Starting phenix.real_space_refine on Fri Sep 27 06:02:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mjq_23882/09_2024/7mjq_23882_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mjq_23882/09_2024/7mjq_23882.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mjq_23882/09_2024/7mjq_23882.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mjq_23882/09_2024/7mjq_23882.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mjq_23882/09_2024/7mjq_23882_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mjq_23882/09_2024/7mjq_23882_neut.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 1.000 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: 5 Type Number sf(0) Gaussians K 1 8.98 5 P 15 5.49 5 C 8878 2.51 5 N 3013 2.21 5 O 3069 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 14976 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 1714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 1714 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 302} Link IDs: {'PTRANS': 11, 'TRANS': 334} Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 1074 Unresolved non-hydrogen angles: 1381 Unresolved non-hydrogen dihedrals: 882 Unresolved non-hydrogen chiralities: 122 Planarities with less than four sites: {'GLN:plan1': 12, 'ASP:plan': 13, 'TYR:plan': 6, 'ASN:plan1': 11, 'TRP:plan': 5, 'HIS:plan': 8, 'PHE:plan': 18, 'GLU:plan': 21, 'ARG:plan': 23} Unresolved non-hydrogen planarities: 554 Chain: "B" Number of atoms: 1667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 1667 Classifications: {'peptide': 337} Incomplete info: {'truncation_to_alanine': 294} Link IDs: {'PTRANS': 10, 'TRANS': 326} Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 1040 Unresolved non-hydrogen angles: 1340 Unresolved non-hydrogen dihedrals: 855 Unresolved non-hydrogen chiralities: 120 Planarities with less than four sites: {'GLN:plan1': 11, 'ASP:plan': 12, 'TYR:plan': 6, 'ASN:plan1': 11, 'TRP:plan': 5, 'HIS:plan': 8, 'PHE:plan': 18, 'GLU:plan': 21, 'ARG:plan': 20} Unresolved non-hydrogen planarities: 532 Chain: "C" Number of atoms: 1674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 1674 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 294} Link IDs: {'PTRANS': 10, 'TRANS': 327} Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 1041 Unresolved non-hydrogen angles: 1341 Unresolved non-hydrogen dihedrals: 855 Unresolved non-hydrogen chiralities: 120 Planarities with less than four sites: {'GLN:plan1': 12, 'ASP:plan': 12, 'TYR:plan': 6, 'ASN:plan1': 11, 'TRP:plan': 5, 'HIS:plan': 8, 'PHE:plan': 18, 'GLU:plan': 21, 'ARG:plan': 20} Unresolved non-hydrogen planarities: 536 Chain: "D" Number of atoms: 1667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 1667 Classifications: {'peptide': 337} Incomplete info: {'truncation_to_alanine': 294} Link IDs: {'PTRANS': 10, 'TRANS': 326} Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 1040 Unresolved non-hydrogen angles: 1340 Unresolved non-hydrogen dihedrals: 855 Unresolved non-hydrogen chiralities: 120 Planarities with less than four sites: {'GLN:plan1': 11, 'ASP:plan': 12, 'TYR:plan': 6, 'ASN:plan1': 11, 'TRP:plan': 5, 'HIS:plan': 8, 'PHE:plan': 18, 'GLU:plan': 21, 'ARG:plan': 20} Unresolved non-hydrogen planarities: 532 Chain: "E" Number of atoms: 7060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1426, 7060 Classifications: {'peptide': 1426} Incomplete info: {'truncation_to_alanine': 1237} Link IDs: {'PTRANS': 44, 'TRANS': 1381} Chain breaks: 6 Unresolved chain link angles: 41 Unresolved non-hydrogen bonds: 4489 Unresolved non-hydrogen angles: 5807 Unresolved non-hydrogen dihedrals: 3756 Unresolved non-hydrogen chiralities: 493 Planarities with less than four sites: {'GLN:plan1': 47, 'ARG:plan': 61, 'TYR:plan': 44, 'ASN:plan1': 66, 'TRP:plan': 28, 'ASP:plan': 56, 'PHE:plan': 75, 'GLU:plan': 66, 'HIS:plan': 33} Unresolved non-hydrogen planarities: 2298 Chain: "G" Number of atoms: 982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 982 Classifications: {'peptide': 198} Incomplete info: {'truncation_to_alanine': 177} Link IDs: {'PTRANS': 6, 'TRANS': 191} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 684 Unresolved non-hydrogen angles: 896 Unresolved non-hydrogen dihedrals: 595 Unresolved non-hydrogen chiralities: 71 Planarities with less than four sites: {'GLN:plan1': 5, 'ARG:plan': 7, 'TYR:plan': 7, 'ASN:plan1': 11, 'TRP:plan': 6, 'ASP:plan': 3, 'PHE:plan': 17, 'GLU:plan': 4, 'HIS:plan': 10} Unresolved non-hydrogen planarities: 368 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' K': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.92, per 1000 atoms: 0.66 Number of scatterers: 14976 At special positions: 0 Unit cell: (110.751, 153.729, 153.729, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) K 1 19.00 P 15 15.00 O 3069 8.00 N 3013 7.00 C 8878 6.00 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 - 3.00 Amino acid : True - 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=3, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG N 1 " - " NAG N 2 " NAG-ASN " NAG F 1 " - " ASN G 9 " " NAG N 1 " - " ASN E 9 " Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.77 Conformation dependent library (CDL) restraints added in 2.8 seconds 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5640 Finding SS restraints... Secondary structure from input PDB file: 91 helices and 19 sheets defined 49.7% alpha, 7.