Starting phenix.real_space_refine on Tue Apr 9 07:13:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lbf_23253/04_2024/7lbf_23253.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lbf_23253/04_2024/7lbf_23253.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lbf_23253/04_2024/7lbf_23253.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lbf_23253/04_2024/7lbf_23253.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lbf_23253/04_2024/7lbf_23253.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lbf_23253/04_2024/7lbf_23253.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.033 sd= 0.674 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: 4 Type Number sf(0) Gaussians S 74 5.16 5 C 9955 2.51 5 N 2596 2.21 5 O 3031 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 15656 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 5203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 647, 5203 Classifications: {'peptide': 647} Link IDs: {'PCIS': 2, 'PTRANS': 30, 'TRANS': 614} Chain breaks: 4 Chain: "B" Number of atoms: 1860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1860 Classifications: {'peptide': 236} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 216} Chain: "C" Number of atoms: 2484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2484 Classifications: {'peptide': 299} Link IDs: {'PCIS': 3, 'PTRANS': 15, 'TRANS': 280} Chain breaks: 3 Chain: "D" Number of atoms: 2142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2142 Classifications: {'peptide': 274} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 258} Chain breaks: 3 Chain: "E" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 798 Classifications: {'peptide': 106} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 98} Chain: "F" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 927 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "G" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 850 Classifications: {'peptide': 111} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 103} Chain: "H" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1001 Classifications: {'peptide': 129} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 125} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 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: "J" 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: "K" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "D" 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 Time building chain proxies: 8.78, per 1000 atoms: 0.56 Number of scatterers: 15656 At special positions: 0 Unit cell: (95.9494, 177.033, 167.574, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 74 16.00 O 3031 8.00 N 2596 7.00 C 9955 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 95 " - pdb=" SG CYS B 47 " distance=2.03 Simple disulfide: pdb=" SG CYS A 195 " - pdb=" SG CYS A 211 " distance=2.03 Simple disulfide: pdb=" SG CYS A 330 " - pdb=" SG CYS A 383 " distance=2.03 Simple disulfide: pdb=" SG CYS A 495 " - pdb=" SG CYS A 522 " distance=2.03 Simple disulfide: pdb=" SG CYS A 571 " - pdb=" SG CYS A 624 " distance=2.03 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS C 343 " distance=2.03 Simple disulfide: pdb=" SG CYS B 154 " - pdb=" SG CYS B 159 " distance=2.03 Simple disulfide: pdb=" SG CYS C 141 " - pdb=" SG CYS C 149 " distance=2.04 Simple disulfide: pdb=" SG CYS C 167 " - pdb=" SG CYS C 218 " distance=2.03 Simple disulfide: pdb=" SG CYS D 49 " - pdb=" SG CYS D 100 " distance=2.03 Simple disulfide: pdb=" SG CYS D 150 " - pdb=" SG CYS D 189 " distance=2.03 Simple disulfide: pdb=" SG CYS D 235 " - pdb=" SG CYS D 290 " distance=2.03 Simple disulfide: pdb=" SG CYS E 46 " - pdb=" SG CYS E 111 " distance=2.03 Simple disulfide: pdb=" SG CYS F 45 " - pdb=" SG CYS F 119 " distance=2.03 Simple disulfide: pdb=" SG CYS G 46 " - pdb=" SG CYS G 116 " distance=2.03 Simple disulfide: pdb=" SG CYS H 45 " - pdb=" SG CYS H 119 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN K 4 " - " MAN K 5 " ALPHA1-3 " BMA K 3 " - " MAN K 4 " " MAN K 6 " - " MAN K 7 " ALPHA1-6 " BMA K 3 " - " MAN K 6 " BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " NAG-ASN " NAG A 801 " - " ASN A 192 " " NAG A 804 " - " ASN A 700 " " NAG B 301 " - " ASN B 74 " " NAG C 601 " - " ASN C 85 " " NAG C 603 " - " ASN C 155 " " NAG C 604 " - " ASN C 217 " " NAG C 605 " - " ASN C 240 " " NAG C 606 " - " ASN C 365 " " NAG C 608 " - " ASN C 452 " " NAG D 601 " - " ASN D 103 " " NAG D 602 " - " ASN D 179 " " NAG I 1 " - " ASN C 348 " " NAG J 1 " - " ASN C 431 " " NAG K 1 " - " ASN C 160 " Time building additional restraints: 6.31 Conformation dependent library (CDL) restraints added in 2.7 seconds 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3650 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 34 sheets defined 27.4% alpha, 25.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.87 Creating SS restraints... Processing helix chain 'A' and resid 93 through 98 Processing helix chain 'A' and resid 99 through 107 removed outlier: 3.602A pdb=" N PHE A 105 " --> pdb=" O LEU A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 122 Processing helix chain 'A' and resid 219 through 221 No H-bonds generated for 'chain 'A' and resid 219 through 221' Processing helix chain 'A' and resid 263 through 266 Processing helix chain 'A' and resid 289 through 294 Processing helix chain 'A' and resid 298 through 303 Processing helix chain 'A' and resid 308 through 316 Processing helix chain 'A' and resid 316 through 328 removed outlier: 3.668A pdb=" N TYR A 320 " --> pdb=" O SER A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 352 Processing helix chain 'A' and resid 354 through 359 removed outlier: 3.843A pdb=" N GLY A 358 " --> pdb=" O GLN A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 385 Processing helix chain 'A' and resid 396 through 409 Processing helix chain 'A' and resid 415 through 429 removed outlier: 3.741A pdb=" N LEU A 419 " --> pdb=" O ASP A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 435 Processing helix chain 'A' and resid 436 through 454 removed outlier: 3.620A pdb=" N LEU A 440 " --> pdb=" O PRO A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 475 removed outlier: 3.664A pdb=" N HIS A 475 " --> pdb=" O GLY A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 495 removed outlier: 3.761A pdb=" N CYS A 495 " --> pdb=" O GLU A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 507 Processing helix chain 'A' and resid 514 through 519 Processing helix chain 'A' and resid 520 through 524 Processing helix chain 'A' and resid 531 through 538 removed outlier: 3.674A pdb=" N LEU A 538 " --> pdb=" O ARG A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 559 Processing helix chain 'A' and resid 644 through 648 Processing helix chain 'A' and resid 671 through 680 Processing helix chain 'A' and resid 681 through 684 Processing helix chain 'A' and resid 707 through 710 Processing helix chain 'B' and resid 46 through 55 Processing helix chain 'B' and resid 66 through 70 Processing helix chain 'B' and resid 85 through 87 No H-bonds generated for 'chain 'B' and resid 85 through 87' Processing helix chain 'B' and resid 102 through 113 Processing helix chain 'B' and resid 117 through 128 Processing helix chain 'B' and resid 132 through 137 Processing helix chain 'B' and resid 163 through 167 Processing helix chain 'B' and resid 172 through 176 removed outlier: 3.509A pdb=" N THR B 175 " --> pdb=" O SER B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 217 No H-bonds generated for 'chain 'B' and resid 215 through 217' Processing helix chain 'B' and resid 218 through 236 removed outlier: 3.874A pdb=" N PHE B 222 " --> pdb=" O GLY B 218 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N HIS B 236 " --> pdb=" O PHE B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 253 removed outlier: 4.147A pdb=" N ARG B 244 " --> pdb=" O PRO B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 258 Processing helix chain 'C' and resid 112 through 114 No H-bonds generated for 'chain 'C' and resid 112 through 114' Processing helix chain 'C' and resid 146 through 159 Processing helix chain 