Starting phenix.real_space_refine on Fri Mar 15 11:01:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lby_23267/03_2024/7lby_23267.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lby_23267/03_2024/7lby_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_23267/03_2024/7lby_23267.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lby_23267/03_2024/7lby_23267.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lby_23267/03_2024/7lby_23267.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lby_23267/03_2024/7lby_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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 5.47, per 1000 atoms: 0.62 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: 4.27 Conformation dependent library (CDL) restraints added in 2.3 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: 1.03 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: 2.76 Time building geometry restraints manager: 4.58 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: 7.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.000 Extract box with map and model: 13.700 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 28.570 Find NCS groups from input model: 0.340 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:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.110 ------------------------------------------------------------------------------- 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.000 TRP B 253 HIS 0.001 0.000 HIS B 509 PHE 0.024 0.001 PHE B 289 TYR 0.005 0.001 TYR B 524 ARG 0.005 0.000 ARG B 257 *********************** 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 : 0.811 Fit side-chains revert: symmetry clash REVERT: B 172 LEU cc_start: 0.8714 (mp) cc_final: 0.8465 (mt) REVERT: B 338 LEU cc_start: 0.8362 (pt) cc_final: 0.7991 (pp) REVERT: B 429 MET cc_start: 0.8745 (tmm) cc_final: 0.8237 (tmm) REVERT: B 482 LEU cc_start: 0.8744 (tp) cc_final: 0.8481 (tt) REVERT: B 676 SER cc_start: 0.8473 (p) cc_final: 0.7910 (p) outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.1760 time to fit residues: 39.4660 Evaluate side-chains 115 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 0.906 ------------------------------------------------------------------------------- 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: 2.9990 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: 0.6987 moved from start: 0.1523 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 : 0.524 5.388 12248 Z= 0.278 Chirality : 0.043 0.144 1497 Planarity : 0.004 0.071 1689 Dihedral : 3.582 19.116 1460 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.50 % Allowed : 6.90 % Favored : 92.60 % Rotamer: Outliers : 0.55 % Allowed : 5.54 % Favored : 93.91 % 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: 0.03 (0.24), residues: 1406 helix: 3.08 (0.22), residues: 557 sheet: -1.03 (0.43), residues: 173 loop : -2.55 (0.22), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 737 HIS 0.003 0.001 HIS B 177 PHE 0.015 0.001 PHE B 221 TYR 0.009 0.001 TYR B 416 ARG 0.003 0.001 ARG B 675 *********************** 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 138 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 135 time to evaluate : 0.989 Fit side-chains REVERT: B 88 VAL cc_start: 0.8356 (t) cc_final: 0.8100 (m) REVERT: B 226 ASN cc_start: 0.7548 (m-40) cc_final: 0.7287 (m-40) REVERT: B 258 SER cc_start: 0.8880 (t) cc_final: 0.8592 (t) REVERT: B 338 LEU cc_start: 0.8341 (pt) cc_final: 0.8034 (pp) REVERT: B 372 PHE cc_start: 0.7443 (m-80) cc_final: 0.7066 (m-80) REVERT: B 466 LYS cc_start: 0.7578 (mmmt) cc_final: 0.7241 (ttmm) REVERT: B 482 LEU cc_start: 0.8959 (tp) cc_final: 0.8723 (tt) outliers start: 3 outliers final: 2 residues processed: 138 average time/residue: 0.1751 time to fit residues: 34.8004 Evaluate side-chains 112 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 110 time to evaluate : 1.019 ------------------------------------------------------------------------------- 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: 20.0000 chunk 106 optimal weight: 0.4980 chunk 87 optimal weight: 1.9990 chunk 35 optimal weight: 8.9990 chunk 128 optimal weight: 0.4980 chunk 138 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 127 optimal weight: 0.0050 chunk 43 optimal weight: 30.0000 chunk 102 optimal weight: 1.9990 overall best weight: 0.