Starting phenix.real_space_refine (version: dev) on Wed Dec 21 12:29:03 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dqx_27663/12_2022/8dqx_27663_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dqx_27663/12_2022/8dqx_27663.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dqx_27663/12_2022/8dqx_27663.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dqx_27663/12_2022/8dqx_27663.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dqx_27663/12_2022/8dqx_27663_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dqx_27663/12_2022/8dqx_27663_trim_updated.pdb" } resolution = 2.1 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.051 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A GLU 369": "OE1" <-> "OE2" Residue "A TYR 372": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 443": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 457": "OE1" <-> "OE2" Residue "A ASP 472": "OD1" <-> "OD2" Residue "A GLU 538": "OE1" <-> "OE2" Residue "A GLU 544": "OE1" <-> "OE2" Residue "A ASP 566": "OD1" <-> "OD2" Residue "A ASP 586": "OD1" <-> "OD2" Residue "A GLU 612": "OE1" <-> "OE2" Residue "A GLU 685": "OE1" <-> "OE2" Residue "A TYR 705": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 740": "OE1" <-> "OE2" Residue "B ASP 22": "OD1" <-> "OD2" Residue "B GLU 28": "OE1" <-> "OE2" Residue "B GLU 65": "OE1" <-> "OE2" Residue "B GLU 77": "OE1" <-> "OE2" Residue "B PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 169": "OE1" <-> "OE2" Residue "B ASP 183": "OD1" <-> "OD2" Residue "B GLU 199": "OE1" <-> "OE2" Residue "B GLU 287": "OE1" <-> "OE2" Residue "C GLU 22": "OE1" <-> "OE2" Residue "C ASP 91": "OD1" <-> "OD2" Residue "C GLU 172": "OE1" <-> "OE2" Residue "C ASP 230": "OD1" <-> "OD2" Residue "C GLU 234": "OE1" <-> "OE2" Residue "C ASP 254": "OD1" <-> "OD2" Residue "C ASP 276": "OD1" <-> "OD2" Residue "C ASP 305": "OD1" <-> "OD2" Residue "C GLU 334": "OE1" <-> "OE2" Residue "D GLU 29": "OE1" <-> "OE2" Residue "D GLU 38": "OE1" <-> "OE2" Residue "D ASP 43": "OD1" <-> "OD2" Residue "D GLU 81": "OE1" <-> "OE2" Residue "D ASP 86": "OD1" <-> "OD2" Residue "D ASP 148": "OD1" <-> "OD2" Residue "D GLU 258": "OE1" <-> "OE2" Residue "D GLU 273": "OE1" <-> "OE2" Residue "D ASP 281": "OD1" <-> "OD2" Residue "D PHE 290": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 21": "OE1" <-> "OE2" Residue "E GLU 142": "OE1" <-> "OE2" Residue "E ASP 172": "OD1" <-> "OD2" Residue "E ASP 204": "OD1" <-> "OD2" Residue "F GLU 3": "OE1" <-> "OE2" Residue "F PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 51": "OE1" <-> "OE2" Residue "F GLU 104": "OE1" <-> "OE2" Residue "F PHE 254": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 51": "OE1" <-> "OE2" Residue "G GLU 113": "OE1" <-> "OE2" Residue "G TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 165": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 43173 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 7919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 7919 Classifications: {'peptide': 497} Link IDs: {'PTRANS': 19, 'TRANS': 477} Chain: "B" Number of atoms: 5039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 5039 Classifications: {'peptide': 315} Link IDs: {'PTRANS': 9, 'TRANS': 305} Chain: "C" Number of atoms: 5254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 5254 Classifications: {'peptide': 330} Link IDs: {'PTRANS': 12, 'TRANS': 317} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 5282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 5282 Classifications: {'peptide': 332} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 319} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 5685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 5685 Classifications: {'peptide': 353} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 14, 'TRANS': 338} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "F" Number of atoms: 4046 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 4046 Classifications: {'peptide': 257} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 8, 'TRANS': 248} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "G" Number of atoms: 4039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 4039 Classifications: {'peptide': 256} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 8, 'TRANS': 247} Chain: "H" Number of atoms: 4060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 4060 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 8, 'TRANS': 249} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 191 Classifications: {'DNA': 6} Modifications used: {'3*END': 1, '5*END': 1} Link IDs: {'rna3p': 5} Chain: "J" Number of atoms: 318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 318 Classifications: {'DNA': 10} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 9} Chain: "K" Number of atoms: 318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 318 Classifications: {'DNA': 10} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 9} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 126 Classifications: {'water': 126} Link IDs: {None: 125} Chain: "B" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 150 Classifications: {'water': 150} Link IDs: {None: 149} Chain: "C" Number of atoms: 156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 156 Classifications: {'water': 156} Link IDs: {None: 155} Chain: "D" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 182 Classifications: {'water': 182} Link IDs: {None: 181} Chain: "E" Number of atoms: 170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 170 Classifications: {'water': 170} Link IDs: {None: 169} Chain: "F" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 50 Classifications: {'water': 50} Link IDs: {None: 49} Chain: "G" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "H" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "I" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "K" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Time building chain proxies: 20.25, per 1000 atoms: 0.47 Number of scatterers: 43173 At special positions: 0 Unit cell: (126.378, 120.596, 142.898, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 101 16.00 P 39 15.00 Mg 4 11.99 O 5000 8.00 N 3595 7.00 C 13291 6.00 H 21143 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: 40.03 Conformation dependent library (CDL) restraints