Starting phenix.real_space_refine (version: 1.21rc1) on Thu Oct 5 20:27:08 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lby_23267/10_2023/7lby_23267.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lby_23267/10_2023/7lby_23267.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lby_23267/10_2023/7lby_23267.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lby_23267/10_2023/7lby_23267.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lby_23267/10_2023/7lby_23267.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lby_23267/10_2023/7lby_23267.pdb" } resolution = 4.2 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= -0.001 sd= 0.042 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 2664 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: 4 Type Number sf(0) Gaussians S 23 5.16 5 C 5441 2.51 5 N 1624 2.21 5 O 1712 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ASP 72": "OD1" <-> "OD2" Residue "B GLU 106": "OE1" <-> "OE2" Residue "B TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 180": "OD1" <-> "OD2" Residue "B ARG 196": "NH1" <-> "NH2" Residue "B TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 240": "OD1" <-> "OD2" Residue "B PHE 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 321": "OD1" <-> "OD2" Residue "B GLU 342": "OE1" <-> "OE2" Residue "B ARG 355": "NH1" <-> "NH2" Residue "B ASP 367": "OD1" <-> "OD2" Residue "B GLU 379": "OE1" <-> "OE2" Residue "B GLU 388": "OE1" <-> "OE2" Residue "B ASP 401": "OD1" <-> "OD2" Residue "B TYR 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 413": "OD1" <-> "OD2" Residue "B TYR 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 464": "OD1" <-> "OD2" Residue "B PHE 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 515": "OD1" <-> "OD2" Residue "B PHE 520": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 535": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 540": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 565": "OE1" <-> "OE2" Residue "B ASP 590": "OD1" <-> "OD2" Residue "B ASP 609": "OD1" <-> "OD2" Residue "B ASP 618": "OD1" <-> "OD2" Residue "B PHE 667": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 688": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 697": "OD1" <-> "OD2" Residue "B ARG 701": "NH1" <-> "NH2" Residue "B ARG 712": "NH1" <-> "NH2" Residue "B GLU 713": "OE1" <-> "OE2" Residue "B TYR 726": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 735": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 8800 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 755, 3724 Classifications: {'peptide': 755} Incomplete info: {'truncation_to_alanine': 648} Link IDs: {'PTRANS': 40, 'TRANS': 714} Chain breaks: 2 Unresolved chain link angles: 40 Unresolved non-hydrogen bonds: 2559 Unresolved non-hydrogen angles: 3319 Unresolved non-hydrogen dihedrals: 2205 Unresolved non-hydrogen chiralities: 231 Planarities with less than four sites: {'GLN:plan1': 28, 'ASP:plan': 25, 'TYR:plan': 28, 'ASN:plan1': 28, 'TRP:plan': 22, 'HIS:plan': 24, 'PHE:plan': 40, 'GLU:plan': 32, 'ARG:plan': 54} Unresolved non-hydrogen planarities: 1423 Chain: "B" Number of atoms: 5076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 663, 5076 Classifications: {'peptide': 663} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PCIS': 1, 'PTRANS': 49, 'TRANS': 612} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 110 Unresolved non-hydrogen angles: 145 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 3, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 39 Time building chain proxies: 5.00, per 1000 atoms: 0.57 Number of scatterers: 8800 At special positions: 0 Unit cell: (135, 150.12, 124.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 23 16.00 O 1712 8.00 N 1624 7.00 C 5441 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 182 " - pdb=" SG CYS B 500 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.08 Conformation dependent library (CDL) restraints added in 1.5 seconds 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2648 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 13 sheets defined 40.6% alpha, 9.