 20490 4.37 - 4.90: 33896 Nonbonded interactions: 81571 Sorted by model distance: nonbonded pdb=" OH TYR C 480 " pdb=" O SER C 507 " model vdw 2.235 2.440 nonbonded pdb=" OH TYR A 480 " pdb=" O SER A 507 " model vdw 2.235 2.440 nonbonded pdb=" O SER A 450 " pdb=" OG SER A 505 " model vdw 2.270 2.440 nonbonded pdb=" O SER C 450 " pdb=" OG SER C 505 " model vdw 2.270 2.440 nonbonded pdb=" OH TYR A 151 " pdb=" OE2 GLU A 483 " model vdw 2.292 2.440 ... (remaining 81566 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 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: 2.870 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: 7.930 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 27.380 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 51.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.119 10030 Z= 0.389 Angle : 0.576 5.316 13620 Z= 0.333 Chirality : 0.045 0.355 1494 Planarity : 0.003 0.043 1740 Dihedral : 13.444 88.707 3600 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.80 % Favored : 95.95 % Rotamer Outliers : 2.33 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.67 (0.20), residues: 1184 helix: -3.59 (0.14), residues: 292 sheet: -2.23 (0.42), residues: 132 loop : -2.06 (0.21), residues: 760 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 140 time to evaluate : 1.086 Fit side-chains outliers start: 25 outliers final: 9 residues processed: 160 average time/residue: 1.2994 time to fit residues: 222.5590 Evaluate side-chains 90 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 81 time to evaluate : 1.268 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 7 residues processed: 3 average time/residue: 0.1326 time to fit residues: 2.2696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 0.0050 chunk 89 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 30 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 35 optimal weight: 0.5980 chunk 56 optimal weight: 6.9990 chunk 68 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 overall best weight: 1.1198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS A 244 HIS A 272 GLN A 358 HIS A 366 GLN A 488 ASN ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 524 ASN A 544 GLN A 572 HIS ** A 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 609 ASN A 659 GLN C 220 HIS C 244 HIS ** C 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 272 GLN C 277 GLN C 358 HIS C 366 GLN C 488 ASN ** C 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 524 ASN C 544 GLN ** C 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 609 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 659 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 10030 Z= 0.190 Angle : 0.508 7.239 13620 Z= 0.268 Chirality : 0.043 0.210 1494 Planarity : 0.004 0.040 1740 Dihedral : 4.118 24.900 1300 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.65 % Favored : 95.19 % Rotamer Outliers : 3.91 % 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: -2.28 (0.22), residues: 1184 helix: -1.08 (0.25), residues: 302 sheet: -1.45 (0.48), residues: 112 loop : -1.78 (0.21), residues: 770 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 90 time to evaluate : 1.246 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 22 residues processed: 118 average time/residue: 1.0029 time to fit residues: 129.8581 Evaluate side-chains 102 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 80 time to evaluate : 1.191 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 18 residues processed: 7 average time/residue: 0.1828 time to fit residues: 3.4626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 59 optimal weight: 30.0000 chunk 33 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 chunk 72 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 107 optimal weight: 0.9980 chunk 115 optimal weight: 4.9990 chunk 95 optimal weight: 0.6980 chunk 106 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 86 optimal weight: 0.8980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN A 277 GLN A 354 GLN ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 ASN C 265 HIS C 354 GLN C 459 ASN ** C 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 530 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.3513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.028 10030 Z= 0.257 Angle : 0.537 8.596 13620 Z= 0.285 Chirality : 0.045 0.248 1494 Planarity : 0.004 0.037 1740 Dihedral : 4.568 24.751 1300 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.15 % Favored : 94.68 % Rotamer Outliers : 3.54 % 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: -1.55 (0.23), residues: 1184 helix: 0.10 (0.28), residues: 312 sheet: -1.25 (0.51), residues: 108 loop : -1.55 (0.22), residues: 764 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 86 time to evaluate : 1.302 Fit side-chains outliers start: 38 outliers final: 20 residues processed: 112 average time/residue: 0.9968 time to fit residues: 122.5383 Evaluate side-chains 99 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 79 time to evaluate : 1.224 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 16 residues processed: 4 average time/residue: 0.1262 time to fit residues: 2.4485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 106 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 55 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 