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.85 Creating SS restraints... Processing helix chain 'A' and resid 23 through 29 Processing helix chain 'A' and resid 57 through 66 removed outlier: 4.186A pdb=" N PHE A 61 " --> pdb=" O LEU A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 98 Processing helix chain 'A' and resid 100 through 106 Processing helix chain 'A' and resid 126 through 139 Processing helix chain 'A' and resid 152 through 183 Processing helix chain 'A' and resid 281 through 288 removed outlier: 3.597A pdb=" N LEU A 285 " --> pdb=" O ALA A 282 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL A 286 " --> pdb=" O THR A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 318 Processing helix chain 'A' and resid 353 through 358 removed outlier: 4.142A pdb=" N GLU A 357 " --> pdb=" O CYS A 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 66 Processing helix chain 'B' and resid 68 through 98 removed outlier: 4.712A pdb=" N VAL B 74 " --> pdb=" O ARG B 70 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N THR B 77 " --> pdb=" O LEU B 73 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N HIS B 98 " --> pdb=" O VAL B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 106 removed outlier: 4.238A pdb=" N GLU B 106 " --> pdb=" O TYR B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 138 Processing helix chain 'B' and resid 152 through 184 Processing helix chain 'B' and resid 281 through 286 removed outlier: 4.382A pdb=" N VAL B 286 " --> pdb=" O ALA B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 316 No H-bonds generated for 'chain 'B' and resid 314 through 316' Processing helix chain 'B' and resid 355 through 361 Processing helix chain 'C' and resid 57 through 66 removed outlier: 3.954A pdb=" N PHE C 61 " --> pdb=" O LEU C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 94 removed outlier: 3.900A pdb=" N LEU C 73 " --> pdb=" O TRP C 69 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N VAL C 74 " --> pdb=" O ARG C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 107 removed outlier: 3.527A pdb=" N LYS C 107 " --> pdb=" O ALA C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 118 removed outlier: 3.744A pdb=" N GLU C 116 " --> pdb=" O LYS C 112 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA C 118 " --> pdb=" O GLY C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 127 through 139 Processing helix chain 'C' and resid 152 through 182 removed outlier: 3.852A pdb=" N ILE C 156 " --> pdb=" O CYS C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 280 removed outlier: 4.291A pdb=" N ASP C 279 " --> pdb=" O PRO C 276 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE C 280 " --> pdb=" O LEU C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 316 No H-bonds generated for 'chain 'C' and resid 314 through 316' Processing helix chain 'C' and resid 354 through 360 Processing helix chain 'D' and resid 58 through 66 removed outlier: 3.872A pdb=" N ASP D 66 " --> pdb=" O THR D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 73 Processing helix chain 'D' and resid 74 through 98 removed outlier: 3.666A pdb=" N LEU D 93 " --> pdb=" O ILE D 89 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N HIS D 98 " --> pdb=" O VAL D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 107 removed outlier: 3.707A pdb=" N ALA D 103 " --> pdb=" O GLY D 99 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N TYR D 104 " --> pdb=" O ASP D 100 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LYS D 107 " --> pdb=" O ALA D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 138 removed outlier: 3.684A pdb=" N GLU D 136 " --> pdb=" O LEU D 132 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL D 137 " --> pdb=" O PHE D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 183 Processing helix chain 'D' and resid 276 through 280 removed outlier: 3.858A pdb=" N ASP D 279 " --> pdb=" O PRO D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 283 through 287 Processing helix chain 'D' and resid 314 through 318 removed outlier: 3.664A pdb=" N ILE D 318 " --> pdb=" O ALA D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 354 through 359 Processing helix chain 'D' and resid 361 through 366 Processing helix chain 'E' and resid 24 through 45 Proline residue: E 33 - end of helix Proline residue: E 43 - end of helix Processing helix chain 'E' and resid 68 through 97 removed outlier: 4.276A pdb=" N TRP E 73 " --> pdb=" O HIS E 69 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ALA E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N SER E 95 " --> pdb=" O ILE E 91 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLN E 96 " --> pdb=" O VAL E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 128 Processing helix chain 'E' and resid 130 through 159 removed outlier: 4.286A pdb=" N LEU E 134 " --> pdb=" O PHE E 130 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU E 135 " --> pdb=" O PRO E 131 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA E 136 " --> pdb=" O LYS E 132 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA E 144 " --> pdb=" O TYR E 140 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N PHE E 145 " --> pdb=" O TRP E 141 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ILE E 146 " --> pdb=" O VAL E 142 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N THR E 147 " --> pdb=" O MET E 143 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY E 159 " --> pdb=" O TYR E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 165 through 191 Processing helix chain 'E' and resid 218 through 225 Processing helix chain 'E' and resid 231 through 237 Processing helix chain 'E' and resid 245 through 249 Processing helix chain 'E' and resid 250 through 255 removed outlier: 3.584A pdb=" N ALA E 254 " --> pdb=" O LYS E 250 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 276 removed outlier: 3.679A pdb=" N TYR E 261 " --> pdb=" O ALA E 257 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU E 264 " --> pdb=" O ASN E 260 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS E 265 " --> pdb=" O TYR E 261 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU E 266 " --> pdb=" O VAL E 262 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 294 removed outlier: 4.242A pdb=" N TYR E 290 " --> pdb=" O TRP E 286 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ARG E 291 " --> pdb=" O LEU E 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 297 through 324 removed outlier: 3.853A pdb=" N PHE E 303 " --> pdb=" O LEU E 299 " (cutoff:3.500A) Proline residue: E 315 - end of helix removed outlier: 3.628A pdb=" N ARG E 324 " --> pdb=" O GLY E 320 " (cutoff:3.500A) Processing helix chain 'E' and resid 342 through 347 removed outlier: 3.994A pdb=" N GLU E 346 " --> pdb=" O LYS E 342 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ASN E 347 " --> pdb=" O GLU E 343 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 342 through 347' Processing helix chain 'E' and resid 347 through 394 removed outlier: 3.825A pdb=" N LEU E 351 " --> pdb=" O ASN E 347 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA E 352 " --> pdb=" O ALA E 348 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N VAL E 353 " --> pdb=" O HIS E 349 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ASN E 379 " --> pdb=" O GLU E 375 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ARG E 394 " --> pdb=" O ASN E 390 " (cutoff:3.500A) Processing helix chain 'E' and resid 408 through 413 Processing helix chain 'E' and resid 417 through 434 Proline residue: E 429 - end of helix Processing helix chain 'E' and resid 434 through 449 removed outlier: 4.082A pdb=" N MET E 440 " --> pdb=" O VAL E 436 " (cutoff:3.500A) Processing helix chain 'E' and resid 452 through 497 removed outlier: 3.877A pdb=" N VAL E 459 " --> pdb=" O VAL E 455 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N ILE E 460 " --> pdb=" O GLY E 456 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL E 461 " --> pdb=" O ALA E 457 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU E 462 " --> pdb=" O ALA E 458 " (cutoff:3.500A) Proline residue: E 465 - end of helix removed outlier: 4.302A pdb=" N THR E 472 " --> pdb=" O TYR E 468 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LYS E 473 " --> pdb=" O PHE E 469 " (cutoff:3.500A) Processing helix chain 'E' and resid 498 through 503 Processing helix chain 'E' and resid 509 through 511 No H-bonds generated for 'chain 'E' and resid 509 through 511' Processing helix chain 'E' and resid 512 through 556 removed outlier: 3.586A pdb=" N SER E 525 " --> pdb=" O LYS E 521 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR E 532 " --> pdb=" O THR E 528 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE E 543 " --> pdb=" O MET E 539 " (cutoff:3.500A) Proline residue: E 544 - end of helix removed outlier: 3.611A pdb=" N ALA E 556 " --> pdb=" O PHE E 552 " (cutoff:3.500A) Processing helix chain 'E' and resid 564 through 579 removed outlier: 3.578A pdb=" N PHE E 569 " --> pdb=" O PRO E 565 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N ALA E 570 " --> pdb=" O ALA E 566 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N SER E 571 " --> pdb=" O GLU E 567 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL E 579 " --> pdb=" O PHE E 575 " (cutoff:3.500A) Processing helix chain 'E' and resid 580 through 607 removed outlier: 4.389A pdb=" N LEU E 584 " --> pdb=" O THR E 580 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG E 590 " --> pdb=" O SER E 586 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N VAL E 593 " --> pdb=" O VAL E 589 " (cutoff:3.500A) Processing helix chain 'E' and resid 706 through 715 removed outlier: 4.224A pdb=" N LEU E 715 " --> pdb=" O LEU E 711 " (cutoff:3.500A) Processing helix chain 'E' and resid 774 through 784 removed outlier: 4.118A pdb=" N ALA E 779 " --> pdb=" O GLN E 775 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N VAL E 780 " --> pdb=" O ARG E 776 " (cutoff:3.500A) Processing helix chain 'E' and resid 809 through 823 Processing helix chain 'E' and resid 843 through 855 Processing helix chain 'E' and resid 893 through 898 Processing helix chain 'E' and resid 900 through 907 Processing helix chain 'E' and resid 909 through 914 Processing helix chain 'E' and resid 962 through 969 Processing helix chain 'E' and resid 973 through 986 removed outlier: 4.506A pdb=" N THR E 977 " --> pdb=" O MET E 973 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER E 984 " --> pdb=" O TRP E 980 " (cutoff:3.500A) Processing helix chain 'E' and resid 988 through 993 Processing helix chain 'E' and resid 993 through 1015 removed outlier: 3.516A pdb=" N THR E1015 " --> pdb=" O LEU E1011 " (cutoff:3.500A) Processing helix chain 'E' and resid 1026 through 1073 removed outlier: 4.340A pdb=" N ILE E1037 " --> pdb=" O ALA E1033 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU E1069 " --> pdb=" O HIS E1065 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ILE E1072 " --> pdb=" O LEU E1068 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE E1073 " --> pdb=" O LEU E1069 " (cutoff:3.500A) Processing helix chain 'E' and resid 1076 through 1083 removed outlier: 3.838A pdb=" N PHE E1080 " --> pdb=" O PRO E1076 " (cutoff:3.500A) Processing helix chain 'E' and resid 1084 through 1102 removed outlier: 4.201A pdb=" N ILE E1088 " --> pdb=" O PRO E1084 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ASP E1095 " --> pdb=" O ARG E1091 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N THR E1096 " --> pdb=" O PHE E1092 " (cutoff:3.500A) Processing helix chain 'E' and resid 1102 through 1128 Processing helix chain 'E' and resid 1129 through 1135 removed outlier: 4.291A pdb=" N ILE E1133 " --> pdb=" O PRO E1129 " (cutoff:3.500A) Processing helix chain 