Starting phenix.real_space_refine on Sat Mar 16 10:15:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fhk_31585/03_2024/7fhk_31585.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fhk_31585/03_2024/7fhk_31585.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fhk_31585/03_2024/7fhk_31585.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fhk_31585/03_2024/7fhk_31585.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fhk_31585/03_2024/7fhk_31585.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fhk_31585/03_2024/7fhk_31585.pdb" } resolution = 3.3 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3394 atoms to isotropic. 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 4 9.91 5 S 44 5.16 5 C 7346 2.51 5 N 1710 2.21 5 O 1954 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 328": "OE1" <-> "OE2" Residue "A GLU 678": "OE1" <-> "OE2" Residue "C GLU 403": "OE1" <-> "OE2" Residue "C PHE 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 11058 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 663, 5467 Classifications: {'peptide': 663} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 20, 'TRANS': 642} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 60 Classifications: {'peptide': 12} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'TRANS': 11} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'UNK:plan-1': 12} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 5467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 663, 5467 Classifications: {'peptide': 663} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 20, 'TRANS': 642} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 60 Classifications: {'peptide': 12} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'TRANS': 11} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'UNK:plan-1': 12} Unresolved non-hydrogen planarities: 12 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.05, per 1000 atoms: 0.55 Number of scatterers: 11058 At special positions: 0 Unit cell: (88.218, 120.666, 116.61, 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 4 19.99 S 44 16.00 O 1954 8.00 N 1710 7.00 C 7346 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.73 Conformation dependent library (CDL) restraints added in 1.9 seconds 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2584 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 0 sheets defined 87.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'A' and resid 20 through 27 Processing helix chain 'A' and resid 29 through 44 Processing helix chain 'A' and resid 48 through 54 Processing helix chain 'A' and resid 57 through 69 removed outlier: 3.520A pdb=" N ALA A 61 " --> pdb=" O PHE A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 88 removed outlier: 3.525A pdb=" N TRP A 74 " --> pdb=" O LEU A 70 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ASN A 85 " --> pdb=" O LEU A 81 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N PHE A 86 " --> pdb=" O LEU A 82 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N PHE A 87 " --> pdb=" O PHE A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 95 removed outlier: 3.766A pdb=" N GLU A 94 " --> pdb=" O PRO A 90 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS A 95 " --> pdb=" O LEU A 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 90 through 95' Processing helix chain 'A' and resid 116 through 137 Processing helix chain 'A' and resid 138 through 143 Processing helix chain 'A' and resid 143 through 150 removed outlier: 3.616A pdb=" N SER A 150 " --> pdb=" O ILE A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 174 Processing helix chain 'A' and resid 186 through 197 removed outlier: 3.598A pdb=" N VAL A 192 " --> pdb=" O PRO A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 238 removed outlier: 4.295A pdb=" N GLY A 214 " --> pdb=" O SER A 210 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N THR A 215 " --> pdb=" O GLY A 211 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ASN A 218 " --> pdb=" O GLY A 214 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE A 219 " --> pdb=" O THR A 215 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU A 222 " --> pdb=" O ASN A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 247 removed outlier: 3.503A pdb=" N LEU A 245 " --> pdb=" O THR A 241 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR A 246 " --> pdb=" O GLN A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 263 removed outlier: 3.769A pdb=" N THR A 263 " --> pdb=" O PHE A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 271 removed outlier: 3.937A pdb=" N VAL A 270 " --> pdb=" O ASN A 266 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N TRP A 271 " --> pdb=" O ASN A 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 266 through 271' Processing helix chain 'A' and resid 271 through 278 Processing helix chain 'A' and resid 281 through 295 removed outlier: 3.719A pdb=" N PHE A 285 " --> pdb=" O SER