added in 3.2 seconds 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4940 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 126 helices and 17 sheets defined 47.6% alpha, 15.1% beta 4 base pairs and 13 stacking pairs defined. Time for finding SS restraints: 19.84 Creating SS restraints... Processing helix chain 'A' and resid 293 through 295 No H-bonds generated for 'chain 'A' and resid 293 through 295' Processing helix chain 'A' and resid 298 through 301 No H-bonds generated for 'chain 'A' and resid 298 through 301' Processing helix chain 'A' and resid 307 through 309 No H-bonds generated for 'chain 'A' and resid 307 through 309' Processing helix chain 'A' and resid 314 through 325 Processing helix chain 'A' and resid 327 through 333 removed outlier: 3.616A pdb=" N ASN A 333 " --> pdb=" O ASN A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 369 Processing helix chain 'A' and resid 385 through 390 Processing helix chain 'A' and resid 392 through 395 Processing helix chain 'A' and resid 401 through 406 Processing helix chain 'A' and resid 426 through 428 No H-bonds generated for 'chain 'A' and resid 426 through 428' Processing helix chain 'A' and resid 431 through 433 No H-bonds generated for 'chain 'A' and resid 431 through 433' Processing helix chain 'A' and resid 436 through 446 Processing helix chain 'A' and resid 461 through 466 Proline residue: A 465 - end of helix Processing helix chain 'A' and resid 480 through 482 No H-bonds generated for 'chain 'A' and resid 480 through 482' Processing helix chain 'A' and resid 484 through 494 Processing helix chain 'A' and resid 500 through 509 removed outlier: 4.301A pdb=" N ASP A 504 " --> pdb=" O ASN A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 526 removed outlier: 3.740A pdb=" N THR A 526 " --> pdb=" O SER A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 542 Processing helix chain 'A' and resid 551 through 558 Processing helix chain 'A' and resid 561 through 564 Processing helix chain 'A' and resid 566 through 571 Processing helix chain 'A' and resid 574 through 583 Processing helix chain 'A' and resid 588 through 595 Processing helix chain 'A' and resid 610 through 631 Processing helix chain 'A' and resid 638 through 648 Proline residue: A 642 - end of helix removed outlier: 3.956A pdb=" N SER A 648 " --> pdb=" O ALA A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 656 Processing helix chain 'A' and resid 669 through 689 Processing helix chain 'A' and resid 698 through 703 Processing helix chain 'A' and resid 706 through 713 removed outlier: 3.636A pdb=" N LYS A 711 " --> pdb=" O PRO A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 715 through 734 removed outlier: 7.976A pdb=" N ALA A 722 " --> pdb=" O LEU A 718 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N ASP A 723 " --> pdb=" O LYS A 719 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ALA A 724 " --> pdb=" O GLN A 720 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N ILE A 725 " --> pdb=" O GLY A 721 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N SER A 726 " --> pdb=" O ALA A 722 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N SER A 727 " --> pdb=" O ASP A 723 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 748 removed outlier: 3.542A pdb=" N PHE A 748 " --> pdb=" O SER A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 751 through 753 No H-bonds generated for 'chain 'A' and resid 751 through 753' Processing helix chain 'A' and resid 756 through 760 Processing helix chain 'A' and resid 764 through 776 Processing helix chain 'B' and resid 11 through 14 No H-bonds generated for 'chain 'B' and resid 11 through 14' Processing helix chain 'B' and resid 20 through 22 No H-bonds generated for 'chain 'B' and resid 20 through 22' Processing helix chain 'B' and resid 27 through 39 Processing helix chain 'B' and resid 55 through 74 removed outlier: 7.313A pdb=" N ARG B 69 " --> pdb=" O GLU B 65 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N SER B 70 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N TYR B 71 " --> pdb=" O LEU B 67 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N ALA B 72 " --> pdb=" O GLY B 68 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N ASP B 73 " --> pdb=" O ARG B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 98 removed outlier: 4.108A pdb=" N ILE B 93 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N LYS B 94 " --> pdb=" O ARG B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 118 No H-bonds generated for 'chain 'B' and resid 116 through 118' Processing helix chain 'B' and resid 121 through 133 removed outlier: 3.517A pdb=" N LEU B 127 " --> pdb=" O ALA B 123 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ARG B 128 " --> pdb=" O GLN B 124 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N ARG B 129 " --> pdb=" O GLN B 125 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N THR B 130 " --> pdb=" O ALA B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 149 No H-bonds generated for 'chain 'B' and resid 147 through 149' Processing helix chain 'B' and resid 152 through 156 Processing helix chain 'B' and resid 168 through 182 Processing helix chain 'B' and resid 188 through 198 Processing helix chain 'B' and resid 202 through 216 Processing helix chain 'B' and resid 221 through 227 removed outlier: 3.843A pdb=" N ILE B 227 " --> pdb=" O ASN B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 241 Processing helix chain 'B' and resid 245 through 255 Processing helix chain 'B' and resid 263 through 276 removed outlier: 3.535A pdb=" N ASN B 276 " --> pdb=" O ARG B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 300 Processing helix chain 'B' and resid 306 through 319 Processing helix chain 'C' and resid 10 through 12 No H-bonds generated for 'chain 'C' and resid 10 through 12' Processing helix chain 'C' and resid 15 through 18 No H-bonds generated for 'chain 'C' and resid 15 through 18' Processing helix chain 'C' and resid 24 through 26 No H-bonds generated for 'chain 'C' and resid 24 through 26' Processing helix chain 'C' and resid 31 through 43 Processing helix chain 'C' and resid 59 through 71 Processing helix chain 'C' and resid 75 through 77 No H-bonds generated for 'chain 'C' and resid 75 through 77' Processing helix chain 'C' and resid 90 through 101 removed