Starting phenix.real_space_refine on Wed Feb 14 02:26:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kkt_0702/02_2024/6kkt_0702.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kkt_0702/02_2024/6kkt_0702.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kkt_0702/02_2024/6kkt_0702.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kkt_0702/02_2024/6kkt_0702.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kkt_0702/02_2024/6kkt_0702.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kkt_0702/02_2024/6kkt_0702.pdb" } resolution = 2.9 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= 0.006 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: 6 Type Number sf(0) Gaussians K 2 8.98 5 S 68 5.16 5 Cl 4 4.86 5 C 5544 2.51 5 N 1284 2.21 5 O 1514 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 492": "NH1" <-> "NH2" Residue "A ARG 528": "NH1" <-> "NH2" Residue "A ARG 543": "NH1" <-> "NH2" Residue "A ARG 608": "NH1" <-> "NH2" Residue "A ARG 610": "NH1" <-> "NH2" Residue "B ARG 492": "NH1" <-> "NH2" Residue "B ARG 528": "NH1" <-> "NH2" Residue "B ARG 543": "NH1" <-> "NH2" Residue "B ARG 608": "NH1" <-> "NH2" Residue "B ARG 610": "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: 8416 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 537, 4068 Classifications: {'peptide': 537} Link IDs: {'PTRANS': 26, 'TRANS': 510} Chain: "B" Number of atoms: 4068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 537, 4068 Classifications: {'peptide': 537} Link IDs: {'PTRANS': 26, 'TRANS': 510} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {'BGC': 1, 'GLC': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {'BGC': 1, 'GLC': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {'BGC': 1, 'GLC': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {'BGC': 1, 'GLC': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 40 Unusual residues: {' K': 1, ' CL': 2, 'DU0': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 40 Unusual residues: {' K': 1, ' CL': 2, 'DU0': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 5.18, per 1000 atoms: 0.62 Number of scatterers: 8416 At special positions: 0 Unit cell: (78.11, 101.65, 102.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) K 2 19.00 Cl 4 17.00 S 68 16.00 O 1514 8.00 N 1284 7.00 C 5544 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 163 " - pdb=" SG CYS A 626 " distance=2.03 Simple disulfide: pdb=" SG CYS A 308 " - pdb=" SG CYS A 323 " distance=2.03 Simple disulfide: pdb=" SG CYS A 343 " - pdb=" SG CYS A 353 " distance=2.03 Simple disulfide: pdb=" SG CYS B 163 " - pdb=" SG CYS B 626 " distance=2.03 Simple disulfide: pdb=" SG CYS B 308 " - pdb=" SG CYS B 323 " distance=2.03 Simple disulfide: pdb=" SG CYS B 343 " - pdb=" SG CYS B 353 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=4, symmetry=0 Links applied ALPHA1-4 " BGC E 1 " - " GLC E 2 " " BGC F 1 " - " GLC F 2 " " BGC I 1 " - " GLC I 2 " " BGC J 1 " - " GLC J 2 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG C 1 " - " ASN A 312 " " NAG D 1 " - " ASN A 361 " " NAG G 1 " - " ASN B 312 " " NAG H 1 " - " ASN B 361 " Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.75 Conformation dependent library (CDL) restraints added in 1.7 seconds 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1968 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 4 sheets defined 70.6% alpha, 2.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'A' and resid 119 through 124 Processing helix chain 'A' and resid 124 through 133 removed outlier: 3.745A pdb=" N PHE A 133 " --> pdb=" O LEU A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 140 Processing helix chain 'A' and resid 140 through 176 removed outlier: 6.953A pdb=" N VAL A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) removed outlier: 8.989A pdb=" N LEU A 151 " --> pdb=" O THR A 147 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLN A 152 " --> pdb=" O ALA A 148 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N CYS A 163 " --> pdb=" O ILE A 159 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N THR A 164 " --> pdb=" O CYS A 160 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU A 165 " --> pdb=" O CYS A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 194 removed outlier: 4.266A pdb=" N PHE A 187 " --> pdb=" O GLY A 183 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N MET A 188 " --> pdb=" O GLY A 184 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE A 189 " --> pdb=" O SER A 185 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLY A 194 " --> pdb=" O SER A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 227 removed outlier: 3.648A pdb=" N ALA A 214 " --> pdb=" O THR A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 269 removed outlier: 3.523A pdb=" N THR A 247 " --> pdb=" O THR A 243 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL A 253 " --> pdb=" O ASN A 249 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N TYR A 254 " --> pdb=" O ASN A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 274 Processing helix chain 'A' and resid 276 through 298 removed outlier: 3.560A pdb=" N PHE A 280 " --> pdb=" O PHE A 276 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU A 281 " --> pdb=" O ALA A 277 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE A 291 " --> pdb=" O SER A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 344 removed outlier: 3.596A pdb=" N SER A 340 " --> pdb=" O THR A 336 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N PHE A 342 " --> pdb=" O LEU A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 360 Processing helix chain 'A' and resid 372 through 379 Processing helix chain 'A' and resid 419 through 428 removed outlier: 3.638A pdb=" N GLY A 425 " --> pdb=" O THR A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 431 No H-bonds generated for 'chain 'A' and resid 429 through 431' Processing helix chain 'A' and resid 434 through 438 removed outlier: 3.613A pdb=" N SER A 438 " --> pdb=" O MET A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 477 removed outlier: 3.513A pdb=" N ILE A 451 " --> pdb=" O ALA A 447 " (cutoff:3.500A) Proline residue: A 452 - end of helix removed outlier: 3.575A pdb=" N ILE A 456 " --> pdb=" O PRO A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 483 Processing helix chain 'A' and resid 484 through 488 removed outlier: 4.412A pdb=" N ASP A 488 " --> pdb=" O LYS A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 500 Processing helix chain 'A' and resid 504 through 537 Proline residue: A 527 - end of helix Processing helix chain 'A' and resid 539 through 547 removed outlier: 4.889A pdb=" N VAL A 544 " --> pdb=" O PHE A 541 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N PHE A 545 " --> pdb=" O LEU A 542 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N HIS A 547 " --> pdb=" O VAL A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 570 removed outlier: 3.506A pdb=" N LEU A 567 " --> pdb=" O LEU A 563 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLY A 568 " --> pdb=" O ILE A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 602 removed outlier: 3.593A pdb=" N ALA A 578 " --> pdb=" O LEU A 574 " (cutoff:3.500A) Proline residue: A 579 - end of helix removed outlier: 4.038A pdb=" N GLN A 599 " --> pdb=" O ALA A 595 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N THR A 600 " --> pdb=" O CYS A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 634 removed outlier: 3.557A pdb=" N SER A 619 " --> pdb=" O HIS A 615 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N MET A 630 " --> pdb=" O CYS A 626 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER A 634 " --> pdb=" O MET A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 652 Processing helix chain 'B' and resid 119 through 124 Processing helix chain 'B' and resid 124 through 133 removed outlier: 3.745A pdb=" N PHE B 133 " --> pdb=" O LEU B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 140 Processing helix chain 'B' and resid 140 through 176 removed outlier: 6.954A pdb=" N VAL B 150 " --> pdb=" O GLY B 146 " (cutoff:3.500A) removed outlier: 8.989A pdb=" N LEU B 151 " --> pdb=" O THR B 147 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLN B 152 " --> pdb=" O ALA B 148 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N CYS B 163 " --> pdb=" O ILE B 159 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N THR B 164 " --> pdb=" O CYS B 160 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU B 165 " --> pdb=" O CYS B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 194 removed outlier: 4.267A pdb=" N PHE B 187 " --> pdb=" O GLY B 183 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N MET B 188 " --> pdb=" O GLY B 184 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE B 189 " --> pdb=" O SER B 185 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLY B 194 " --> pdb=" O SER B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 227 removed outlier: 3.649A pdb=" N ALA B 214 " --> pdb=" O THR B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 269 removed outlier: 3.523A pdb=" N THR B 247 " --> pdb=" O THR B 243 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL B 253 " --> pdb=" O ASN B 249 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N TYR B 254 " --> pdb=" O ASN B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 274 Processing helix chain 'B' and resid 276 through 298 removed outlier: 3.560A pdb=" N PHE B 280 " --> pdb=" O PHE B 276 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU B 281 " --> pdb=" O ALA B 277 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE B 291 " --> pdb=" O SER B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 344 removed outlier: 3.597A pdb=" N SER B 340 " --> pdb=" O THR B 336 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N PHE B 342 " --> pdb=" O LEU B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 360 Processing helix chain 'B' and resid 372 through 379 Processing helix chain 'B' and resid 419 through 428 removed outlier: 3.638A pdb=" N GLY B 425 " --> pdb=" O THR B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 431 No H-bonds generated for 'chain 'B' and resid 429 through 431' Processing helix chain 'B' and resid 434 through 438 removed outlier: 3.614A pdb=" N SER B 438 " --> pdb=" O MET B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 477 removed outlier: 3.513A pdb=" N ILE B 451 " --> pdb=" O ALA B 447 " (cutoff:3.500A) Proline residue: B 452 - end of helix removed outlier: 3.576A pdb=" N ILE B 456 " --> pdb=" O PRO B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 483 Processing