'E' and resid 1135 through 1177 removed outlier: 4.154A pdb=" N GLY E1139 " --> pdb=" O LEU E1135 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL E1140 " --> pdb=" O ALA E1136 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N LYS E1154 " --> pdb=" O ARG E1150 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN E1164 " --> pdb=" O ASP E1160 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N LEU E1165 " --> pdb=" O ASP E1161 " (cutoff:3.500A) Proline residue: E1166 - end of helix removed outlier: 3.722A pdb=" N CYS E1169 " --> pdb=" O LEU E1165 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA E1175 " --> pdb=" O PHE E1171 " (cutoff:3.500A) Processing helix chain 'E' and resid 1186 through 1238 removed outlier: 3.866A pdb=" N LYS E1191 " --> pdb=" O GLU E1187 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLN E1192 " --> pdb=" O THR E1188 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG E1193 " --> pdb=" O ARG E1189 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLU E1196 " --> pdb=" O GLN E1192 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ASP E1199 " --> pdb=" O LEU E1195 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ALA E1204 " --> pdb=" O THR E1200 " (cutoff:3.500A) Processing helix chain 'E' and resid 1240 through 1280 removed outlier: 4.255A pdb=" N ASN E1256 " --> pdb=" O LEU E1252 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N TYR E1257 " --> pdb=" O THR E1253 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N LEU E1258 " --> pdb=" O ILE E1254 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N ASN E1259 " --> pdb=" O THR E1255 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N TRP E1260 " --> pdb=" O ASN E1256 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS E1277 " --> pdb=" O GLY E1273 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N VAL E1278 " --> pdb=" O ALA E1274 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER E1280 " --> pdb=" O LYS E1276 " (cutoff:3.500A) Processing helix chain 'E' and resid 1343 through 1354 removed outlier: 4.150A pdb=" N LYS E1348 " --> pdb=" O THR E1344 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N SER E1349 " --> pdb=" O GLY E1345 " (cutoff:3.500A) Processing helix chain 'E' and resid 1380 through 1385 Processing helix chain 'E' and resid 1415 through 1421 Processing helix chain 'E' and resid 1453 through 1459 Processing helix chain 'E' and resid 1475 through 1494 removed outlier: 4.091A pdb=" N ALA E1492 " --> pdb=" O MET E1488 " (cutoff:3.500A) Processing helix chain 'E' and resid 1527 through 1533 Processing helix chain 'E' and resid 1538 through 1542 removed outlier: 3.573A pdb=" N ARG E1542 " --> pdb=" O SER E1539 " (cutoff:3.500A) Processing helix chain 'G' and resid 23 through 42 removed outlier: 4.012A pdb=" N ALA G 28 " --> pdb=" O CYS G 24 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N LEU G 29 " --> pdb=" O PHE G 25 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ASN G 30 " --> pdb=" O VAL G 26 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N LEU G 31 " --> pdb=" O ASP G 27 " (cutoff:3.500A) Proline residue: G 33 - end of helix Processing helix chain 'G' and resid 65 through 97 removed outlier: 3.688A pdb=" N ASN G 70 " --> pdb=" O PHE G 66 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEU G 71 " --> pdb=" O PRO G 67 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ILE G 74 " --> pdb=" O ASN G 70 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N PHE G 77 " --> pdb=" O TRP G 73 " (cutoff:3.500A) Processing helix chain 'G' and resid 104 through 128 Processing helix chain 'G' and resid 135 through 158 removed outlier: 4.054A pdb=" N LEU G 139 " --> pdb=" O LEU G 135 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N TYR G 140 " --> pdb=" O ALA G 136 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N PHE G 145 " --> pdb=" O TRP G 141 " (cutoff:3.500A) Processing helix chain 'G' and resid 164 through 192 Processing sheet with id=AA1, first strand: chain 'A' and resid 191 through 193 Processing sheet with id=AA2, first strand: chain 'A' and resid 198 through 202 removed outlier: 3.905A pdb=" N VAL A 198 " --> pdb=" O MET A 209 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 244 through 248 removed outlier: 4.629A pdb=" N ILE A 227 " --> pdb=" O ILE A 248 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N SER A 222 " --> pdb=" O VAL A 299 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N VAL A 299 " --> pdb=" O SER A 222 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 323 through 324 Processing sheet with id=AA5, first strand: chain 'A' and resid 328 through 330 Processing sheet with id=AA6, first strand: chain 'B' and resid 265 through 270 removed outlier: 3.782A pdb=" N PHE B 210 " --> pdb=" O ILE B 267 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ILE B 199 " --> pdb=" O GLN B 319 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 246 through 248 removed outlier: 4.515A pdb=" N ILE B 227 " --> pdb=" O ILE B 248 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N SER B 222 " --> pdb=" O VAL B 299 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N VAL B 299 " --> pdb=" O SER B 222 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 46 through 48 removed outlier: 3.718A pdb=" N LYS C 48 " --> pdb=" O VAL D 337 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 197 through 198 removed outlier: 5.845A pdb=" N ALA C 197 " --> pdb=" O GLN C 319 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 209 through 212 Processing sheet with id=AB2, first strand: chain 'C' and resid 245 through 248 removed outlier: 4.442A pdb=" N ILE C 227 " --> pdb=" O ILE C 248 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ALA