Starting phenix.real_space_refine on Fri Jul 26 21:35:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u5y_41939/07_2024/8u5y_41939.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u5y_41939/07_2024/8u5y_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_41939/07_2024/8u5y_41939.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u5y_41939/07_2024/8u5y_41939.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u5y_41939/07_2024/8u5y_41939.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u5y_41939/07_2024/8u5y_41939.cif" } 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-dev-5388/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: 26.17, per 1000 atoms: 0.76 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: 27.13 Conformation dependent library (CDL) restraints added in 5.1 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: 2.98 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: 14.14 Time building geometry restraints manager: 28.58 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: 15907 32.23 - 64.46: 521 64.46 - 96.69: 19 96.69 - 128.92: 0 128.92 - 161.15: 1 Dihedral angle restraints: 16448 sinusoidal: 9147 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 16445 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: 16.210 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: 1.180 Check model and map are aligned: 0.230 Set scattering table: 0.310 Process input model: 121.100 Find NCS groups from input model: 1.860 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 144.300 ------------------------------------------------------------------------------- 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 : 2.646 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 REVERT: B 224 LEU cc_start: 0.9076 (tp) cc_final: 0.8828 (tp) REVERT: A 49 VAL cc_start: 0.9273 (t) cc_final: 0.8849 (p) REVERT: A 89 LYS cc_start: 0.8736 (mtpp) cc_final: 0.8470 (mmtt) REVERT: A 103 VAL cc_start: 0.8434 (t) cc_final: 0.8174 (t) REVERT: A 334 ASP cc_start: 0.8575 (m-30) cc_final: 0.8372 (m-30) REVERT: C 695 HIS cc_start: 0.6082 (t70) cc_final: 0.5666 (t-170) outliers start: 11 outliers final: 9 residues processed: 162 average time/residue: 0.9805 time to fit residues: 215.1188 Evaluate side-chains 116 residues out of total 1934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 107 time to evaluate : 2.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 CYS Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 283 CYS Chi-restraints excluded: chain A residue 373 CYS Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 347 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 176 optimal weight: 0.9980 chunk 158 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 54 optimal weight: 0.6980 chunk 106 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 163 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 99 optimal weight: 0.0770 chunk 121 optimal weight: 1.9990 chunk 189 optimal weight: 4.9990 overall best weight: 0.9140 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.0820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17804 Z= 0.219 Angle : 0.528 5.749 24250 Z= 0.270 Chirality : 0.044 0.146 2666 Planarity : 0.004 0.065 3059 Dihedral : 9.650 161.731 2481 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 0.78 % Allowed : 13.95 % Favored : 85.28 % 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: -1.39 (0.19), residues: 2073 helix: 0.53 (0.31), residues: 310 sheet: -1.64 (0.22), residues: 555 loop : -0.90 (0.18), residues: 1208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 228 HIS 0.004 0.001 HIS C 564 PHE 0.009 0.001 PHE A 416 TYR 0.015 0.001 TYR C 509 ARG 0.006 0.000 ARG B 679 *********************** 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 122 residues out of total 1934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 107 time to evaluate : 2.699 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: B 224 LEU cc_start: 0.9156 (tp) cc_final: 0.8937 (tp) REVERT: A 49 VAL cc_start: 0.9299 (t) cc_final: 0.8896 (p) REVERT: A 89 LYS cc_start: 0.8749 (mtpp) cc_final: 0.8466 (mmtt) REVERT: A 103 VAL cc_start: 0.8415 (t) cc_final: 0.8148 (t) REVERT: A 334 ASP cc_start: 0.8591 (m-30) cc_final: 0.8388 (m-30) REVERT: C 369 MET cc_start: 0.8077 (OUTLIER) cc_final: 0.7744 (ttp) REVERT: C 695 HIS cc_start: 0.6083 (t70) cc_final: 0.5673 (t-170) outliers start: 15 outliers final: 10 residues processed: 120 average time/residue: 0.9700 time to fit residues: 161.9503 Evaluate side-chains 110 residues out of total 1934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 99 time to evaluate : 2.