helix chain 'B' and resid 484 through 488 removed outlier: 4.413A pdb=" N ASP B 488 " --> pdb=" O LYS B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 500 Processing helix chain 'B' and resid 504 through 537 Proline residue: B 527 - end of helix Processing helix chain 'B' and resid 539 through 547 removed outlier: 4.889A pdb=" N VAL B 544 " --> pdb=" O PHE B 541 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N PHE B 545 " --> pdb=" O LEU B 542 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N HIS B 547 " --> pdb=" O VAL B 544 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 570 removed outlier: 3.506A pdb=" N LEU B 567 " --> pdb=" O LEU B 563 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLY B 568 " --> pdb=" O ILE B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 602 removed outlier: 3.593A pdb=" N ALA B 578 " --> pdb=" O LEU B 574 " (cutoff:3.500A) Proline residue: B 579 - end of helix removed outlier: 4.038A pdb=" N GLN B 599 " --> pdb=" O ALA B 595 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N THR B 600 " --> pdb=" O CYS B 596 " (cutoff:3.500A) Processing helix chain 'B' and resid 615 through 634 removed outlier: 3.558A pdb=" N SER B 619 " --> pdb=" O HIS B 615 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N MET B 630 " --> pdb=" O CYS B 626 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER B 634 " --> pdb=" O MET B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 652 Processing sheet with id=AA1, first strand: chain 'A' and resid 313 through 314 Processing sheet with id=AA2, first strand: chain 'A' and resid 326 through 328 Processing sheet with id=AA3, first strand: chain 'B' and resid 313 through 314 Processing sheet with id=AA4, first strand: chain 'B' and resid 326 through 328 494 hydrogen bonds defined for protein. 1434 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: 2.30 Time building geometry restraints manager: 3.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 2474 1.35 - 1.48: 2385 1.48 - 1.60: 3663 1.60 - 1.73: 0 1.73 - 1.86: 104 Bond restraints: 8626 Sorted by residual: bond pdb=" C5 GLC F 2 " pdb=" O5 GLC F 2 " ideal model delta sigma weight residual 1.415 1.503 -0.088 2.00e-02 2.50e+03 1.94e+01 bond pdb=" C5 GLC I 2 " pdb=" O5 GLC I 2 " ideal model delta sigma weight residual 1.415 1.503 -0.088 2.00e-02 2.50e+03 1.94e+01 bond pdb=" C1 BGC E 1 " pdb=" O5 BGC E 1 " ideal model delta sigma weight residual 1.408 1.494 -0.086 2.00e-02 2.50e+03 1.85e+01 bond pdb=" C1 BGC J 1 " pdb=" O5 BGC J 1 " ideal model delta sigma weight residual 1.408 1.494 -0.086 2.00e-02 2.50e+03 1.85e+01 bond pdb=" C1 GLC I 2 " pdb=" O5 GLC I 2 " ideal model delta sigma weight residual 1.402 1.485 -0.083 2.00e-02 2.50e+03 1.71e+01 ... (remaining 8621 not shown) Histogram of bond angle deviations from ideal: 94.07 - 102.07: 42 102.07 - 110.07: 2049 110.07 - 118.08: 4506 118.08 - 126.08: 5051 126.08 - 134.08: 146 Bond angle restraints: 11794 Sorted by residual: angle pdb=" N VAL B 431 " pdb=" CA VAL B 431 " pdb=" C VAL B 431 " ideal model delta sigma weight residual 113.43 107.83 5.60 1.09e+00 8.42e-01 2.64e+01 angle pdb=" N VAL A 431 " pdb=" CA VAL A 431 " pdb=" C VAL A 431 " ideal model delta sigma weight residual 113.43 107.83 5.60 1.09e+00 8.42e-01 2.64e+01 angle pdb=" C VAL A 490 " pdb=" N SER A 491 " pdb=" CA SER A 491 " ideal model delta sigma weight residual 122.08 127.25 -5.17 1.47e+00 4.63e-01 1.24e+01 angle pdb=" C VAL B 490 " pdb=" N SER B 491 " pdb=" CA SER B 491 " ideal model delta sigma weight residual 122.08 127.24 -5.16 1.47e+00 4.63e-01 1.23e+01 angle pdb=" CA PRO A 230 " pdb=" C PRO A 230 " pdb=" N PRO A 231 " ideal model delta sigma weight residual 117.93 122.12 -4.19 1.20e+00 6.94e-01 1.22e+01 ... (remaining 11789 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.22: 5237 34.22 - 68.43: 53 68.43 - 102.65: 42 102.65 - 136.86: 32 136.86 - 171.08: 2 Dihedral angle restraints: 5366 sinusoidal: 2284 harmonic: 3082 Sorted by residual: dihedral pdb=" C26 DU0 A2000 " pdb=" C24 DU0 A2000 " pdb=" C25 DU0 A2000 " pdb=" O23 DU0 A2000 " ideal model delta sinusoidal sigma weight residual 189.32 18.24 171.08 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" C26 DU0 B2000 " pdb=" C24 DU0 B2000 " pdb=" C25 DU0 B2000 " pdb=" O23 DU0 B2000 " ideal model delta sinusoidal sigma weight residual 189.32 18.24 171.08 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" CA VAL A 490 " pdb=" C VAL A 490 " pdb=" N SER A 491 " pdb=" CA SER A 491 " ideal model delta harmonic sigma weight residual 180.00 157.47 22.53 0 5.00e+00 4.00e-02 2.03e+01 ... (remaining 5363 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 1233 0.086 - 0.173: 215 0.173 - 0.259: 14 0.259 - 0.345: 2 0.345 - 0.432: 2 Chirality restraints: 1466 Sorted by residual: chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.45 0.05 2.00e-02 2.50e+03 6.38e+00 chirality pdb=" C1 NAG H 2 " pdb=" O4 NAG H 1 " pdb=" C2 NAG H 2 " pdb=" O5 NAG H 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.45 0.05 2.00e-02 2.50e+03 5.60e+00 chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN A 312 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.83 0.43 2.00e-01 2.50e+01 4.66e+00 ... (remaining 1463 not shown) Planarity restraints: 1408 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 