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'A' and resid 18 through 42 Processing helix chain 'A' and resid 124 through 142 Proline residue: A 129 - end of helix Proline residue: A 133 - end of helix removed outlier: 3.859A pdb=" N HIS A 142 " --> pdb=" O ILE A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 153 removed outlier: 3.510A pdb=" N SER A 152 " --> pdb=" O HIS A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 169 Proline residue: A 159 - end of helix Processing helix chain 'A' and resid 178 through 191 Processing helix chain 'A' and resid 196 through 219 removed outlier: 3.894A pdb=" N MET A 200 " --> pdb=" O TYR A 196 " (cutoff:3.500A) Proline residue: A 204 - end of helix Processing helix chain 'A' and resid 222 through 227 Processing helix chain 'A' and resid 228 through 256 Proline residue: A 250 - end of helix Proline residue: A 253 - end of helix Processing helix chain 'A' and resid 287 through 300 removed outlier: 3.576A pdb=" N SER A 300 " --> pdb=" O TRP A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 328 Processing helix chain 'A' and resid 343 through 352 Processing helix chain 'A' and resid 353 through 355 No H-bonds generated for 'chain 'A' and resid 353 through 355' Processing helix chain 'A' and resid 373 through 377 removed outlier: 3.632A pdb=" N SER A 376 " --> pdb=" O ILE A 373 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU A 377 " --> pdb=" O TYR A 374 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 373 through 377' Processing helix chain 'A' and resid 400 through 407 Processing helix chain 'A' and resid 416 through 421 Processing helix chain 'A' and resid 422 through 430 removed outlier: 3.703A pdb=" N ASN A 426 " --> pdb=" O GLY A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 468 removed outlier: 3.825A pdb=" N GLN A 462 " --> pdb=" O LEU A 458 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU A 463 " --> pdb=" O LYS A 459 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN A 467 " --> pdb=" O LEU A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 513 Processing helix chain 'A' and resid 519 through 551 removed outlier: 3.903A pdb=" N THR A 535 " --> pdb=" O VAL A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 582 Processing helix chain 'A' and resid 589 through 610 removed outlier: 4.249A pdb=" N GLY A 593 " --> pdb=" O ASN A 589 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG A 601 " --> pdb=" O LYS A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 659 Proline residue: A 646 - end of helix Processing helix chain 'A' and resid 663 through 688 Proline residue: A 670 - end of helix Processing helix chain 'A' and resid 791 through 802 removed outlier: 3.822A pdb=" N ARG A 802 " --> pdb=" O ARG A 798 " (cutoff:3.500A) Processing helix chain 'A' and resid 805 through 831 removed outlier: 3.592A pdb=" N GLY A 830 " --> pdb=" O PHE A 826 " (cutoff:3.500A) Processing helix chain 'A' and resid 838 through 860 Processing helix chain 'A' and resid 861 through 863 No H-bonds generated for 'chain 'A' and resid 861 through 863' Processing helix chain 'B' and resid 145 through 149 removed outlier: 3.692A pdb=" N LEU B 149 " --> pdb=" O LYS B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 259 Processing helix chain 'B' and resid 260 through 262 No H-bonds generated for 'chain 'B' and resid 260 through 262' Processing helix chain 'B' and resid 321 through 335 Processing helix chain 'B' and resid 532 through 538 Processing helix chain 'B' and resid 560 through 578 removed outlier: 3.558A pdb=" N MET B 564 " --> pdb=" O ASN B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 614 No H-bonds generated for 'chain 'B' and resid 612 through 614' Processing helix chain 'B' and resid 615 through 630 removed outlier: 3.907A pdb=" N LEU B 619 " --> pdb=" O LYS B 615 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU B 620 " --> pdb=" O GLN B 616 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N VAL B 621 " --> pdb=" O ILE B 617 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLN B 622 " --> pdb=" O ASP B 618 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TRP B 627 " --> pdb=" O ALA B 623 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N THR B 630 " --> pdb=" O SER B 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 684 through 697 removed outlier: 3.517A pdb=" N TYR B 688 " --> pdb=" O SER B 684 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ASP B 697 " --> pdb=" O ASP B 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 731 through 743 removed outlier: 4.047A pdb=" N VAL B 736 " --> pdb=" O TRP B 732 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N TRP B 737 " --> pdb=" O PHE B 733 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N TYR B 738 " --> pdb=" O GLU B 734 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ASN B 742 " --> pdb=" O TYR B 738 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N HIS B 743 " --> pdb=" O ALA B 739 " (cutoff:3.500A) Processing helix chain 'B' and resid 743 through 772 Processing sheet with id=AA1, first strand: chain 'A' and resid 277 through 282 removed outlier: 3.766A pdb=" N ALA A 279 " --> pdb=" O SER A 309 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL A 311 " --> pdb=" O