outlier: 3.872A pdb=" N ILE C 97 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N LYS C 98 " --> pdb=" O ARG C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 121 No H-bonds generated for 'chain 'C' and resid 119 through 121' Processing helix chain 'C' and resid 124 through 136 removed outlier: 3.600A pdb=" N ARG C 131 " --> pdb=" O GLN C 127 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N ARG C 132 " --> pdb=" O ASN C 128 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N VAL C 133 " --> pdb=" O ALA C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 152 No H-bonds generated for 'chain 'C' and resid 150 through 152' Processing helix chain 'C' and resid 155 through 159 Processing helix chain 'C' and resid 171 through 185 Processing helix chain 'C' and resid 191 through 201 Processing helix chain 'C' and resid 205 through 218 Processing helix chain 'C' and resid 229 through 236 Processing helix chain 'C' and resid 241 through 253 Processing helix chain 'C' and resid 256 through 270 removed outlier: 4.012A pdb=" N LYS C 270 " --> pdb=" O VAL C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 287 removed outlier: 4.066A pdb=" N ASP C 287 " --> pdb=" O LYS C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 312 removed outlier: 3.700A pdb=" N LYS C 312 " --> pdb=" O TYR C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 334 removed outlier: 3.826A pdb=" N ASN C 333 " --> pdb=" O ALA C 329 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N GLU C 334 " --> pdb=" O SER C 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 30 No H-bonds generated for 'chain 'D' and resid 27 through 30' Processing helix chain 'D' and resid 36 through 38 No H-bonds generated for 'chain 'D' and resid 36 through 38' Processing helix chain 'D' and resid 43 through 55 removed outlier: 4.379A pdb=" N VAL D 48 " --> pdb=" O HIS D 44 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR D 52 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LEU D 53 " --> pdb=" O LEU D 49 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N LYS D 54 " --> pdb=" O LYS D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 87 Proline residue: D 85 - end of helix Processing helix chain 'D' and resid 89 through 91 No H-bonds generated for 'chain 'D' and resid 89 through 91' Processing helix chain 'D' and resid 103 through 115 removed outlier: 4.057A pdb=" N VAL D 110 " --> pdb=" O VAL D 106 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N LYS D 111 " --> pdb=" O ARG D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 128 Processing helix chain 'D' and resid 142 through 144 No H-bonds generated for 'chain 'D' and resid 142 through 144' Processing helix chain 'D' and resid 147 through 159 removed outlier: 3.703A pdb=" N ARG D 154 " --> pdb=" O GLN D 150 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N ARG D 155 " --> pdb=" O SER D 151 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N THR D 156 " --> pdb=" O ALA D 152 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU D 158 " --> pdb=" O ARG D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 175 No H-bonds generated for 'chain 'D' and resid 173 through 175' Processing helix chain 'D' and resid 178 through 183 Processing helix chain 'D' and resid 194 through 207 removed outlier: 3.671A pdb=" N ILE D 198 " --> pdb=" O ALA D 194 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N ASP D 199 " --> pdb=" O SER D 195 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N ARG D 200 " --> pdb=" O ASN D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 224 Processing helix chain 'D' and resid 228 through 245 Processing helix chain 'D' and resid 253 through 259 Processing helix chain 'D' and resid 265 through 277 Processing helix chain 'D' and resid 280 through 293 removed outlier: 3.787A pdb=" N LYS D 292 " --> pdb=" O ASN D 288 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N SER D 293 " --> pdb=" O THR D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 309 Processing helix chain 'D' and resid 316 through 335 removed outlier: 3.574A pdb=" N ASN D 335 " --> pdb=" O SER D 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 339 through 351 Processing helix chain 'E' and resid 4 through 7 No H-bonds generated for 'chain 'E' and resid 4 through 7' Processing helix chain 'E' and resid 20 through 31 Processing helix chain 'E' and resid 49 through 61 Processing helix chain 'E' and resid 63 through 66 Processing helix chain 'E' and resid 98 through 118 removed outlier: 6.891A pdb=" N ASN E 103 " --> pdb=" O ASP E 100 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ARG E 106 " --> pdb=" O ASN E 103 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLU E 111 " --> pdb=" O VAL E 108 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N LEU E 112 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N LEU E 113 " --> pdb=" O GLN E 110 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS E 114 " --> pdb=" O GLU E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 145 No H-bonds generated for 'chain 'E' and resid 143 through 145' Processing helix chain 'E' and resid 148 through 160 removed outlier: 3.679A pdb=" N ARG E 155 " --> pdb=" O GLN E 151 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ARG E 156 " --> pdb=" O ALA E 152 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N THR E 157 " --> pdb=" O ALA E 153 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU E 159 " --> pdb=" O ARG E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 184 Processing helix chain 'E' and resid 195 through 208 Processing helix chain 'E' and resid 216 through 225 Processing helix chain 'E' and resid 230 through 243 Processing helix chain 'E' and resid 258 through 272 Processing helix chain 'E' and resid 276 through 292 Processing helix chain 'E' and resid 296 through 309 removed outlier: 3.507A pdb=" N ASP E 309 " --> pdb=" O PHE E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 315 through 334 Processing helix chain 'E' and resid 338 through 352 Processing helix chain 'F' and resid 10 through 18 Processing helix chain 'F' and resid 20 through 22 No H-bonds generated for 'chain 'F' and resid 20 through 22' Processing helix chain 'F' and resid 54 through 56 No H-bonds generated for 'chain 'F' and resid 54 through 56' Processing helix chain 'F' and