'C' and resid 198 through 215 Processing helix chain 'C' and resid 222 through 230 Processing helix chain 'C' and resid 240 through 251 Processing helix chain 'C' and resid 321 through 335 Processing helix chain 'C' and resid 336 through 343 removed outlier: 6.479A pdb=" N GLU C 340 " --> pdb=" O TYR C 337 " (cutoff:3.500A) Proline residue: C 341 - end of helix Processing helix chain 'C' and resid 353 through 360 Processing helix chain 'C' and resid 361 through 364 Processing helix chain 'C' and resid 377 through 379 No H-bonds generated for 'chain 'C' and resid 377 through 379' Processing helix chain 'C' and resid 413 through 436 Processing helix chain 'C' and resid 453 through 458 removed outlier: 3.661A pdb=" N SER C 458 " --> pdb=" O SER C 454 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 95 Processing helix chain 'D' and resid 104 through 106 No H-bonds generated for 'chain 'D' and resid 104 through 106' Processing helix chain 'D' and resid 251 through 255 Processing helix chain 'E' and resid 102 through 106 Processing helix chain 'F' and resid 51 through 55 removed outlier: 3.901A pdb=" N TYR F 55 " --> pdb=" O PHE F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 110 through 114 Processing helix chain 'G' and resid 107 through 111 removed outlier: 4.087A pdb=" N VAL G 111 " --> pdb=" O THR G 108 " (cutoff:3.500A) Processing helix chain 'H' and resid 110 through 114 removed outlier: 3.669A pdb=" N THR H 114 " --> pdb=" O ALA H 111 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 50 through 52 Processing sheet with id=AA2, first strand: chain 'A' and resid 64 through 66 removed outlier: 4.145A pdb=" N SER A 64 " --> pdb=" O VAL A 89 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N GLN A 86 " --> pdb=" O GLN A 82 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N SER A 77 " --> pdb=" O PHE B 181 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N LEU B 183 " --> pdb=" O SER A 77 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ASN A 79 " --> pdb=" O LEU B 183 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N VAL B 178 " --> pdb=" O ALA B 194 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ALA B 194 " --> pdb=" O VAL B 178 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY B 180 " --> pdb=" O VAL B 192 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N PHE B 189 " --> pdb=" O VAL B 210 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 136 through 137 removed outlier: 5.985A pdb=" N ILE A 268 " --> pdb=" O VAL A 279 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N VAL A 279 " --> pdb=" O ILE A 268 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG A 270 " --> pdb=" O LEU A 277 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 182 through 184 Processing sheet with id=AA5, first strand: chain 'A' and resid 194 through 197 Processing sheet with id=AA6, first strand: chain 'A' and resid 527 through 528 Processing sheet with id=AA7, first strand: chain 'A' and resid 637 through 638 removed outlier: 6.501A pdb=" N THR A 637 " --> pdb=" O GLU A 705 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 82 through 83 removed outlier: 6.243A pdb=" N LEU B 82 " --> pdb=" O GLY B 170 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 99 through 100 removed outlier: 6.565A pdb=" N VAL B 99 " --> pdb=" O ARG C 234 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 151 through 155 Processing sheet with id=AB2, first strand: chain 'C' and resid 83 through 85 Processing sheet with id=AB3, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.978A pdb=" N GLY C 142 " --> pdb=" O TYR C 122 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 171 through 172 Processing sheet with id=AB5, first strand: chain 'C' and resid 184 through 189 removed outlier: 3.501A pdb=" N THR C 192 " --> pdb=" O VAL C 189 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 369 through 370 Processing sheet with id=AB7, first strand: chain 'C' and resid 381 through 383 Processing sheet with id=AB8, first strand: chain 'D' and resid 29 through 31 removed outlier: 3.683A