C 223 " --> pdb=" O ILE C 259 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE C 259 " --> pdb=" O ALA C 223 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 245 through 248 removed outlier: 4.442A pdb=" N ILE C 227 " --> pdb=" O ILE C 248 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N SER C 222 " --> pdb=" O VAL C 299 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N VAL C 299 " --> pdb=" O SER C 222 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 233 through 234 Processing sheet with id=AB5, first strand: chain 'C' and resid 323 through 324 Processing sheet with id=AB6, first strand: chain 'C' and resid 329 through 330 Processing sheet with id=AB7, first strand: chain 'D' and resid 201 through 202 Processing sheet with id=AB8, first strand: chain 'D' and resid 240 through 248 removed outlier: 4.554A pdb=" N THR D 233 " --> pdb=" O PRO D 242 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ILE D 227 " --> pdb=" O ILE D 248 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ALA D 223 " --> pdb=" O ILE D 259 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 240 through 248 removed outlier: 4.554A pdb=" N THR D 233 " --> pdb=" O PRO D 242 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ILE D 227 " --> pdb=" O ILE D 248 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N SER D 222 " --> pdb=" O VAL D 299 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N VAL D 299 " --> pdb=" O SER D 222 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE D 305 " --> pdb=" O VAL D 300 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 1513 through 1516 removed outlier: 6.679A pdb=" N VAL E1514 " --> pdb=" O LEU E1521 " (cutoff:3.500A) 1112 hydrogen bonds defined for protein. 3222 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: 5.36 Time building geometry restraints manager: 5.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.25: 2972 1.25 - 1.34: 2995 1.34 - 1.43: 125 1.43 - 1.52: 5328 1.52 - 1.61: 3558 Bond restraints: 14978 Sorted by residual: bond pdb=" C4 ATP E1601 " pdb=" C5 ATP E1601 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.84e+01 bond pdb=" C4 ATP A3002 " pdb=" C5 ATP A3002 " ideal model delta sigma weight residual 1.388 1.464 -0.076 1.00e-02 1.00e+04 5.82e+01 bond pdb=" C4 ATP B 501 " pdb=" C5 ATP B 501 " ideal model delta sigma weight residual 1.388 1.463 -0.075 1.00e-02 1.00e+04 5.66e+01 bond pdb=" C4 ATP C 501 " pdb=" C5 ATP C 501 " ideal model delta sigma weight residual 1.388 1.460 -0.072 1.00e-02 1.00e+04 5.23e+01 bond pdb=" C4 ATP D 501 " pdb=" C5 ATP D 501 " ideal model delta sigma weight residual 1.388 1.460 -0.072 1.00e-02 1.00e+04 5.22e+01 ... (remaining 14973 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.60: 20469 4.60 - 9.20: 357 9.20 - 13.80: 39 13.80 - 18.40: 7 18.40 - 23.00: 11 Bond angle restraints: 20883 Sorted by residual: angle pdb=" PB ATP D 501 " pdb=" O3B ATP D 501 " pdb=" PG ATP D 501 " ideal model delta sigma weight residual 139.87 116.87 23.00 1.00e+00 1.00e+00 5.29e+02 angle pdb=" PA ATP B 501 " pdb=" O3A ATP B 501 " pdb=" PB ATP B 501 " ideal model delta sigma weight residual 136.83 114.87 21.96 1.00e+00 1.00e+00 4.82e+02 angle pdb=" PB ATP B 501 " pdb=" O3B ATP B 501 " pdb=" PG ATP B 501 " ideal model delta sigma weight residual 139.87 118.03 21.84 1.00e+00 1.00e+00 4.77e+02 angle pdb=" PB ATP C 501 " pdb=" O3B ATP C 501 " pdb=" PG ATP C 501 " ideal model delta sigma weight residual 139.87 118.41 21.46 1.00e+00 1.00e+00 4.61e+02 angle pdb=" PB ATP E1601 " pdb=" O3B ATP E1601 " pdb=" PG ATP E1601 " ideal model delta sigma weight residual 139.87 119.09 20.78 1.00e+00 1.00e+00 4.32e+02 ... (remaining 20878 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.67: 8786 23.67 - 47.33: 57 47.33 - 71.00: 10 71.00 - 94.67: 17 94.67 - 118.33: 13 Dihedral angle restraints: 8883 sinusoidal: 273 harmonic: 8610 Sorted by residual: dihedral pdb=" C ASN G 22 " pdb=" N ASN G 22 " pdb=" CA ASN G 22 " pdb=" CB ASN G 22 " ideal model delta harmonic sigma weight residual -122.60 -111.06 -11.54 0 2.50e+00 1.60e-01 2.13e+01 dihedral pdb=" CA CYS E1407 " pdb=" C CYS E1407 " pdb=" N LYS E1408 " pdb=" CA LYS E1408 " ideal model delta harmonic sigma weight residual 180.00 157.67 22.33 0 5.00e+00 4.00e-02 1.99e+01 dihedral pdb=" CA LYS C 48 " pdb=" C LYS C 48 " pdb=" N ASN C 49 " pdb=" CA ASN C 49 " ideal model delta harmonic sigma weight residual 180.00 159.11 20.89 0 5.00e+00 4.00e-02 1.75e+01 ... (remaining 8880 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.902: 2858 0.902 - 1.805: 0 1.805 - 2.707: 0 2.707 - 3.609: 0 3.609 - 4.511: 2 Chirality restraints: 2860 Sorted by residual: chirality pdb=" C1 NAG N 1 " pdb=" ND2 ASN E 9 " pdb=" C2 NAG N 1 " pdb=" O5 NAG N 1 " both_signs ideal model delta sigma weight residual False -2.40 2.11 -4.51 2.00e-01 2.50e+01 5.09e+02 chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN G 9 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 2.02 -4.42 2.00e-01 2.50e+01 4.89e+02 chirality pdb=" C1 NAG N 2 " pdb=" O4 NAG N 1 " pdb=" C2 NAG N 2 " pdb=" O5 NAG N 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-02 2.50e+03 1.84e+02 ... (remaining 2857 not shown) Planarity restraints: 2988 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG N 1 " 0.355 2.00e-02 2.50e+03 3.06e-01 1.17e+03 pdb=" C7 NAG N 1 " -0.085 2.00e-02 2.50e+03 pdb=" C8 NAG N 1 " 0.114 2.00e-02 2.50e+03 pdb=" N2 NAG N 1 " -0.545 2.00e-02 2.50e+03 pdb=" O7 NAG N 1 " 0.160 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 2 " -0.323 2.00e-02 2.50e+03 2.70e-01 9.12e+02 pdb=" C7 NAG F 2 " 0.088 2.00e-02 2.50e+03 pdb=" C8 NAG F 2 " -0.200 2.00e-02 2.50e+03 pdb=" N2 NAG F 2 " 0.460 2.00e-02 2.50e+03 pdb=" O7 NAG F 2 