Starting phenix.real_space_refine on Wed Feb 14 17:10:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yuz_10936/02_2024/6yuz_10936.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yuz_10936/02_2024/6yuz_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_10936/02_2024/6yuz_10936.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yuz_10936/02_2024/6yuz_10936.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yuz_10936/02_2024/6yuz_10936.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yuz_10936/02_2024/6yuz_10936.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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-dev-5238/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 dihedrals: 12 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 dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 5.65, per 1000 atoms: 0.58 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: 3.71 Conformation dependent library (CDL) restraints added in 1.8 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: 1.19 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: 2.63 Time building geometry restraints manager: 4.01 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 - 22.41: 5624 22.41 - 44.83: 318 44.83 - 67.24: 52 67.24 - 89.66: 16 89.66 - 112.07: 16 Dihedral angle restraints: 6026 sinusoidal: 2542 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 6023 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: 1.600 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: 7.290 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 28.940 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.320 ------------------------------------------------------------------------------- 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 : 15.649 112.073 3768 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 % Allowed : 14.15 % Favored : 83.52 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 264 HIS 0.002 0.001 HIS A 276 PHE 0.009 0.001 PHE C 407 TYR 0.006 0.001 TYR C 579 ARG 0.002 0.000 ARG A 621 *********************** 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 : 1.150 Fit side-chains REVERT: A 574 ARG cc_start: 0.7886 (OUTLIER) cc_final: 0.7480 (ptm160) REVERT: A 619 ARG cc_start: 0.7435 (mtp-110) cc_final: 0.7133 (mmm-85) REVERT: A 626 SER cc_start: 0.8141 (m) cc_final: 0.7485 (t) REVERT: C 437 GLU cc_start: 0.7149 (mm-30) cc_final: 0.6875 (mm-30) REVERT: C 574 ARG cc_start: 0.7751 (OUTLIER) cc_final: 0.7380 (ptm160) outliers start: 25 outliers final: 9 residues processed: 160 average time/residue: 1.2834 time to fit residues: 219.5300 Evaluate side-chains 92 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 81 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 449 ASP Chi-restraints excluded: chain A residue 574 ARG Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 574 ARG Chi-restraints excluded: chain C residue 628 ASP Chi-restraints excluded: chain C residue 677 VAL 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: 0.0970 chunk 56 optimal weight: 6.9990 chunk 68 optimal weight: 0.9990 chunk 107 optimal weight: 8.9990 overall best weight: 1.0196 ------------------------------------------------------------------------------- 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 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: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.2643 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= 0.181 Angle : 0.522 7.033 13620 Z= 0.270 Chirality : 0.044 0.247 1494 Planarity : 0.004 0.040 1740 Dihedral : 7.638 59.445 1487 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.81 % Favored : 95.02 % Rotamer: Outliers : 3.72 % Allowed : 15.74 % Favored : 80.54 % 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: -2.32 (0.22), residues: 1184 helix: -1.20 (0.25), residues: 302 sheet: -1.42 (0.48), residues: 112 loop : -1.77 (0.21), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 303 HIS 0.005 0.001 HIS A 276 PHE 0.017 0.002 PHE C 407 TYR 0.013 0.001 TYR A 582 ARG 0.003 0.000 ARG A 574 *********************** 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 130 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 90 time to evaluate : 1.120 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 574 ARG cc_start: 0.7927 (OUTLIER) cc_final: 0.7704 (ptt90) REVERT: A 619 ARG cc_start: 