pdb=" N PHE D 81 " --> pdb=" O GLY D 51 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 36 through 38 removed outlier: 6.411A pdb=" N LYS D 37 " --> pdb=" O TYR D 120 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ARG D 115 " --> pdb=" O CYS D 100 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N CYS D 100 " --> pdb=" O ARG D 115 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 136 through 141 Processing sheet with id=AC2, first strand: chain 'D' and resid 136 through 141 Processing sheet with id=AC3, first strand: chain 'D' and resid 145 through 148 Processing sheet with id=AC4, first strand: chain 'D' and resid 216 through 219 Processing sheet with id=AC5, first strand: chain 'D' and resid 224 through 226 Processing sheet with id=AC6, first strand: chain 'D' and resid 246 through 248 Processing sheet with id=AC7, first strand: chain 'E' and resid 27 through 30 removed outlier: 3.716A pdb=" N ALA E 93 " --> pdb=" O SER E 90 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 33 through 35 removed outlier: 6.399A pdb=" N LEU E 56 " --> pdb=" O TYR E 72 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N TYR E 72 " --> pdb=" O LEU E 56 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N TRP E 58 " --> pdb=" O LEU E 70 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 26 through 29 Processing sheet with id=AD1, first strand: chain 'F' and resid 33 through 34 removed outlier: 6.906A pdb=" N ILE F 57 " --> pdb=" O ILE F 73 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N ILE F 73 " --> pdb=" O ILE F 57 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N TRP F 59 " --> pdb=" O MET F 71 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 33 through 34 removed outlier: 3.754A pdb=" N ASP F 135 " --> pdb=" O ARG F 121 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 27 through 30 removed outlier: 3.841A pdb=" N ASP G 98 " --> pdb=" O SER G 95 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 33 through 35 removed outlier: 5.885A pdb=" N LEU G 34 " --> pdb=" O GLU G 133 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'G' and resid 81 through 82 removed outlier: 6.453A pdb=" N TRP G 63 " --> pdb=" O LEU G 75 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N TYR G 77 " --> pdb=" O LEU G 61 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N LEU G 61 " --> pdb=" O TYR G 77 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 26 through 30 Processing sheet with id=AD7, first strand: chain 'H' and resid 34 through 35 removed outlier: 4.011A pdb=" N SER H 56 " --> pdb=" O ASP H 122 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N VAL H 57 " --> pdb=" O SER H 73 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N SER H 73 " --> pdb=" O VAL H 57 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N TRP H 59 " --> pdb=" O VAL H 71 " (cutoff:3.500A) 643 hydrogen bonds defined for protein. 1647 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: 5.86 Time building geometry restraints manager: 6.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 4967 1.35 - 1.47: 3997 1.47 - 1.59: 6937 1.59 - 1.71: 0 1.71 - 1.83: 111 Bond restraints: 16012 Sorted by residual: bond pdb=" N THR B 38 " pdb=" CA THR B 38 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.08e+00 bond pdb=" N ASP E 24 " pdb=" CA ASP E 24 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.05e+00 bond pdb=" N GLU H 24 " pdb=" CA GLU H 24 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.91e+00 bond pdb=" N ASN C 81 " pdb=" CA ASN C 81 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.91e+00 bond pdb=" N ASP G 24 " pdb=" CA ASP G 24 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.90e+00 ... (remaining 16007 not shown) Histogram of bond angle deviations from ideal: 99.03 - 106.03: 399 106.03 - 113.03: 8864 113.03 - 120.03: 5351 120.03 - 127.03: 6984 127.03 - 134.03: 185 Bond angle restraints: 21783 Sorted by residual: angle pdb=" C3 MAN K 4 " pdb=" C2 MAN K 4 " pdb=" O2 MAN K 4 " ideal model delta sigma weight residual 111.77 104.78 6.99 3.00e+00 1.11e-01 5.42e+00 