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG N 2 " 0.232 2.00e-02 2.50e+03 1.98e-01 4.89e+02 pdb=" C7 NAG N 2 " -0.049 2.00e-02 2.50e+03 pdb=" C8 NAG N 2 " -0.035 2.00e-02 2.50e+03 pdb=" N2 NAG N 2 " -0.326 2.00e-02 2.50e+03 pdb=" O7 NAG N 2 " 0.178 2.00e-02 2.50e+03 ... (remaining 2985 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.27: 4 2.27 - 2.99: 9314 2.99 - 3.70: 24739 3.70 - 4.42: 30177 4.42 - 5.14: 45188 Nonbonded interactions: 109422 Sorted by model distance: nonbonded pdb=" CB ASN E 672 " pdb=" O GLU E 722 " model vdw 1.552 3.440 nonbonded pdb=" O4 NAG F 2 " pdb=" O6 NAG F 2 " model vdw 2.104 3.040 nonbonded pdb=" O GLN E1336 " pdb=" N VAL E1496 " model vdw 2.219 3.120 nonbonded pdb=" N LYS E 707 " pdb=" O1A ATP E1601 " model vdw 2.250 3.120 nonbonded pdb=" O VAL E 153 " pdb=" CB TRP E 156 " model vdw 2.298 3.440 ... (remaining 109417 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 30 through 297 and (name N or name CA or name C or name O \ or name CB )) or resid 298 through 366 or resid 3002)) selection = chain 'B' selection = (chain 'C' and ((resid 30 through 40 and (name N or name CA or name C or name O \ or name CB )) or resid 41 through 366 or resid 501)) selection = chain 'D' } ncs_group { reference = chain 'F' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 0.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.540 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 38.440 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6425 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 : 0.009 0.109 14978 Z= 0.693 Angle : 1.551 22.995 20883 Z= 1.145 Chirality : 0.148 4.511 2860 Planarity : 0.012 0.306 2986 Dihedral : 11.990 118.331 3243 Min Nonbonded Distance : 1.552 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.43 % Favored : 90.57 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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 (0.15), residues: 2958 helix: 1.11 (0.15), residues: 1307 sheet: -1.49 (0.34), residues: 239 loop : -2.74 (0.15), residues: 1412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 69 PHE 0.000 0.000 PHE A 36 TYR 0.000 0.000 TYR A 102 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 2605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 1.547 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.1330 time to fit residues: 24.2762 Evaluate side-chains 87 residues out of total 2605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 1.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 248 optimal weight: 50.0000 chunk 222 optimal weight: 10.0000 chunk 123 optimal weight: 30.0000 chunk 76 optimal weight: 9.9990 chunk 150 optimal weight: 9.9990 chunk 119 optimal weight: 10.0000 chunk 230 optimal weight: 30.0000 chunk 89 optimal weight: 0.9980 chunk 140 optimal weight: 20.0000 chunk 171 optimal weight: 50.0000 chunk 266 optimal weight: 50.0000 overall best weight: 8.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6618 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.095 14978 Z= 0.262 Angle : 0.659 11.636 20883 Z= 0.388 Chirality : 0.048 0.310 2860 Planarity : 0.004 0.046 2986 Dihedral : 10.982 105.360 3224 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 0.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 0.00 % Allowed : 14.29 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.15), residues: 2958 helix: 0.99 (0.14), residues: 1349 sheet: -0.88 (0.36), residues: 212 loop : -2.72 (0.15), residues: 1397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 69 PHE 0.000 0.000 PHE A 36 TYR 0.000 0.000 TYR A 102 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 2605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 1.824 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.1312 time to fit residues: 24.0328 Evaluate side-chains 86 residues out of total 2605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 1.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 148 optimal weight: 40.0000 chunk 82 optimal weight: 50.0000 chunk 222 optimal weight: 20.0000 chunk 181 optimal weight: 20.0000 chunk 73 optimal weight: 30.0000 chunk 267 optimal weight: 20.0000 chunk 288 optimal weight: 0.0370 chunk 238 optimal weight: 6.9990 chunk 265 optimal weight: 50.0000 chunk 91 optimal weight: 3.9990 chunk 214 optimal weight: 3.9990 overall best weight: 7.0068 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6689 moved from start: 0.3115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 14978 Z= 0.218 Angle : 0.566 11.592 20883 Z= 0.334 Chirality : 0.047 0.474 2860 Planarity : 0.003 0.034 2986 Dihedral : 10.522 110.513 3224 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 0.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -0.59 (0.16), residues: 2958 helix: 1.77 (0.14), residues: 1345 sheet: -0.77 (0.37), residues: 214 loop : -2.70 (0.15), residues: 1399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 69 PHE 0.000 0.000 PHE A 36 TYR 0.000 0.000 TYR A 102 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 2605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 1.488 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.1285 time to fit residues: 23.1249 Evaluate side-chains 86 residues out of total 2605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 1.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 264 optimal weight: 0.0370 chunk 201 optimal weight: 50.0000 chunk 138 optimal weight: 50.0000 chunk 29 optimal weight: 50.0000 chunk 127 optimal weight: 5.9990 chunk 179 optimal weight: 50.0000 chunk 268 optimal weight: 50.0000 chunk 284 optimal weight: 40.0000 chunk 140 optimal weight: 6.9990 chunk 254 optimal weight: 10.0000 chunk 76 optimal weight: 9.9990 overall best weight: 6.6068 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6729 moved from start: 0.3924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 14978 Z= 0.176 Angle : 0.550 17.622 20883 Z= 0.316 Chirality : 0.047 0.388 2860 Planarity : 0.002 0.029 2986 Dihedral : 9.751 88.589 3224 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 0.