A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 335 Processing helix chain 'A' and resid 343 through 358 removed outlier: 3.857A pdb=" N LYS A 349 " --> pdb=" O ASN A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 376 removed outlier: 4.231A pdb=" N GLY A 369 " --> pdb=" O LYS A 365 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASP A 373 " --> pdb=" O GLY A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 399 removed outlier: 3.772A pdb=" N ALA A 389 " --> pdb=" O LYS A 385 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASP A 390 " --> pdb=" O ASP A 386 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU A 391 " --> pdb=" O GLU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 416 Processing helix chain 'A' and resid 417 through 429 Processing helix chain 'A' and resid 429 through 456 removed outlier: 3.964A pdb=" N GLY A 433 " --> pdb=" O SER A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 487 removed outlier: 4.058A pdb=" N TRP A 464 " --> pdb=" O ALA A 460 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N PHE A 471 " --> pdb=" O ALA A 467 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLY A 472 " --> pdb=" O GLU A 468 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR A 485 " --> pdb=" O LEU A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 494 removed outlier: 4.209A pdb=" N GLU A 494 " --> pdb=" O ASN A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 517 Processing helix chain 'A' and resid 528 through 538 removed outlier: 4.377A pdb=" N TYR A 532 " --> pdb=" O GLU A 528 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU A 533 " --> pdb=" O TRP A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 547 Processing helix chain 'A' and resid 551 through 565 Proline residue: A 563 - end of helix Processing helix chain 'A' and resid 565 through 587 Processing helix chain 'A' and resid 595 through 601 removed outlier: 4.047A pdb=" N PHE A 599 " --> pdb=" O ASN A 595 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLU A 600 " --> pdb=" O LYS A 596 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR A 601 " --> pdb=" O LYS A 597 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 595 through 601' Processing helix chain 'A' and resid 601 through 607 removed outlier: 3.786A pdb=" N GLU A 605 " --> pdb=" O THR A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 612 Processing helix chain 'A' and resid 615 through 628 Processing helix chain 'A' and resid 632 through 644 removed outlier: 3.957A pdb=" N MET A 636 " --> pdb=" O TRP A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 647 No H-bonds generated for 'chain 'A' and resid 645 through 647' Processing helix chain 'A' and resid 648 through 660 removed outlier: 3.957A pdb=" N PHE A 652 " --> pdb=" O SER A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 686 removed outlier: 3.601A pdb=" N LEU A 681 " --> pdb=" O THR A 677 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU A 685 " --> pdb=" O LEU A 681 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LYS A 686 " --> pdb=" O GLU A 682 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 17 Processing helix chain 'C' and resid 20 through 27 Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'C' and resid 48 through 54 Processing helix chain 'C' and resid 57 through 69 removed outlier: 3.517A pdb=" N ALA C 61 " --> pdb=" O PHE C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 88 removed outlier: 3.511A pdb=" N TRP C 74 " --> pdb=" O LEU C 70 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ASN C 85 " --> pdb=" O LEU C 81 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N PHE C 86 " --> pdb=" O LEU C 82 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N PHE C 87 " --> pdb=" O PHE C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 95 removed outlier: 3.749A pdb=" N GLU C 94 " --> pdb=" O PRO C 90 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS C 95 " --> pdb=" O LEU C 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 90 through 95' Processing helix chain 'C' and resid 116 through 137 Processing helix chain 'C' and resid 138 through 143 Processing helix chain 'C' and resid 143 through 150 removed outlier: 3.552A pdb=" N THR C 149 " --> pdb=" O ARG C 145 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER C 150 " --> pdb=" O ILE C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 174 Processing helix chain 'C' and resid 186 through 199 removed outlier: 3.775A pdb=" N ILE C 199 " --> pdb=" O PHE C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 238 removed outlier: 4.930A pdb=" N GLY C 214 " --> pdb=" O SER C 210 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N THR C 215 " --> pdb=" O GLY C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 247 Processing helix chain 'C' and resid 250 through 264 Processing helix chain 'C' and resid 266 through 271 removed outlier: 3.944A pdb=" N VAL C 270 " --> pdb=" O ASN C 266 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N