angle pdb=" C3 BMA K 3 " pdb=" C2 BMA K 3 " pdb=" O2 BMA K 3 " ideal model delta sigma weight residual 112.95 106.23 6.72 3.00e+00 1.11e-01 5.02e+00 angle pdb=" N GLN A 145 " pdb=" CA GLN A 145 " pdb=" C GLN A 145 " ideal model delta sigma weight residual 107.73 110.68 -2.95 1.34e+00 5.57e-01 4.85e+00 angle pdb=" CA CYS D 150 " pdb=" C CYS D 150 " pdb=" N ARG D 151 " ideal model delta sigma weight residual 114.76 117.26 -2.50 1.14e+00 7.69e-01 4.80e+00 angle pdb=" C3 MAN K 6 " pdb=" C2 MAN K 6 " pdb=" O2 MAN K 6 " ideal model delta sigma weight residual 111.77 105.22 6.55 3.00e+00 1.11e-01 4.77e+00 ... (remaining 21778 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.18: 9406 21.18 - 42.37: 463 42.37 - 63.55: 82 63.55 - 84.73: 29 84.73 - 105.91: 8 Dihedral angle restraints: 9988 sinusoidal: 4332 harmonic: 5656 Sorted by residual: dihedral pdb=" CB CYS B 144 " pdb=" SG CYS B 144 " pdb=" SG CYS C 343 " pdb=" CB CYS C 343 " ideal model delta sinusoidal sigma weight residual -86.00 -155.94 69.94 1 1.00e+01 1.00e-02 6.31e+01 dihedral pdb=" CB CYS A 571 " pdb=" SG CYS A 571 " pdb=" SG CYS A 624 " pdb=" CB CYS A 624 " ideal model delta sinusoidal sigma weight residual -86.00 -148.26 62.26 1 1.00e+01 1.00e-02 5.13e+01 dihedral pdb=" CB CYS A 195 " pdb=" SG CYS A 195 " pdb=" SG CYS A 211 " pdb=" CB CYS A 211 " ideal model delta sinusoidal sigma weight residual 93.00 148.00 -55.00 1 1.00e+01 1.00e-02 4.09e+01 ... (remaining 9985 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 2197 0.057 - 0.114: 301 0.114 - 0.170: 57 0.170 - 0.227: 1 0.227 - 0.284: 1 Chirality restraints: 2557 Sorted by residual: chirality pdb=" C5 BMA K 3 " pdb=" C4 BMA K 3 " pdb=" C6 BMA K 3 " pdb=" O5 BMA K 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" C1 NAG C 601 " pdb=" ND2 ASN C 85 " pdb=" C2 NAG C 601 " pdb=" O5 NAG C 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-01 2.50e+01 8.20e-01 chirality pdb=" C1 NAG C 606 " pdb=" ND2 ASN C 365 " pdb=" C2 NAG C 606 " pdb=" O5 NAG C 606 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-01 2.50e+01 6.05e-01 ... (remaining 2554 not shown) Planarity restraints: 2749 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 363 " 0.031 5.00e-02 4.00e+02 4.68e-02 3.51e+00 pdb=" N PRO A 364 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 364 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 364 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE F 123 " 0.017 2.00e-02 2.50e+03 1.25e-02 2.74e+00 pdb=" CG PHE F 123 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 PHE F 123 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE F 123 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE F 123 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE F 123 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE F 123 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN E 102 " -0.007 2.00e-02 2.50e+03 1.48e-02 2.18e+00 pdb=" CD GLN E 102 " 0.026 2.00e-02 2.50e+03 pdb=" OE1 GLN E 102 " -0.010 2.00e-02 2.50e+03 pdb=" NE2 GLN E 102 " -0.009 2.00e-02 2.50e+03 ... (remaining 2746 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 253 2.66 - 3.22: 14970 3.22 - 3.78: 23470 3.78 - 4.34: 34581 4.34 - 4.90: 56461 Nonbonded interactions: 129735 Sorted by model distance: nonbonded pdb=" NE2 GLN F 62 " pdb=" O GLN F 66 " model vdw 2.098 2.520 nonbonded pdb=" NH1 ARG A 264 " pdb=" OE1 GLU A 276 " model vdw 2.144 2.520 nonbonded pdb=" O LEU A 626 " pdb=" OG1 THR A 627 " model vdw 2.217 2.440 nonbonded pdb=" O GLN G 29 " pdb=" NE2 GLN G 128 " model vdw 2.226 2.520 nonbonded pdb=" O PRO C 345 " pdb=" NH2 ARG C 349 " model vdw 2.229 2.520 ... (remaining 129730 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 'I' selection = chain 'J' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.860 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: 0.020 Extract box with map and model: 4.830 Check model and map are aligned: 0.230 Set scattering table: 0.140 Process input model: 43.720 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.070 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:12.