Starting phenix.real_space_refine on Sat Dec 16 07:46:45 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u5y_41939/12_2023/8u5y_41939.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u5y_41939/12_2023/8u5y_41939.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u5y_41939/12_2023/8u5y_41939.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u5y_41939/12_2023/8u5y_41939.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u5y_41939/12_2023/8u5y_41939.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u5y_41939/12_2023/8u5y_41939.pdb" } resolution = 3.01 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= 0.003 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 16 5.49 5 S 78 5.16 5 C 11057 2.51 5 N 2937 2.21 5 O 3251 1.98 5 H 17152 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 519": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 210": "OE1" <-> "OE2" Residue "A GLU 327": "OE1" <-> "OE2" Residue "A TYR 476": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 479": "OD1" <-> "OD2" Residue "A TYR 519": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 178": "OE1" <-> "OE2" Residue "C GLU 285": "OE1" <-> "OE2" Residue "C PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 526": "OE1" <-> "OE2" Residue "C GLU 534": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 34491 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 11430 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 700, 11429 Classifications: {'peptide': 700} Link IDs: {'PTRANS': 50, 'TRANS': 649} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 700, 11429 Classifications: {'peptide': 700} Link IDs: {'PTRANS': 50, 'TRANS': 649} Chain breaks: 1 bond proxies already assigned to first conformer: 11575 Chain: "A" Number of atoms: 11320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 697, 11320 Classifications: {'peptide': 697} Link IDs: {'PTRANS': 50, 'TRANS': 646} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 11229 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 692, 11228 Classifications: {'peptide': 692} Link IDs: {'PTRANS': 50, 'TRANS': 641} Chain breaks: 2 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 14 Conformer: "B" Number of residues, atoms: 692, 11228 Classifications: {'peptide': 692} Link IDs: {'PTRANS': 50, 'TRANS': 641} Chain breaks: 2 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 14 bond proxies already assigned to first conformer: 11368 Chain: "D" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 512 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Time building chain proxies: 23.50, per 1000 atoms: 0.68 Number of scatterers: 34491 At special positions: 0 Unit cell: (104.14, 142.68, 154.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 78 16.00 P 16 15.00 O 3251 8.00 N 2937 7.00 C 11057 6.00 H 17152 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 29.48 Conformation dependent library (CDL) restraints added in 5.9 seconds 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3998 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 13 sheets defined 21.0% alpha, 17.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.76 Creating SS restraints... Processing helix chain 'B' and resid 44 through 53 Processing helix chain 'B' and resid 114 through 120 removed outlier: 4.131A pdb=" N VAL B 118 " --> pdb=" O LEU B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 174 Processing helix chain 'B' and resid 220 through 227 Processing helix chain 'B' and resid 282 through 287 Processing helix chain 'B' and resid 343 through 347 Processing helix chain 'B' and resid 348 through 352 Processing helix chain 'B' and resid 362 through 367 Processing helix chain 'B' and resid 425 through 430 Processing helix chain 'B' and resid 479 through 495 Processing helix chain 'B' and resid 515 through 521 Processing helix chain 'B' and resid 524 through 529 removed outlier: 4.689A pdb=" N LEU B 529 " --> pdb=" O VAL B 525 " (cutoff:3.500A) Processing helix chain 'B' and resid 534 through 542 removed outlier: 3.699A pdb=" N LEU B 542 " --> pdb=" O GLU B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 682 through 689 Processing helix chain 'B' and resid 702 through 706 removed outlier: 3.815A pdb=" N ILE B 706 " --> pdb=" O PRO B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 711 through 713 No H-bonds generated for 'chain 'B' and resid 711 through 713' Processing helix chain 'B' and resid 714 through 721 Processing helix chain 'B' and resid 773 through 780 Processing helix chain 'B' and resid 807 through 822 removed outlier: 3.820A pdb=" N LEU B 822 " --> pdb=" O ALA B 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 56 Processing helix chain 'A' and resid 112 through 114 No H-bonds generated for 'chain 'A' and resid 112 through 114' Processing helix chain 'A' and resid 115 through 120 Processing helix chain 'A' and resid 220 through 227 Processing helix chain 'A' and resid 282 through 287 Processing helix chain 'A' and resid 343 through 347 Processing helix chain 'A' and resid 348 through 352 Processing helix chain 'A' and resid 362 through 369 removed outlier: 3.867A pdb=" N ASP A 368 " --> pdb=" O SER A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 430 Processing