TRP C 271 " --> pdb=" O ASN C 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 266 through 271' Processing helix chain 'C' and resid 271 through 278 Processing helix chain 'C' and resid 280 through 295 removed outlier: 4.208A pdb=" N PHE C 284 " --> pdb=" O TRP C 280 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE C 285 " --> pdb=" O SER C 281 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU C 290 " --> pdb=" O VAL C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 335 Processing helix chain 'C' and resid 343 through 358 Processing helix chain 'C' and resid 364 through 376 removed outlier: 3.505A pdb=" N PHE C 368 " --> pdb=" O SER C 364 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N GLY C 369 " --> pdb=" O LYS C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 399 Processing helix chain 'C' and resid 411 through 416 Processing helix chain 'C' and resid 417 through 429 Processing helix chain 'C' and resid 429 through 456 removed outlier: 4.204A pdb=" N GLY C 433 " --> pdb=" O SER C 429 " (cutoff:3.500A) Processing helix chain 'C' and resid 460 through 487 removed outlier: 4.479A pdb=" N TRP C 464 " --> pdb=" O ALA C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 494 removed outlier: 4.083A pdb=" N GLU C 494 " --> pdb=" O ASN C 490 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 517 removed outlier: 3.554A pdb=" N ARG C 498 " --> pdb=" O GLU C 494 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE C 499 " --> pdb=" O GLY C 495 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR C 517 " --> pdb=" O ALA C 513 " (cutoff:3.500A) Processing helix chain 'C' and resid 528 through 538 removed outlier: 4.296A pdb=" N TYR C 532 " --> pdb=" O GLU C 528 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU C 533 " --> pdb=" O TRP C 529 " (cutoff:3.500A) Processing helix chain 'C' and resid 539 through 547 Processing helix chain 'C' and resid 551 through 587 Proline residue: C 563 - end of helix Proline residue: C 567 - end of helix Processing helix chain 'C' and resid 595 through 601 removed outlier: 4.065A pdb=" N PHE C 599 " --> pdb=" O ASN C 595 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLU C 600 " --> pdb=" O LYS C 596 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR C 601 " --> pdb=" O LYS C 597 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 595 through 601' Processing helix chain 'C' and resid 601 through 607 removed outlier: 3.645A pdb=" N GLU C 605 " --> pdb=" O THR C 601 " (cutoff:3.500A) Processing helix chain 'C' and resid 608 through 612 Processing helix chain 'C' and resid 615 through 628 Processing helix chain 'C' and resid 632 through 644 removed outlier: 3.890A pdb=" N MET C 636 " --> pdb=" O TRP C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 646 through 659 removed outlier: 4.129A pdb=" N THR C 650 " --> pdb=" O TRP C 646 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N TYR C 651 " --> pdb=" O TRP C 647 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N PHE C 652 " --> pdb=" O SER C 648 " (cutoff:3.500A) Processing helix chain 'C' and resid 662 through 686 Processing helix chain 'D' and resid 7 through 17 769 hydrogen bonds defined for protein. 2259 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.47 Time building geometry restraints manager: 5.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3351 1.34 - 1.46: 2092 1.46 - 1.57: 5835 1.57 - 1.69: 0 1.69 - 1.81: 72 Bond restraints: 11350 Sorted by residual: bond pdb=" C LYS A 98 " pdb=" N PRO A 99 " ideal model delta sigma weight residual 1.330 1.346 -0.016 1.23e-02 6.61e+03 1.65e+00 bond pdb=" CG LEU C 440 " pdb=" CD1 LEU C 440 " ideal model delta sigma weight residual 1.521 1.484 0.037 3.30e-02 9.18e+02 1.24e+00 bond pdb=" CB GLU C 468 " pdb=" CG GLU C 468 " ideal model delta sigma weight residual 1.520 1.487 0.033 3.00e-02 1.11e+03 1.23e+00 bond pdb=" N PHE A 57 " pdb=" CA PHE A 57 " ideal model delta sigma weight residual 1.457 1.471 -0.013 1.29e-02 6.01e+03 1.07e+00 bond pdb=" N PHE C 57 " pdb=" CA PHE C 57 " ideal model delta sigma weight residual 1.457 1.471 -0.013 1.29e-02 6.01e+03 1.04e+00 ... (remaining 11345 not shown) Histogram of bond angle deviations from ideal: 100.07 - 106.86: 220 106.86 - 113.65: 6176 113.65 - 120.44: 4659 120.44 - 127.24: 4275 127.24 - 134.03: 110 Bond angle restraints: 15440 Sorted by residual: angle pdb=" C THR C 246 " pdb=" N VAL C 247 " pdb=" CA VAL C 247 " ideal model delta sigma weight residual 123.16 120.08 3.08 1.06e+00 8.90e-01 8.43e+00 angle pdb=" C THR A 246 " pdb=" N VAL A 247 " pdb=" CA VAL A 247 " ideal model delta sigma weight residual 123.16 120.11 3.05 1.06e+00 8.90e-01 8.29e+00 angle pdb=" N VAL C 286 " pdb=" CA VAL C 286 " pdb=" C VAL C 286 " ideal model delta sigma weight residual 113.00 109.55 3.45 1.30e+00 5.92e-01 7.04e+00 angle pdb=" N GLN C 393 " pdb=" CA GLN C 393 " pdb=" CB GLN C 393 " ideal model delta sigma weight residual 110.12 113.99 -3.87 1.47e+00 4.63e-01 6.93e+00 