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16012 Z= 0.213 Angle : 0.557 6.986 21783 Z= 0.277 Chirality : 0.043 0.284 2557 Planarity : 0.003 0.047 2735 Dihedral : 13.180 105.915 6290 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.00 % Allowed : 0.06 % Favored : 99.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.65 % 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: 0.66 (0.19), residues: 1887 helix: 1.29 (0.27), residues: 397 sheet: 0.62 (0.23), residues: 483 loop : 0.09 (0.20), residues: 1007 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 330 HIS 0.003 0.001 HIS C 447 PHE 0.027 0.001 PHE F 123 TYR 0.016 0.001 TYR H 136 ARG 0.011 0.000 ARG F 124 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 300 time to evaluate : 1.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 64 LYS cc_start: 0.9269 (tmmt) cc_final: 0.8529 (tmmt) REVERT: C 147 MET cc_start: 0.8743 (mmm) cc_final: 0.8530 (mmm) REVERT: C 377 MET cc_start: 0.8237 (mmp) cc_final: 0.7793 (mmp) REVERT: C 462 TRP cc_start: 0.8412 (p90) cc_final: 0.8140 (p90) REVERT: D 31 LEU cc_start: 0.9196 (tt) cc_final: 0.8989 (tp) REVERT: D 33 ASN cc_start: 0.7998 (t0) cc_final: 0.7613 (t0) REVERT: D 58 GLN cc_start: 0.8174 (tp40) cc_final: 0.7959 (tp40) REVERT: D 176 GLN cc_start: 0.8415 (mt0) cc_final: 0.8206 (mt0) REVERT: G 70 GLN cc_start: 0.8363 (mt0) cc_final: 0.8108 (mt0) outliers start: 0 outliers final: 1 residues processed: 300 average time/residue: 1.4408 time to fit residues: 473.6978 Evaluate side-chains 235 residues out of total 1711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 234 time to evaluate : 1.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 134 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 158 optimal weight: 3.9990 chunk 142 optimal weight: 5.9990 chunk 79 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 96 optimal weight: 0.7980 chunk 76 optimal weight: 0.8980 chunk 147 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 109 optimal weight: 0.8980 chunk 170 optimal weight: 0.9980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN B 115 ASN C 383 ASN D 106 GLN D 116 HIS D 162 HIS F 24 GLN F 62 GLN F 66 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 16012 Z= 0.303 Angle : 0.616 8.406 21783 Z= 0.317 Chirality : 0.046 0.184 2557 Planarity : 0.004 0.043 2735 Dihedral : 7.267 76.032 2709 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.22 % Allowed : 9.65 % Favored : 88.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.65 % 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: 0.58 (0.20), residues: 1887 helix: 1.37 (0.27), residues: 406 sheet: 0.65 (0.23), residues: 481 loop : -0.08 (0.20), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 183 HIS 0.009 0.001 HIS D 162 PHE 0.026 0.002 PHE H 52 TYR 0.023 0.002 TYR D 206 ARG 0.010 0.001 ARG E 41 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 239 time to evaluate : 1.788 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 285 GLN cc_start: 0.9039 (OUTLIER) cc_final: 0.8719 (tt0) REVERT: A 534 ARG cc_start: 0.7883 (mtp180) cc_final: 0.7664 (mtm180) REVERT: C 377 MET cc_start: 0.8033 (mmp) cc_final: 0.7741 (mmp) REVERT: C 462 TRP cc_start: 0.8467 (p90) cc_final: 0.8266 (p90) REVERT: D 31 LEU cc_start: 0.9199 (tt) cc_final: 0.8988 (OUTLIER) REVERT: D 33 ASN cc_start: 0.8038 (t0) cc_final: 0.7624 (t0) REVERT: D 58 GLN cc_start: 0.8207 (tp40) cc_final: 0.7909 (tp40) REVERT: D 176 GLN cc_start: 0.8223 (mt0) cc_final: 0.7937 (mt0) REVERT: E 68 LYS cc_start: 0.8462 (ttpt) cc_final: 0.8064 (ttpt) REVERT: F 50 TYR cc_start: 0.8738 (p90) cc_final: 0.7974 (p90) REVERT: F 104 MET cc_start: 0.8489 (tmm) cc_final: 0.8078 (tmm) REVERT: G 70 GLN cc_start: 0.8222 (mt0) cc_final: 0.8000 (mt0) REVERT: H 25 GLU cc_start: 0.8151 (mp0) cc_final: 0.7766 (mp0) outliers start: 38 outliers final: 18 residues processed: 257 average time/residue: 1.4264 time to fit residues: 402.0243 Evaluate side-chains 238 residues out of total 1711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 220 time to evaluate : 1.