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 0.00 % Allowed : 14.29 % Favored : 85.71 % 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: -0.53 (0.16), residues: 2958 helix: 1.84 (0.14), residues: 1352 sheet: -1.21 (0.36), residues: 218 loop : -2.63 (0.16), residues: 1388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 69 PHE 0.000 0.000 PHE A 36 TYR 0.000 0.000 TYR A 102 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 2605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 1.476 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.1314 time to fit residues: 23.6594 Evaluate side-chains 87 residues out of total 2605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 1.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 236 optimal weight: 50.0000 chunk 161 optimal weight: 40.0000 chunk 4 optimal weight: 30.0000 chunk 211 optimal weight: 50.0000 chunk 117 optimal weight: 40.0000 chunk 242 optimal weight: 30.0000 chunk 196 optimal weight: 50.0000 chunk 0 optimal weight: 80.0000 chunk 145 optimal weight: 6.9990 chunk 255 optimal weight: 10.0000 chunk 71 optimal weight: 6.9990 overall best weight: 16.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6876 moved from start: 0.4757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 14978 Z= 0.359 Angle : 0.769 14.910 20883 Z= 0.478 Chirality : 0.051 0.336 2860 Planarity : 0.004 0.035 2986 Dihedral : 10.838 98.202 3224 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 1.28 Ramachandran Plot: Outliers : 0.10 % Allowed : 12.20 % Favored : 87.69 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -1.76 (0.15), residues: 2958 helix: 0.55 (0.14), residues: 1337 sheet: -1.50 (0.38), residues: 195 loop : -2.96 (0.15), residues: 1426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 69 PHE 0.000 0.000 PHE A 36 TYR 0.000 0.000 TYR A 102 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 2605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 1.622 Fit side-chains REVERT: G 9 ASN cc_start: 0.6269 (t0) cc_final: 0.5939 (t0) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.1295 time to fit residues: 23.3941 Evaluate side-chains 87 residues out of total 2605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 1.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 95 optimal weight: 30.0000 chunk 255 optimal weight: 8.9990 chunk 56 optimal weight: 20.0000 chunk 166 optimal weight: 0.0870 chunk 70 optimal weight: 5.9990 chunk 284 optimal weight: 40.0000 chunk 236 optimal weight: 7.9990 chunk 131 optimal weight: 20.0000 chunk 23 optimal weight: 40.0000 chunk 94 optimal weight: 0.8980 chunk 149 optimal weight: 7.9990 overall best weight: 4.5964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6771 moved from start: 0.4821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 14978 Z= 0.138 Angle : 0.503 11.178 20883 Z= 0.296 Chirality : 0.046 0.459 2860 Planarity : 0.002 0.033 2986 Dihedral : 9.719 92.689 3224 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 0.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -0.74 (0.16), residues: 2958 helix: 1.72 (0.15), residues: 1331 sheet: -1.51 (0.36), residues: 211 loop : -2.69 (0.16), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 69 PHE 0.000 0.000 PHE A 36 TYR 0.000 0.000 TYR A 102 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 2605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 1.621 Fit side-chains revert: symmetry clash REVERT: G 9 ASN cc_start: 0.5865 (t0) cc_final: 0.5490 (t0) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.1340 time to fit residues: 24.3190 Evaluate side-chains 87 residues out of total 2605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 1.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 274 optimal weight: 50.0000 chunk 32 optimal weight: 20.0000 chunk 162 optimal weight: 40.0000 chunk 207 optimal weight: 7.9990 chunk 160 optimal weight: 40.0000 chunk 239 optimal weight: 50.0000 chunk 158 optimal weight: 20.0000 chunk 283 optimal weight: 40.0000 chunk 177 optimal weight: 8.9990 chunk 172 optimal weight: 20.0000 chunk 130 optimal weight: 30.0000 overall best weight: 15.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6890 moved from start: 0.5292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 14978 Z= 0.325 Angle : 0.719 13.005 20883 Z= 0.444 Chirality : 0.049 0.382 2860 Planarity : 0.004 0.039 2986 Dihedral : 10.583 90.130 3224 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 1.24 Ramachandran Plot: Outliers : 0.10 % Allowed : 13.73 % Favored : 86.17 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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 (0.15), residues: 2958 helix: 0.64 (0.14), residues: 1326 sheet: -1.69 (0.38), residues: 187 loop : -3.03 (0.15), residues: 1445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 69 PHE 0.000 0.000 PHE A 36 TYR 0.000 0.000 TYR A 102 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 2605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 1.584 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.1302 time to fit residues: 23.8456 Evaluate side-chains 87 residues out of total 2605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 1.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 175 optimal weight: 30.0000 chunk 113 optimal weight: 8.9990 chunk 169 optimal weight: 40.0000 chunk 85 optimal weight: 40.0000 chunk 55 optimal weight: 30.0000 chunk 54 optimal weight: 3.9990 chunk 180 optimal weight: 40.0000 chunk 193 optimal weight: 40.0000 chunk 140 optimal weight: 7.9990 chunk 26 optimal weight: 40.0000 chunk 222 optimal weight: 20.0000 overall best weight: 14.