resid 72 through 81 Processing helix chain 'F' and resid 141 through 153 removed outlier: 3.692A pdb=" N GLN F 153 " --> pdb=" O ARG F 149 " (cutoff:3.500A) Processing helix chain 'F' and resid 191 through 193 No H-bonds generated for 'chain 'F' and resid 191 through 193' Processing helix chain 'F' and resid 209 through 221 removed outlier: 4.108A pdb=" N LYS F 217 " --> pdb=" O LEU F 213 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N GLY F 218 " --> pdb=" O ASP F 214 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N SER F 219 " --> pdb=" O ILE F 215 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N SER F 220 " --> pdb=" O ILE F 216 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N LEU F 221 " --> pdb=" O LYS F 217 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 19 removed outlier: 3.898A pdb=" N PHE G 19 " --> pdb=" O ILE G 15 " (cutoff:3.500A) Processing helix chain 'G' and resid 54 through 56 No H-bonds generated for 'chain 'G' and resid 54 through 56' Processing helix chain 'G' and resid 72 through 81 Processing helix chain 'G' and resid 141 through 152 Processing helix chain 'G' and resid 191 through 193 No H-bonds generated for 'chain 'G' and resid 191 through 193' Processing helix chain 'G' and resid 209 through 221 removed outlier: 3.742A pdb=" N LYS G 217 " --> pdb=" O LEU G 213 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N GLY G 218 " --> pdb=" O ASP G 214 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N SER G 219 " --> pdb=" O ILE G 215 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N SER G 220 " --> pdb=" O ILE G 216 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N LEU G 221 " --> pdb=" O LYS G 217 " (cutoff:3.500A) Processing helix chain 'H' and resid 9 through 19 removed outlier: 3.793A pdb=" N PHE H 19 " --> pdb=" O ILE H 15 " (cutoff:3.500A) Processing helix chain 'H' and resid 72 through 81 Processing helix chain 'H' and resid 141 through 152 Processing helix chain 'H' and resid 191 through 193 No H-bonds generated for 'chain 'H' and resid 191 through 193' Processing helix chain 'H' and resid 209 through 221 removed outlier: 3.949A pdb=" N LYS H 217 " --> pdb=" O LEU H 213 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N GLY H 218 " --> pdb=" O ASP H 214 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N SER H 219 " --> pdb=" O ILE H 215 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N SER H 220 " --> pdb=" O ILE H 216 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N LEU H 221 " --> pdb=" O LYS H 217 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 471 through 474 removed outlier: 6.532A pdb=" N LEU A 451 " --> pdb=" O ALA A 349 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N LEU A 351 " --> pdb=" O LEU A 451 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N LEU A 453 " --> pdb=" O LEU A 351 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ASP A 373 " --> pdb=" O VAL A 420 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N ILE A 422 " --> pdb=" O ASP A 373 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N LEU A 375 " --> pdb=" O ILE A 422 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 599 through 601 Processing sheet with id= C, first strand: chain 'B' and resid 159 through 162 removed outlier: 6.382A pdb=" N LYS B 109 " --> pdb=" O ARG B 139 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N ALA B 141 " --> pdb=" O LYS B 109 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N VAL B 111 " --> pdb=" O ALA B 141 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N ALA B 143 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N LEU B 113 " --> pdb=" O ALA B 143 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 162 through 166 removed outlier: 6.569A pdb=" N LYS C 112 " --> pdb=" O ARG C 142 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N CYS C 144 " --> pdb=" O LYS C 112 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ILE C 114 " --> pdb=" O CYS C 144 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N LEU C 146 " --> pdb=" O ILE C 114 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N LEU C 116 " --> pdb=" O LEU C 146 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 185 through 189 removed outlier: 6.356A pdb=" N LYS D 135 " --> pdb=" O ARG D 165 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N CYS D 167 " --> pdb=" O LYS D 135 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ILE D 137 " --> pdb=" O CYS D 167 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N ILE D 169 " --> pdb=" O ILE D 137 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N LEU D 139 " --> pdb=" O ILE D 169 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'E' and resid 186 through 189 removed outlier: 6.325A pdb=" N LYS E 136 " --> pdb=" O ARG E 166 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N ILE E 168 " --> pdb=" O LYS E 136 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N VAL E 138 " --> pdb=" O ILE E 168 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N VAL E 170 " --> pdb=" O VAL E 138 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILE E 140 " --> pdb=" O VAL E 170 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'E' and resid 69 through 76 Processing sheet with id= H, first strand: chain 'F' and resid 59 through 62 removed outlier: 3.719A pdb=" N GLU F 59 " --> pdb=" O LYS F 5 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'F' and resid 66 through 71 removed outlier: 5.582A pdb=" N LEU F 25 " --> pdb=" O VAL F 40 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N VAL F 40 " --> pdb=" O LEU F 25 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ASP F 240 " --> pdb=" O ARG F 224 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ARG F 224 " --> pdb=" O ASP F 240 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'F' and resid 203 through 208 removed outlier: 6.119A pdb=" N SER F 157 " --> pdb=" O ASP F 172 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N ASP F 172 " --> pdb=" O SER F 157 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'G' and resid 59 through 62 removed outlier: 3.557A pdb=" N GLU G 59 " --> pdb=" O LYS G 5 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'G' and resid 66 through 71 removed outlier: 5.615A pdb=" N LEU G 25 " --> pdb=" O VAL G 40 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N