helix chain 'A' and resid 473 through 477 Processing helix chain 'A' and resid 479 through 495 removed outlier: 3.930A pdb=" N LYS A 483 " --> pdb=" O ASP A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 522 removed outlier: 3.818A pdb=" N SER A 522 " --> pdb=" O LYS A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 528 removed outlier: 6.338A pdb=" N GLU A 526 " --> pdb=" O ILE A 523 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU A 528 " --> pdb=" O VAL A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 542 removed outlier: 3.589A pdb=" N LEU A 542 " --> pdb=" O GLU A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 689 Processing helix chain 'A' and resid 702 through 706 removed outlier: 3.775A pdb=" N ILE A 706 " --> pdb=" O PRO A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 723 Processing helix chain 'A' and resid 738 through 742 removed outlier: 3.816A pdb=" N PHE A 742 " --> pdb=" O LEU A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 773 through 780 Processing helix chain 'A' and resid 809 through 822 removed outlier: 3.623A pdb=" N LEU A 822 " --> pdb=" O ALA A 818 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 54 Processing helix chain 'C' and resid 112 through 114 No H-bonds generated for 'chain 'C' and resid 112 through 114' Processing helix chain 'C' and resid 115 through 120 Processing helix chain 'C' and resid 170 through 175 Processing helix chain 'C' and resid 220 through 227 Processing helix chain 'C' and resid 282 through 287 Processing helix chain 'C' and resid 362 through 367 Processing helix chain 'C' and resid 425 through 430 Processing helix chain 'C' and resid 473 through 477 removed outlier: 3.545A pdb=" N THR C 477 " --> pdb=" O GLN C 474 " (cutoff:3.500A) Processing helix chain 'C' and resid 479 through 495 Processing helix chain 'C' and resid 515 through 523 Processing helix chain 'C' and resid 534 through 542 Processing helix chain 'C' and resid 702 through 706 Processing helix chain 'C' and resid 711 through 714 Processing helix chain 'C' and resid 715 through 722 removed outlier: 3.736A pdb=" N TYR C 722 " --> pdb=" O LEU C 718 " (cutoff:3.500A) Processing helix chain 'C' and resid 738 through 742 Processing helix chain 'C' and resid 773 through 780 Processing helix chain 'C' and resid 807 through 822 removed outlier: 4.498A pdb=" N GLY C 813 " --> pdb=" O ARG C 809 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N ILE C 816 " --> pdb=" O ALA C 812 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU C 822 " --> pdb=" O ALA C 818 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 128 through 129 removed outlier: 5.595A pdb=" N VAL B 71 " --> pdb=" O SER B 100 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N SER B 100 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ALA B 73 " --> pdb=" O THR B 98 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N TYR B 95 " --> pdb=" O LEU B 110 " (cutoff:3.500A) removed outlier: 8.385A pdb=" N ILE B 150 " --> pdb=" O LYS B 107 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N TYR B 109 " --> pdb=" O ILE B 150 " (cutoff:3.500A) removed outlier: 8.243A pdb=" N ASN B 152 " --> pdb=" O TYR B 109 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ARG B 133 " --> pdb=" O ASP B 151 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL B 153 " --> pdb=" O ILE B 131 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ILE B 131 " --> pdb=" O VAL B 153 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 237 through 244 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 237 through 244 current: chain 'B' and resid 261 through 269 removed outlier: 3.520A pdb=" N GLY B 272 " --> pdb=" O ASP B 269 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 272 through 278 current: chain 'B' and resid 322 through 330 Processing sheet with id=AA3, first strand: chain 'B' and resid 360 through 361 removed outlier: 4.533A pdb=" N ILE B 378 " --> pdb=" O THR B 361 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 375 through 384 current: chain 'B' and resid 399 through 408 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 416 through 421 current: chain 'B' and resid 455 through 460 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 455 through 460 current: chain 'B' and resid 708 through 709 Processing sheet with id=AA4, first strand: chain 'B' and resid 547 through 561 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 679 through 681 current: chain 'B' and resid 762 through 768 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 762 through 768 current: chain 'B' and resid 841 through 849 Processing sheet with id=AA5, first strand: chain 'A' and resid 128 through 129 removed outlier: 6.309A pdb=" N THR A 98 " --> pdb=" O LEU A 72 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N VAL A 74 " --> pdb=" O ASP A 96 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ASP A 96 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ARG A 76 " --> pdb=" O CYS A 94 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N CYS A 94 " --> pdb=" O ARG A 76 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N TYR A 95 " --> pdb=" O LEU A 110 " (cutoff:3.500A) removed outlier: 10.792A pdb=" N LEU A 148 " --> pdb=" O GLN A 105 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N LYS A 107 " --> pdb=" O LEU A 148 " (cutoff:3.500A) removed outlier: 8.308A pdb=" N ILE A 150 " --> pdb=" O LYS A 107 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N TYR A 109 " --> pdb=" O ILE A 150 " (cutoff:3.500A) removed outlier: 8.298A pdb=" N ASN A 152 " --> pdb=" O TYR A 109 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N ARG A 133 " --> pdb=" O ASP A 151 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N VAL A 153 " --> pdb=" O ILE A 131 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ILE A 131 " --> pdb=" O VAL A 153 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 237 through 244 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 237 through 244 current: chain 'A' and resid 261 through 269 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 272 through 278 current: chain 'A' and resid 322 through 327 Processing sheet with id=AA7, first strand: chain 'A' and resid 360 through 361 removed outlier: 4.592A pdb=" N ILE A 378 " --> pdb=" O THR A 361 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N HIS A 406 " --> pdb=" O VAL A 382 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N VAL A 384 " --> pdb=" O TRP A 404 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N TRP A 404 " --> pdb=" O VAL A 384 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ARG A 386 " --> pdb=" O TYR A 402 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N TYR A 402 " --> pdb=" O ARG A 386 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N GLN A 388 " --> pdb=" O TRP A 400 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N TRP A 400 " --> pdb=" O GLN A 388 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 416 through 421 current: chain 'A' and resid 455 through 460 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 455 through 460 current: chain 'A' and resid 708 through 709 Processing sheet with id=AA8, first strand: chain 'A' and resid 547 through 562 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 679 through 681 current: chain 'A' and resid 762 through 768 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 762 through 768 current: chain 'A' and resid 841 through 849 Processing sheet with id=AA9, first strand: chain 'C' and resid 93 through 100 removed outlier: 4.156A pdb=" N ALA C 73 " --> pdb=" O THR C 98 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N SER C 100 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N VAL C 71 " --> pdb=" O SER C 100 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 109 through 110 removed outlier: 6.378A pdb=" N TYR C 109 " --> pdb=" O ILE C 150 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N ASN C 152 " --> pdb=" O TYR C 109 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N ARG C 133 " --> pdb=" O ASP C 151 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 239 through 244 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 239 through 244 current: chain 'C' and resid 261 through 268 Processing sheet with id=AB3, first strand: chain 'C' and resid 375 through 384 removed outlier: 6.178A pdb=" N HIS C 406 " --> pdb=" O VAL C 382 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N VAL C 384 " --> pdb=" O TRP C 404 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N TRP C 404 " --> pdb=" O VAL C 384 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 418 through 421 current: chain 'C' and resid 457 through 460 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 457 through 460 current: chain 'C' and resid 708 through 709 Processing sheet with id=AB4, first strand: chain 'C' and resid 679 through 681 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 679 through 681 current: chain 'C' and resid 767 through 768 removed outlier: 7.212A pdb=" N ALA C 767 " --> pdb=" O LEU C 845 " (cutoff:3.500A) removed outlier: 8.451A pdb=" N LYS C 847 " --> pdb=" O ALA C 767 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N LYS C 840 " --> pdb=" O LEU C 836 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ILE C 830 " --> pdb=" O HIS C 846 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N ILE C 848 " --> pdb=" O VAL C 828 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N VAL C 828 " --> pdb=" O ILE C 848 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE C 827 " --> pdb=" O GLY C 554 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE C 550 " --> pdb=" O LEU C 831 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N THR C 754 " --> pdb=" O THR C 557 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N ILE C 762 " --> pdb=" O GLY C 757 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ASP C 694 " --> pdb=" O ALA C 763 " (cutoff:3.500A) removed outlier: 8.424A pdb=" N ASP C 765 " --> pdb=" O ASP C 694 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU C 696 " --> pdb=" O ASP C 765 " (cutoff:3.500A) 318 hydrogen bonds defined for protein. 849 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: 12.52 Time building geometry restraints manager: 30.