0.7653 (mtp-110) cc_final: 0.7337 (mmm-85) REVERT: A 626 SER cc_start: 0.8021 (m) cc_final: 0.7283 (t) REVERT: C 574 ARG cc_start: 0.7890 (OUTLIER) cc_final: 0.7466 (ptt90) REVERT: C 579 TYR cc_start: 0.6927 (p90) cc_final: 0.6631 (p90) outliers start: 40 outliers final: 15 residues processed: 117 average time/residue: 1.0817 time to fit residues: 137.8186 Evaluate side-chains 96 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 79 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 574 ARG Chi-restraints excluded: chain A residue 664 ASP Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 261 ASN Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 574 ARG Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 664 ASP Chi-restraints excluded: chain C residue 683 THR 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: 0.6980 chunk 89 optimal weight: 0.5980 chunk 72 optimal weight: 4.9990 chunk 29 optimal weight: 6.9990 chunk 107 optimal weight: 2.9990 chunk 115 optimal weight: 6.9990 chunk 95 optimal weight: 2.9990 chunk 106 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 86 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 358 HIS C 459 ASN ** C 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 530 ASN ** C 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10030 Z= 0.151 Angle : 0.462 7.976 13620 Z= 0.243 Chirality : 0.042 0.211 1494 Planarity : 0.003 0.038 1740 Dihedral : 6.648 59.168 1480 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.65 % Favored : 95.19 % Rotamer: Outliers : 2.79 % Allowed : 16.85 % Favored : 80.35 % 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: -1.47 (0.23), residues: 1184 helix: 0.31 (0.29), residues: 306 sheet: -1.17 (0.51), residues: 108 loop : -1.57 (0.21), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 431 HIS 0.004 0.001 HIS A 276 PHE 0.015 0.001 PHE A 407 TYR 0.010 0.001 TYR A 166 ARG 0.003 0.000 ARG C 619 *********************** 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 115 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 85 time to evaluate : 1.213 Fit side-chains REVERT: A 415 MET cc_start: 0.6726 (OUTLIER) cc_final: 0.6371 (mmp) REVERT: A 435 MET cc_start: 0.9211 (ttp) cc_final: 0.8848 (ttp) REVERT: A 610 MET cc_start: 0.8300 (OUTLIER) cc_final: 0.7912 (mtm) REVERT: A 619 ARG cc_start: 0.7646 (mtp-110) cc_final: 0.7368 (mmm-85) REVERT: A 626 SER cc_start: 0.8051 (m) cc_final: 0.7296 (t) REVERT: A 653 LYS cc_start: 0.8608 (ptpp) cc_final: 0.8324 (mtmt) REVERT: C 333 LYS cc_start: 0.8443 (OUTLIER) cc_final: 0.8227 (mptp) REVERT: C 415 MET cc_start: 0.6932 (OUTLIER) cc_final: 0.6709 (mmp) outliers start: 30 outliers final: 15 residues processed: 107 average time/residue: 1.0867 time to fit residues: 126.4384 Evaluate side-chains 96 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 77 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 415 MET Chi-restraints excluded: chain A residue 610 MET Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain A residue 664 ASP Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 312 SER Chi-restraints excluded: chain C residue 333 LYS Chi-restraints excluded: chain C residue 415 MET Chi-restraints excluded: chain C residue 449 ASP Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 660 THR Chi-restraints excluded: chain C residue 664 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 106 optimal weight: 0.0980 chunk 80 optimal weight: 4.9990 chunk 55 optimal weight: 8.9990 chunk 11 optimal weight: 4.9990 chunk 51 optimal weight: 7.9990 chunk 72 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 114 optimal weight: 8.9990 chunk 56 optimal weight: 9.9990 chunk 102 optimal weight: 7.9990 chunk 30 optimal weight: 3.9990 overall best weight: 3.