VAL G 40 " --> pdb=" O LEU G 25 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N ASP G 240 " --> pdb=" O ARG G 224 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ARG G 224 " --> pdb=" O ASP G 240 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 203 through 208 removed outlier: 5.912A pdb=" N SER G 157 " --> pdb=" O ASP G 172 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N ASP G 172 " --> pdb=" O SER G 157 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'H' and resid 59 through 61 removed outlier: 3.782A pdb=" N GLU H 104 " --> pdb=" O THR H 87 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA H 112 " --> pdb=" O PHE H 103 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'H' and resid 25 through 30 Processing sheet with id= P, first strand: chain 'H' and resid 37 through 40 removed outlier: 4.552A pdb=" N ASP H 240 " --> pdb=" O ARG H 224 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ARG H 224 " --> pdb=" O ASP H 240 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'H' and resid 203 through 208 removed outlier: 5.825A pdb=" N SER H 157 " --> pdb=" O ASP H 172 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N ASP H 172 " --> pdb=" O SER H 157 " (cutoff:3.500A) 980 hydrogen bonds defined for protein. 2727 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 11 hydrogen bonds 22 hydrogen bond angles 0 basepair planarities 4 basepair parallelities 13 stacking parallelities Total time for adding SS restraints: 18.71 Time building geometry restraints manager: 39.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.06: 21104 1.06 - 1.27: 3584 1.27 - 1.49: 8513 1.49 - 1.71: 9341 1.71 - 1.92: 159 Bond restraints: 42701 Sorted by residual: bond pdb=" C2' AGS B 402 " pdb=" C3' AGS B 402 " ideal model delta sigma weight residual 1.530 1.241 0.289 1.30e-02 5.92e+03 4.94e+02 bond pdb=" C2' AGS A 901 " pdb=" C3' AGS A 901 " ideal model delta sigma weight residual 1.530 1.241 0.289 1.30e-02 5.92e+03 4.93e+02 bond pdb=" C2' AGS D 402 " pdb=" C3' AGS D 402 " ideal model delta sigma weight residual 1.530 1.245 0.285 1.30e-02 5.92e+03 4.81e+02 bond pdb=" C2' AGS C 402 " pdb=" C3' AGS C 402 " ideal model delta sigma weight residual 1.530 1.245 0.285 1.30e-02 5.92e+03 4.79e+02 bond pdb=" C6 AGS D 402 " pdb=" N6 AGS D 402 " ideal model delta sigma weight residual 1.335 1.466 -0.131 1.00e-02 1.00e+04 1.73e+02 ... (remaining 42696 not shown) Histogram of bond angle deviations from ideal: 99.10 - 106.08: 497 106.08 - 113.06: 51456 113.06 - 120.04: 12474 120.04 - 127.02: 12819 127.02 - 134.00: 232 Bond angle restraints: 77478 Sorted by residual: angle pdb=" C5 AGS C 402 " pdb=" C4 AGS C 402 " pdb=" N3 AGS C 402 " ideal model delta sigma weight residual 126.80 119.06 7.74 7.41e-01 1.82e+00 1.09e+02 angle pdb=" C5 AGS B 402 " pdb=" N7 AGS B 402 " pdb=" C8 AGS B 402 " ideal model delta sigma weight residual 103.67 108.12 -4.45 4.26e-01 5.51e+00 1.09e+02 angle pdb=" N1 AGS B 402 " pdb=" C2 AGS B 402 " pdb=" N3 AGS B 402 " ideal model delta sigma weight residual 128.80 120.09 8.71 8.41e-01 1.41e+00 1.07e+02 angle pdb=" C5 AGS A 901 " pdb=" N7 AGS A 901 " pdb=" C8 AGS A 901 " ideal model delta sigma weight residual 103.67 108.04 -4.37 4.26e-01 5.51e+00 1.05e+02 angle pdb=" C5 AGS D 402 " pdb=" N7 AGS D 402 " pdb=" C8 AGS D 402 " ideal model delta sigma weight residual 103.67 108.03 -4.36 4.26e-01 5.51e+00 1.05e+02 ... (remaining 77473 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.27: 15991 26.27 - 52.54: 802 52.54 - 78.82: 132 78.82 - 105.09: 24 105.09 - 131.36: 3 Dihedral angle restraints: 16952 sinusoidal: 8342 harmonic: 8610 Sorted by residual: dihedral pdb=" C5' GDP E 401 " pdb=" O5' GDP E 401 " pdb=" PA GDP E 401 " pdb=" O3A GDP E 401 " ideal model delta sinusoidal sigma weight residual 179.98 -76.01 -104.01 1 2.00e+01 2.50e-03 2.98e+01 dihedral pdb=" CA PHE A 419 " pdb=" C PHE A 419 " pdb=" N VAL A 420 " pdb=" CA VAL A 420 " ideal model delta harmonic sigma weight residual 180.00 154.93 25.07 0 5.00e+00 4.00e-02 2.51e+01 dihedral pdb=" CA GLN D 25 " pdb=" C GLN D 25 " pdb=" N PRO D 26 " pdb=" CA PRO D 26 " ideal model delta harmonic sigma weight residual 180.00 158.10 21.90 0 5.00e+00 4.00e-02 1.92e+01 ... (remaining 16949 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 2942 0.060 - 0.120: 404 0.120 - 0.179: 50 0.179 - 0.239: 5 0.239 - 0.299: 4 Chirality restraints: 3405 Sorted by residual: chirality pdb=" C2' AGS B 402 " pdb=" C1' AGS B 402 " pdb=" C3' AGS B 402 " pdb=" O2' AGS B 402 " both_signs ideal model delta sigma weight residual False -2.67 -2.38 -0.30 2.00e-01 2.50e+01 2.23e+00 chirality pdb=" C2' AGS A 901 " pdb=" C1' AGS A 901 " pdb=" C3' AGS A 901 " pdb=" O2' AGS A 901 " both_signs ideal model delta sigma weight residual False -2.67 -2.38 -0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" C2' AGS D 402 " pdb=" C1' AGS D 402 " pdb=" C3' AGS D 402 " pdb=" O2' AGS D 402 " both_signs ideal model delta sigma weight residual False -2.67 -2.40 -0.28 2.00e-01 2.50e+01 1.94e+00 ... (remaining 3402 not shown) Planarity restraints: 6144 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG G 61 " -0.198 9.50e-02 1.11e+02 6.62e-02 5.31e+00 pdb=" NE ARG G 61 " 0.015 2.00e-02 2.50e+03 pdb=" CZ ARG G 61 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG G 61 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG G 61 " 0.000 2.00e-02 2.50e+03 pdb="HH11 ARG G 61 " 0.006 2.00e-02 2.50e+03 pdb="HH12 ARG G 61 " 0.000 2.00e-02 2.50e+03 pdb="HH21 ARG G 61 " -0.001 2.00e-02 2.50e+03 pdb="HH22 ARG G 61 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN C 95 " -0.009 2.00e-02 2.50e+03 1.85e-02 3.42e+00 pdb=" C ASN C 95 " 0.032 2.00e-02 2.50e+03 pdb=" O ASN C 95 " -0.012 2.00e-02 2.50e+03 pdb=" N GLN C 96 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC K 5 " 0.019 2.00e-02 2.50e+03 9.66e-03 2.57e+00 pdb=" N1 DC K 5 " -0.024 2.00e-02 2.50e+03 pdb=" C2 DC K 5 " 0.001 2.00e-02 2.50e+03 pdb=" O2 DC K 5 " -0.002 2.00e-02 2.50e+03 pdb=" N3 DC K 5 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DC K 5 " -0.002 2.00e-02 2.50e+03 pdb=" N4 DC K 5 " 0.006 2.00e-02 2.50e+03 pdb=" C5 DC K 5 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DC K 5 " -0.002 2.00e-02 2.50e+03 pdb=" H5 DC K 5 " 0.003 2.00e-02 2.50e+03 pdb=" H6 DC K 5 " -0.001 2.00e-02 2.50e+03 ... (remaining 6141 not shown) Histogram of nonbonded interaction distances: 1.46 - 2.09: 912 2.09 - 2.71: 71864 2.71 - 3.34: 130541 3.34 - 3.97: 171700 3.97 - 4.60: 264636 Nonbonded interactions: 639653 Sorted by model distance: nonbonded pdb=" OE1 GLU B 169 " pdb=" H GLU B 169 " model vdw 1.457 1.850 nonbonded pdb=" OE1 GLU F 55 " pdb=" H GLU F 55 " model vdw 1.490 1.850 nonbonded pdb="HH12 ARG C 267 " pdb=" OD2 ASP C 316 " model vdw 1.528 1.850 nonbonded pdb=" OE1 GLU G 8 " pdb=" H GLU G 8 " model vdw 1.528 1.850 nonbonded pdb=" HZ3 LYS B 100 " pdb=" OD1 ASP G 120 " model vdw 1.584 1.850 ... (remaining 639648 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 'F' and resid 1 through 255) selection = (chain 'G' and resid 1 through 255) selection = (chain 'H' and resid 1 through 255) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 39 5.49 5 Mg 4 5.21 5 S 101 5.16 5 C 13291 2.51 5 N 3595 2.21 5 O 5000 1.98 5 H 21143 0.53 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.270 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: 0.730 Extract box with map and model: 16.180 Check model and map are aligned: 0.630 Convert atoms to be neutral: 0.360 Process input model: 154.020 Find NCS groups from input model: 1.320 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Set scattering table: 0.020 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:13.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 189.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 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 : 0.008 0.289 21558 Z= 0.505 Angle : 0.681 9.127 29260 Z= 0.439 Chirality : 0.043 0.299 3405 Planarity : 0.004 0.087 3628 Dihedral : 17.172 131.359 8181 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer Outliers : 1.26 % 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: 1.11 (0.16), residues: 2582 helix: 1.13 (0.15), residues: 1204 sheet: 0.64 (0.21), residues: 536 loop : 0.45 (0.23), residues: 842 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 360 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Evaluate side-chains 342 residues out of total 2309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 313 time to evaluate : 3.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 8 residues processed: 337 average time/residue: 3.3101 time to fit residues: 1256.4079 Evaluate side-chains 185 residues out of total 2309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 177 time to evaluate : 3.539 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 8 residues processed: 0 time to fit residues: 4.2731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 217 optimal weight: 2.9990 chunk 195 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 202 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 150 optimal weight: 0.6980 chunk 234 optimal weight: 6.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 398 ASN ** A 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 60 HIS E 32 GLN F 255 ASN G 24 GLN G 84 ASN H 58 GLN ** H 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 21558 Z= 0.264 Angle : 0.556 6.875 29260 Z= 0.293 Chirality : 0.041 0.144 3405 Planarity : 0.003 0.052 3628 Dihedral : 11.715 141.291 3077 Min Nonbonded Distance : 1.737 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer Outliers : 1.78 % 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 (0.17), residues: 2582 helix: 1.43 (0.15), residues: 1209 sheet: 0.82 (0.22), residues: 540 loop : 0.60 (0.23), residues: 833 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 360 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Evaluate side-chains 225 residues out of total 2309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 184 time to evaluate : 3.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 14 residues processed: 220 average time/residue: 3.2413 time to fit residues: 811.6961 Evaluate side-chains 181 residues out of total 2309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 167 time to evaluate : 3.463 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 14 residues processed: 0 time to fit residues: 4.3789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 130 optimal weight: 0.5980 chunk 72 optimal weight: 1.9990 chunk 194 optimal weight: 4.9990 chunk 159 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 chunk 234 optimal weight: 5.9990 chunk 253 optimal weight: 4.9990 chunk 209 optimal weight: 4.9990 chunk 232 optimal weight: 6.9990 chunk 80 optimal weight: 1.9990 chunk 188 optimal weight: 0.6980 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 398 ASN ** A 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 255 ASN G 24 GLN G 84 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 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 0.026 21558 Z= 0.194 Angle : 0.504 6.226 29260 Z= 0.265 Chirality : 0.039 0.143 3405 Planarity : 0.003 0.042 3628 Dihedral : 11.547 134.823 3077 Min Nonbonded Distance : 1.750 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer Outliers : 1.35 % 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: 1.67 (0.17), residues: 2582 helix: 1.65 (0.15), residues: 1210 sheet: 0.89 (0.22), residues: 545 loop : 0.63 (0.24), residues: 827 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 360 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Evaluate side-chains 208 residues out of total 2309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 177 time to evaluate : 3.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 20 residues processed: 203 average time/residue: 3.1407 time to fit residues: 723.5580 Evaluate side-chains 187 residues out of total 2309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 167 time to evaluate : 3.539 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 17 residues processed: 3 average time/residue: 1.7255 time to fit residues: 10.6985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 231 optimal weight: 10.0000 chunk 176 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 112 optimal weight: 1.9990 chunk 157 optimal weight: 2.9990 chunk 235 optimal weight: 3.9990 chunk 249 optimal weight: 4.9990 chunk 123 optimal weight: 3.9990 chunk 223 optimal weight: 8.9990 chunk 67 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 313 ASN A 398 ASN ** A 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 ASN E 32 GLN F 255 ASN G 24 GLN G 84 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.046 21558 Z= 0.364 Angle : 0.555 6.352 29260 Z= 0.294 Chirality : 0.042 0.167 3405 Planarity : 0.004 0.038 3628 Dihedral : 11.574 132.907 3077 Min Nonbonded Distance : 1.655 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer Outliers : 1.56 % 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: 1.53 (0.17), residues: 2582 helix: 1.53 (0.15), residues: 1205 sheet: 0.89 (0.22), residues: 542 loop : 0.51 (0.23), residues: 835 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 360 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Evaluate side-chains 210 residues out of total 2309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 174 time to evaluate : 3.