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6885 moved from start: 0.5529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 14978 Z= 0.303 Angle : 0.705 11.526 20883 Z= 0.428 Chirality : 0.050 0.570 2860 Planarity : 0.004 0.046 2986 Dihedral : 10.705 98.411 3224 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 1.24 Ramachandran Plot: Outliers : 0.03 % Allowed : 11.87 % Favored : 88.10 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.96 (0.15), residues: 2958 helix: 0.50 (0.14), residues: 1326 sheet: -1.64 (0.39), residues: 186 loop : -3.16 (0.15), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 69 PHE 0.000 0.000 PHE A 36 TYR 0.000 0.000 TYR A 102 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 2605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 1.512 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.1297 time to fit residues: 23.6482 Evaluate side-chains 88 residues out of total 2605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 1.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 257 optimal weight: 40.0000 chunk 271 optimal weight: 50.0000 chunk 247 optimal weight: 40.0000 chunk 264 optimal weight: 40.0000 chunk 158 optimal weight: 20.0000 chunk 115 optimal weight: 40.0000 chunk 207 optimal weight: 10.0000 chunk 81 optimal weight: 20.0000 chunk 238 optimal weight: 40.0000 chunk 249 optimal weight: 40.0000 chunk 263 optimal weight: 9.9990 overall best weight: 19.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6963 moved from start: 0.6088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.102 14978 Z= 0.412 Angle : 0.856 11.648 20883 Z= 0.535 Chirality : 0.054 0.538 2860 Planarity : 0.005 0.048 2986 Dihedral : 11.744 83.533 3224 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 2.06 Ramachandran Plot: Outliers : 0.07 % Allowed : 16.80 % Favored : 83.13 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -2.87 (0.14), residues: 2958 helix: -0.40 (0.13), residues: 1323 sheet: -1.94 (0.40), residues: 179 loop : -3.51 (0.14), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 69 PHE 0.000 0.000 PHE A 36 TYR 0.000 0.000 TYR A 102 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 2605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 1.608 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.1492 time to fit residues: 26.6329 Evaluate side-chains 87 residues out of total 2605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 1.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 173 optimal weight: 0.9990 chunk 279 optimal weight: 10.0000 chunk 170 optimal weight: 40.0000 chunk 132 optimal weight: 20.0000 chunk 194 optimal weight: 0.8980 chunk 292 optimal weight: 30.0000 chunk 269 optimal weight: 30.0000 chunk 233 optimal weight: 8.9990 chunk 24 optimal weight: 7.9990 chunk 180 optimal weight: 0.0980 chunk 143 optimal weight: 9.9990 overall best weight: 3.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6808 moved from start: 0.5969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 14978 Z= 0.134 Angle : 0.519 9.576 20883 Z= 0.303 Chirality : 0.047 0.405 2860 Planarity : 0.003 0.070 2986 Dihedral : 10.215 87.042 3224 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 0.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.16), residues: 2958 helix: 1.35 (0.15), residues: 1329 sheet: -1.88 (0.37), residues: 199 loop : -3.11 (0.15), residues: 1430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 69 PHE 0.000 0.000 PHE A 36 TYR 0.000 0.000 TYR A 102 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 2605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 1.512 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.1331 time to fit residues: 23.9028 Evaluate side-chains 87 residues out of total 2605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 1.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 185 optimal weight: 8.9990 chunk 248 optimal weight: 50.0000 chunk 71 optimal weight: 5.9990 chunk 215 optimal weight: 0.8980 chunk 34 optimal weight: 40.0000 chunk 64 optimal weight: 40.0000 chunk 233 optimal weight: 40.0000 chunk 97 optimal weight: 40.0000 chunk 239 optimal weight: 30.0000 chunk 29 optimal weight: 40.0000 chunk 43 optimal weight: 30.0000 overall best weight: 15.1792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.214423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.177640 restraints weight = 237281.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.181480 restraints weight = 152889.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.181320 restraints weight = 125715.790| |-----------------------------------------------------------------------------| r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.6161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 14978 Z= 0.316 Angle : 0.707 12.552 20883 Z= 0.435 Chirality : 0.049 0.359 2860 Planarity : 0.004 0.063 2986 Dihedral : 10.810 86.198 3224 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 1.47 Ramachandran Plot: Outliers : 0.10 % Allowed : 15.38 % Favored : 84.52 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.10 (0.15), residues: 2958 helix: 0.49 (0.14), residues: 1337 sheet: -1.88 (0.39), residues: 183 loop : -3.35 (0.15), residues: 1438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 69 PHE 0.000 0.000 PHE A 36 TYR 0.000 0.000 TYR A 102 =============================================================================== Job complete usr+sys time: 1821.87 seconds wall clock time: 32 minutes 58.83 seconds (1978.83 seconds total)