Starting phenix.real_space_refine on Sat Mar 16 17:03:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mjq_23882/03_2024/7mjq_23882_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mjq_23882/03_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_23882/03_2024/7mjq_23882.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mjq_23882/03_2024/7mjq_23882.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mjq_23882/03_2024/7mjq_23882_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mjq_23882/03_2024/7mjq_23882_neut_updated.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 9.51, per 1000 atoms: 0.64 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 - 3.50 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=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: 7.15 Conformation dependent library (CDL) restraints added in 4.2 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... running ksdssp... Secondary structure from input PDB file: 88 helices and 11 sheets defined 45.2% alpha, 5.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.23 Creating SS restraints... Processing helix chain 'A' and resid 24 through 28 Processing helix chain 'A' and resid 57 through 65 Processing helix chain 'A' and resid 69 through 97 Processing helix chain 'A' and resid 101 through 105 Processing helix chain 'A' and resid 127 through 138 Processing helix chain 'A' and resid 153 through 182 Processing helix chain 'A' and resid 282 through 287 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 315 through 317 No H-bonds generated for 'chain 'A' and resid 315 through 317' Processing helix chain 'A' and resid 354 through 357 No H-bonds generated for 'chain 'A' and resid 354 through 357' Processing helix chain 'B' and resid 57 through 65 Processing helix chain 'B' and resid 69 through 97 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) Processing helix chain 'B' and resid 100 through 105 Processing helix chain 'B' and resid 127 through 137 Processing helix chain 'B' and resid 153 through 183 Processing helix chain 'B' and resid 282 through 285 No H-bonds generated for 'chain 'B' and resid 282 through 285' Processing helix chain 'B' and resid 315 through 317 No H-bonds generated for 'chain 'B' and resid 315 through 317' Processing helix chain 'B' and resid 356 through 360 Processing helix chain 'C' and resid 57 through 65 Processing helix chain 'C' and resid 69 through 95 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 100 through 106 Processing helix chain 'C' and resid 111 through 117 Processing helix chain 'C' and resid 128 through 138 Processing helix chain 'C' and resid 153 through 183 Processing helix chain 'C' and resid 276 through 279 removed outlier: 4.291A pdb=" N ASP C 279 " --> pdb=" O PRO C 276 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 276 through 279' Processing helix chain 'C' and resid 315 through 317 No H-bonds generated for 'chain 'C' and resid 315 through 317' Processing helix chain 'C' and resid 355 through 359 Processing helix chain 'D' and resid 57 through 65 removed outlier: 4.113A pdb=" N ILE D 60 " --> pdb=" O LEU D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 72 No H-bonds generated for 'chain 'D' and resid 69 through 72' Processing helix chain 'D' and resid 75 through 97 removed outlier: 3.666A pdb=" N LEU D 93 " --> pdb=" O ILE D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 106 removed outlier: 3.941A pdb=" N TYR D 104 " --> pdb=" O ASP D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 139 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 153 through 184 removed outlier: 4.618A pdb=" N ALA D 184 " --> pdb=" O LYS D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 279 No H-bonds generated for 'chain 'D' and resid 277 through 279' Processing helix chain 'D' and resid 284 through 286 No H-bonds generated for 'chain 'D' and resid 284 through 286' Processing helix chain 'D' and resid 315 through 317 No H-bonds generated for 'chain 'D' and resid 315 through 317' Processing helix chain 'D' and resid 355 through 358 No H-bonds generated for 'chain 'D' and resid 355 through 358' Processing helix chain 'D' and resid 362 through 365 No H-bonds generated for 'chain 'D' and resid 362 through 365' Processing helix chain 'E' and resid 25 through 45 Proline residue: E 33 - end of helix Proline residue: E 43 - end of helix Processing helix chain 'E' and resid 69 through 96 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 103 through 127 Proline residue: E 107 - end of helix Processing helix chain 'E' and resid 131 through 158 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) Processing helix chain 'E' and resid 166 through 