angle pdb=" CA LYS C 385 " pdb=" CB LYS C 385 " pdb=" CG LYS C 385 " ideal model delta sigma weight residual 114.10 119.04 -4.94 2.00e+00 2.50e-01 6.10e+00 ... (remaining 15435 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.42: 6027 17.42 - 34.84: 455 34.84 - 52.25: 70 52.25 - 69.67: 6 69.67 - 87.09: 8 Dihedral angle restraints: 6566 sinusoidal: 2570 harmonic: 3996 Sorted by residual: dihedral pdb=" CA SER A 56 " pdb=" C SER A 56 " pdb=" N PHE A 57 " pdb=" CA PHE A 57 " ideal model delta harmonic sigma weight residual 180.00 163.15 16.85 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" CA SER C 56 " pdb=" C SER C 56 " pdb=" N PHE C 57 " pdb=" CA PHE C 57 " ideal model delta harmonic sigma weight residual 180.00 163.20 16.80 0 5.00e+00 4.00e-02 1.13e+01 dihedral pdb=" CA LYS C 98 " pdb=" C LYS C 98 " pdb=" N PRO C 99 " pdb=" CA PRO C 99 " ideal model delta harmonic sigma weight residual 180.00 163.31 16.69 0 5.00e+00 4.00e-02 1.11e+01 ... (remaining 6563 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1276 0.038 - 0.077: 381 0.077 - 0.115: 76 0.115 - 0.153: 14 0.153 - 0.192: 1 Chirality restraints: 1748 Sorted by residual: chirality pdb=" CA LYS C 98 " pdb=" N LYS C 98 " pdb=" C LYS C 98 " pdb=" CB LYS C 98 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.19e-01 chirality pdb=" CA VAL C 404 " pdb=" N VAL C 404 " pdb=" C VAL C 404 " pdb=" CB VAL C 404 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.65e-01 chirality pdb=" CA VAL A 404 " pdb=" N VAL A 404 " pdb=" C VAL A 404 " pdb=" CB VAL A 404 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.58e-01 ... (remaining 1745 not shown) Planarity restraints: 1914 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR C 651 " 0.008 2.00e-02 2.50e+03 1.64e-02 2.69e+00 pdb=" C TYR C 651 " -0.028 2.00e-02 2.50e+03 pdb=" O TYR C 651 " 0.011 2.00e-02 2.50e+03 pdb=" N PHE C 652 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG C 531 " -0.008 2.00e-02 2.50e+03 1.53e-02 2.35e+00 pdb=" C ARG C 531 " 0.027 2.00e-02 2.50e+03 pdb=" O ARG C 531 " -0.010 2.00e-02 2.50e+03 pdb=" N TYR C 532 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP C 607 " 0.006 2.00e-02 2.50e+03 1.29e-02 1.66e+00 pdb=" C ASP C 607 " -0.022 2.00e-02 2.50e+03 pdb=" O ASP C 607 " 0.008 2.00e-02 2.50e+03 pdb=" N TYR C 608 " 0.007 2.00e-02 2.50e+03 ... (remaining 1911 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1579 2.75 - 3.29: 11731 3.29 - 3.82: 18218 3.82 - 4.36: 20059 4.36 - 4.90: 35187 Nonbonded interactions: 86774 Sorted by model distance: nonbonded pdb=" OH TYR C 216 " pdb=" O VAL C 657 " model vdw 2.210 2.440 nonbonded pdb=" O PHE C 426 " pdb=" OG SER C 429 " model vdw 2.225 2.440 nonbonded pdb=" O TYR A 107 " pdb=" ND2 ASN A 614 " model vdw 2.231 2.520 nonbonded pdb=" OE2 GLU C 478 " pdb=" NH2 ARG C 537 " model vdw 2.252 2.520 nonbonded pdb=" O TYR C 107 " pdb=" ND2 ASN C 614 " model vdw 2.253 2.520 ... (remaining 86769 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' } ncs_group { reference = chain 'B' selection = chain 'D' } 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: 1.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.000 Extract box with map and model: 3.600 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 32.590 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.060 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 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 : 0.004 0.037 11350 Z= 0.225 Angle : 0.596 7.132 15440 Z= 0.335 Chirality : 0.038 0.192 1748 Planarity : 0.003 0.031 1914 Dihedral : 12.525 87.090 3982 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % 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: 1.22 (0.23), residues: 1318 helix: 1.18 (0.16), residues: 972 sheet: None (None), residues: 0 loop : -0.01 (0.36), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 492 HIS 0.005 0.002 HIS C 134 PHE 0.019 0.001 PHE C 248 TYR 0.017 0.002 TYR C 256 ARG 0.003 0.000 ARG A 191 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 1.314 Fit side-chains REVERT: A 149 THR cc_start: 0.8234 (m) cc_final: 0.7903 (p) REVERT: A 321 GLN cc_start: 0.8098 (tm-30) cc_final: 0.7775 (tm-30) REVERT: A 406 SER cc_start: 0.7673 (t) cc_final: 0.6224 (t) REVERT: A 620 MET cc_start: 0.8906 (mmm) cc_final: 0.8676 (mmt) REVERT: A 637 GLU cc_start: 0.7542 (tm-30) cc_final: 0.6692 (tm-30) REVERT: C 149 THR cc_start: 0.8179 (m) cc_final: 0.7868 (p) REVERT: C 321 GLN cc_start: 0.7893 (tm-30) cc_final: 0.7655 (tm-30) REVERT: C 406 SER cc_start: 0.7776 (t) cc_final: 0.7462 (t) REVERT: C 629 MET cc_start: 0.8850 (mmm) cc_final: 0.8537 (mmm) REVERT: C 637 GLU cc_start: 0.7387 (tm-30) cc_final: 0.6847 (tm-30) REVERT: C 641 ASP cc_start: 0.7434 (m-30) cc_final: 0.7143 (m-30) outliers start: 0 outliers final: 0 residues processed: 178 average time/residue: 0.1818 time to fit residues: 50.0109 Evaluate side-chains 128 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 113 optimal weight: 5.9990 chunk 101 optimal weight: 9.9990 chunk 56 optimal weight: 4.9990 chunk 34 optimal weight: 8.9990 chunk 68 optimal weight: 10.0000 chunk 54 optimal weight: 0.0000 chunk 105 optimal weight: 10.0000 chunk 40 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 121 optimal weight: 0.7980 overall best weight: 1.