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 17089 1.03 - 1.23: 91 1.23 - 1.42: 7367 1.42 - 1.61: 10295 1.61 - 1.81: 114 Bond restraints: 34956 Sorted by residual: bond pdb=" N HIS B 564 " pdb=" H HIS B 564 " ideal model delta sigma weight residual 0.860 1.035 -0.175 2.00e-02 2.50e+03 7.68e+01 bond pdb=" N SER B 566 " pdb=" H SER B 566 " ideal model delta sigma weight residual 0.860 1.035 -0.175 2.00e-02 2.50e+03 7.66e+01 bond pdb=" N SER B 565 " pdb=" H SER B 565 " ideal model delta sigma weight residual 0.860 1.035 -0.175 2.00e-02 2.50e+03 7.65e+01 bond pdb=" NE2 HIS B 564 " pdb=" HE2 HIS B 564 " ideal model delta sigma weight residual 0.860 1.015 -0.155 2.00e-02 2.50e+03 6.00e+01 bond pdb=" CD2 HIS B 564 " pdb=" HD2 HIS B 564 " ideal model delta sigma weight residual 0.930 1.082 -0.152 2.00e-02 2.50e+03 5.74e+01 ... (remaining 34951 not shown) Histogram of bond angle deviations from ideal: 100.36 - 107.11: 948 107.11 - 113.86: 42210 113.86 - 120.61: 10873 120.61 - 127.36: 9077 127.36 - 134.11: 263 Bond angle restraints: 63371 Sorted by residual: angle pdb=" N PRO B 563 " pdb=" CA PRO B 563 " pdb=" C PRO B 563 " ideal model delta sigma weight residual 112.47 104.71 7.76 2.06e+00 2.36e-01 1.42e+01 angle pdb=" C SER C 270 " pdb=" CA SER C 270 " pdb=" CB SER C 270 " ideal model delta sigma weight residual 116.34 111.17 5.17 1.40e+00 5.10e-01 1.36e+01 angle pdb=" N VAL A 103 " pdb=" CA VAL A 103 " pdb=" C VAL A 103 " ideal model delta sigma weight residual 111.67 108.25 3.42 9.50e-01 1.11e+00 1.30e+01 angle pdb=" N ILE A 428 " pdb=" CA ILE A 428 " pdb=" C ILE A 428 " ideal model delta sigma weight residual 111.62 108.90 2.72 7.90e-01 1.60e+00 1.19e+01 angle pdb=" N VAL A 87 " pdb=" CA VAL A 87 " pdb=" C VAL A 87 " ideal model delta sigma weight residual 112.35 108.36 3.99 1.20e+00 6.94e-01 1.10e+01 ... (remaining 63366 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.23: 15693 32.23 - 64.46: 423 64.46 - 96.69: 19 96.69 - 128.92: 0 128.92 - 161.15: 1 Dihedral angle restraints: 16136 sinusoidal: 8835 harmonic: 7301 Sorted by residual: dihedral pdb=" C4' DT D 5 " pdb=" C3' DT D 5 " pdb=" O3' DT D 5 " pdb=" P DT D 6 " ideal model delta sinusoidal sigma weight residual 220.00 58.85 161.15 1 3.50e+01 8.16e-04 1.53e+01 dihedral pdb=" CA ASP C 409 " pdb=" CB ASP C 409 " pdb=" CG ASP C 409 " pdb=" OD1 ASP C 409 " ideal model delta sinusoidal sigma weight residual -30.00 -88.55 58.55 1 2.00e+01 2.50e-03 1.15e+01 dihedral pdb=" CB GLU B 842 " pdb=" CG GLU B 842 " pdb=" CD GLU B 842 " pdb=" OE1 GLU B 842 " ideal model delta sinusoidal sigma weight residual 0.00 89.11 -89.11 1 3.00e+01 1.11e-03 1.05e+01 ... (remaining 16133 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1538 0.028 - 0.057: 719 0.057 - 0.085: 152 0.085 - 0.113: 196 0.113 - 0.142: 61 Chirality restraints: 2666 Sorted by residual: chirality pdb=" CA ILE A 342 " pdb=" N ILE A 342 " pdb=" C ILE A 342 " pdb=" CB ILE A 342 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.02e-01 chirality pdb=" CA ILE B 706 " pdb=" N ILE B 706 " pdb=" C ILE B 706 " pdb=" CB ILE B 706 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.92e-01 chirality pdb=" CA ILE A 340 " pdb=" N ILE A 340 " pdb=" C ILE A 340 " pdb=" CB ILE A 340 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.64e-01 ... (remaining 2663 not shown) Planarity restraints: 4988 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A 207 " -0.027 5.00e-02 4.00e+02 4.03e-02 2.59e+00 pdb=" N PRO A 208 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 208 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 208 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS C 283 " 0.026 5.00e-02 4.00e+02 3.97e-02 2.53e+00 pdb=" N PRO C 284 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO C 284 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 284 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN B 474 " 0.026 5.00e-02 4.00e+02 3.88e-02 2.41e+00 pdb=" N PRO B 475 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO B 475 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 475 " 0.022 5.00e-02 4.00e+02 ... (remaining 4985 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.19: 1806 2.19 - 2.79: 72593 2.79 - 3.39: 98297 3.39 - 4.00: 132454 4.00 - 4.60: 199266 Nonbonded interactions: 504416 Sorted by model distance: nonbonded pdb=" O VAL C 384 " pdb=" H GLY C 504 " model vdw 1.585 1.850 nonbonded pdb=" O PRO B 513 " pdb=" HH TYR B 849 " model vdw 1.626 1.850 nonbonded pdb="HD22 ASN C 500 " pdb=" O PRO C 796 " model vdw 1.627 1.850 nonbonded pdb=" O THR C 441 " pdb=" HG SER C 464 " model vdw 1.644 1.850 nonbonded pdb=" O VAL B 384 " pdb=" H GLY B 504 " model vdw 1.659 1.850 ... (remaining 504411 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 43 through 154 or resid 156 through 564 or (resid 565 and \ (name N or name CA or name C or name O or name CB or name H or name HA )) or res \ id 676 through 682 or (resid 683 and (name N or name CA or name C or name O or n \ ame CB or name CG or name CD or name OE1 or name NE2)) or (resid 691 and (name N \ or name CA or name C or name O )) or (resid 692 and (name N or name CA or name \ C or name O or name CB or name CG or name CD1 or name CD2 or name HA or name HB2 \ or name HB3 or name HG or name HD11 or name HD12 or name HD13 or name HD21 or n \ ame HD22 or name HD23)) or resid 693 through 759 or (resid 760 through 761 and ( \ name N or name CA or name C or name O or name CB or name H or name HA )) or resi \ d 762 through 825 or (resid 826 and (name N or name CA or name C or name O or na \ me CB or name H or name HA )) or resid 827 through 851)) selection = (chain 'B' and (resid 43 through 138 or (resid 139 and (name N or name CA or nam \ e C or name O or name CB or name CG or name OD1 or name ND2)) or (resid 143 and \ (name N or name CA or name C or name O or name CB or name CG1 or name CG2 or nam \ e CD1)) or (resid 144 and (name N or name CA or name C or name O )) or resid 145 \ through 154 or resid 156 through 451 or (resid 452 and (name N or name CA or na \ me C or name O or name CB or name H or name HA )) or resid 453 through 473 or (r \ esid 474 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 475 through 524 or (resid 525 and (name N or name CA or name C o \ r name O or name CB or name H or name HA )) or resid 526 through 564 or (resid 5 \ 65 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 676 through 682 or (resid 683 and (name N or name CA or name C or name \ O or name CB or name CG or name CD or name OE1 or name NE2)) or (resid 691 and \ (name N or name CA or name C or name O )) or (resid 692 and (name N or name CA o \ r name C or name O or name CB or name CG or name CD1 or name CD2 or name HA or n \ ame HB2 or name HB3 or name HG or name HD11 or name HD12 or name HD13 or name HD \ 21 or name HD22 or name HD23)) or resid 693 through 759 or (resid 760 through 76 \ 1 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 762 through 825 or (resid 826 and (name N or name CA or name C or name \ O or name CB or name H or name HA )) or resid 827 through 851)) selection = (chain 'C' and (resid 43 through 138 or (resid 139 and (name N or name CA or nam \ e C or name O or name CB or name CG or name OD1 or name ND2)) or (resid 143 and \ (name N or name CA or name C or name O or name CB or name CG1 or name CG2 or nam \ e CD1)) or (resid 144 and (name N or name CA or name C or name O )) or resid 145 \ through 154 or resid 156 through 451 or (resid 452 and (name N or name CA or na \ me C or name O or name CB or name H or name HA )) or resid 453 through 473 or (r \ esid 474 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 475 through 524 or (resid 525 and (name N or name CA or name C o \ r name O or name CB or name H or name HA )) or resid 526 through 851)) } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.500 Extract box with map and model: 30.060 Check model and map are aligned: 0.510 Set scattering table: 0.300 Process input model: 118.670 Find NCS groups from input model: 1.860 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 163.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 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 0.030 17804 Z= 0.187 Angle : 0.569 7.765 24250 Z= 0.328 Chirality : 0.043 0.142 2666 Planarity : 0.004 0.040 3059 Dihedral : 14.423 161.147 6810 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.57 % Allowed : 13.06 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.19), residues: 2073 helix: 0.37 (0.31), residues: 306 sheet: -1.64 (0.22), residues: 546 loop : -0.91 (0.18), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 228 HIS 0.002 0.001 HIS B 564 PHE 0.007 0.001 PHE A 416 TYR 0.014 0.001 TYR B 509 ARG 0.002 0.000 ARG A 715 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 452 is missing expected H atoms. Skipping. Residue VAL 525 is missing expected H atoms. Skipping. Residue SER 565 is missing expected H atoms. Skipping. Evaluate side-chains 162 residues out of total 1934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 151 time to evaluate : 3.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 9 residues processed: 162 average time/residue: 1.0094 time to fit residues: 222.3510 Evaluate side-chains 112 residues out of total 1934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 103 time to evaluate : 2.658 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 9 outliers final: 1 residues processed: 9 average time/residue: 0.3938 time to fit residues: 10.5804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 176 optimal weight: 1.9990 chunk 158 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 106 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 163 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 189 optimal weight: 4.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 695 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.0939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 17804 Z= 0.307 Angle : 0.550 5.676 24250 Z= 0.283 Chirality : 0.045 0.145 2666 Planarity : 0.005 0.068 3059 Dihedral : 9.508 162.090 2470 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 0.62 % Allowed : 13.95 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.19), residues: 2073 helix: 0.48 (0.31), residues: 310 sheet: -1.71 (0.21), residues: 551 loop : -0.97 (0.18), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 279 HIS 0.004 0.001 HIS C 564 PHE 0.010 0.001 PHE C 438 TYR 0.015 0.001 TYR C 509 ARG 0.008 0.000 ARG C 171 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 452 is missing expected H atoms. Skipping. Residue VAL 525 is missing expected H atoms. Skipping. Residue SER 565 is missing expected H atoms. Skipping. Evaluate side-chains 115 residues out of total 1934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 103 time to evaluate : 2.