230 " 0.047 5.00e-02 4.00e+02 7.02e-02 7.89e+00 pdb=" N PRO A 231 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO A 231 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 231 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 230 " 0.047 5.00e-02 4.00e+02 7.01e-02 7.87e+00 pdb=" N PRO B 231 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO B 231 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 231 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 408 " -0.043 5.00e-02 4.00e+02 6.34e-02 6.43e+00 pdb=" N PRO B 409 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO B 409 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 409 " -0.036 5.00e-02 4.00e+02 ... (remaining 1405 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.90: 3212 2.90 - 3.46: 9186 3.46 - 4.02: 15199 4.02 - 4.58: 21702 4.58 - 5.14: 31072 Nonbonded interactions: 80371 Sorted by model distance: nonbonded pdb=" O ILE B 169 " pdb=" OG SER B 172 " model vdw 2.343 2.440 nonbonded pdb=" O ILE A 169 " pdb=" OG SER A 172 " model vdw 2.345 2.440 nonbonded pdb=" O2 GLC F 2 " pdb=" O4 GLC F 2 " model vdw 2.383 2.440 nonbonded pdb=" O2 GLC I 2 " pdb=" O4 GLC I 2 " model vdw 2.383 2.440 nonbonded pdb=" N ASP B 354 " pdb=" OD1 ASP B 354 " model vdw 2.396 2.520 ... (remaining 80366 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'I' selection = chain 'J' } 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: 0.600 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: 0.000 Extract box with map and model: 2.550 Check model and map are aligned: 0.130 Set scattering table: 0.070 Process input model: 27.190 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.070 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:17.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 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 : 0.011 0.103 8626 Z= 0.683 Angle : 1.178 10.322 11794 Z= 0.624 Chirality : 0.066 0.432 1466 Planarity : 0.008 0.070 1404 Dihedral : 18.463 171.079 3380 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.34 % Allowed : 2.49 % Favored : 97.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.62 (0.20), residues: 1070 helix: -2.23 (0.15), residues: 680 sheet: None (None), residues: 0 loop : -2.43 (0.28), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP B 339 HIS 0.005 0.001 HIS A 241 PHE 0.038 0.004 PHE B 473 TYR 0.028 0.003 TYR B 466 ARG 0.007 0.001 ARG B 252 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 217 time to evaluate : 0.929 Fit side-chains REVERT: A 190 SER cc_start: 0.8834 (t) cc_final: 0.8254 (p) REVERT: A 275 LYS cc_start: 0.8109 (ttpt) cc_final: 0.7793 (tttp) REVERT: A 553 GLU cc_start: 0.8286 (mt-10) cc_final: 0.7687 (tt0) REVERT: B 190 SER cc_start: 0.8809 (t) cc_final: 0.8163 (p) REVERT: B 275 LYS cc_start: 0.8151 (ttpt) cc_final: 0.7939 (tttp) outliers start: 3 outliers final: 2 residues processed: 219 average time/residue: 1.1512 time to fit residues: 267.9717 Evaluate side-chains 138 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 136 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain B residue 315 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 chunk 27 optimal weight: 8.9990 chunk 54 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 83 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 537 ASN A 547 HIS A 615 HIS B 547 HIS B 551 ASN B 615 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 8626 Z= 0.239 Angle : 0.709 8.722 11794 Z= 0.332 Chirality : 0.045 0.227 1466 Planarity : 0.005 0.048 1404 Dihedral : 15.467 142.366 1652 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 4.31 % Allowed : 10.43 % Favored : 85.26 % 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: -0.99 (0.24), residues: 1070 helix: 0.15 (0.19), residues: 678 sheet: None (None), residues: 0 loop : -2.05 (0.28), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 381 HIS 0.002 0.001 HIS A 241 PHE 0.015 0.002 PHE A 341 TYR 0.012 0.002 TYR A 651 ARG 0.004 0.001 ARG B 528 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 150 time to evaluate : 0.906 Fit side-chains REVERT: A 190 SER cc_start: 0.8853 (t) cc_final: 0.8297 (p) REVERT: A 275 LYS cc_start: 0.8192 (ttpt) cc_final: 0.7971 (ttmm) REVERT: A 531 GLN cc_start: 0.8343 (tp40) cc_final: 0.8081 (tt0) REVERT: A 553 GLU cc_start: 0.8287 (mt-10) cc_final: 0.7639 (tt0) REVERT: B 376 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8915 (tp) outliers start: 38 outliers final: 7 residues processed: 173 average time/residue: 1.3689 time to fit residues: 250.3103 Evaluate side-chains 143 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 135 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 351 ASP Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 351 ASP Chi-restraints excluded: chain B residue 376 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 53 optimal weight: 8.9990 chunk 29 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 65 optimal weight: 8.9990 chunk 26 optimal weight: 0.9980 chunk 96 optimal weight: 0.0170 chunk 104 optimal weight: 2.9990 chunk 85 optimal weight: 7.9990 chunk 95 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 overall best weight: 1.6024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN A 537 ASN B 319 GLN ** B 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 