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 GLN A 488 ASN ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 ASN C 265 HIS C 354 GLN ** C 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.4036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.047 10030 Z= 0.493 Angle : 0.665 10.649 13620 Z= 0.350 Chirality : 0.054 0.517 1494 Planarity : 0.005 0.039 1740 Dihedral : 7.245 59.654 1472 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 3.72 % Allowed : 16.85 % Favored : 79.42 % 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: -1.54 (0.24), residues: 1184 helix: 0.26 (0.29), residues: 308 sheet: -1.61 (0.47), residues: 140 loop : -1.52 (0.22), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 239 HIS 0.017 0.002 HIS C 265 PHE 0.021 0.002 PHE C 407 TYR 0.013 0.002 TYR C 166 ARG 0.008 0.001 ARG A 379 *********************** 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 119 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 79 time to evaluate : 1.155 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 MET cc_start: 0.9023 (mtt) cc_final: 0.8820 (mtt) REVERT: A 184 ASP cc_start: 0.7625 (OUTLIER) cc_final: 0.7418 (p0) REVERT: A 265 HIS cc_start: 0.8235 (OUTLIER) cc_final: 0.7949 (t70) REVERT: A 309 ASP cc_start: 0.7307 (OUTLIER) cc_final: 0.7083 (m-30) REVERT: A 381 MET cc_start: 0.8823 (ttt) cc_final: 0.8471 (ttt) REVERT: A 574 ARG cc_start: 0.8063 (OUTLIER) cc_final: 0.7858 (mtp-110) REVERT: A 628 ASP cc_start: 0.7841 (m-30) cc_final: 0.7593 (m-30) REVERT: A 653 LYS cc_start: 0.8685 (ptpp) cc_final: 0.8374 (mtmt) REVERT: C 123 MET cc_start: 0.9019 (mtt) cc_final: 0.8781 (mtt) REVERT: C 184 ASP cc_start: 0.7627 (OUTLIER) cc_final: 0.7386 (p0) REVERT: C 381 MET cc_start: 0.8822 (ttp) cc_final: 0.8477 (ttt) REVERT: C 606 ASN cc_start: 0.8762 (t0) cc_final: 0.8561 (t0) REVERT: C 682 TYR cc_start: 0.8097 (m-80) cc_final: 0.7882 (m-10) outliers start: 40 outliers final: 19 residues processed: 110 average time/residue: 0.9578 time to fit residues: 115.6218 Evaluate side-chains 95 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 71 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 139 ASN Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 574 ARG Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain A residue 664 ASP Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 139 ASN Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 261 ASN Chi-restraints excluded: chain C residue 312 SER Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 660 THR Chi-restraints excluded: chain C residue 683 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 94 optimal weight: 0.8980 chunk 64 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 97 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 0 optimal weight: 30.0000 chunk 58 optimal weight: 8.9990 chunk 102 optimal weight: 0.6980 chunk 28 optimal weight: 3.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- 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 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.3956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10030 Z= 0.208 Angle : 0.497 9.105 13620 Z= 0.261 Chirality : 0.045 0.417 1494 Planarity : 0.004 0.050 1740 Dihedral : 6.672 59.895 1472 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 3.54 % Allowed : 17.50 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.24), residues: 1184 helix: 0.66 (0.30), residues: 310 sheet: -1.51 (0.47), residues: 132 loop : -1.35 (0.22), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 431 HIS 0.006 0.001 HIS A 265 PHE 0.015 0.001 PHE C 407 TYR 0.010 0.001 TYR C 582 ARG 0.010 0.000 ARG C 619 *********************** 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 119 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 81 time to evaluate : 1.149 Fit side-chains REVERT: A 123 MET cc_start: 0.8914 (mtt) cc_final: 0.8699 (mtt) REVERT: A 381 MET cc_start: 0.8835 (ttt) cc_final: 0.8565 (ttt) REVERT: A 610 MET cc_start: 0.8347 (OUTLIER) cc_final: 0.8027 (mtm) REVERT: A 628 ASP cc_start: 0.7924 (m-30) cc_final: 0.7571 (m-30) REVERT: A 653 LYS cc_start: 0.8658 (ptpp) cc_final: 0.8431 (mtmt) REVERT: C 184 ASP cc_start: 0.7537 (OUTLIER) cc_final: 0.7269 (p0) REVERT: C 381 MET cc_start: 0.8833 (ttp) cc_final: 0.8561 (ttt) outliers start: 38 outliers final: 21 residues processed: 114 average time/residue: 0.9019 time to fit residues: 113.7934 Evaluate side-chains 100 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 77 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 139 ASN Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 610 MET Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain A residue 664 ASP Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 139 ASN Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 312 SER Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 660 THR Chi-restraints excluded: chain C residue 683 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 