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 244 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7019 moved from start: 0.1998 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= 0.199 Angle : 0.522 7.037 12248 Z= 0.273 Chirality : 0.043 0.143 1497 Planarity : 0.004 0.072 1689 Dihedral : 3.588 21.826 1460 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.25 % Favored : 92.39 % Rotamer: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % 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: 0.12 (0.24), residues: 1406 helix: 3.23 (0.22), residues: 562 sheet: -1.14 (0.42), residues: 167 loop : -2.56 (0.22), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 191 HIS 0.003 0.001 HIS B 306 PHE 0.023 0.002 PHE B 254 TYR 0.016 0.001 TYR B 378 ARG 0.003 0.000 ARG B 675 *********************** 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 134 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 1.009 Fit side-chains REVERT: B 88 VAL cc_start: 0.8501 (t) cc_final: 0.8224 (m) REVERT: B 226 ASN cc_start: 0.7641 (m-40) cc_final: 0.7333 (m-40) REVERT: B 263 GLN cc_start: 0.8882 (mp10) cc_final: 0.8385 (mp10) REVERT: B 464 ASP cc_start: 0.7229 (m-30) cc_final: 0.7027 (m-30) REVERT: B 482 LEU cc_start: 0.9038 (tp) cc_final: 0.8706 (tt) REVERT: B 547 ASP cc_start: 0.8183 (p0) cc_final: 0.7974 (p0) REVERT: B 580 PHE cc_start: 0.8467 (t80) cc_final: 0.8238 (t80) outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.1818 time to fit residues: 35.0655 Evaluate side-chains 106 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 0.994 ------------------------------------------------------------------------------- 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: 0.8980 chunk 96 optimal weight: 2.9990 chunk 66 optimal weight: 20.0000 chunk 14 optimal weight: 0.9990 chunk 61 optimal weight: 30.0000 chunk 86 optimal weight: 3.9990 chunk 128 optimal weight: 0.7980 chunk 136 optimal weight: 1.9990 chunk 67 optimal weight: 0.0040 chunk 122 optimal weight: 5.9990 chunk 36 optimal weight: 40.0000 overall best weight: 0.9396 ------------------------------------------------------------------------------- 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 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 305 ASN B 672 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7050 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8914 Z= 0.192 Angle : 0.523 6.536 12248 Z= 0.270 Chirality : 0.043 0.151 1497 Planarity : 0.004 0.074 1689 Dihedral : 3.632 19.582 1460 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.69 % Favored : 92.96 % Rotamer: Outliers : 0.18 % Allowed : 4.06 % Favored : 95.76 % 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: 0.12 (0.24), residues: 1406 helix: 3.26 (0.22), residues: 557 sheet: -1.17 (0.43), residues: 159 loop : -2.53 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 191 HIS 0.002 0.001 HIS B 306 PHE 0.019 0.001 PHE B 174 TYR 0.021 0.001 TYR B 378 ARG 0.012 0.001 ARG B 196 *********************** 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 130 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 129 time to evaluate : 1.050 Fit side-chains REVERT: B 263 GLN cc_start: 0.8758 (mp10) cc_final: 0.8447 (mp10) REVERT: B 482 LEU cc_start: 0.9057 (tp) cc_final: 0.8781 (tt) REVERT: B 547 ASP cc_start: 0.8211 (p0) cc_final: 0.7962 (p0) REVERT: B 580 PHE cc_start: 0.8448 (t80) cc_final: 0.8235 (t80) outliers start: 1 outliers final: 0 residues processed: 130 average time/residue: 0.1602 time to fit residues: 31.6685 Evaluate side-chains 107 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 0.813 ------------------------------------------------------------------------------- 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: 4.9990 chunk 77 optimal weight: 2.9990 chunk 1 optimal weight: 50.0000 chunk 101 optimal weight: 0.8980 chunk 56 optimal weight: 9.9990 chunk 116 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 69 optimal weight: 30.0000 chunk 122 optimal weight: 2.9990 chunk 34 optimal weight: 20.0000 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 129 GLN B 244 GLN ** B 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.3546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.062 8914 Z= 0.504 Angle : 0.754 9.924 12248 Z= 0.407 Chirality : 0.049 0.178 1497 Planarity : 0.005 0.071 1689 Dihedral : 4.953 24.884 1460 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.36 % Allowed : 10.17 % Favored : 89.47 % Rotamer: Outliers : 0.18 % Allowed : 6.27 % 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: -0.45 (0.24), residues: 1406 helix: 2.82 (0.23), residues: 562 sheet: -1.90 (0.38), residues: 164 loop : -2.81 (0.22), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 627 HIS 0.006 0.002 HIS B 306 PHE 0.029 0.003 PHE B 580 TYR 0.021 0.003 TYR B 378 ARG 0.006 0.001 ARG B 196 *********************** 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 110 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 109 time to evaluate : 0.994 Fit side-chains REVERT: B 210 LYS cc_start: 0.7872 (pttp) cc_final: 0.7572 (tppt) REVERT: B 489 MET cc_start: 0.7103 (pmm) cc_final: 0.6850 (pmm) REVERT: B 627 TRP cc_start: 0.8906 (t-100) cc_final: 0.8677 (t-100) REVERT: B 690 MET cc_start: 0.7763 (ptt) cc_final: 0.7559 (ptt) outliers start: 1 outliers final: 0 residues processed: 110 average time/residue: 0.1541 time to fit residues: 25.9992 Evaluate side-chains 83 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 1.016 ------------------------------------------------------------------------------- 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: 10.0000 chunk 122 optimal weight: 0.5980 chunk 26 optimal weight: 0.6980 chunk 80 