190 Processing helix chain 'E' and resid 219 through 224 Processing helix chain 'E' and resid 232 through 236 Processing helix chain 'E' and resid 246 through 248 No H-bonds generated for 'chain 'E' and resid 246 through 248' Processing helix chain 'E' and resid 251 through 276 removed outlier: 3.826A pdb=" N ALA E 257 " --> pdb=" O ILE E 253 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N VAL E 258 " --> pdb=" O ALA E 254 " (cutoff:3.500A) 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 287 through 293 removed outlier: 4.049A pdb=" N ARG E 291 " --> pdb=" O LEU E 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 298 through 325 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) removed outlier: 3.945A pdb=" N VAL E 325 " --> pdb=" O ILE E 321 " (cutoff:3.500A) Processing helix chain 'E' and resid 343 through 346 No H-bonds generated for 'chain 'E' and resid 343 through 346' Processing helix chain 'E' and resid 348 through 393 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) Processing helix chain 'E' and resid 409 through 412 No H-bonds generated for 'chain 'E' and resid 409 through 412' Processing helix chain 'E' and resid 418 through 433 Proline residue: E 429 - end of helix Processing helix chain 'E' and resid 435 through 448 removed outlier: 4.082A pdb=" N MET E 440 " --> pdb=" O VAL E 436 " (cutoff:3.500A) Processing helix chain 'E' and resid 453 through 502 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) removed outlier: 3.561A pdb=" N GLY E 498 " --> pdb=" O GLU E 494 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ILE E 499 " --> pdb=" O ILE E 495 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N LYS E 500 " --> pdb=" O LEU E 496 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LEU E 501 " --> pdb=" O LYS E 497 " (cutoff:3.500A) Processing helix chain 'E' and resid 510 through 557 removed outlier: 5.177A pdb=" N SER E 514 " --> pdb=" O PHE E 511 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ALA E 542 " --> pdb=" O MET E 539 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N ILE E 543 " --> pdb=" O ASN E 540 " (cutoff:3.500A) Proline residue: E 544 - end of helix Processing helix chain 'E' and resid 565 through 578 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) Processing helix chain 'E' and resid 581 through 607 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 707 through 714 Processing helix chain 'E' and resid 762 through 765 No H-bonds generated for 'chain 'E' and resid 762 through 765' Processing helix chain 'E' and resid 775 through 783 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 810 through 822 Processing helix chain 'E' and resid 844 through 854 Processing helix chain 'E' and resid 894 through 898 Processing helix chain 'E' and resid 901 through 906 Processing helix chain 'E' and resid 910 through 917 removed outlier: 6.153A pdb=" N GLN E 915 " --> pdb=" O ARG E 912 " (cutoff:3.500A) Processing helix chain 'E' and resid 963 through 968 Processing helix chain 'E' and resid 974 through 985 removed outlier: 3.502A pdb=" N SER E 984 " --> pdb=" O TRP E 980 " (cutoff:3.500A) Processing helix chain 'E' and resid 989 through 992 No H-bonds generated for 'chain 'E' and resid 989 through 992' Processing helix chain 'E' and resid 994 through 1014 Processing helix chain 'E' and resid 1027 through 1072 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) Processing helix chain 'E' and resid 1077 through 1082 Processing helix chain 'E' and resid 1085 through 1101 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 1103 through 1127 Processing helix chain 'E' and resid 1129 through 1176 removed outlier: 3.849A pdb=" N LEU E1135 " --> pdb=" O LEU E1132 " (cutoff:3.500A) Proline residue: E1137 - end of helix removed outlier: 6.046A pdb=" N SER E1153 " --> pdb=" O ARG E1150 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N GLN E1164 " --> pdb=" O ASP E1161 " (cutoff:3.500A) Proline residue: E1166 - end of helix removed outlier: 4.335A pdb=" N THR E1174 " --> pdb=" O PHE E1171 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ALA E1175 " --> pdb=" O SER E1172 " (cutoff:3.500A) Processing helix chain 'E' and resid 1187 through 1237 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 1241 through 1279 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) Processing helix chain 'E' and resid 1344 through 1353 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 1381 through 1384 Processing helix chain 'E' and resid 1416 through 1420 Processing helix chain 'E' and resid 1454 through 1458 Processing helix chain 'E' and resid 1476 through 1493 removed outlier: 4.091A pdb=" N ALA E1492 " --> pdb=" O MET