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 CYS Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 283 CYS Chi-restraints excluded: chain A residue 373 CYS Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 369 MET Chi-restraints excluded: chain C residue 773 CYS 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: 0.7980 chunk 157 optimal weight: 4.9990 chunk 129 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 190 optimal weight: 5.9990 chunk 205 optimal weight: 0.9990 chunk 169 optimal weight: 0.1980 chunk 188 optimal weight: 0.7980 chunk 64 optimal weight: 3.9990 chunk 152 optimal weight: 0.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17804 Z= 0.192 Angle : 0.507 5.138 24250 Z= 0.259 Chirality : 0.044 0.151 2666 Planarity : 0.004 0.049 3059 Dihedral : 9.589 161.616 2478 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 0.83 % Allowed : 14.00 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.19), residues: 2073 helix: 0.60 (0.31), residues: 310 sheet: -1.51 (0.22), residues: 555 loop : -0.91 (0.18), residues: 1208 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 0.009 0.001 PHE A 416 TYR 0.017 0.001 TYR C 849 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 117 residues out of total 1934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 101 time to evaluate : 2.782 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: B 103 VAL cc_start: 0.9331 (OUTLIER) cc_final: 0.9110 (t) REVERT: A 49 VAL cc_start: 0.9302 (t) cc_final: 0.8902 (p) REVERT: A 89 LYS cc_start: 0.8752 (mtpp) cc_final: 0.8465 (mmtt) REVERT: A 103 VAL cc_start: 0.8402 (t) cc_final: 0.8134 (t) REVERT: A 129 MET cc_start: 0.8993 (ptp) cc_final: 0.8762 (ptm) REVERT: A 334 ASP cc_start: 0.8592 (m-30) cc_final: 0.8387 (m-30) REVERT: C 369 MET cc_start: 0.8094 (OUTLIER) cc_final: 0.7763 (ttp) outliers start: 16 outliers final: 9 residues processed: 116 average time/residue: 0.9441 time to fit residues: 151.8218 Evaluate side-chains 108 residues out of total 1934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 97 time to evaluate : 2.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 CYS Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 444 LYS Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 369 MET Chi-restraints excluded: chain C residue 773 CYS 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: 0.9990 chunk 90 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 190 optimal weight: 6.9990 chunk 202 optimal weight: 1.9990 chunk 99 optimal weight: 0.7980 chunk 180 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN C 695 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.1275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17804 Z= 0.289 Angle : 0.529 5.799 24250 Z= 0.270 Chirality : 0.044 0.148 2666 Planarity : 0.004 0.048 3059 Dihedral : 9.581 162.079 2475 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 0.93 % Allowed : 14.10 % 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: -1.36 (0.19), residues: 2073 helix: 0.61 (0.31), residues: 310 sheet: -1.53 (0.22), residues: 558 loop : -0.95 (0.18), residues: 1205 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 0.012 0.001 PHE C 742 TYR 0.016 0.001 TYR C 849 ARG 0.004 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 118 residues out of total 1934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 100 time to evaluate : 2.987 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: B 103 VAL cc_start: 0.9366 (OUTLIER) cc_final: 0.9149 (t) REVERT: A 89 LYS cc_start: 0.8754 (mtpp) cc_final: 0.8458 (mmtt) REVERT: A 103 VAL cc_start: 0.8459 (t) cc_final: 0.8202 (t) REVERT: A 334 ASP cc_start: 0.8611 (m-30) cc_final: 0.8405 (m-30) REVERT: A 467 PHE cc_start: 0.7668 (m-80) cc_final: 0.7403 (m-80) REVERT: C 695 HIS cc_start: 0.6495 (t70) cc_final: 0.6245 (t70) outliers start: 18 outliers final: 11 residues processed: 117 average time/residue: 0.9147 time to fit residues: 149.1456 Evaluate side-chains 110 residues out of total 1934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 98 time to evaluate : 2.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 CYS Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 283 CYS Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 773 CYS 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: 0.0770 chunk 150 optimal weight: 3.9990 chunk 83 optimal weight: 0.4980 chunk 172 optimal weight: 3.9990 chunk 139 optimal weight: 3.9990 chunk 0 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 181 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 overall best weight: 1.3142 ------------------------------------------------------------------------------- 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: 0.8340 moved from start: 0.1416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17804 Z= 0.267 Angle : 0.521 6.153 24250 Z= 0.266 Chirality : 0.044 0.147 2666 Planarity : 0.004 0.048 3059 Dihedral : 9.587 161.545 2475 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 0.98 % Allowed : 14.20 % 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: -1.38 (0.19), residues: 2073 helix: 0.63 (0.31), residues: 310 sheet: -1.53 (0.22), residues: 556 loop : -0.98 (0.18), residues: 1207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 279 HIS 0.003 0.001 HIS C 223 PHE 0.011 0.001 PHE B 416 TYR 0.013 0.001 TYR B 478 ARG 0.003 0.000 ARG A 735 *********************** 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 119 residues out of total 1934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 100 time to evaluate : 2.669 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: B 58 ARG cc_start: 0.8520 (mtp-110) cc_final: 0.8169 (mtp-110) REVERT: A 89 LYS cc_start: 0.8748 (mtpp) cc_final: 0.8453 (mmtt) REVERT: A 103 VAL cc_start: 0.8442 (t) cc_final: 0.8178 (t) REVERT: A 334 ASP cc_start: 0.8624 (m-30) cc_final: 0.8411 (m-30) REVERT: A 467 PHE cc_start: 0.7680 (m-80) cc_final: 0.7408 (m-80) REVERT: C 396 ARG cc_start: 0.8030 (mmm160) cc_final: 0.7722 (mmp-170) REVERT: C 695 HIS cc_start: 0.6644 (t70) cc_final: 0.6381 (t70) outliers start: 19 outliers final: 10 residues processed: 117 average time/residue: 0.9034 time to fit residues: 148.0388 Evaluate side-chains 106 residues out of total 1934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 96 time to evaluate : 2.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain A residue 226 MET Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 773 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 67 optimal weight: 0.9980 chunk 181 optimal weight: 4.9990 chunk 39 optimal weight: 0.5980 chunk 118 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 202 optimal weight: 0.7980 chunk 167 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 106 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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: 0.8331 moved from start: 0.1513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17804 Z= 0.204 Angle : 0.503 6.582 24250 Z= 0.255 Chirality : 0.044 0.150 2666 Planarity : 0.004 0.047 3059 Dihedral : 9.498 161.242 2473 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 0.88 % Allowed : 14.20 % 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: -1.28 (0.19), residues: 2073 helix: 0.78 (0.31), residues: 310 sheet: -1.54 (0.21), residues: 577 loop : -0.86 (0.19), residues: 1186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 228 HIS 0.002 0.001 HIS C 223 PHE 0.010 0.001 PHE B 416 TYR 0.013 0.001 TYR B 478 ARG 0.004 0.000 ARG A 735 *********************** 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 115 residues out of total 1934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 98 time to evaluate : 2.475 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: B 58 ARG cc_start: 0.8509 (mtp-110) cc_final: 0.8178 (mtp-110) REVERT: A 89 LYS cc_start: 0.8746 (mtpp) cc_final: 0.8449 (mmtt) REVERT: A 103 VAL cc_start: 0.8435 (t) cc_final: 0.8184 (t) REVERT: A 334 ASP cc_start: 0.8621 (m-30) cc_final: 0.8411 (m-30) REVERT: A 467 PHE cc_start: 0.7687 (m-80) cc_final: 0.7398 (m-80) REVERT: C 695 HIS cc_start: 0.6659 (t70) cc_final: 0.6397 (t70) outliers start: 17 outliers final: 14 residues processed: 113 average time/residue: 0.9096 time to fit residues: 142.5729 Evaluate side-chains 111 residues out of total 1934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 97 time to evaluate : 2.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 283 CYS Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain A residue 120 GLN Chi-restraints excluded: chain A residue 226 MET Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 711 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 194 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 chunk 147 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 170 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 201 optimal weight: 4.9990 chunk 126 optimal weight: 1.9990 chunk 122 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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: 0.8386 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 17804 Z= 0.466 Angle : 0.585 5.546 24250 Z= 0.304 Chirality : 0.046 0.178 2666 Planarity : 0.005 0.057 3059 Dihedral : 9.688 162.531 2473 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 0.78 % Allowed : 14.72 % Favored : 84.50 % 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: -1.55 (0.19), residues: 2073 helix: 0.51 (0.30), residues: 311 sheet: -1.62 (0.22), residues: 560 loop : -1.11 (0.18), residues: 1202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 279 HIS 0.005 0.001 HIS A 846 PHE 0.013 0.002 PHE B 213 TYR 0.015 0.002 TYR B 478 ARG 0.006 0.001 ARG A 403 *********************** 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 109 residues out of total 1934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 94 time to evaluate : 2.907 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: A 89 LYS cc_start: 0.8743 (mtpp) cc_final: 0.8447 (mmtt) REVERT: A 103 VAL cc_start: 0.8456 (t) cc_final: 0.8191 (t) REVERT: A 334 ASP cc_start: 0.8642 (m-30) cc_final: 0.8418 (m-30) REVERT: A 467 PHE cc_start: 0.7700 (m-80) cc_final: 0.7410 (m-80) REVERT: C 695 HIS cc_start: 0.6760 (t70) cc_final: 0.6487 (t70) outliers start: 15 outliers final: 12 residues processed: 107 average time/residue: 0.9527 time to fit residues: 144.7107 Evaluate side-chains 103 residues out of total 1934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 91 time to evaluate : 4.