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 136 optimal weight: 4.9990 chunk 113 optimal weight: 0.0570 chunk 63 optimal weight: 7.9990 chunk 11 optimal weight: 1.9990 chunk 71 optimal weight: 20.0000 chunk 131 optimal weight: 1.9990 overall best weight: 0.6298 ------------------------------------------------------------------------------- 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 397 ASN ** B 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7152 moved from start: 0.3411 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= 0.160 Angle : 0.573 9.869 12248 Z= 0.292 Chirality : 0.044 0.167 1497 Planarity : 0.004 0.075 1689 Dihedral : 4.155 21.313 1460 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.33 % Favored : 93.31 % 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: -0.05 (0.24), residues: 1406 helix: 3.05 (0.22), residues: 563 sheet: -1.36 (0.42), residues: 148 loop : -2.57 (0.22), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 737 HIS 0.003 0.001 HIS B 306 PHE 0.023 0.001 PHE B 174 TYR 0.010 0.001 TYR B 725 ARG 0.004 0.001 ARG B 675 *********************** 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 117 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 1.026 Fit side-chains REVERT: B 264 ASN cc_start: 0.7959 (m-40) cc_final: 0.7737 (m-40) REVERT: B 547 ASP cc_start: 0.8334 (p0) cc_final: 0.8126 (p0) REVERT: B 627 TRP cc_start: 0.8786 (t-100) cc_final: 0.8584 (t-100) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.1618 time to fit residues: 28.7208 Evaluate side-chains 96 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 1.078 ------------------------------------------------------------------------------- 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: 8.9990 chunk 77 optimal weight: 0.6980 chunk 99 optimal weight: 0.9990 chunk 114 optimal weight: 0.0970 chunk 76 optimal weight: 3.9990 chunk 135 optimal weight: 0.0170 chunk 85 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 62 optimal weight: 0.7980 chunk 84 optimal weight: 0.2980 chunk 54 optimal weight: 5.9990 overall best weight: 0.3816 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7103 moved from start: 0.3392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8914 Z= 0.135 Angle : 0.536 7.500 12248 Z= 0.272 Chirality : 0.043 0.169 1497 Planarity : 0.004 0.075 1689 Dihedral : 3.791 19.961 1460 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.11 % Favored : 92.53 % Rotamer: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % 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: 0.14 (0.24), residues: 1406 helix: 3.26 (0.22), residues: 556 sheet: -1.30 (0.43), residues: 150 loop : -2.44 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP B 760 HIS 0.002 0.001 HIS B 306 PHE 0.019 0.001 PHE B 174 TYR 0.009 0.001 TYR B 416 ARG 0.002 0.000 ARG B 675 *********************** 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 : 1.067 Fit side-chains REVERT: B 414 ILE cc_start: 0.9037 (mm) cc_final: 0.8834 (mm) REVERT: B 690 MET cc_start: 0.7278 (ptt) cc_final: 0.6935 (ptt) outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.1529 time to fit residues: 27.7161 Evaluate side-chains 94 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 0.983 ------------------------------------------------------------------------------- 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: 0.6980 chunk 26 optimal weight: 0.3980 chunk 86 optimal weight: 0.0070 chunk 92 optimal weight: 0.0870 chunk 67 optimal weight: 20.0000 chunk 12 optimal weight: 5.9990 chunk 106 optimal weight: 1.9990 chunk 123 optimal weight: 0.9990 chunk 130 optimal weight: 2.9990 chunk 118 optimal weight: 0.9990 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7093 moved from start: 0.3447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8914 Z= 0.139 Angle : 0.551 10.574 12248 Z= 0.274 Chirality : 0.043 0.168 1497 Planarity : 0.004 0.074 1689 Dihedral : 3.684 18.611 1460 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.40 % Favored : 93.24 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % 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: 0.25 (0.24), residues: 1406 helix: 3.34 (0.22), residues: 556 sheet: -1.38 (0.42), residues: 160 loop : -2.33 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP B 760 HIS 0.002 0.001 HIS B 306 PHE 0.022 0.001 PHE B 540 TYR 0.007 0.001 TYR B 726 ARG 0.002 0.000 ARG B 675 *********************** 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 119 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 1.093 Fit side-chains revert: symmetry clash REVERT: B 414 ILE cc_start: 0.9104 (mm) cc_final: 0.8786 (mm) outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.1438 time to fit residues: 26.7247 Evaluate side-chains 94 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 0.925 ------------------------------------------------------------------------------- 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: 0.1980 chunk 130 optimal weight: 0.0670 chunk 76 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 