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.1339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 11350 Z= 0.262 Angle : 0.596 7.353 15440 Z= 0.315 Chirality : 0.039 0.192 1748 Planarity : 0.004 0.068 1914 Dihedral : 4.136 17.438 1468 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.18 % Allowed : 7.15 % Favored : 91.67 % 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: 2.14 (0.24), residues: 1318 helix: 1.91 (0.16), residues: 998 sheet: None (None), residues: 0 loop : -0.05 (0.38), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 492 HIS 0.004 0.001 HIS C 134 PHE 0.025 0.002 PHE C 408 TYR 0.019 0.002 TYR C 256 ARG 0.003 0.000 ARG C 498 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 123 time to evaluate : 1.288 Fit side-chains REVERT: A 154 LEU cc_start: 0.9003 (mt) cc_final: 0.8764 (mt) REVERT: A 443 ASN cc_start: 0.8979 (t0) cc_final: 0.8746 (t0) REVERT: A 538 MET cc_start: 0.8551 (mtm) cc_final: 0.8269 (mtm) REVERT: A 629 MET cc_start: 0.8897 (mmm) cc_final: 0.8681 (mmm) REVERT: C 287 LEU cc_start: 0.9140 (tp) cc_final: 0.8928 (mt) REVERT: C 321 GLN cc_start: 0.7913 (tm-30) cc_final: 0.7664 (tm-30) REVERT: C 515 PHE cc_start: 0.7564 (t80) cc_final: 0.7294 (t80) REVERT: C 620 MET cc_start: 0.8515 (mmm) cc_final: 0.8049 (mmt) REVERT: C 637 GLU cc_start: 0.7425 (tm-30) cc_final: 0.7017 (tm-30) outliers start: 14 outliers final: 11 residues processed: 133 average time/residue: 0.1783 time to fit residues: 36.9745 Evaluate side-chains 129 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 118 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 478 GLU Chi-restraints excluded: chain A residue 658 ILE Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 198 SER Chi-restraints excluded: chain C residue 327 LEU Chi-restraints excluded: chain C residue 658 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 67 optimal weight: 10.0000 chunk 37 optimal weight: 4.9990 chunk 101 optimal weight: 10.0000 chunk 82 optimal weight: 9.9990 chunk 33 optimal weight: 1.9990 chunk 121 optimal weight: 0.5980 chunk 131 optimal weight: 0.6980 chunk 108 optimal weight: 0.9990 chunk 120 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 97 optimal weight: 6.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11350 Z= 0.217 Angle : 0.550 7.438 15440 Z= 0.287 Chirality : 0.038 0.183 1748 Planarity : 0.004 0.040 1914 Dihedral : 4.033 16.503 1468 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.18 % Allowed : 9.93 % Favored : 88.89 % 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 (0.24), residues: 1318 helix: 2.10 (0.17), residues: 988 sheet: None (None), residues: 0 loop : -0.13 (0.37), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 492 HIS 0.002 0.001 HIS C 416 PHE 0.023 0.001 PHE A 368 TYR 0.023 0.002 TYR C 415 ARG 0.005 0.000 ARG C 424 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 134 time to evaluate : 1.422 Fit side-chains REVERT: A 154 LEU cc_start: 0.9004 (mt) cc_final: 0.8758 (mt) REVERT: A 321 GLN cc_start: 0.7848 (tm-30) cc_final: 0.7616 (tm-30) REVERT: A 443 ASN cc_start: 0.8890 (t0) cc_final: 0.8668 (t0) REVERT: A 566 MET cc_start: 0.7972 (tpp) cc_final: 0.7724 (mmm) REVERT: A 629 MET cc_start: 0.8842 (mmm) cc_final: 0.8603 (mmm) REVERT: A 682 GLU cc_start: 0.8452 (mm-30) cc_final: 0.7923 (tt0) REVERT: C 287 LEU cc_start: 0.9181 (tp) cc_final: 0.8972 (mt) REVERT: C 321 GLN cc_start: 0.7925 (tm-30) cc_final: 0.7660 (tm-30) REVERT: C 637 GLU cc_start: 0.7636 (tm-30) cc_final: 0.7252 (tm-30) outliers start: 14 outliers final: 9 residues processed: 143 average time/residue: 0.1771 time to fit residues: 39.1640 Evaluate side-chains 127 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 118 time to evaluate : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 198 SER Chi-restraints excluded: chain C residue 272 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 63 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 58 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 chunk 122 optimal weight: 0.7980 chunk 129 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 34 optimal weight: 10.0000 chunk 107 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 11350 Z= 0.220 Angle : 0.546 8.456 15440 Z= 0.283 Chirality : 0.038 0.175 1748 Planarity : 0.003 0.038 1914 Dihedral : 3.990 16.265 1468 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.60 % Allowed : 12.29 % Favored : 86.11 % 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: 2.36 (0.24), residues: 1318 helix: 2.09 (0.16), residues: 1012 sheet: None (None), residues: 0 loop : -0.18 (0.39), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 492 HIS 0.002 0.001 HIS C 