8626 Z= 0.276 Angle : 0.639 6.638 11794 Z= 0.306 Chirality : 0.044 0.199 1466 Planarity : 0.004 0.044 1404 Dihedral : 11.823 132.673 1648 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 5.44 % Allowed : 11.00 % Favored : 83.56 % 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: 0.14 (0.25), residues: 1070 helix: 1.13 (0.20), residues: 678 sheet: None (None), residues: 0 loop : -1.80 (0.28), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 381 HIS 0.003 0.001 HIS B 241 PHE 0.011 0.002 PHE B 467 TYR 0.020 0.002 TYR A 651 ARG 0.008 0.001 ARG B 528 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 136 time to evaluate : 0.884 Fit side-chains REVERT: A 275 LYS cc_start: 0.8197 (ttpt) cc_final: 0.7937 (ttmm) REVERT: A 553 GLU cc_start: 0.8293 (mt-10) cc_final: 0.7578 (tt0) REVERT: A 566 GLU cc_start: 0.9152 (tp30) cc_final: 0.8819 (tp30) REVERT: B 492 ARG cc_start: 0.8871 (OUTLIER) cc_final: 0.8635 (mmt180) outliers start: 48 outliers final: 18 residues processed: 169 average time/residue: 1.3943 time to fit residues: 248.5890 Evaluate side-chains 150 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 131 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 330 ASP Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 351 ASP Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 610 ARG Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 351 ASP Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 492 ARG Chi-restraints excluded: chain B residue 583 MET Chi-restraints excluded: chain B residue 600 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 5.9990 chunk 72 optimal weight: 0.9980 chunk 50 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 chunk 46 optimal weight: 0.7980 chunk 64 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 chunk 102 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 85 optimal weight: 10.0000 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN A 319 GLN A 521 GLN ** A 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 537 ASN B 319 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.2970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 8626 Z= 0.238 Angle : 0.620 8.262 11794 Z= 0.294 Chirality : 0.044 0.194 1466 Planarity : 0.004 0.040 1404 Dihedral : 10.393 131.559 1648 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 4.31 % Allowed : 13.72 % Favored : 81.97 % 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: 0.71 (0.26), residues: 1070 helix: 1.62 (0.20), residues: 678 sheet: None (None), residues: 0 loop : -1.64 (0.28), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 381 HIS 0.002 0.001 HIS B 241 PHE 0.009 0.001 PHE B 428 TYR 0.015 0.001 TYR A 651 ARG 0.004 0.000 ARG B 528 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 132 time to evaluate : 1.004 Fit side-chains REVERT: A 275 LYS cc_start: 0.8175 (ttpt) cc_final: 0.7909 (ttmm) REVERT: A 405 LYS cc_start: 0.8667 (OUTLIER) cc_final: 0.8311 (ttpp) REVERT: A 566 GLU cc_start: 0.9132 (tp30) cc_final: 0.8812 (tp30) REVERT: B 122 MET cc_start: 0.8611 (tpp) cc_final: 0.8324 (mmm) REVERT: B 377 GLN cc_start: 0.7586 (tp40) cc_final: 0.7121 (mm110) REVERT: B 378 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.8052 (mt-10) outliers start: 38 outliers final: 15 residues processed: 152 average time/residue: 1.3963 time to fit residues: 224.1905 Evaluate side-chains 146 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 129 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 330 ASP Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 351 ASP Chi-restraints excluded: chain A residue 405 LYS Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 610 ARG Chi-restraints excluded: chain A residue 623 MET Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 309 MET Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 351 ASP Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 378 GLU Chi-restraints excluded: chain B residue 408 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 58 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 52 optimal weight: 0.5980 chunk 91 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN A 521 GLN A 537 ASN A 551 ASN B 319 GLN B 551 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8626 Z= 0.212 Angle : 0.612 8.218 11794 Z= 0.287 Chirality : 0.043 0.177 1466 Planarity : 0.004 0.038 1404 Dihedral : 9.463 128.840 1648 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 4.20 % Allowed : 14.17 % Favored : 81.63 % 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: 1.13 (0.26), residues: 1070 helix: 1.93 (0.20), residues: 678 sheet: None (None), residues: 0 loop : -1.47 (0.29), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 381 HIS 0.002 0.001 HIS A 241 PHE 0.012 0.001 PHE A 541 TYR 0.019 0.001 TYR A 651 ARG 0.003 0.000 ARG B 528 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 137 time to evaluate : 1.007 Fit side-chains REVERT: A 275 LYS cc_start: 0.8198 (ttpt) cc_final: 0.7978 (ttpt) REVERT: A 378 GLU cc_start: 0.8329 (mt-10) cc_final: 0.8107 (mt-10) REVERT: A 405 LYS cc_start: 0.8651 (OUTLIER) cc_final: 0.8313 (ttpp) REVERT: A 531 GLN cc_start: 0.8456 (tt0) cc_final: 0.7978 (tt0) REVERT: A 566 GLU cc_start: 0.9128 (tp30) cc_final: 0.8805 (tp30) REVERT: B 122 MET cc_start: 0.8636 (tpp) cc_final: 0.8346 (mmm) REVERT: B 377 GLN cc_start: 0.7681 (tp40) cc_final: 0.7245 (mm110) REVERT: B 378 GLU cc_start: 0.8289 (mt-10) cc_final: 0.8053 (mt-10) REVERT: B 492 ARG cc_start: 0.8774 (OUTLIER) cc_final: 0.8497 (mmt180) REVERT: B 531 GLN cc_start: 0.8465 (mt0) cc_final: 0.8134 (tt0) outliers start: 37 outliers final: 18 residues processed: 154 average time/residue: 1.4855 time to fit residues: 240.8194 Evaluate side-chains 150 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 130 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 330 ASP Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 351 ASP Chi-restraints excluded: chain A residue 405 LYS Chi-restraints excluded: chain A residue 610 ARG Chi-restraints excluded: chain A residue 623 MET Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 309 MET Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 351 ASP Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 492 ARG Chi-restraints excluded: chain B residue 583 MET Chi-restraints excluded: chain B residue 610 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 92 optimal weight: 0.7980 chunk 20 optimal weight: 0.2980 chunk 60 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 102 optimal weight: 3.9990 chunk 85 optimal weight: 0.5980 chunk 47 optimal weight: 0.5980 chunk 8 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 53 optimal weight: 6.9990 chunk 98 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 439 ASN A 537 ASN A 551 ASN B 319 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.3355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8626 Z= 0.173 Angle : 0.588 8.123 11794 Z= 0.274 Chirality : 0.042 0.162 1466 Planarity : 0.004 0.035 1404 Dihedral : 8.358 127.674 1648 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 4.20 % Allowed : 14.29 % Favored : 81.52 % 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: 1.49 (0.26), residues: 1070 helix: 2.23 (0.20), residues: 678 sheet: None (None), residues: 0 loop : -1.35 (0.29), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 381 HIS 0.001 0.000 HIS A 547 PHE 0.009 0.001 PHE A 541 TYR 0.020 0.001 TYR A 651 ARG 0.003 0.000 ARG B 543 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 142 time to evaluate : 0.963 Fit side-chains REVERT: A 275 LYS cc_start: 0.8192 (ttpt) cc_final: 0.7960 (ttpt) REVERT: A 566 GLU cc_start: 0.9121 (tp30) cc_final: 0.8820 (tp30) REVERT: A 613 TYR cc_start: 0.8567 (m-10) cc_final: 0.8242 (m-10) REVERT: B 122 MET cc_start: 0.8656 (tpp) cc_final: 0.8384 (mmm) REVERT: B 190 SER cc_start: 0.8895 (t) cc_final: 0.8309 (p) REVERT: B 262 MET cc_start: 0.8788 (mtp) cc_final: 0.8448 (mtt) REVERT: B 377 GLN cc_start: 0.7582 (tp40) cc_final: 0.7168 (mm110) REVERT: B 378 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.8051 (mt-10) REVERT: B 492 ARG cc_start: 0.8757 (OUTLIER) cc_final: 0.8512 (mmt180) REVERT: B 566 GLU cc_start: 0.9114 (tp30) cc_final: 0.8839 (tp30) outliers start: 37 outliers final: 16 residues processed: 162 average time/residue: 1.4721 time to fit residues: 251.0909 Evaluate side-chains 149 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 131 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 351 ASP Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 583 MET Chi-restraints excluded: chain B residue 196 GLU Chi-restraints excluded: chain B residue 215 MET Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 309 MET Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 351 ASP Chi-restraints excluded: chain B residue 378 GLU Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 492 ARG Chi-restraints excluded: chain B residue 583 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 11 optimal weight: 0.3980 chunk 58 optimal weight: 4.9990 chunk 74 optimal weight: 5.9990 chunk 86 optimal weight: 0.6980 chunk 57 optimal weight: 0.7980 chunk 102 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 40 optimal weight: 0.0370 chunk 61 optimal weight: 2.9990 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 537 ASN A 551 ASN B 319 GLN B 551 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.3421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 8626 Z= 0.212 Angle : 1.189 59.199 11794 Z= 0.649 Chirality : 0.046 0.450 1466 Planarity : 0.004 0.036 1404 Dihedral : 8.639 127.295 1648 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.74 % Allowed : 16.10 % Favored : 80.16 % 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: 1.58 (0.26), residues: 1070 helix: 2.32 (0.20), residues: 678 sheet: None (None), residues: 0 loop : -1.34 (0.29), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 381 HIS 0.001 0.000 HIS A 547 PHE 0.011 0.001 PHE A 258 TYR 0.013 0.001 TYR A 613 ARG 0.003 0.000 ARG B 543 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 133 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 275 LYS cc_start: 0.8180 (ttpt) cc_final: 0.7911 (ttpt) REVERT: A 566 GLU cc_start: 0.9118 (tp30) cc_final: 0.8820 (tp30) REVERT: B 122 MET cc_start: 0.8664 (tpp) cc_final: 0.8387 (mmm) REVERT: B 190 SER cc_start: 0.8891 (t) cc_final: 0.8312 (p) REVERT: B 262 MET cc_start: 0.8802 (mtp) cc_final: 0.8447 (mtt) REVERT: B 377 GLN cc_start: 0.7613 (tp40) cc_final: 0.7229 (mm110) REVERT: B 378 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.8049 (mt-10) REVERT: B 492 ARG