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 5 residues processed: 113 average time/residue: 0.9988 time to fit residues: 157.8992 Evaluate side-chains 102 residues out of total 1934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 97 time to evaluate : 3.034 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 5 average time/residue: 0.3829 time to fit residues: 7.2860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 105 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 157 optimal weight: 5.9990 chunk 129 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 190 optimal weight: 6.9990 chunk 205 optimal weight: 0.6980 chunk 169 optimal weight: 0.0270 chunk 188 optimal weight: 0.7980 chunk 64 optimal weight: 0.9990 chunk 152 optimal weight: 2.9990 overall best weight: 1.1042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.1145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 17804 Z= 0.237 Angle : 0.521 5.111 24250 Z= 0.267 Chirality : 0.044 0.150 2666 Planarity : 0.004 0.049 3059 Dihedral : 9.488 161.435 2470 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 0.31 % Allowed : 14.26 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.19), residues: 2073 helix: 0.54 (0.31), residues: 310 sheet: -1.59 (0.22), residues: 556 loop : -1.00 (0.18), residues: 1207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 228 HIS 0.009 0.001 HIS C 223 PHE 0.010 0.001 PHE A 467 TYR 0.014 0.001 TYR B 509 ARG 0.004 0.000 ARG C 171 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 452 is missing expected H atoms. Skipping. Residue VAL 525 is missing expected H atoms. Skipping. Residue SER 565 is missing expected H atoms. Skipping. Evaluate side-chains 107 residues out of total 1934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 101 time to evaluate : 2.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 107 average time/residue: 0.9944 time to fit residues: 146.9459 Evaluate side-chains 98 residues out of total 1934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 95 time to evaluate : 3.142 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 3 average time/residue: 0.6086 time to fit residues: 6.7991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 187 optimal weight: 5.9990 chunk 142 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 90 optimal weight: 2.9990 chunk 127 optimal weight: 3.9990 chunk 190 optimal weight: 7.9990 chunk 202 optimal weight: 3.9990 chunk 99 optimal weight: 0.7980 chunk 180 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.1400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 17804 Z= 0.267 Angle : 0.526 6.148 24250 Z= 0.268 Chirality : 0.044 0.146 2666 Planarity : 0.004 0.048 3059 Dihedral : 9.494 161.482 2470 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 0.41 % Allowed : 14.36 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.19), residues: 2073 helix: 0.54 (0.31), residues: 310 sheet: -1.54 (0.22), residues: 547 loop : -1.01 (0.18), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 279 HIS 0.005 0.001 HIS C 223 PHE 0.011 0.001 PHE B 416 TYR 0.014 0.001 TYR B 478 ARG 0.003 0.000 ARG B 396 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 452 is missing expected H atoms. Skipping. Residue VAL 525 is missing expected H atoms. Skipping. Residue SER 565 is missing expected H atoms. Skipping. Evaluate side-chains 105 residues out of total 1934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 97 time to evaluate : 3.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 2 residues processed: 104 average time/residue: 0.9824 time to fit residues: 141.7379 Evaluate side-chains 95 residues out of total 1934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 93 time to evaluate : 2.693 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 2 average time/residue: 0.4089 time to fit residues: 5.1602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 168 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 2 optimal weight: 0.0070 chunk 150 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 172 optimal weight: 3.9990 chunk 139 optimal weight: 3.9990 chunk 0 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 chunk 181 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 overall best weight: 1.5604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 17804 Z= 0.314 Angle : 0.533 6.422 24250 Z= 0.274 Chirality : 0.044 0.146 2666 Planarity : 0.004 0.050 3059 Dihedral : 9.531 161.553 2470 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 0.52 % Allowed : 14.00 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.19), residues: 2073 helix: 0.56 (0.31), residues: 310 sheet: -1.50 (0.22), residues: 549 loop : -1.03 (0.18), residues: 1214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 279 HIS 0.004 0.001 HIS C 223 PHE 0.018 0.001 PHE A 467 TYR 0.013 0.001 TYR C 795 ARG 0.003 0.000 ARG A 76 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 452 is missing expected H atoms. Skipping. Residue VAL 525 is missing expected H atoms. Skipping. Residue SER 565 is missing expected H atoms. Skipping. Evaluate side-chains 103 residues out of total 1934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 93 time to evaluate : 2.