51 optimal weight: 10.0000 chunk 72 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 114 optimal weight: 6.9990 chunk 56 optimal weight: 3.9990 chunk 102 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 HIS A 488 ASN ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 488 ASN ** C 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.4112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.049 10030 Z= 0.484 Angle : 0.658 11.012 13620 Z= 0.347 Chirality : 0.052 0.441 1494 Planarity : 0.005 0.047 1740 Dihedral : 5.151 21.542 1300 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.59 % Favored : 93.24 % Rotamer Outliers : 4.10 % 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: -1.52 (0.24), residues: 1184 helix: 0.19 (0.29), residues: 308 sheet: -1.56 (0.48), residues: 132 loop : -1.48 (0.22), residues: 744 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 86 time to evaluate : 1.232 Fit side-chains outliers start: 44 outliers final: 24 residues processed: 122 average time/residue: 1.0308 time to fit residues: 138.1794 Evaluate side-chains 103 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 79 time to evaluate : 1.206 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 20 residues processed: 4 average time/residue: 0.4626 time to fit residues: 3.6253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 94 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 chunk 78 optimal weight: 0.6980 chunk 0 optimal weight: 9.9990 chunk 58 optimal weight: 6.9990 chunk 102 optimal weight: 6.9990 chunk 28 optimal weight: 0.8980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 530 ASN ** C 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.4006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 10030 Z= 0.204 Angle : 0.507 9.159 13620 Z= 0.265 Chirality : 0.044 0.227 1494 Planarity : 0.003 0.039 1740 Dihedral : 4.581 17.414 1300 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.24 % Favored : 94.59 % Rotamer Outliers : 3.35 % 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: -1.24 (0.24), residues: 1184 helix: 0.57 (0.30), residues: 314 sheet: -1.56 (0.47), residues: 132 loop : -1.35 (0.22), residues: 738 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 86 time to evaluate : 1.269 Fit side-chains outliers start: 36 outliers final: 24 residues processed: 117 average time/residue: 0.9257 time to fit residues: 119.5510 Evaluate side-chains 105 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 81 time to evaluate : 1.118 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 24 residues processed: 0 time to fit residues: 1.4959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 38 optimal weight: 0.5980 chunk 102 optimal weight: 7.9990 chunk 22 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 chunk 114 optimal weight: 9.9990 chunk 94 optimal weight: 2.9990 chunk 52 optimal weight: 8.9990 chunk 9 optimal weight: 0.0670 chunk 37 optimal weight: 0.6980 chunk 59 optimal weight: 30.0000 overall best weight: 1.0520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.4029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 10030 Z= 0.180 Angle : 0.495 9.548 13620 Z= 0.260 Chirality : 0.043 0.214 1494 Planarity : 0.003 0.046 1740 Dihedral : 4.392 17.300 1300 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.41 % Favored : 94.43 % Rotamer Outliers : 3.07 % 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: -0.97 (0.25), residues: 1184 helix: 0.84 (0.30), residues: 310 sheet: -1.25 (0.50), residues: 118 loop : -1.23 (0.23), residues: 756 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 86 time to evaluate : 1.218 Fit side-chains outliers start: 33 outliers final: 26 residues processed: 114 average time/residue: 1.0220 time to fit residues: 127.9192 Evaluate side-chains 105 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 79 time to evaluate : 1.231 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 25 residues processed: 1 average time/residue: 0.2317 time to fit residues: 1.9852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 110 optimal weight: 8.9990 chunk 12 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 64 optimal weight: 5.9990 chunk 96 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 chunk 113 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 chunk 69 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.4208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.036 10030 Z= 0.301 Angle : 0.553 10.460 13620 Z= 0.293 Chirality : 0.046 0.237 1494 Planarity : 0.004 0.046 1740 Dihedral : 4.750 18.947 1300 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.66 % Favored : 94.17 % Rotamer Outliers : 3.35 % 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: -1.07 (0.24), residues: 1184 helix: 0.70 (0.30), residues: 312 sheet: -1.43 (0.48), residues: 128 loop : -1.24 (0.23), residues: 744 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 79 time to evaluate : 1.273 Fit side-chains outliers start: 36 outliers final: 26 residues processed: 110 average time/residue: 1.0002 time to fit residues: 121.0278 Evaluate side-chains 102 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 76 time to evaluate : 1.207 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 25 residues processed: 1 average time/residue: 0.2296 time to fit residues: 