ALA A 279 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 390 through 392 removed outlier: 3.546A pdb=" N PHE A 478 " --> pdb=" O LEU A 391 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 700 through 704 removed outlier: 6.586A pdb=" N TYR A 702 " --> pdb=" O THR A 722 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N THR A 722 " --> pdb=" O TYR A 702 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA A 704 " --> pdb=" O ASN A 720 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N GLU A 729 " --> pdb=" O VAL A 721 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 716 through 717 Processing sheet with id=AA5, first strand: chain 'B' and resid 88 through 89 Processing sheet with id=AA6, first strand: chain 'B' and resid 95 through 101 removed outlier: 4.078A pdb=" N PHE B 100 " --> pdb=" O ASN B 168 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ASN B 168 " --> pdb=" O PHE B 100 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU B 173 " --> pdb=" O LYS B 131 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL B 132 " --> pdb=" O GLY B 140 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N GLY B 140 " --> pdb=" O VAL B 132 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 153 through 159 removed outlier: 4.207A pdb=" N THR B 153 " --> pdb=" O TYR B 117 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N TYR B 117 " --> pdb=" O THR B 153 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ALA B 111 " --> pdb=" O ILE B 159 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N LYS B 110 " --> pdb=" O THR B 203 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 267 through 269 removed outlier: 4.116A pdb=" N LEU B 268 " --> pdb=" O MET B 233 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N PHE B 235 " --> pdb=" O LEU B 268 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N VAL B 234 " --> pdb=" O PHE B 280 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N VAL B 279 " --> pdb=" O VAL B 317 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL B 316 " --> pdb=" O GLU B 302 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 383 through 384 Processing sheet with id=AB1, first strand: chain 'B' and resid 395 through 396 removed outlier: 3.942A pdb=" N LEU B 396 " --> pdb=" O ASN B 480 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASN B 480 " --> pdb=" O LEU B 396 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 437 through 442 removed outlier: 3.880A pdb=" N GLN B 439 " --> pdb=" O ILE B 431 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N MET B 429 " --> pdb=" O PHE B 441 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ARG B 428 " --> pdb=" O GLU B 487 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLU B 487 " --> pdb=" O ARG B 428 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ASP B 430 " --> pdb=" O ASP B 485 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ASP B 485 " --> pdb=" O ASP B 430 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 527 through 528 removed outlier: 4.022A pdb=" N ILE B 527 " --> pdb=" O VAL B 727 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL B 727 " --> pdb=" O ILE B 527 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 586 through 588 removed outlier: 6.163A pdb=" N THR B 553 " --> pdb=" O THR B 588 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ILE B 552 " --> pdb=" O MET B 602 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ILE B 604 " --> pdb=" O ILE B 552 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N VAL B 554 " --> pdb=" O ILE B 604 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ILE B 601 " --> pdb=" O SER B 676 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE B 678 " --> pdb=" O ILE B 601 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ALA B 662 " --> pdb=" O ILE B 711 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL B 710 " --> pdb=" O ASN B 717 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASN B 717 " --> pdb=" O VAL B 710 " (cutoff:3.500A) 434 hydrogen bonds defined for protein. 1269 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: 2.73 Time building geometry restraints manager: 3.