38 optimal weight: 0.4980 chunk 102 optimal weight: 8.9990 chunk 22 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 114 optimal weight: 9.9990 chunk 94 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 59 optimal weight: 30.0000 overall best weight: 1.6986 ------------------------------------------------------------------------------- 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** ** C 578 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.4078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10030 Z= 0.253 Angle : 0.523 9.933 13620 Z= 0.276 Chirality : 0.045 0.253 1494 Planarity : 0.004 0.049 1740 Dihedral : 6.567 57.275 1472 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 2.89 % Allowed : 18.72 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.24), residues: 1184 helix: 0.82 (0.30), residues: 308 sheet: -1.51 (0.47), residues: 132 loop : -1.25 (0.23), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 303 HIS 0.007 0.001 HIS C 276 PHE 0.015 0.001 PHE C 407 TYR 0.010 0.001 TYR A 582 ARG 0.010 0.001 ARG C 619 *********************** 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 112 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 81 time to evaluate : 1.103 Fit side-chains REVERT: A 123 MET cc_start: 0.8954 (mtt) cc_final: 0.8730 (mtt) REVERT: A 184 ASP cc_start: 0.7553 (OUTLIER) cc_final: 0.7307 (p0) REVERT: A 381 MET cc_start: 0.8775 (ttp) cc_final: 0.8490 (ttt) REVERT: A 628 ASP cc_start: 0.7920 (m-30) cc_final: 0.7548 (m-30) REVERT: A 653 LYS cc_start: 0.8677 (ptpp) cc_final: 0.8449 (mtmt) REVERT: C 184 ASP cc_start: 0.7531 (OUTLIER) cc_final: 0.7285 (p0) REVERT: C 381 MET cc_start: 0.8809 (ttp) cc_final: 0.8532 (ttt) REVERT: C 634 ASP cc_start: 0.7877 (p0) cc_final: 0.7330 (p0) outliers start: 31 outliers final: 20 residues processed: 106 average time/residue: 0.8926 time to fit residues: 104.5656 Evaluate side-chains 101 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 79 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 577 SER Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain A residue 664 ASP Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 312 SER Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 654 ASN Chi-restraints excluded: chain C residue 660 THR Chi-restraints excluded: chain C residue 664 ASP 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: 2.9990 chunk 65 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 chunk 64 optimal weight: 2.9990 chunk 96 optimal weight: 0.8980 chunk 63 optimal weight: 4.9990 chunk 113 optimal weight: 2.9990 chunk 71 optimal weight: 6.9990 chunk 69 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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: 0.8624 moved from start: 0.4202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10030 Z= 0.279 Angle : 0.534 10.137 13620 Z= 0.282 Chirality : 0.046 0.271 1494 Planarity : 0.004 0.060 1740 Dihedral : 6.419 57.401 1470 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 3.35 % Allowed : 18.25 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.24), residues: 1184 helix: 0.86 (0.30), residues: 308 sheet: -1.50 (0.47), residues: 132 loop : -1.24 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 303 HIS 0.007 0.001 HIS A 265 PHE 0.016 0.002 PHE A 407 TYR 0.010 0.001 TYR A 582 ARG 0.011 0.001 ARG C 619 *********************** 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 116 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 80 time to evaluate : 1.172 Fit side-chains REVERT: A 123 MET cc_start: 0.8948 (mtt) cc_final: 0.8721 (mtt) REVERT: A 184 ASP cc_start: 0.7576 (OUTLIER) cc_final: 0.7342 (p0) REVERT: A 381 MET cc_start: 0.8758 (ttp) cc_final: 0.8479 (ttt) REVERT: A 610 MET cc_start: 0.8331 (OUTLIER) cc_final: 0.8092 (mpp) REVERT: A 628 ASP cc_start: 0.7919 (m-30) cc_final: 0.7531 (m-30) REVERT: A 653 LYS cc_start: 0.8683 (ptpp) cc_final: 0.8451 (mtmt) REVERT: C 184 ASP cc_start: 0.7546 (OUTLIER) cc_final: 0.7307 (p0) REVERT: C 381 MET cc_start: 0.8784 (ttp) cc_final: 0.8507 (ttt) REVERT: C 610 MET cc_start: 0.8454 (mpp) cc_final: 0.8169 (mtm) REVERT: C 634 ASP cc_start: 0.7866 (p0) cc_final: 0.7384 (p0) outliers start: 36 outliers final: 26 residues processed: 114 average time/residue: 0.9307 time to fit residues: 117.0986 Evaluate side-chains 109 