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 5 residues processed: 101 average time/residue: 0.9583 time to fit residues: 135.1823 Evaluate side-chains 95 residues out of total 1934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 90 time to evaluate : 2.976 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 5 average time/residue: 0.3968 time to fit residues: 7.4533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 67 optimal weight: 0.6980 chunk 181 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 chunk 118 optimal weight: 1.9990 chunk 49 optimal weight: 0.3980 chunk 202 optimal weight: 2.9990 chunk 167 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 106 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17804 Z= 0.200 Angle : 0.506 5.241 24250 Z= 0.258 Chirality : 0.044 0.150 2666 Planarity : 0.004 0.049 3059 Dihedral : 9.479 161.031 2470 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 0.26 % Allowed : 14.20 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.19), residues: 2073 helix: 0.69 (0.31), residues: 310 sheet: -1.49 (0.22), residues: 567 loop : -0.93 (0.18), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 228 HIS 0.003 0.001 HIS A 358 PHE 0.024 0.001 PHE A 467 TYR 0.013 0.001 TYR B 509 ARG 0.004 0.000 ARG B 396 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 452 is missing expected H atoms. Skipping. Residue VAL 525 is missing expected H atoms. Skipping. Residue SER 565 is missing expected H atoms. Skipping. Evaluate side-chains 97 residues out of total 1934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 92 time to evaluate : 3.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 96 average time/residue: 0.9786 time to fit residues: 130.5224 Evaluate side-chains 90 residues out of total 1934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 88 time to evaluate : 2.969 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 2 average time/residue: 0.4480 time to fit residues: 5.3147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 194 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 115 optimal weight: 0.9990 chunk 147 optimal weight: 2.9990 chunk 114 optimal weight: 0.7980 chunk 170 optimal weight: 5.9990 chunk 112 optimal weight: 2.9990 chunk 201 optimal weight: 4.9990 chunk 126 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 714 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 760 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 17804 Z= 0.383 Angle : 0.557 5.323 24250 Z= 0.287 Chirality : 0.045 0.162 2666 Planarity : 0.005 0.060 3059 Dihedral : 9.589 161.997 2470 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 0.26 % Allowed : 14.83 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.19), residues: 2073 helix: 0.61 (0.31), residues: 309 sheet: -1.55 (0.22), residues: 558 loop : -1.07 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 279 HIS 0.004 0.001 HIS A 846 PHE 0.012 0.001 PHE B 416 TYR 0.014 0.002 TYR B 478 ARG 0.005 0.001 ARG A 76 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 452 is missing expected H atoms. Skipping. Residue VAL 525 is missing expected H atoms. Skipping. Residue SER 565 is missing expected H atoms. Skipping. Evaluate side-chains 94 residues out of total 1934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 89 time to evaluate : 3.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 94 average time/residue: 0.9843 time to fit residues: 128.2606 Evaluate side-chains 89 residues out of total 1934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 87 time to evaluate : 2.770 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 2 average time/residue: 0.3577 time to fit residues: 4.9212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 124 optimal weight: 2.9990 chunk 80 optimal weight: 0.2980 chunk 120 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 128 optimal weight: 0.0870 chunk 137 optimal weight: 0.5980 chunk 99 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 chunk 158 optimal weight: 0.9980 chunk 183 optimal weight: 2.9990 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 17804 Z= 0.165 Angle : 0.502 7.382 24250 Z= 0.255 Chirality : 0.044 0.152 2666 Planarity : 0.004 0.050 3059 Dihedral : 9.475 160.677 2470 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 0.16 % Allowed : 14.77 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.19), residues: 2073 helix: 0.80 (0.31), residues: 311 sheet: -1.57 (0.21), residues: 579 loop : -0.88 (0.19), residues: 1183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 228 HIS 0.004 0.001 HIS A 358 PHE 0.017 0.001 PHE A 467 TYR 0.014 0.001 TYR B 509 ARG 0.004 0.000 ARG B 396 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 452 is missing expected H atoms. Skipping. Residue VAL 525 is missing expected H atoms. Skipping. Residue SER 565 is missing expected H atoms. Skipping. Evaluate side-chains 90 residues out of total 1934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 87 time to evaluate : 2.