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3201 1.34 - 1.46: 1632 1.46 - 1.58: 4037 1.58 - 1.69: 0 1.69 - 1.81: 44 Bond restraints: 8914 Sorted by residual: bond pdb=" CA VAL A 343 " pdb=" CB VAL A 343 " ideal model delta sigma weight residual 1.537 1.508 0.028 5.00e-03 4.00e+04 3.22e+01 bond pdb=" C THR A 540 " pdb=" O THR A 540 " ideal model delta sigma weight residual 1.236 1.272 -0.036 1.15e-02 7.56e+03 9.71e+00 bond pdb=" N THR A 540 " pdb=" CA THR A 540 " ideal model delta sigma weight residual 1.459 1.491 -0.031 1.19e-02 7.06e+03 6.89e+00 bond pdb=" N SER A 635 " pdb=" CA SER A 635 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.28e-02 6.10e+03 6.04e+00 bond pdb=" N GLY A 636 " pdb=" CA GLY A 636 " ideal model delta sigma weight residual 1.454 1.481 -0.027 1.24e-02 6.50e+03 4.60e+00 ... (remaining 8909 not shown) Histogram of bond angle deviations from ideal: 100.41 - 107.13: 227 107.13 - 113.84: 5011 113.84 - 120.56: 3329 120.56 - 127.27: 3622 127.27 - 133.99: 59 Bond angle restraints: 12248 Sorted by residual: angle pdb=" N PRO A 445 " pdb=" CA PRO A 445 " pdb=" CB PRO A 445 " ideal model delta sigma weight residual 102.25 110.63 -8.38 7.00e-01 2.04e+00 1.43e+02 angle pdb=" N PRO A 764 " pdb=" CA PRO A 764 " pdb=" CB PRO A 764 " ideal model delta sigma weight residual 103.36 110.96 -7.60 8.30e-01 1.45e+00 8.38e+01 angle pdb=" N PRO A 337 " pdb=" CA PRO A 337 " pdb=" CB PRO A 337 " ideal model delta sigma weight residual 103.36 110.62 -7.26 8.30e-01 1.45e+00 7.66e+01 angle pdb=" N PRO A 706 " pdb=" CA PRO A 706 " pdb=" CB PRO A 706 " ideal model delta sigma weight residual 103.25 112.37 -9.12 1.05e+00 9.07e-01 7.55e+01 angle pdb=" N PRO A 763 " pdb=" CA PRO A 763 " pdb=" CB PRO A 763 " ideal model delta sigma weight residual 103.08 111.30 -8.22 9.70e-01 1.06e+00 7.18e+01 ... (remaining 12243 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 5008 17.93 - 35.86: 233 35.86 - 53.79: 43 53.79 - 71.71: 13 71.71 - 89.64: 7 Dihedral angle restraints: 5304 sinusoidal: 1226 harmonic: 4078 Sorted by residual: dihedral pdb=" N PRO A 342 " pdb=" C PRO A 342 " pdb=" CA PRO A 342 " pdb=" CB PRO A 342 " ideal model delta harmonic sigma weight residual 115.10 124.59 -9.49 0 2.50e+00 1.60e-01 1.44e+01 dihedral pdb=" CB GLU B 183 " pdb=" CG GLU B 183 " pdb=" CD GLU B 183 " pdb=" OE1 GLU B 183 " ideal model delta sinusoidal sigma weight residual 0.00 89.64 -89.64 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" N PRO A 307 " pdb=" C PRO A 307 " pdb=" CA PRO A 307 " pdb=" CB PRO A 307 " ideal model delta harmonic sigma weight residual 115.10 123.23 -8.13 0 2.50e+00 1.60e-01 1.06e+01 ... (remaining 5301 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1195 0.052 - 0.104: 227 0.104 - 0.155: 31 0.155 - 0.207: 11 0.207 - 0.259: 33 Chirality restraints: 1497 Sorted by residual: chirality pdb=" CA PRO A 307 " pdb=" N PRO A 307 " pdb=" C PRO A 307 " pdb=" CB PRO A 307 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CA PRO A 342 " pdb=" N PRO A 342 " pdb=" C PRO A 342 " pdb=" CB PRO A 342 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CA PRO A 660 " pdb=" N PRO A 660 " pdb=" C PRO A 660 " pdb=" CB PRO A 660 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.25 2.00e-01 2.50e+01 1.62e+00 ... (remaining 1494 not shown) Planarity restraints: 1689 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 83 " -0.047 5.00e-02 4.00e+02 7.15e-02 8.19e+00 pdb=" N PRO B 84 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO B 84 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 84 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 538 " -0.013 2.00e-02 2.50e+03 2.58e-02 6.66e+00 pdb=" C ALA A 538 " 0.045 2.00e-02 2.50e+03 pdb=" O ALA A 538 " -0.017 2.00e-02 2.50e+03 pdb=" N HIS A 539 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 537 " -0.008 2.00e-02 2.50e+03 1.66e-02 2.76e+00 pdb=" C ASP A 537 " 0.029 2.00e-02 2.50e+03 pdb=" O ASP A 537 " -0.011 2.00e-02 2.50e+03 pdb=" N ALA A 538 " -0.010 2.00e-02 2.50e+03 ... (remaining 1686 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 174 2.70 - 3.25: 8609 3.25 - 3.80: 13241 3.80 - 4.35: 14118 4.35 - 4.90: 24343 Nonbonded interactions: 60485 Sorted by model distance: nonbonded pdb=" O PHE B 705 " pdb=" OG SER B 718 " model vdw 2.148 2.440 nonbonded pdb=" ND2 ASN B 569 " pdb=" OD1 ASN B 692 " model vdw 2.221 2.520 nonbonded pdb=" OG SER B 432 " pdb=" O ARG B 483 " model vdw 2.232 2.440 nonbonded pdb=" OG1 THR B 118 " pdb=" OD1 ASP B 193 " model vdw 2.272 2.440 nonbonded pdb=" O ASN B 67 " pdb=" OH TYR B 311 " model vdw 2.289 2.440 ... (remaining 60480 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 group one per residue 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: 3.