E1488 " (cutoff:3.500A) Processing helix chain 'E' and resid 1528 through 1532 Processing helix chain 'E' and resid 1539 through 1541 No H-bonds generated for 'chain 'E' and resid 1539 through 1541' Processing helix chain 'G' and resid 23 through 42 removed outlier: 4.287A pdb=" N ALA G 28 " --> pdb=" O PHE G 25 " (cutoff:3.500A) Proline residue: G 33 - end of helix Processing helix chain 'G' and resid 66 through 96 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 127 Processing helix chain 'G' and resid 134 through 157 removed outlier: 3.781A pdb=" N LEU G 137 " --> pdb=" O LEU G 134 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ALA G 144 " --> pdb=" O TRP G 141 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS G 148 " --> pdb=" O PHE G 145 " (cutoff:3.500A) Processing helix chain 'G' and resid 165 through 191 Processing sheet with id= A, first strand: chain 'A' and resid 191 through 193 Processing sheet with id= B, 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= C, 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) Processing sheet with id= D, first strand: chain 'A' and resid 328 through 330 Processing sheet with id= E, first strand: chain 'B' and resid 318 through 320 removed outlier: 6.062A pdb=" N ALA B 197 " --> pdb=" O GLN B 319 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N PHE B 210 " --> pdb=" O ILE B 267 " (cutoff:3.500A) Processing sheet with id= F, 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) Processing sheet with id= G, first strand: chain 'B' and resid 233 through 235 Processing sheet with id= H, first strand: chain 'C' and resid 209 through 212 Processing sheet with id= I, 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) Processing sheet with id= J, first strand: chain 'D' and resid 244 through 248 removed outlier: 4.393A pdb=" N ILE D 227 " --> pdb=" O ILE D 248 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE D 305 " --> pdb=" O VAL D 300 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 1513 through 1516 removed outlier: 4.998A pdb=" N LYS E1516 " --> pdb=" O ILE E1520 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N ILE E1520 " --> pdb=" O LYS E1516 " (cutoff:3.500A) 1000 hydrogen bonds defined for protein. 2556 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: 5.44 Time building geometry restraints manager: 7.64 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: 92.70 - 101.50: 15 101.50 - 110.31: 3633 110.31 - 119.12: 8705 119.12 - 127.93: 8506 127.93 - 136.74: 24 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: 9383 2.99 - 3.70: 24777 3.70 - 4.42: 30437 4.42 - 5.14: 45237 Nonbonded interactions: 109838 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 2.440 nonbonded pdb=" O GLN E1336 " pdb=" N VAL E1496 " model vdw 2.219 2.520 nonbonded pdb=" N LYS E 707 " pdb=" O1A ATP E1601 " model vdw 2.250 2.520 nonbonded pdb=" O VAL E 153 " pdb=" CB TRP E 156 " model vdw 2.298 3.440 ... (remaining 109833 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 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: 0.000 Normalize map: mean=0, sd=1: 0.030 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: 0.010 Extract box with map and model: 1.240 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 47.030 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.980 ------------------------------------------------------------------------------- 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= 0.700 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 : 1.770 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.1258 time to fit residues: 22.8845 Evaluate side-chains 87 residues out of total 2605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 1.633 ------------------------------------------------------------------------------- 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: 5.9990 chunk 123 optimal weight: 30.0000 chunk 76 optimal weight: 7.9990 chunk 150 optimal weight: 10.0000 chunk 119 optimal weight: 20.0000 chunk 230 optimal weight: 30.0000 chunk 89 optimal weight: 10.0000 chunk 140 optimal weight: 10.0000 chunk 171 optimal weight: 50.0000 chunk 266 optimal weight: 0.9990 overall best weight: 6.9994 ------------------------------------------------------------------------------- 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: 0.6587 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 14978 Z= 0.277 Angle : 0.611 11.602 20883 Z= 0.362 Chirality : 0.048 0.455 2860 Planarity : 0.004 0.045 2986 Dihedral : 10.858 102.999 3224 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 1.