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 80 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 139 ASN Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 577 SER Chi-restraints excluded: chain A residue 610 MET Chi-restraints excluded: chain A residue 634 ASP Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 139 ASN Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 312 SER Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 577 SER Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 654 ASN Chi-restraints excluded: chain C residue 660 THR Chi-restraints excluded: chain C residue 664 ASP 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: 3.9990 chunk 34 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 89 optimal weight: 0.9980 chunk 103 optimal weight: 5.9990 overall best weight: 2.0044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 ASN ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.4285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10030 Z= 0.288 Angle : 0.540 10.360 13620 Z= 0.286 Chirality : 0.046 0.266 1494 Planarity : 0.004 0.056 1740 Dihedral : 6.256 56.537 1470 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 2.89 % Allowed : 18.72 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.24), residues: 1184 helix: 0.86 (0.30), residues: 308 sheet: -1.49 (0.48), residues: 132 loop : -1.21 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 303 HIS 0.006 0.001 HIS C 265 PHE 0.016 0.001 PHE C 407 TYR 0.010 0.001 TYR A 682 ARG 0.011 0.001 ARG A 619 *********************** 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 111 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 80 time to evaluate : 1.269 Fit side-chains REVERT: A 123 MET cc_start: 0.8962 (mtt) cc_final: 0.8748 (mtt) REVERT: A 184 ASP cc_start: 0.7597 (OUTLIER) cc_final: 0.7378 (p0) REVERT: A 381 MET cc_start: 0.8749 (ttp) cc_final: 0.8481 (ttt) REVERT: A 610 MET cc_start: 0.8342 (OUTLIER) cc_final: 0.8102 (mpp) REVERT: A 628 ASP cc_start: 0.7906 (m-30) cc_final: 0.7530 (m-30) REVERT: A 653 LYS cc_start: 0.8726 (ptpp) cc_final: 0.8479 (mtmt) REVERT: C 184 ASP cc_start: 0.7571 (OUTLIER) cc_final: 0.7361 (p0) REVERT: C 381 MET cc_start: 0.8734 (ttp) cc_final: 0.8447 (ttt) REVERT: C 610 MET cc_start: 0.8465 (mpp) cc_final: 0.8162 (mtm) REVERT: C 634 ASP cc_start: 0.7911 (p0) cc_final: 0.7485 (p0) outliers start: 31 outliers final: 24 residues processed: 109 average time/residue: 0.9060 time to fit residues: 109.0853 Evaluate side-chains 102 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 75 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 139 ASN Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 577 SER Chi-restraints excluded: chain A residue 610 MET Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 139 ASN Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 312 SER Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 577 SER Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 660 THR Chi-restraints excluded: chain C residue 664 ASP Chi-restraints excluded: chain C residue 683 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 105 optimal weight: 0.9990 chunk 63 optimal weight: 7.9990 chunk 46 optimal weight: 2.9990 chunk 83 optimal weight: 0.2980 chunk 32 optimal weight: 4.9990 chunk 95 optimal weight: 4.9990 chunk 100 optimal weight: 0.4980 chunk 69 optimal weight: 0.8980 chunk 112 optimal weight: 0.6980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 HIS ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.4195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10030 Z= 0.146 Angle : 0.464 9.386 13620 Z= 0.246 Chirality : 0.042 0.216 1494 Planarity : 0.004 0.061 1740 Dihedral : 5.443 51.538 1470 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 2.05 % Allowed : 19.93 % Favored : 78.03 % 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: 1.18 (0.31), residues: 310 sheet: -1.20 (0.44), residues: 152 loop : -1.12 (0.23), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 431 HIS 0.006 0.001 HIS A 265 PHE 0.014 0.001 PHE C 407 TYR 0.008 0.001 TYR A 151 ARG 0.013 0.000 ARG A 619 *********************** 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 108 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 86 time to evaluate : 1.158 Fit side-chains REVERT: A 381 MET cc_start: 0.8752 (ttp) cc_final: 0.8524 (ttt) REVERT: A 628 ASP