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 13.790 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 24.900 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6785 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 : 0.003 0.036 8914 Z= 0.212 Angle : 0.780 9.122 12248 Z= 0.603 Chirality : 0.054 0.259 1497 Planarity : 0.003 0.072 1689 Dihedral : 12.333 89.643 2653 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 1.28 % Allowed : 6.19 % Favored : 92.53 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.11 % 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: -0.24 (0.24), residues: 1406 helix: 2.83 (0.22), residues: 539 sheet: -1.18 (0.40), residues: 194 loop : -2.55 (0.23), residues: 673 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 0.982 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.1750 time to fit residues: 39.3586 Evaluate side-chains 114 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 1.005 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 119 optimal weight: 0.7980 chunk 106 optimal weight: 0.0010 chunk 59 optimal weight: 0.7980 chunk 36 optimal weight: 5.9990 chunk 72 optimal weight: 30.0000 chunk 57 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 67 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 overall best weight: 1.1190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 168 ASN B 244 GLN ** B 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 305 ASN B 729 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6995 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8914 Z= 0.225 Angle : 0.541 5.846 12248 Z= 0.284 Chirality : 0.044 0.148 1497 Planarity : 0.004 0.071 1689 Dihedral : 3.663 19.707 1460 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.50 % Allowed : 6.69 % Favored : 92.82 % Rotamer: Outliers : 0.55 % Allowed : 5.72 % Favored : 93.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.11 % 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: -0.00 (0.24), residues: 1406 helix: 3.04 (0.22), residues: 556 sheet: -1.05 (0.43), residues: 173 loop : -2.55 (0.22), residues: 677 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 137 time to evaluate : 0.958 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 140 average time/residue: 0.1801 time to fit residues: 36.2589 Evaluate side-chains 111 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 109 time to evaluate : 0.943 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0785 time to fit residues: 1.5661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 71 optimal weight: 30.0000 chunk 39 optimal weight: 2.9990 chunk 106 optimal weight: 0.0020 chunk 87 optimal weight: 1.9990 chunk 35 optimal weight: 6.9990 chunk 128 optimal weight: 0.5980 chunk 138 optimal weight: 2.9990 chunk 114 optimal weight: 0.0050 chunk 127 optimal weight: 0.0570 chunk 43 optimal weight: 40.0000 chunk 102 optimal weight: 0.7980 overall best weight: 0.2920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 244 GLN ** B 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 509 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6898 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8914 Z= 0.121 Angle : 0.493 8.128 12248 Z= 0.249 Chirality : 0.042 0.141 1497 Planarity : 0.003 0.071 1689 Dihedral : 3.328 20.251 1460 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.40 % Favored : 93.24 % Rotamer: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.11 % 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: 0.16 (0.24), residues: 1406 helix: 3.24 (0.22), residues: 562 sheet: -1.22 (0.43), residues: 163 loop : -2.48 (0.22), residues: 681 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 0.994 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 0.1890 time to fit residues: 38.3629 Evaluate side-chains 111 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 0.977 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 126 optimal weight: 2.9990 chunk 96 optimal weight: 0.8980 chunk 66 optimal weight: 6.9990 chunk 14 optimal weight: 0.9980 chunk 61 optimal weight: 40.0000 chunk 86 optimal weight: 5.9990 chunk 128 optimal weight: 0.9980 chunk 136 optimal weight: 2.9990 chunk 67 optimal weight: 30.0000 chunk 122 optimal weight: 0.0570 chunk 36 optimal weight: 8.9990 overall best weight: 1.1900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7085 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 0.040 8914 Z= 0.230 Angle : 0.561 10.730 12248 Z= 0.291 Chirality : 0.043 0.149 1497 Planarity : 0.004 0.071 1689 Dihedral : 3.738 20.064 1460 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.04 % Favored : 92.60 % Rotamer: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.11 % 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: 0.11 (0.24), residues: 1406 helix: 3.22 (0.22), residues: 562 sheet: -1.27 (0.41), residues: 175 loop : -2.54 (0.23), residues: 669 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 0.901 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.1697 time to fit residues: 31.1259 Evaluate side-chains 99 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 0.997 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 