chunk 99 optimal weight: 0.2980 chunk 38 optimal weight: 50.0000 chunk 114 optimal weight: 0.0870 chunk 119 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 133 optimal weight: 0.9980 chunk 81 optimal weight: 0.8980 overall best weight: 0.3096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7073 moved from start: 0.3456 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= 0.133 Angle : 0.545 9.819 12248 Z= 0.271 Chirality : 0.043 0.165 1497 Planarity : 0.004 0.073 1689 Dihedral : 3.630 20.175 1460 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.47 % Favored : 93.17 % 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: 0.33 (0.24), residues: 1406 helix: 3.41 (0.22), residues: 556 sheet: -1.32 (0.42), residues: 159 loop : -2.30 (0.23), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 627 HIS 0.002 0.000 HIS B 306 PHE 0.021 0.001 PHE B 540 TYR 0.019 0.001 TYR B 725 ARG 0.002 0.000 ARG B 257 *********************** 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 117 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 0.970 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 414 ILE cc_start: 0.9075 (mm) cc_final: 0.8818 (mm) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.1425 time to fit residues: 26.1527 Evaluate side-chains 94 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 0.981 ------------------------------------------------------------------------------- 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: 0.0570 chunk 93 optimal weight: 0.9980 chunk 140 optimal weight: 0.9980 chunk 129 optimal weight: 0.7980 chunk 111 optimal weight: 0.8980 chunk 11 optimal weight: 7.9990 chunk 86 optimal weight: 0.0570 chunk 68 optimal weight: 10.0000 chunk 88 optimal weight: 0.0970 chunk 119 optimal weight: 0.3980 chunk 34 optimal weight: 30.0000 overall best weight: 0.2814 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7052 moved from start: 0.3509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8914 Z= 0.130 Angle : 0.539 7.903 12248 Z= 0.270 Chirality : 0.043 0.163 1497 Planarity : 0.004 0.073 1689 Dihedral : 3.516 18.145 1460 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.12 % Favored : 93.53 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % 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: 0.39 (0.24), residues: 1406 helix: 3.44 (0.22), residues: 557 sheet: -1.18 (0.43), residues: 159 loop : -2.28 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 627 HIS 0.002 0.000 HIS B 306 PHE 0.020 0.001 PHE B 540 TYR 0.013 0.001 TYR B 725 ARG 0.002 0.000 ARG B 675 ********************** 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 123 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 0.988 Fit side-chains revert: symmetry clash REVERT: B 395 SER cc_start: 0.8291 (m) cc_final: 0.7738 (m) REVERT: B 414 ILE cc_start: 0.9101 (mm) cc_final: 0.8753 (mm) REVERT: B 479 THR cc_start: 0.8699 (m) cc_final: 0.8471 (m) REVERT: B 690 MET cc_start: 0.7372 (ptt) cc_final: 0.7009 (ptt) outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.1383 time to fit residues: 26.7920 Evaluate side-chains 99 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 0.948 ------------------------------------------------------------------------------- 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: 6.9990 chunk 16 optimal weight: 10.0000 chunk 31 optimal weight: 50.0000 chunk 112 optimal weight: 3.9990 chunk 46 optimal weight: 20.0000 chunk 115 optimal weight: 0.9990 chunk 14 optimal weight: 9.9990 chunk 20 optimal weight: 2.9990 chunk 98 optimal weight: 0.9980 chunk 6 optimal weight: 20.0000 chunk 80 optimal weight: 0.6980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 244 GLN B 481 GLN ** B 668 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.164418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.148525 restraints weight = 21048.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.145655 restraints weight = 45071.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.146083 restraints weight = 48974.245| |-----------------------------------------------------------------------------| r_work (final): 0.3883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 moved from start: 0.3926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 8914 Z= 0.359 Angle : 0.656 7.858 12248 Z= 0.343 Chirality : 0.046 0.219 1497 Planarity : 0.004 0.042 1689 Dihedral : 4.185 22.778 1460 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.43 % Allowed : 8.39 % Favored : 91.18 % Rotamer: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % 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: 0.18 (0.25), residues: 1406 helix: 3.29 (0.22), residues: 558 sheet: -1.34 (0.41), residues: 170 loop : -2.42 (0.23), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 732 HIS 0.006 0.002 HIS B 306 PHE 0.032 0.002 PHE B 540 TYR 0.019 0.002 TYR B 725 ARG 0.005 0.001 ARG B 406 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1932.34 seconds wall clock time: 35 minutes 0.87 seconds (2100.87 seconds total)