416 PHE 0.023 0.001 PHE A 368 TYR 0.021 0.002 TYR C 415 ARG 0.002 0.000 ARG A 498 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 125 time to evaluate : 1.169 Fit side-chains revert: symmetry clash REVERT: A 321 GLN cc_start: 0.7882 (tm-30) cc_final: 0.7620 (tm-30) REVERT: A 443 ASN cc_start: 0.8903 (t0) cc_final: 0.8701 (t0) REVERT: A 629 MET cc_start: 0.8839 (mmm) cc_final: 0.8564 (mmm) REVERT: A 682 GLU cc_start: 0.8414 (mm-30) cc_final: 0.7962 (tt0) REVERT: C 287 LEU cc_start: 0.9169 (tp) cc_final: 0.8938 (mt) REVERT: C 321 GLN cc_start: 0.7918 (tm-30) cc_final: 0.7645 (tm-30) REVERT: C 629 MET cc_start: 0.8836 (mmm) cc_final: 0.8603 (mmm) REVERT: C 637 GLU cc_start: 0.7729 (tm-30) cc_final: 0.7298 (tm-30) outliers start: 19 outliers final: 14 residues processed: 139 average time/residue: 0.1933 time to fit residues: 40.5966 Evaluate side-chains 132 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 118 time to evaluate : 1.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 393 GLN Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 198 SER Chi-restraints excluded: chain C residue 272 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 73 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 chunk 96 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 110 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 66 optimal weight: 10.0000 chunk 116 optimal weight: 0.0050 chunk 32 optimal weight: 2.9990 chunk 43 optimal weight: 6.9990 overall best weight: 1.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 11350 Z= 0.246 Angle : 0.558 8.973 15440 Z= 0.289 Chirality : 0.038 0.169 1748 Planarity : 0.003 0.036 1914 Dihedral : 3.988 17.510 1468 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.19 % Allowed : 12.79 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.30 (0.24), residues: 1318 helix: 2.03 (0.17), residues: 1016 sheet: None (None), residues: 0 loop : -0.19 (0.38), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 492 HIS 0.003 0.001 HIS C 416 PHE 0.022 0.001 PHE A 368 TYR 0.027 0.002 TYR C 415 ARG 0.006 0.000 ARG C 424 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 130 time to evaluate : 1.297 Fit side-chains REVERT: A 321 GLN cc_start: 0.7867 (tm-30) cc_final: 0.7602 (tm-30) REVERT: A 351 PHE cc_start: 0.8393 (t80) cc_final: 0.8155 (t80) REVERT: A 443 ASN cc_start: 0.9011 (t0) cc_final: 0.8706 (t0) REVERT: A 629 MET cc_start: 0.8834 (mmm) cc_final: 0.8567 (mmm) REVERT: A 682 GLU cc_start: 0.8424 (mm-30) cc_final: 0.7977 (tt0) REVERT: C 287 LEU cc_start: 0.9183 (tp) cc_final: 0.8945 (mt) REVERT: C 321 GLN cc_start: 0.7919 (tm-30) cc_final: 0.7683 (tm-30) REVERT: C 629 MET cc_start: 0.8832 (mmm) cc_final: 0.8593 (mmm) REVERT: C 637 GLU cc_start: 0.7778 (tm-30) cc_final: 0.7326 (tm-30) outliers start: 26 outliers final: 18 residues processed: 150 average time/residue: 0.1923 time to fit residues: 43.8959 Evaluate side-chains 140 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 122 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 198 SER Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain C residue 514 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 116 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 31 optimal weight: 9.9990 chunk 129 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 chunk 68 optimal weight: 9.9990 chunk 124 optimal weight: 7.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11350 Z= 0.196 Angle : 0.543 9.461 15440 Z= 0.278 Chirality : 0.037 0.158 1748 Planarity : 0.003 0.037 1914 Dihedral : 3.944 18.552 1468 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.85 % Allowed : 13.38 % Favored : 84.76 % 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: 2.35 (0.24), residues: 1318 helix: 2.09 (0.17), residues: 1016 sheet: None (None), residues: 0 loop : -0.22 (0.38), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 492 HIS 0.003 0.001 HIS C 416 PHE 0.021 0.001 PHE A 368 TYR 0.020 0.002 TYR A 415 ARG 0.013 0.000 ARG C 424 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 135 time to evaluate : 1.442 Fit side-chains REVERT: A 321 GLN cc_start: 0.7860 (tm-30) cc_final: 0.7584 (tm-30) REVERT: A 351 PHE cc_start: 0.8361 (t80) cc_final: 0.8151 (t80) REVERT: A 443 ASN cc_start: 0.8996 (t0) cc_final: 0.8490 (t0) REVERT: A 538 MET cc_start: 0.8446 (mtm) cc_final: 0.8147 (ptp) REVERT: A 629 MET cc_start: 0.8806 (mmm) cc_final: 0.8542 (mmm) REVERT: A 680 ASP cc_start: 0.8309 (p0) cc_final: 0.8107 (p0) REVERT: A 682 GLU cc_start: 0.8419 (mm-30) cc_final: 0.7964 (tt0) REVERT: C 287 LEU cc_start: 0.9149 (tp) cc_final: 0.8903 (mt) REVERT: C 321 GLN cc_start: 0.7911 (tm-30) cc_final: 0.7666 (tm-30) REVERT: C 629 MET cc_start: 0.8824 (mmm) cc_final: 0.8576 (mmm) REVERT: C 637 GLU cc_start: 0.7742 (tm-30) cc_final: 0.6879 (tm-30) outliers start: 22 outliers final: 15 residues processed: 155 average time/residue: 0.1873 time to fit residues: 44.2617 Evaluate side-chains 141 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 