1.9318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 70 optimal weight: 3.9990 chunk 45 optimal weight: 0.0270 chunk 67 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 overall best weight: 1.5844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 215 HIS ** C 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.4220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 10030 Z= 0.239 Angle : 0.523 10.096 13620 Z= 0.277 Chirality : 0.044 0.214 1494 Planarity : 0.004 0.060 1740 Dihedral : 4.612 17.650 1300 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.66 % Favored : 94.17 % Rotamer Outliers : 2.70 % 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: -0.95 (0.24), residues: 1184 helix: 0.83 (0.30), residues: 312 sheet: -1.30 (0.48), residues: 130 loop : -1.18 (0.23), residues: 742 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 80 time to evaluate : 1.323 Fit side-chains outliers start: 29 outliers final: 25 residues processed: 108 average time/residue: 1.0092 time to fit residues: 120.3129 Evaluate side-chains 102 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 77 time to evaluate : 1.233 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 25 residues processed: 0 time to fit residues: 1.6549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 4.9990 chunk 99 optimal weight: 0.0050 chunk 105 optimal weight: 1.9990 chunk 63 optimal weight: 8.9990 chunk 46 optimal weight: 2.9990 chunk 83 optimal weight: 0.5980 chunk 32 optimal weight: 0.4980 chunk 95 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 112 optimal weight: 0.8980 overall best weight: 0.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.4164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 10030 Z= 0.157 Angle : 0.477 9.775 13620 Z= 0.254 Chirality : 0.042 0.195 1494 Planarity : 0.003 0.060 1740 Dihedral : 4.316 17.066 1300 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.74 % Favored : 94.09 % Rotamer Outliers : 2.61 % 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: -0.75 (0.25), residues: 1184 helix: 1.12 (0.30), residues: 310 sheet: -1.35 (0.46), residues: 134 loop : -1.07 (0.23), residues: 740 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 85 time to evaluate : 1.208 Fit side-chains outliers start: 28 outliers final: 24 residues processed: 113 average time/residue: 0.9837 time to fit residues: 122.4376 Evaluate side-chains 106 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 82 time to evaluate : 1.224 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 24 residues processed: 0 time to fit residues: 1.6560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 68 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 77 optimal weight: 4.9990 chunk 117 optimal weight: 0.0060 chunk 108 optimal weight: 1.9990 chunk 93 optimal weight: 0.0170 chunk 9 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 chunk 99 optimal weight: 8.9990 overall best weight: 0.9838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.4198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 10030 Z= 0.173 Angle : 0.488 10.194 13620 Z= 0.259 Chirality : 0.043 0.197 1494 Planarity : 0.003 0.064 1740 Dihedral : 4.312 16.865 1300 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.74 % Favored : 94.09 % Rotamer Outliers : 2.33 % 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: -0.72 (0.25), residues: 1184 helix: 1.19 (0.30), residues: 310 sheet: -1.37 (0.46), residues: 134 loop : -1.07 (0.23), residues: 740 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 80 time to evaluate : 1.305 Fit side-chains outliers start: 25 outliers final: 24 residues processed: 104 average time/residue: 1.0186 time to fit residues: 116.5913 Evaluate side-chains 103 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 79 time to evaluate : 1.283 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 24 residues processed: 0 time to fit residues: 1.6027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 28 optimal weight: 0.6980 chunk 86 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 26 optimal weight: 6.9990 chunk 93 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 96 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 82 optimal weight: 6.9990 chunk 5 optimal weight: 4.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.093421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.070865 restraints weight = 16327.940| |-----------------------------------------------------------------------------| r_work (start): 0.2895 rms_B_bonded: 2.42 r_work: 0.2766 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2623 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.4248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 10030 Z= 0.209 Angle : 0.504 10.470 13620 Z= 0.269 Chirality : 0.043 0.198 1494 Planarity : 0.004 0.065 1740 Dihedral : 4.436 17.350 1300 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.41 % Favored : 94.43 % Rotamer Outliers : 2.33 % 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: -0.73 (0.25), residues: 1184 helix: 1.17 (0.30), residues: 310 sheet: -1.23 (0.50), residues: 118 loop : -1.11 (0.23), residues: 756 =============================================================================== Job complete usr+sys time: 3151.90 seconds wall clock time: 57 minutes 0.88 seconds (3420.88 seconds total)