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 18 residues processed: 205 average time/residue: 3.2516 time to fit residues: 758.5061 Evaluate side-chains 188 residues out of total 2309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 170 time to evaluate : 3.799 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 16 residues processed: 2 average time/residue: 0.6002 time to fit residues: 6.6103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 207 optimal weight: 2.9990 chunk 141 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 185 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 212 optimal weight: 0.2980 chunk 172 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 223 optimal weight: 8.9990 chunk 62 optimal weight: 0.7980 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 398 ASN A 408 ASN ** A 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 255 ASN G 24 GLN G 84 ASN H 58 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 21558 Z= 0.206 Angle : 0.501 6.510 29260 Z= 0.265 Chirality : 0.039 0.143 3405 Planarity : 0.003 0.035 3628 Dihedral : 11.499 130.989 3077 Min Nonbonded Distance : 1.715 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer Outliers : 1.30 % 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: 1.67 (0.17), residues: 2582 helix: 1.68 (0.15), residues: 1200 sheet: 0.93 (0.22), residues: 542 loop : 0.55 (0.23), residues: 840 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 360 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Evaluate side-chains 207 residues out of total 2309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 177 time to evaluate : 4.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 21 residues processed: 203 average time/residue: 3.0825 time to fit residues: 714.5110 Evaluate side-chains 190 residues out of total 2309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 169 time to evaluate : 3.540 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 19 residues processed: 2 average time/residue: 0.6052 time to fit residues: 6.4504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 83 optimal weight: 1.9990 chunk 224 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 146 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 249 optimal weight: 1.9990 chunk 207 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 131 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 398 ASN ** A 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 GLN E 32 GLN G 24 GLN H 58 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.029 21558 Z= 0.259 Angle : 0.506 6.138 29260 Z= 0.267 Chirality : 0.040 0.143 3405 Planarity : 0.003 0.037 3628 Dihedral : 11.476 130.849 3077 Min Nonbonded Distance : 1.697 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer Outliers : 1.30 % 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: 1.68 (0.17), residues: 2582 helix: 1.70 (0.15), residues: 1200 sheet: 0.94 (0.22), residues: 542 loop : 0.54 (0.23), residues: 840 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 360 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Evaluate side-chains 203 residues out of total 2309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 173 time to evaluate : 3.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 22 residues processed: 199 average time/residue: 3.1796 time to fit residues: 726.3168 Evaluate side-chains 190 residues out of total 2309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 168 time to evaluate : 3.759 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 19 residues processed: 3 average time/residue: 1.0498 time to fit residues: 9.1041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 240 optimal weight: 0.0570 chunk 28 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 chunk 182 optimal weight: 3.9990 chunk 141 optimal weight: 1.9990 chunk 210 optimal weight: 0.3980 chunk 139 optimal weight: 1.9990 chunk 248 optimal weight: 3.9990 chunk 155 optimal weight: 1.9990 chunk 151 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 overall best weight: 1.2904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 398 ASN A 408 ASN ** A 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 GLN H 58 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 21558 Z= 0.194 Angle : 0.490 8.194 29260 Z= 0.258 Chirality : 0.039 0.143 3405 Planarity : 0.003 0.060 3628 Dihedral : 11.437 130.307 3077 Min Nonbonded Distance : 1.725 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer Outliers : 1.26 % 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: 1.77 (0.17), residues: 2582 helix: 1.80 (0.15), residues: 1200 sheet: 0.95 (0.22), residues: 542 loop : 0.56 (0.23), residues: 840 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 360 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Evaluate side-chains 198 residues out of total 2309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 169 time to evaluate : 3.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 21 residues processed: 193 average time/residue: 3.1688 time to fit residues: 696.2038 Evaluate side-chains 184 residues out of total 2309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 163 time to evaluate : 3.422 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 19 residues processed: 2 average time/residue: 1.3875 time to fit residues: 8.3920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 153 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 148 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 158 optimal weight: 4.9990 chunk 169 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 195 optimal weight: 1.9990 chunk 226 optimal weight: 4.