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 90 average time/residue: 1.0480 time to fit residues: 130.3462 Evaluate side-chains 88 residues out of total 1934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 86 time to evaluate : 2.846 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 2 average time/residue: 0.4216 time to fit residues: 5.1887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 192 optimal weight: 3.9990 chunk 176 optimal weight: 0.0470 chunk 187 optimal weight: 0.6980 chunk 112 optimal weight: 2.9990 chunk 81 optimal weight: 7.9990 chunk 147 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 169 optimal weight: 0.5980 chunk 177 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 198 optimal weight: 7.9990 overall best weight: 0.8680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17804 Z= 0.208 Angle : 0.503 5.844 24250 Z= 0.256 Chirality : 0.044 0.147 2666 Planarity : 0.004 0.048 3059 Dihedral : 9.446 161.400 2470 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 0.05 % Allowed : 14.98 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.19), residues: 2073 helix: 0.84 (0.30), residues: 311 sheet: -1.54 (0.21), residues: 577 loop : -0.86 (0.19), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 228 HIS 0.002 0.001 HIS A 358 PHE 0.016 0.001 PHE A 467 TYR 0.013 0.001 TYR B 478 ARG 0.004 0.000 ARG B 396 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 452 is missing expected H atoms. Skipping. Residue VAL 525 is missing expected H atoms. Skipping. Residue SER 565 is missing expected H atoms. Skipping. Evaluate side-chains 88 residues out of total 1934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 87 time to evaluate : 3.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 88 average time/residue: 1.0521 time to fit residues: 127.5788 Evaluate side-chains 87 residues out of total 1934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 86 time to evaluate : 2.590 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.3725 time to fit residues: 4.4847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 121 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 137 optimal weight: 0.8980 chunk 208 optimal weight: 4.9990 chunk 191 optimal weight: 0.5980 chunk 165 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 128 optimal weight: 0.6980 chunk 101 optimal weight: 1.9990 chunk 131 optimal weight: 0.7980 chunk 176 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 17804 Z= 0.182 Angle : 0.495 6.100 24250 Z= 0.251 Chirality : 0.044 0.147 2666 Planarity : 0.004 0.049 3059 Dihedral : 9.414 161.318 2470 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 0.16 % Allowed : 15.03 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.19), residues: 2073 helix: 0.92 (0.31), residues: 311 sheet: -1.53 (0.21), residues: 581 loop : -0.80 (0.19), residues: 1181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 228 HIS 0.002 0.000 HIS A 358 PHE 0.011 0.001 PHE A 467 TYR 0.013 0.001 TYR B 509 ARG 0.005 0.000 ARG B 396 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 452 is missing expected H atoms. Skipping. Residue VAL 525 is missing expected H atoms. Skipping. Residue SER 565 is missing expected H atoms. Skipping. Evaluate side-chains 95 residues out of total 1934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 92 time to evaluate : 2.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 95 average time/residue: 1.0718 time to fit residues: 139.1996 Evaluate side-chains 87 residues out of total 1934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 86 time to evaluate : 3.162 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.3915 time to fit residues: 4.6541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 50 optimal weight: 1.9990 chunk 152 optimal weight: 1.9990 chunk 24 optimal weight: 0.2980 chunk 46 optimal weight: 0.9980 chunk 166 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 170 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 145 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 105 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.082599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.062848 restraints weight = 150821.398| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 3.12 r_work: 0.3127 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3129 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3129 r_free = 0.3129 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3129 r_free = 0.3129 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3129 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17804 Z= 0.202 Angle : 0.500 6.644 24250 Z= 0.254 Chirality : 0.044 0.147 2666 Planarity : 0.004 0.065 3059 Dihedral : 9.407 161.599 2470 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 0.05 % Allowed : 15.19 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.19), residues: 2073 helix: 0.95 (0.31), residues: 311 sheet: -1.54 (0.21), residues: 582 loop : -0.79 (0.19), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 228 HIS 0.002 0.000 HIS B 714 PHE 0.011 0.001 PHE A 467 TYR 0.013 0.001 TYR B 478 ARG 0.012 0.000 ARG B 490 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7154.27 seconds wall clock time: 128 minutes 59.54 seconds (7739.54 seconds total)