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 283 CYS Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain A residue 226 MET Chi-restraints excluded: chain A residue 233 ASN Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 338 ASN Chi-restraints excluded: chain C residue 347 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 124 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 120 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 39 optimal weight: 0.5980 chunk 128 optimal weight: 0.6980 chunk 137 optimal weight: 0.5980 chunk 99 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 158 optimal weight: 0.7980 chunk 183 optimal weight: 2.9990 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: 0.8350 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17804 Z= 0.193 Angle : 0.511 5.056 24250 Z= 0.261 Chirality : 0.044 0.151 2666 Planarity : 0.004 0.050 3059 Dihedral : 9.555 161.011 2471 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 0.78 % Allowed : 14.88 % Favored : 84.34 % 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: -1.39 (0.19), residues: 2073 helix: 0.71 (0.31), residues: 310 sheet: -1.63 (0.21), residues: 580 loop : -0.93 (0.19), residues: 1183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 228 HIS 0.002 0.001 HIS A 154 PHE 0.013 0.001 PHE B 416 TYR 0.014 0.001 TYR C 795 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 107 residues out of total 1934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 92 time to evaluate : 2.565 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: B 58 ARG cc_start: 0.8526 (mtp-110) cc_final: 0.8247 (mtp-110) REVERT: B 684 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8971 (tt) REVERT: A 89 LYS cc_start: 0.8732 (mtpp) cc_final: 0.8441 (mmtt) REVERT: A 103 VAL cc_start: 0.8458 (t) cc_final: 0.8212 (t) REVERT: A 467 PHE cc_start: 0.7706 (m-80) cc_final: 0.7399 (m-80) REVERT: C 225 GLU cc_start: 0.8720 (tp30) cc_final: 0.8391 (tp30) REVERT: C 695 HIS cc_start: 0.6730 (t70) cc_final: 0.6459 (t70) outliers start: 15 outliers final: 13 residues processed: 106 average time/residue: 0.9834 time to fit residues: 146.4789 Evaluate side-chains 104 residues out of total 1934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 90 time to evaluate : 2.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain B residue 684 LEU Chi-restraints excluded: chain A residue 120 GLN Chi-restraints excluded: chain A residue 226 MET Chi-restraints excluded: chain A residue 233 ASN Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 773 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 192 optimal weight: 5.9990 chunk 176 optimal weight: 2.9990 chunk 187 optimal weight: 0.4980 chunk 112 optimal weight: 1.9990 chunk 81 optimal weight: 6.9990 chunk 147 optimal weight: 2.9990 chunk 57 optimal weight: 0.5980 chunk 169 optimal weight: 0.9990 chunk 177 optimal weight: 0.8980 chunk 123 optimal weight: 1.9990 chunk 198 optimal weight: 4.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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: 0.8354 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17804 Z= 0.232 Angle : 0.512 8.593 24250 Z= 0.261 Chirality : 0.044 0.147 2666 Planarity : 0.004 0.049 3059 Dihedral : 9.522 161.245 2471 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 0.83 % Allowed : 14.88 % Favored : 84.29 % 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: -1.35 (0.19), residues: 2073 helix: 0.71 (0.31), residues: 312 sheet: -1.61 (0.21), residues: 580 loop : -0.89 (0.19), residues: 1181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 228 HIS 0.002 0.001 HIS A 154 PHE 0.010 0.001 PHE B 416 TYR 0.013 0.001 TYR B 509 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 107 residues out of total 1934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 91 time to evaluate : 2.761 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: B 58 ARG cc_start: 0.8542 (mtp-110) cc_final: 0.8280 (mtp-110) REVERT: B 684 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8970 (tt) REVERT: A 89 LYS cc_start: 0.8732 (mtpp) cc_final: 0.8440 (mmtt) REVERT: A 103 VAL cc_start: 0.8460 (t) cc_final: 0.8217 (t) REVERT: A 467 PHE cc_start: 0.7720 (m-80) cc_final: 0.7416 (m-80) REVERT: C 225 GLU cc_start: 0.8724 (tp30) cc_final: 0.8407 (tp30) REVERT: C 695 HIS cc_start: 0.6781 (t70) cc_final: 0.6516 (t70) outliers start: 16 outliers final: 13 residues processed: 106 average time/residue: 0.9461 time to fit residues: 138.1816 Evaluate side-chains 104 residues out of total 1934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 90 time to evaluate : 2.