cc_start: 0.8768 (OUTLIER) cc_final: 0.8519 (mmt180) REVERT: B 566 GLU cc_start: 0.9114 (tp30) cc_final: 0.8836 (tp30) outliers start: 33 outliers final: 20 residues processed: 150 average time/residue: 1.4574 time to fit residues: 229.9914 Evaluate side-chains 156 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 134 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 351 ASP Chi-restraints excluded: chain A residue 361 ASN Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 583 MET Chi-restraints excluded: chain A residue 623 MET Chi-restraints excluded: chain B residue 215 MET Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 309 MET Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 351 ASP Chi-restraints excluded: chain B residue 361 ASN Chi-restraints excluded: chain B residue 378 GLU Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 492 ARG Chi-restraints excluded: chain B residue 583 MET Chi-restraints excluded: chain B residue 623 MET Chi-restraints excluded: chain B residue 642 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 30 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 chunk 69 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 80 optimal weight: 0.5980 chunk 92 optimal weight: 0.9990 chunk 97 optimal weight: 0.7980 chunk 89 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 537 ASN A 551 ASN B 319 GLN ** B 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 551 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.3404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 8626 Z= 0.212 Angle : 1.189 59.200 11794 Z= 0.649 Chirality : 0.046 0.450 1466 Planarity : 0.004 0.036 1404 Dihedral : 8.639 127.295 1648 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.61 % Allowed : 17.23 % Favored : 80.16 % 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: 1.58 (0.26), residues: 1070 helix: 2.32 (0.20), residues: 678 sheet: None (None), residues: 0 loop : -1.34 (0.29), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 381 HIS 0.001 0.000 HIS A 547 PHE 0.011 0.001 PHE A 258 TYR 0.013 0.001 TYR A 613 ARG 0.003 0.000 ARG B 543 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 132 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 275 LYS cc_start: 0.8179 (ttpt) cc_final: 0.7911 (ttpt) REVERT: A 566 GLU cc_start: 0.9118 (tp30) cc_final: 0.8820 (tp30) REVERT: B 122 MET cc_start: 0.8664 (tpp) cc_final: 0.8387 (mmm) REVERT: B 190 SER cc_start: 0.8888 (t) cc_final: 0.8312 (p) REVERT: B 262 MET cc_start: 0.8803 (mtp) cc_final: 0.8447 (mtt) REVERT: B 377 GLN cc_start: 0.7613 (tp40) cc_final: 0.7229 (mm110) REVERT: B 378 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.8049 (mt-10) REVERT: B 492 ARG cc_start: 0.8768 (OUTLIER) cc_final: 0.8519 (mmt180) REVERT: B 566 GLU cc_start: 0.9114 (tp30) cc_final: 0.8837 (tp30) outliers start: 23 outliers final: 20 residues processed: 144 average time/residue: 1.5158 time to fit residues: 229.3587 Evaluate side-chains 155 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 133 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 351 ASP Chi-restraints excluded: chain A residue 361 ASN Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 583 MET Chi-restraints excluded: chain A residue 623 MET Chi-restraints excluded: chain B residue 215 MET Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 309 MET Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 351 ASP Chi-restraints excluded: chain B residue 361 ASN Chi-restraints excluded: chain B residue 378 GLU Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 492 ARG Chi-restraints excluded: chain B residue 583 MET Chi-restraints excluded: chain B residue 623 MET Chi-restraints excluded: chain B residue 642 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 5.9990 chunk 97 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 74 optimal weight: 4.9990 chunk 29 optimal weight: 0.4980 chunk 86 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 94 optimal weight: 0.9980 chunk 62 optimal weight: 0.7980 chunk 100 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 537 ASN A 551 ASN B 319 GLN ** B 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 551 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.3403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 8626 Z= 0.212 Angle : 1.189 59.200 11794 Z= 0.649 Chirality : 0.046 0.450 1466 Planarity : 0.004 0.036 1404 Dihedral : 8.639 127.295 1648 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.61 % Allowed : 17.35 % Favored : 80.05 % 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: 1.58 (0.26), residues: 1070 helix: 2.32 (0.20), residues: 678 sheet: None (None), residues: 0 loop : -1.34 (0.29), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 381 HIS 0.001 0.000 HIS A 547 PHE 0.011 0.001 PHE A 258 TYR 0.013 0.001 TYR A 613 ARG 0.003 0.000 ARG B 543 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 131 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 275 LYS cc_start: 0.8179 (ttpt) cc_final: 0.7911 (ttpt) REVERT: A 566 GLU cc_start: 0.9118 (tp30) cc_final: 0.8820 (tp30) REVERT: B 122 MET cc_start: 0.8664 (tpp) cc_final: 0.8387 (mmm) REVERT: B 190 SER cc_start: 0.8887 (t) cc_final: 0.8312 (p) REVERT: B 262 MET cc_start: 0.8803 (mtp) cc_final: 0.8447 (mtt) REVERT: B 377 GLN cc_start: 0.7613 (tp40) cc_final: 0.7229 (mm110) REVERT: B 378 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.8049 (mt-10) REVERT: B 492 ARG cc_start: 0.8768 (OUTLIER) cc_final: 0.8519 (mmt180) REVERT: B 566 GLU cc_start: 0.9114 (tp30) cc_final: 0.8837 (tp30) outliers start: 23 outliers final: 20 residues processed: 143 average time/residue: 1.6228 time to fit residues: 243.4336 Evaluate side-chains 155 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 133 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 351 ASP Chi-restraints excluded: chain A residue 361 ASN Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 583 MET Chi-restraints excluded: chain A residue 623 MET Chi-restraints excluded: chain B residue 215 MET Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 309 MET Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 351 ASP Chi-restraints excluded: chain B residue 361 ASN Chi-restraints excluded: chain B residue 378 GLU Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 492 ARG Chi-restraints excluded: chain B residue 583 MET Chi-restraints excluded: chain B residue 623 MET Chi-restraints excluded: chain B residue 642 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 61 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 69 optimal weight: 0.2980 chunk 105 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 64 optimal weight: 0.4980 chunk 51 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 537 ASN A 551 ASN B 319 GLN ** B 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 551 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.3403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 8626 Z= 0.212 Angle : 1.189 59.200 11794 Z= 0.649 Chirality : 0.046 0.450 1466 Planarity : 0.004 0.036 1404 Dihedral : 8.639 127.295 1648 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.61 % Allowed : 17.35 % Favored : 80.05 % 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: 1.58 (0.26), residues: 1070 helix: 2.32 (0.20), residues: 678 sheet: None (None), residues: 0 loop : -1.34 (0.29), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 381 HIS 0.001 0.000 HIS A 547 PHE 0.011 0.001 PHE A 258 TYR 0.013 0.001 TYR A 613 ARG 0.003 0.000 ARG B 543 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 131 time to evaluate : 0.972 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 275 LYS cc_start: 0.8179 (ttpt) cc_final: 0.7911 (ttpt) REVERT: A 566 GLU cc_start: 0.9118 (tp30) cc_final: 0.8820 (tp30) REVERT: B 122 MET cc_start: 0.8664 (tpp) cc_final: 0.8387 (mmm) REVERT: B 190 SER cc_start: 0.8887 (t) cc_final: 0.8312 (p) REVERT: B 262 MET cc_start: 0.8803 (mtp) cc_final: 0.8447 (mtt) REVERT: B 377 GLN cc_start: 0.7613 (tp40) cc_final: 0.7229 (mm110) REVERT: B 378 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.8049 (mt-10) REVERT: B 492 ARG cc_start: 0.8768 (OUTLIER) cc_final: 0.8519 (mmt180) REVERT: B 566 GLU cc_start: 0.9114 (tp30) cc_final: 0.8837 (tp30) outliers start: 23 outliers final: 20 residues processed: 143 average time/residue: 1.6084 time to fit residues: 241.6523 Evaluate side-chains 155 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 133 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 351 ASP Chi-restraints excluded: chain A residue 361 ASN Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 583 MET Chi-restraints excluded: chain A residue 623 MET Chi-restraints excluded: chain B residue 215 MET Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 309 MET Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 351 ASP Chi-restraints excluded: chain B residue 361 ASN Chi-restraints excluded: chain B residue 378 GLU Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 492 ARG Chi-restraints excluded: chain B residue 583 MET Chi-restraints excluded: chain B residue 623 MET Chi-restraints excluded: chain B residue 642 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 25 optimal weight: 0.6980 chunk 77 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 35 optimal weight: 0.5980 chunk 86 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 15 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 537 ASN A 551 ASN B 319 GLN ** B 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 551 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.119086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.088257 restraints weight = 10886.067| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 2.40 r_work: 0.2811 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2661 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.3403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 8626 Z= 0.212 Angle : 1.189 59.200 11794 Z= 0.649 Chirality : 0.046 0.450 1466 Planarity : 0.004 0.036 1404 Dihedral : 8.639 127.295 1648 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.61 % Allowed : 17.35 % Favored : 80.05 % 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: 1.58 (0.26), residues: 1070 helix: 2.32 (0.20), residues: 678 sheet: None (None), residues: 0 loop : -1.34 (0.29), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 381 HIS 0.001 0.000 HIS A 547 PHE 0.011 0.001 PHE A 258 TYR 0.013 0.001 TYR A 613 ARG 0.003 0.000 ARG B 543 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3932.18 seconds wall clock time: 70 minutes 23.03 seconds (4223.03 seconds total)