113 optimal weight: 5.9990 chunk 77 optimal weight: 0.0470 chunk 1 optimal weight: 50.0000 chunk 101 optimal weight: 0.8980 chunk 56 optimal weight: 9.9990 chunk 116 optimal weight: 5.9990 chunk 94 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 69 optimal weight: 30.0000 chunk 122 optimal weight: 3.9990 chunk 34 optimal weight: 20.0000 overall best weight: 2.5884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 244 GLN B 397 ASN ** B 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.3470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 8914 Z= 0.457 Angle : 0.737 11.571 12248 Z= 0.389 Chirality : 0.048 0.180 1497 Planarity : 0.005 0.074 1689 Dihedral : 4.788 23.836 1460 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.36 % Allowed : 9.53 % Favored : 90.11 % Rotamer: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.11 % 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: -0.31 (0.24), residues: 1406 helix: 2.92 (0.23), residues: 561 sheet: -1.57 (0.39), residues: 168 loop : -2.77 (0.22), residues: 677 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 0.940 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 0.1504 time to fit residues: 25.1199 Evaluate side-chains 87 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.910 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 45 optimal weight: 9.9990 chunk 122 optimal weight: 0.3980 chunk 26 optimal weight: 20.0000 chunk 80 optimal weight: 1.9990 chunk 33 optimal weight: 20.0000 chunk 136 optimal weight: 0.1980 chunk 113 optimal weight: 2.9990 chunk 63 optimal weight: 20.0000 chunk 11 optimal weight: 4.9990 chunk 71 optimal weight: 20.0000 chunk 131 optimal weight: 4.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 397 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.3813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 8914 Z= 0.363 Angle : 0.666 11.789 12248 Z= 0.352 Chirality : 0.046 0.189 1497 Planarity : 0.005 0.072 1689 Dihedral : 4.629 27.859 1460 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.36 % Allowed : 8.75 % Favored : 90.90 % Rotamer: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.11 % 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: -0.28 (0.24), residues: 1406 helix: 2.96 (0.23), residues: 555 sheet: -1.86 (0.38), residues: 170 loop : -2.64 (0.22), residues: 681 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 0.961 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.1408 time to fit residues: 25.0692 Evaluate side-chains 93 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 0.907 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 15 optimal weight: 9.9990 chunk 77 optimal weight: 6.9990 chunk 99 optimal weight: 0.9990 chunk 114 optimal weight: 0.5980 chunk 76 optimal weight: 0.0980 chunk 135 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 62 optimal weight: 0.0570 chunk 84 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 overall best weight: 0.5500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 GLN ** B 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7157 moved from start: 0.3725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8914 Z= 0.153 Angle : 0.565 10.791 12248 Z= 0.289 Chirality : 0.043 0.172 1497 Planarity : 0.004 0.074 1689 Dihedral : 4.075 23.747 1460 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.04 % Favored : 92.60 % Rotamer: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.11 % 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: -0.01 (0.24), residues: 1406 helix: 3.08 (0.22), residues: 562 sheet: -1.18 (0.43), residues: 141 loop : -2.57 (0.22), residues: 703 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 1.006 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.1410 time to fit residues: 26.8589 Evaluate side-chains 96 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 1.019 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 81 optimal weight: 1.9990 chunk 40 optimal weight: 8.9990 chunk 26 optimal weight: 0.9990 chunk 86 optimal weight: 0.0010 chunk 92 optimal weight: 0.6980 chunk 67 optimal weight: 30.0000 chunk 12 optimal weight: 6.9990 chunk 106 optimal weight: 0.3980 chunk 123 optimal weight: 0.6980 chunk 130 optimal weight: 2.9990 chunk 118 optimal weight: 5.9990 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7144 moved from start: 0.3736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8914 Z= 0.153 Angle : 0.557 12.813 12248 Z= 0.279 Chirality : 0.043 0.168 1497 Planarity : 0.003 0.037 1689 Dihedral : 3.853 23.176 1460 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.04 % Favored : 92.60 % Rotamer: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.11 % 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: 0.09 (0.24), residues: 1406 helix: 3.22 (0.22), residues: 557 sheet: -1.26 (0.42), residues: 156 loop : -2.51 (0.22), residues: 693 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 0.980 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.1468 time to fit residues: 27.0637 Evaluate side-chains 95 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 1.061 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 126 optimal weight: 3.9990 chunk 130 optimal weight: 0.3980 chunk 76 optimal weight: 0.0570 chunk 55 optimal weight: 0.9990 chunk 99 optimal weight: 0.8980 chunk 38 optimal weight: 50.0000 chunk 114 optimal weight: 0.7980 chunk 119 optimal weight: 0.7980 chunk 83 optimal weight: 0.0030 chunk 133 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 overall best weight: 0.4108 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 168 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7119 moved from start: 0.3735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8914 Z= 0.140 Angle : 0.551 12.318 12248 Z= 0.277 Chirality : 0.043 0.166 1497 Planarity : 0.003 0.039 1689 Dihedral : 3.769 21.791 1460 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.83 % Favored : 92.82 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.11 % 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: 0.17 (0.24), residues: 1406 helix: 3.26 (0.22), residues: 557 sheet: -1.15 (0.41), residues: 166 loop : -2.47 (0.23), residues: 683 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 1.037 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.1483 time to fit residues: 27.9360 Evaluate side-chains 97 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 1.055 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 63 optimal weight: 10.0000 chunk 93 optimal weight: 0.8980 chunk 140 optimal weight: 3.9990 chunk 129 optimal weight: 0.7980 chunk 111 optimal weight: 1.9990 chunk 11 optimal weight: 6.9990 chunk 86 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 88 optimal weight: 0.9990 chunk 119 optimal weight: 0.9980 chunk 34 optimal weight: 30.0000 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 381 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7187 moved from start: 0.3878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8914 Z= 0.221 Angle : 0.578 11.822 12248 Z= 0.295 Chirality : 0.044 0.172 1497 Planarity : 0.004 0.040 1689 Dihedral : 3.921 23.741 1460 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.75 % Favored : 91.89 % Rotamer: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.11 % 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: 0.13 (0.24), residues: 1406 helix: 3.28 (0.22), residues: 558 sheet: -1.45 (0.39), residues: 183 loop : -2.48 (0.23), residues: 665 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 1.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.1514 time to fit residues: 27.8052 Evaluate side-chains 96 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 1.009 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 103 optimal weight: 0.0370 chunk 16 optimal weight: 7.9990 chunk 31 optimal weight: 50.0000 chunk 112 optimal weight: 0.8980 chunk 46 optimal weight: 20.0000 chunk 115 optimal weight: 2.9990 chunk 14 optimal weight: 10.0000 chunk 20 optimal weight: 0.0470 chunk 98 optimal weight: 0.0470 chunk 6 optimal weight: 8.9990 chunk 80 optimal weight: 0.0040 overall best weight: 0.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 244 GLN B 381 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.169905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.156187 restraints weight = 21043.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.153432 restraints weight = 40274.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.150001 restraints weight = 42366.990| |-----------------------------------------------------------------------------| r_work (final): 0.3925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6979 moved from start: 0.3844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8914 Z= 0.136 Angle : 0.570 12.341 12248 Z= 0.284 Chirality : 0.043 0.163 1497 Planarity : 0.003 0.038 1689 Dihedral : 3.707 19.838 1460 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.54 % Favored : 93.10 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.11 % 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: 0.24 (0.24), residues: 1406 helix: 3.32 (0.22), residues: 557 sheet: -1.08 (0.41), residues: 170 loop : -2.44 (0.23), residues: 679 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1871.17 seconds wall clock time: 34 minutes 17.00 seconds (2057.00 seconds total)