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 14.29 % Allowed : 0.00 % 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: -1.02 (0.15), residues: 2958 helix: 1.20 (0.15), residues: 1321 sheet: -0.91 (0.36), residues: 220 loop : -2.62 (0.15), residues: 1417 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 88 residues out of total 2605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 87 time to evaluate : 1.782 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 87 average time/residue: 0.1357 time to fit residues: 24.9516 Evaluate side-chains 86 residues out of total 2605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 1.790 ------------------------------------------------------------------------------- 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: 30.0000 chunk 82 optimal weight: 30.0000 chunk 222 optimal weight: 10.0000 chunk 181 optimal weight: 40.0000 chunk 73 optimal weight: 0.0030 chunk 267 optimal weight: 50.0000 chunk 288 optimal weight: 0.1980 chunk 238 optimal weight: 40.0000 chunk 265 optimal weight: 50.0000 chunk 91 optimal weight: 0.0770 chunk 214 optimal weight: 10.0000 overall best weight: 4.0556 ------------------------------------------------------------------------------- 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: 0.6592 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.077 14978 Z= 0.153 Angle : 0.483 7.922 20883 Z= 0.287 Chirality : 0.047 0.451 2860 Planarity : 0.003 0.030 2986 Dihedral : 9.975 105.088 3224 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 1.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % 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 : 0.00 % 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: -0.41 (0.16), residues: 2958 helix: 1.80 (0.15), residues: 1326 sheet: -0.59 (0.37), residues: 222 loop : -2.41 (0.16), residues: 1410 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 : 1.682 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.1326 time to fit residues: 24.2016 Evaluate side-chains 87 residues out of total 2605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 1.556 ------------------------------------------------------------------------------- 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: 8.9990 chunk 201 optimal weight: 50.0000 chunk 138 optimal weight: 50.0000 chunk 29 optimal weight: 30.0000 chunk 127 optimal weight: 30.0000 chunk 179 optimal weight: 50.0000 chunk 268 optimal weight: 50.0000 chunk 284 optimal weight: 40.0000 chunk 140 optimal weight: 40.0000 chunk 254 optimal weight: 40.0000 chunk 76 optimal weight: 30.0000 overall best weight: 27.7998 ------------------------------------------------------------------------------- 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: 0.6965 moved from start: 0.4954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.179 14978 Z= 0.599 Angle : 1.079 13.416 20883 Z= 0.687 Chirality : 0.059 0.570 2860 Planarity : 0.008 0.043 2986 Dihedral : 12.863 92.911 3224 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.54 % Allowed : 16.09 % Favored : 83.37 % 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 : 0.14 % 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: -3.41 (0.14), residues: 2958 helix: -1.32 (0.13), residues: 1297 sheet: -1.67 (0.39), residues: 191 loop : -3.33 (0.14), residues: 1470 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 : 1.695 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.1389 time to fit residues: 25.7236 Evaluate side-chains 86 residues out of total 2605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 1.601 ------------------------------------------------------------------------------- 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: 1.9990 chunk 161 optimal weight: 8.9990 chunk 4 optimal weight: 3.9990 chunk 211 optimal weight: 7.9990 chunk 117 optimal weight: 8.9990 chunk 242 optimal weight: 5.9990 chunk 196 optimal weight: 50.0000 chunk 0 optimal weight: 60.0000 chunk 145 optimal weight: 4.9990 chunk 255 optimal weight: 50.0000 chunk 71 optimal weight: 7.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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: 0.6801 moved from start: 0.4741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 14978 Z= 0.158 Angle : 0.540 9.758 20883 Z= 0.322 Chirality : 0.047 0.552 2860 Planarity : 0.003 0.032 2986 Dihedral : 11.096 94.235 3224 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 1.