126 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 198 SER Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 541 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 14 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 94 optimal weight: 0.6980 chunk 109 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 129 optimal weight: 0.2980 chunk 80 optimal weight: 0.1980 chunk 78 optimal weight: 0.9990 chunk 59 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 353 GLN C 393 GLN ** C 618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 11350 Z= 0.146 Angle : 0.530 9.884 15440 Z= 0.268 Chirality : 0.037 0.253 1748 Planarity : 0.004 0.056 1914 Dihedral : 3.869 17.532 1468 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.09 % Allowed : 15.15 % Favored : 83.75 % 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: 2.70 (0.24), residues: 1318 helix: 2.31 (0.17), residues: 996 sheet: None (None), residues: 0 loop : 0.17 (0.39), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 492 HIS 0.003 0.001 HIS A 416 PHE 0.021 0.001 PHE A 368 TYR 0.023 0.001 TYR A 415 ARG 0.011 0.000 ARG C 424 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 138 time to evaluate : 1.342 Fit side-chains REVERT: A 321 GLN cc_start: 0.7896 (tm-30) cc_final: 0.7647 (tm-30) REVERT: A 351 PHE cc_start: 0.8342 (t80) cc_final: 0.8122 (t80) REVERT: A 363 ILE cc_start: 0.7477 (tp) cc_final: 0.6796 (tt) REVERT: A 443 ASN cc_start: 0.8929 (t0) cc_final: 0.8585 (t0) REVERT: A 629 MET cc_start: 0.8783 (mmm) cc_final: 0.8456 (mmm) REVERT: A 682 GLU cc_start: 0.8416 (mm-30) cc_final: 0.8036 (tt0) REVERT: C 287 LEU cc_start: 0.9074 (tp) cc_final: 0.8831 (mt) REVERT: C 321 GLN cc_start: 0.7904 (tm-30) cc_final: 0.7651 (tm-30) REVERT: C 629 MET cc_start: 0.8804 (mmm) cc_final: 0.8536 (mmm) REVERT: C 637 GLU cc_start: 0.7671 (tm-30) cc_final: 0.7186 (tm-30) REVERT: C 680 ASP cc_start: 0.8264 (p0) cc_final: 0.8002 (p0) outliers start: 13 outliers final: 12 residues processed: 149 average time/residue: 0.1673 time to fit residues: 38.5621 Evaluate side-chains 139 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 127 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 198 SER Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain C residue 541 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 0.9980 chunk 38 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 82 optimal weight: 5.9990 chunk 87 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 12 optimal weight: 4.9990 chunk 101 optimal weight: 10.0000 chunk 117 optimal weight: 3.9990 chunk 123 optimal weight: 2.9990 chunk 112 optimal weight: 0.7980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 11350 Z= 0.246 Angle : 0.569 9.867 15440 Z= 0.291 Chirality : 0.038 0.271 1748 Planarity : 0.004 0.047 1914 Dihedral : 3.874 17.907 1468 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.09 % Allowed : 15.99 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.33 (0.24), residues: 1318 helix: 2.08 (0.17), residues: 1016 sheet: None (None), residues: 0 loop : -0.29 (0.38), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 271 HIS 0.003 0.001 HIS A 416 PHE 0.025 0.001 PHE A 368 TYR 0.026 0.002 TYR A 415 ARG 0.018 0.001 ARG A 424 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 130 time to evaluate : 1.277 Fit side-chains REVERT: A 321 GLN cc_start: 0.7863 (tm-30) cc_final: 0.7577 (tm-30) REVERT: A 324 ARG cc_start: 0.8264 (tpp80) cc_final: 0.7998 (tpp80) REVERT: A 351 PHE cc_start: 0.8293 (t80) cc_final: 0.8059 (t80) REVERT: A 629 MET cc_start: 0.8810 (mmm) cc_final: 0.8605 (mmm) REVERT: A 682 GLU cc_start: 0.8500 (mm-30) cc_final: 0.8031 (tt0) REVERT: C 287 LEU cc_start: 0.9107 (tp) cc_final: 0.8853 (mt) REVERT: C 321 GLN cc_start: 0.7901 (tm-30) cc_final: 0.7671 (tm-30) REVERT: C 456 GLU cc_start: 0.7665 (mm-30) cc_final: 0.7402 (tt0) REVERT: C 629 MET cc_start: 0.8824 (mmm) cc_final: 0.8526 (mmm) REVERT: C 680 ASP cc_start: 0.8334 (p0) cc_final: 0.8025 (p0) outliers start: 13 outliers final: 13 residues processed: 141 average time/residue: 0.1714 time to fit residues: 37.8673 Evaluate side-chains 137 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 124 time to evaluate : 1.