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 283 CYS Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain B residue 684 LEU Chi-restraints excluded: chain A residue 226 MET Chi-restraints excluded: chain A residue 233 ASN Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 773 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 121 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 208 optimal weight: 4.9990 chunk 191 optimal weight: 7.9990 chunk 165 optimal weight: 0.0020 chunk 17 optimal weight: 1.9990 chunk 128 optimal weight: 0.3980 chunk 101 optimal weight: 2.9990 chunk 131 optimal weight: 0.9990 chunk 176 optimal weight: 2.9990 overall best weight: 1.0794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 105 GLN C 451 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.1913 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= 0.234 Angle : 0.510 7.099 24250 Z= 0.260 Chirality : 0.044 0.147 2666 Planarity : 0.004 0.050 3059 Dihedral : 9.513 161.461 2471 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 0.83 % Allowed : 14.88 % Favored : 84.29 % 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: -1.33 (0.19), residues: 2073 helix: 0.74 (0.31), residues: 312 sheet: -1.60 (0.21), residues: 580 loop : -0.89 (0.19), residues: 1181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 279 HIS 0.002 0.001 HIS B 714 PHE 0.011 0.001 PHE B 416 TYR 0.014 0.001 TYR B 478 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 110 residues out of total 1934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 94 time to evaluate : 2.758 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: B 58 ARG cc_start: 0.8548 (mtp-110) cc_final: 0.8324 (mtp-110) REVERT: B 684 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8972 (tt) REVERT: A 89 LYS cc_start: 0.8736 (mtpp) cc_final: 0.8424 (mmtt) REVERT: A 103 VAL cc_start: 0.8449 (t) cc_final: 0.8229 (t) REVERT: A 467 PHE cc_start: 0.7729 (m-80) cc_final: 0.7428 (m-80) REVERT: A 528 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8416 (pt) REVERT: C 225 GLU cc_start: 0.8733 (tp30) cc_final: 0.8412 (tp30) REVERT: C 695 HIS cc_start: 0.6877 (t70) cc_final: 0.6612 (t70) outliers start: 16 outliers final: 13 residues processed: 109 average time/residue: 0.9688 time to fit residues: 146.5593 Evaluate side-chains 106 residues out of total 1934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 91 time to evaluate : 2.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 283 CYS Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain B residue 684 LEU Chi-restraints excluded: chain A residue 226 MET Chi-restraints excluded: chain A residue 233 ASN Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 773 CYS 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: 0.9990 chunk 46 optimal weight: 0.9990 chunk 166 optimal weight: 0.8980 chunk 69 optimal weight: 0.6980 chunk 170 optimal weight: 0.0570 chunk 21 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 145 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 overall best weight: 0.6298 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.082548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.062853 restraints weight = 151198.372| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 3.14 r_work: 0.3126 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3126 ------------------------------------------------------------------------------- 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: 11 | |-----------------------------------------------------------------------------| r_final: 0.3129 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17804 Z= 0.177 Angle : 0.498 7.659 24250 Z= 0.252 Chirality : 0.044 0.148 2666 Planarity : 0.004 0.048 3059 Dihedral : 9.457 161.243 2471 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 0.73 % Allowed : 14.88 % Favored : 84.40 % 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: -1.25 (0.19), residues: 2073 helix: 0.82 (0.31), residues: 312 sheet: -1.57 (0.21), residues: 584 loop : -0.82 (0.19), residues: 1177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 228 HIS 0.002 0.000 HIS C 406 PHE 0.010 0.001 PHE B 416 TYR 0.013 0.001 TYR B 478 ARG 0.004 0.000 ARG B 396 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7182.44 seconds wall clock time: 126 minutes 38.77 seconds (7598.77 seconds total)