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.30 % Favored : 90.70 % 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: -1.89 (0.15), residues: 2958 helix: 0.50 (0.15), residues: 1309 sheet: -1.80 (0.35), residues: 209 loop : -3.00 (0.15), residues: 1440 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 88 residues out of total 2605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 1.669 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.1312 time to fit residues: 23.8819 Evaluate side-chains 86 residues out of total 2605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 1.794 ------------------------------------------------------------------------------- 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: 50.0000 chunk 56 optimal weight: 30.0000 chunk 166 optimal weight: 6.9990 chunk 70 optimal weight: 40.0000 chunk 284 optimal weight: 50.0000 chunk 236 optimal weight: 6.9990 chunk 131 optimal weight: 40.0000 chunk 23 optimal weight: 7.9990 chunk 94 optimal weight: 3.9990 chunk 149 optimal weight: 9.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- 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: 0.6825 moved from start: 0.4971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 14978 Z= 0.185 Angle : 0.544 13.917 20883 Z= 0.325 Chirality : 0.046 0.377 2860 Planarity : 0.003 0.043 2986 Dihedral : 10.371 97.032 3224 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.12 % Favored : 86.88 % 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: -1.61 (0.16), residues: 2958 helix: 0.82 (0.15), residues: 1313 sheet: -1.69 (0.36), residues: 215 loop : -2.95 (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 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 : 1.565 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.1255 time to fit residues: 22.8426 Evaluate side-chains 86 residues out of total 2605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 1.551 ------------------------------------------------------------------------------- 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: 4.9990 chunk 32 optimal weight: 40.0000 chunk 162 optimal weight: 40.0000 chunk 207 optimal weight: 20.0000 chunk 160 optimal weight: 50.0000 chunk 239 optimal weight: 50.0000 chunk 158 optimal weight: 20.0000 chunk 283 optimal weight: 40.0000 chunk 177 optimal weight: 40.0000 chunk 172 optimal weight: 8.9990 chunk 130 optimal weight: 0.8980 overall best weight: 10.9792 ------------------------------------------------------------------------------- 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: 0.6866 moved from start: 0.5298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 14978 Z= 0.244 Angle : 0.615 12.594 20883 Z= 0.374 Chirality : 0.048 0.379 2860 Planarity : 0.004 0.040 2986 Dihedral : 10.730 89.981 3224 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.39 % Favored : 86.61 % 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: -1.96 (0.15), residues: 2958 helix: 0.43 (0.15), residues: 1296 sheet: -1.62 (0.37), residues: 208 loop : -3.02 (0.15), residues: 1454 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 87 residues out of total 2605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 1.558 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.1328 time to fit residues: 23.9634 Evaluate side-chains 87 residues out of total 2605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 1.637 ------------------------------------------------------------------------------- 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: 40.0000 chunk 113 optimal weight: 7.9990 chunk 169 optimal weight: 30.0000 chunk 85 optimal weight: 40.0000 chunk 55 optimal weight: 4.9990 chunk 54 optimal weight: 20.0000 chunk 180 optimal weight: 50.0000 chunk 193 optimal weight: 40.0000 chunk 140 optimal weight: 30.0000 chunk 26 optimal weight: 0.0670 chunk 222 optimal weight: 9.9990 overall best weight: 8.6128 ------------------------------------------------------------------------------- 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: 0.6844 moved from start: 0.5428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14978 Z= 0.205 Angle : 0.586 18.052 20883 Z= 0.342 Chirality : 0.049 0.730 2860 Planarity : 0.003 0.041 2986 Dihedral : 10.152 95.284 3224 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.03 % Allowed : 12.71 % Favored : 87.25 % 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 : 0.03 % 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 (0.16), residues: 2958 helix: 0.67 (0.15), residues: 1317 sheet: -1.67 (0.37), residues: 204 loop : -3.03 (0.15), residues: 1437 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 87 residues out of total 2605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 1.543 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.1316 time to fit residues: 23.8553 Evaluate side-chains 86 residues out of total 2605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 1.517 ------------------------------------------------------------------------------- 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: 50.0000 chunk 271 optimal weight: 40.0000 chunk 247 optimal weight: 40.0000 chunk 264 optimal weight: 9.9990 chunk 158 optimal weight: 7.9990 chunk 115 optimal weight: 40.0000 chunk 207 optimal weight: 50.0000 chunk 81 optimal weight: 30.0000 chunk 238 optimal weight: 30.0000 chunk 249 optimal weight: 50.0000 chunk 263 optimal weight: 50.0000 overall best weight: 23.5996 ------------------------------------------------------------------------------- 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: 0.6985 moved from start: 0.6011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.124 14978 Z= 0.497 Angle : 0.945 11.730 20883 Z= 0.596 Chirality : 0.056 0.502 2860 Planarity : 0.006 0.044 2986 Dihedral : 11.798 85.748 3224 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.27 % Allowed : 18.53 % Favored : 81.20 % 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 : 0.17 % 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: -3.41 (0.14), residues: 2958 helix: -0.96 (0.14), residues: 1280 sheet: -2.12 (0.37), residues: 188 loop : -3.61 (0.14), residues: 1490 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 87 residues out of total 2605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 1.493 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.1341 time to fit residues: 24.2310 Evaluate side-chains 87 residues out of total 2605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 1.654 ------------------------------------------------------------------------------- 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: 8.9990 chunk 279 optimal weight: 7.9990 chunk 170 optimal weight: 30.0000 chunk 132 optimal weight: 30.0000 chunk 194 optimal weight: 20.0000 chunk 292 optimal weight: 10.0000 chunk 269 optimal weight: 30.0000 chunk 233 optimal weight: 40.0000 chunk 24 optimal weight: 9.9990 chunk 180 optimal weight: 9.9990 chunk 143 optimal weight: 20.0000 overall best weight: 9.3992 ------------------------------------------------------------------------------- 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: 0.6884 moved from start: 0.5942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14978 Z= 0.220 Angle : 0.608 11.925 20883 Z= 0.365 Chirality : 0.048 0.437 2860 Planarity : 0.004 0.035 2986 Dihedral : 10.744 89.918 3224 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.49 % Favored : 86.51 % 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 : 0.03 % 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: -2.48 (0.15), residues: 2958 helix: 0.06 (0.14), residues: 1300 sheet: -1.98 (0.37), residues: 192 loop : -3.37 (0.15), residues: 1466 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 : 1.742 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.1399 time to fit residues: 25.3820 Evaluate side-chains 87 residues out of total 2605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 1.616 ------------------------------------------------------------------------------- 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: 0.5980 chunk 248 optimal weight: 6.9990 chunk 71 optimal weight: 5.9990 chunk 215 optimal weight: 50.0000 chunk 34 optimal weight: 40.0000 chunk 64 optimal weight: 50.0000 chunk 233 optimal weight: 40.0000 chunk 97 optimal weight: 40.0000 chunk 239 optimal weight: 40.0000 chunk 29 optimal weight: 40.0000 chunk 43 optimal weight: 10.0000 overall best weight: 12.7192 ------------------------------------------------------------------------------- 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 = 0.4185 r_free = 0.4185 target = 0.213514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.176388 restraints weight = 237753.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.180150 restraints weight = 151828.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.180137 restraints weight = 128804.694| |-----------------------------------------------------------------------------| r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.6128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 14978 Z= 0.277 Angle : 0.666 12.105 20883 Z= 0.406 Chirality : 0.049 0.324 2860 Planarity : 0.004 0.039 2986 Dihedral : 10.808 86.461 3224 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.03 % Allowed : 17.78 % Favored : 82.18 % 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: -2.65 (0.15), residues: 2958 helix: -0.07 (0.14), residues: 1289 sheet: -2.08 (0.37), residues: 192 loop : -3.43 (0.15), residues: 1477 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: 1858.79 seconds wall clock time: 33 minutes 53.97 seconds (2033.97 seconds total)