cc_start: 0.7895 (m-30) cc_final: 0.7530 (m-30) REVERT: C 96 SER cc_start: 0.6483 (OUTLIER) cc_final: 0.6062 (t) REVERT: C 333 LYS cc_start: 0.8684 (OUTLIER) cc_final: 0.8444 (mptp) REVERT: C 610 MET cc_start: 0.8537 (mpp) cc_final: 0.8290 (mtm) outliers start: 22 outliers final: 15 residues processed: 107 average time/residue: 1.0033 time to fit residues: 117.4692 Evaluate side-chains 96 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 79 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 634 ASP Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 312 SER Chi-restraints excluded: chain C residue 333 LYS Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 683 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 68 optimal weight: 3.9990 chunk 53 optimal weight: 8.9990 chunk 77 optimal weight: 0.6980 chunk 117 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 93 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 72 optimal weight: 0.0980 chunk 57 optimal weight: 5.9990 chunk 74 optimal weight: 7.9990 chunk 99 optimal weight: 7.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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: 0.8606 moved from start: 0.4279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10030 Z= 0.228 Angle : 0.510 10.452 13620 Z= 0.269 Chirality : 0.044 0.246 1494 Planarity : 0.004 0.069 1740 Dihedral : 5.467 50.647 1470 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 1.77 % Allowed : 20.76 % Favored : 77.47 % 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: -0.78 (0.25), residues: 1184 helix: 1.11 (0.30), residues: 310 sheet: -1.22 (0.45), residues: 152 loop : -1.12 (0.23), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 303 HIS 0.006 0.001 HIS A 265 PHE 0.015 0.001 PHE C 407 TYR 0.012 0.001 TYR A 682 ARG 0.014 0.001 ARG A 619 ********************** 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 99 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 80 time to evaluate : 1.114 Fit side-chains REVERT: A 381 MET cc_start: 0.8737 (ttp) cc_final: 0.8483 (ttt) REVERT: A 628 ASP cc_start: 0.7942 (m-30) cc_final: 0.7576 (m-30) REVERT: C 381 MET cc_start: 0.8713 (ttp) cc_final: 0.8485 (ttt) REVERT: C 610 MET cc_start: 0.8518 (mpp) cc_final: 0.8220 (mtm) REVERT: C 634 ASP cc_start: 0.8058 (OUTLIER) cc_final: 0.7544 (p0) outliers start: 19 outliers final: 16 residues processed: 99 average time/residue: 0.9569 time to fit residues: 104.0618 Evaluate side-chains 96 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 79 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 634 ASP Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 312 SER Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 634 ASP Chi-restraints excluded: chain C residue 683 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 28 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 26 optimal weight: 6.9990 chunk 93 optimal weight: 0.0670 chunk 39 optimal weight: 2.9990 chunk 96 optimal weight: 0.6980 chunk 11 optimal weight: 3.9990 chunk 17 optimal weight: 0.0970 chunk 82 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 overall best weight: 0.7518 ------------------------------------------------------------------------------- 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 = 0.3321 r_free = 0.3321 target = 0.095114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.072480 restraints weight = 16330.463| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 2.45 r_work: 0.2798 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2655 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.4207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10030 Z= 0.154 Angle : 0.470 9.796 13620 Z= 0.249 Chirality : 0.042 0.215 1494 Planarity : 0.004 0.065 1740 Dihedral : 5.105 47.799 1470 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 1.68 % Allowed : 21.04 % Favored : 77.28 % 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: -0.66 (0.25), residues: 1184 helix: 1.30 (0.31), residues: 310 sheet: -1.23 (0.42), residues: 164 loop : -1.05 (0.24), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 431 HIS 0.005 0.001 HIS A 265 PHE 0.013 0.001 PHE C 407 TYR 0.010 0.001 TYR C 579 ARG 0.014 0.000 ARG A 619 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3239.81 seconds wall clock time: 58 minutes 57.66 seconds (3537.66 seconds total)