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 398 ASN ** A 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 GLN H 58 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.036 21558 Z= 0.308 Angle : 0.523 7.489 29260 Z= 0.275 Chirality : 0.041 0.149 3405 Planarity : 0.003 0.058 3628 Dihedral : 11.459 131.475 3077 Min Nonbonded Distance : 1.668 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer Outliers : 1.26 % 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: 1.67 (0.17), residues: 2582 helix: 1.71 (0.15), residues: 1200 sheet: 0.92 (0.22), residues: 541 loop : 0.52 (0.23), residues: 841 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 360 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Evaluate side-chains 195 residues out of total 2309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 166 time to evaluate : 4.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 23 residues processed: 191 average time/residue: 3.1172 time to fit residues: 680.8162 Evaluate side-chains 186 residues out of total 2309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 163 time to evaluate : 3.451 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 20 residues processed: 3 average time/residue: 1.0964 time to fit residues: 8.8770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 238 optimal weight: 7.9990 chunk 217 optimal weight: 2.9990 chunk 231 optimal weight: 9.9990 chunk 139 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 181 optimal weight: 3.9990 chunk 71 optimal weight: 0.6980 chunk 209 optimal weight: 0.9990 chunk 219 optimal weight: 8.9990 chunk 230 optimal weight: 0.9990 chunk 152 optimal weight: 1.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 398 ASN A 408 ASN ** A 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 GLN H 58 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 21558 Z= 0.202 Angle : 0.499 7.951 29260 Z= 0.261 Chirality : 0.039 0.144 3405 Planarity : 0.003 0.059 3628 Dihedral : 11.394 130.458 3077 Min Nonbonded Distance : 1.716 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer Outliers : 1.09 % 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: 1.78 (0.17), residues: 2582 helix: 1.82 (0.15), residues: 1200 sheet: 0.90 (0.22), residues: 543 loop : 0.60 (0.23), residues: 839 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 360 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Evaluate side-chains 198 residues out of total 2309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 173 time to evaluate : 3.652 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 outliers start: 25 outliers final: 21 residues processed: 195 average time/residue: 3.2501 time to fit residues: 729.6195 Evaluate side-chains 186 residues out of total 2309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 165 time to evaluate : 3.550 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 20 residues processed: 1 average time/residue: 0.6799 time to fit residues: 5.5238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 245 optimal weight: 0.4980 chunk 149 optimal weight: 2.9990 chunk 116 optimal weight: 0.7980 chunk 170 optimal weight: 1.9990 chunk 257 optimal weight: 4.9990 chunk 236 optimal weight: 8.9990 chunk 204 optimal weight: 2.9990 chunk 21 optimal weight: 0.3980 chunk 158 optimal weight: 3.9990 chunk 125 optimal weight: 3.9990 chunk 162 optimal weight: 0.4980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 398 ASN A 408 ASN ** A 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 84 ASN G 24 GLN H 58 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 21558 Z= 0.152 Angle : 0.481 8.992 29260 Z= 0.251 Chirality : 0.039 0.142 3405 Planarity : 0.003 0.056 3628 Dihedral : 11.298 129.782 3077 Min Nonbonded Distance : 1.775 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer Outliers : 1.13 % 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: 1.94 (0.17), residues: 2582 helix: 1.96 (0.15), residues: 1205 sheet: 1.00 (0.22), residues: 542 loop : 0.64 (0.24), residues: 835 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 360 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Evaluate side-chains 201 residues out of total 2309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 175 time to evaluate : 3.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 21 residues processed: 196 average time/residue: 3.3079 time to fit residues: 738.7324 Evaluate side-chains 190 residues out of total 2309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 169 time to evaluate : 3.887 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 19 residues processed: 2 average time/residue: 1.2973 time to fit residues: 8.0273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 218 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 188 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 205 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 210 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 179 optimal weight: 2.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 398 ASN A 408 ASN ** A 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 GLN H 58 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.080923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2598 r_free = 0.2598 target = 0.053042 restraints weight = 96730.107| |-----------------------------------------------------------------------------| r_work (start): 0.2551 rms_B_bonded: 2.23 r_work: 0.2418 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2290 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8884 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.029 21558 Z= 0.256 Angle : 0.514 8.902 29260 Z= 0.267 Chirality : 0.040 0.142 3405 Planarity : 0.003 0.055 3628 Dihedral : 11.331 130.834 3077 Min Nonbonded Distance : 1.713 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer Outliers : 1.04 % 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: 1.86 (0.17), residues: 2582 helix: 1.88 (0.15), residues: 1204 sheet: 1.00 (0.22), residues: 537 loop : 0.57 (0.23), residues: 841 =============================================================================== Job complete usr+sys time: 14570.28 seconds wall clock time: 254 minutes 31.98 seconds (15271.98 seconds total)