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 198 SER Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain C residue 541 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 2.9990 chunk 123 optimal weight: 0.9990 chunk 72 optimal weight: 0.9990 chunk 52 optimal weight: 5.9990 chunk 94 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 108 optimal weight: 0.8980 chunk 113 optimal weight: 0.8980 chunk 119 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 127 optimal weight: 0.9980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11350 Z= 0.173 Angle : 0.546 10.011 15440 Z= 0.277 Chirality : 0.037 0.255 1748 Planarity : 0.004 0.062 1914 Dihedral : 3.856 16.704 1468 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.43 % Allowed : 15.74 % Favored : 82.83 % 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: 2.35 (0.24), residues: 1318 helix: 2.10 (0.17), residues: 1016 sheet: None (None), residues: 0 loop : -0.29 (0.39), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 464 HIS 0.002 0.001 HIS C 134 PHE 0.020 0.001 PHE A 368 TYR 0.015 0.001 TYR A 415 ARG 0.014 0.000 ARG A 424 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 133 time to evaluate : 1.292 Fit side-chains REVERT: A 321 GLN cc_start: 0.7843 (tm-30) cc_final: 0.7604 (tm-30) REVERT: A 324 ARG cc_start: 0.8274 (tpp80) cc_final: 0.8012 (tpp80) REVERT: A 351 PHE cc_start: 0.8264 (t80) cc_final: 0.7986 (t80) REVERT: A 682 GLU cc_start: 0.8459 (mm-30) cc_final: 0.8010 (tt0) REVERT: C 287 LEU cc_start: 0.9086 (tp) cc_final: 0.8836 (mt) REVERT: C 321 GLN cc_start: 0.7894 (tm-30) cc_final: 0.7665 (tm-30) REVERT: C 456 GLU cc_start: 0.7615 (mm-30) cc_final: 0.7361 (tt0) REVERT: C 629 MET cc_start: 0.8823 (mmm) cc_final: 0.8582 (mmm) REVERT: C 637 GLU cc_start: 0.7722 (tm-30) cc_final: 0.7242 (tm-30) outliers start: 17 outliers final: 15 residues processed: 148 average time/residue: 0.1830 time to fit residues: 41.8194 Evaluate side-chains 142 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 127 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 198 SER Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 541 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 1.9990 chunk 60 optimal weight: 0.3980 chunk 88 optimal weight: 0.0570 chunk 133 optimal weight: 20.0000 chunk 122 optimal weight: 0.8980 chunk 106 optimal weight: 7.9990 chunk 11 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 113 optimal weight: 0.0050 overall best weight: 0.6714 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 ASN ** A 618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 117 ASN ** C 618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 11350 Z= 0.152 Angle : 0.537 10.445 15440 Z= 0.270 Chirality : 0.036 0.249 1748 Planarity : 0.004 0.058 1914 Dihedral : 3.747 15.916 1468 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.26 % Allowed : 15.99 % Favored : 82.74 % 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: 2.75 (0.24), residues: 1318 helix: 2.38 (0.17), residues: 984 sheet: None (None), residues: 0 loop : 0.15 (0.38), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 464 HIS 0.001 0.000 HIS A 410 PHE 0.020 0.001 PHE A 368 TYR 0.013 0.001 TYR C 357 ARG 0.014 0.000 ARG A 424 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 132 time to evaluate : 1.350 Fit side-chains REVERT: A 321 GLN cc_start: 0.7889 (tm-30) cc_final: 0.7642 (tm-30) REVERT: A 324 ARG cc_start: 0.8294 (tpp80) cc_final: 0.8022 (tpp80) REVERT: A 350 LEU cc_start: 0.8370 (tt) cc_final: 0.8104 (tt) REVERT: A 351 PHE cc_start: 0.8217 (t80) cc_final: 0.7856 (t80) REVERT: A 456 GLU cc_start: 0.7606 (mm-30) cc_final: 0.7365 (tt0) REVERT: A 682 GLU cc_start: 0.8544 (mm-30) cc_final: 0.8053 (tt0) REVERT: C 287 LEU cc_start: 0.9014 (tp) cc_final: 0.8765 (mt) REVERT: C 321 GLN cc_start: 0.7912 (tm-30) cc_final: 0.7676 (tm-30) REVERT: C 456 GLU cc_start: 0.7603 (mm-30) cc_final: 0.7354 (tt0) REVERT: C 629 MET cc_start: 0.8823 (mmm) cc_final: 0.8560 (mmm) REVERT: C 637 GLU cc_start: 0.7685 (tm-30) cc_final: 0.7198 (tm-30) outliers start: 15 outliers final: 12 residues processed: 145 average time/residue: 0.1801 time to fit residues: 40.1375 Evaluate side-chains 135 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 123 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 198 SER Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 470 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 32 optimal weight: 0.6980 chunk 98 optimal weight: 7.9990 chunk 15 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 106 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 109 optimal weight: 0.9990 chunk 13 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 618 ASN ** 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 = 0.3586 r_free = 0.3586 target = 0.124410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.093969 restraints weight = 18297.743| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 2.36 r_work: 0.3011 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11350 Z= 0.204 Angle : 0.561 10.089 15440 Z= 0.283 Chirality : 0.038 0.251 1748 Planarity : 0.004 0.051 1914 Dihedral : 3.776 16.377 1468 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.26 % Allowed : 16.16 % Favored : 82.58 % 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: 2.44 (0.24), residues: 1318 helix: 2.20 (0.17), residues: 1004 sheet: None (None), residues: 0 loop : -0.27 (0.38), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 271 HIS 0.002 0.001 HIS A 134 PHE 0.021 0.001 PHE A 368 TYR 0.018 0.002 TYR C 357 ARG 0.014 0.000 ARG A 424 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2078.66 seconds wall clock time: 38 minutes 27.37 seconds (2307.37 seconds total)