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 285 GLN Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 414 ASP Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 133 MET Chi-restraints excluded: chain D residue 143 ASP Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain G residue 102 LYS Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 51 THR Chi-restraints excluded: chain H residue 77 ASP Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 145 GLN Chi-restraints excluded: chain H residue 147 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 94 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 142 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 171 optimal weight: 1.9990 chunk 184 optimal weight: 1.9990 chunk 152 optimal weight: 0.6980 chunk 169 optimal weight: 0.0980 chunk 58 optimal weight: 2.9990 chunk 137 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 GLN ** A 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 480 HIS B 115 ASN ** C 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 116 HIS D 162 HIS F 24 GLN F 66 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 16012 Z= 0.265 Angle : 0.571 8.839 21783 Z= 0.293 Chirality : 0.044 0.183 2557 Planarity : 0.004 0.045 2735 Dihedral : 6.817 66.159 2707 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.63 % Allowed : 12.22 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.65 % 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: 0.50 (0.20), residues: 1887 helix: 1.42 (0.27), residues: 406 sheet: 0.52 (0.24), residues: 481 loop : -0.15 (0.20), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 183 HIS 0.004 0.001 HIS C 447 PHE 0.023 0.002 PHE H 52 TYR 0.020 0.001 TYR D 206 ARG 0.008 0.001 ARG E 41 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 247 time to evaluate : 1.768 Fit side-chains revert: symmetry clash REVERT: A 285 GLN cc_start: 0.9087 (OUTLIER) cc_final: 0.8887 (tt0) REVERT: A 529 ASP cc_start: 0.7885 (p0) cc_final: 0.7563 (p0) REVERT: B 54 CYS cc_start: 0.8245 (p) cc_final: 0.7939 (p) REVERT: B 64 LYS cc_start: 0.9383 (tmmm) cc_final: 0.9181 (tmmm) REVERT: C 147 MET cc_start: 0.8864 (mmm) cc_final: 0.8458 (mmm) REVERT: D 31 LEU cc_start: 0.9169 (tt) cc_final: 0.8952 (tp) REVERT: D 33 ASN cc_start: 0.8039 (t0) cc_final: 0.7618 (t0) REVERT: D 48 ARG cc_start: 0.7609 (OUTLIER) cc_final: 0.7217 (ptm-80) REVERT: D 58 GLN cc_start: 0.8231 (tp40) cc_final: 0.7888 (tp40) REVERT: D 165 GLU cc_start: 0.7663 (mp0) cc_final: 0.6691 (mp0) REVERT: D 176 GLN cc_start: 0.8284 (mt0) cc_final: 0.7981 (mt0) REVERT: D 215 ASP cc_start: 0.7590 (p0) cc_final: 0.7310 (p0) REVERT: E 68 LYS cc_start: 0.8471 (ttpt) cc_final: 0.8063 (ttpt) REVERT: F 50 TYR cc_start: 0.8762 (p90) cc_final: 0.7807 (p90) REVERT: F 104 MET cc_start: 0.8403 (tmm) cc_final: 0.8049 (tmm) REVERT: H 25 GLU cc_start: 0.8130 (mp0) cc_final: 0.7764 (mp0) outliers start: 45 outliers final: 23 residues processed: 272 average time/residue: 1.3804 time to fit residues: 416.7466 Evaluate side-chains 251 residues out of total 1711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 226 time to evaluate : 2.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 285 GLN Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 414 ASP Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 48 ARG Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain G residue 134 ILE Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 69 GLU Chi-restraints excluded: chain H residue 77 ASP Chi-restraints excluded: chain H residue 145 GLN Chi-restraints excluded: chain H residue 147 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 168 optimal weight: 0.1980 chunk 128 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 171 optimal weight: 0.6980 chunk 181 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 162 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 106 GLN D 116 HIS ** F 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 66 GLN ** G 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 97 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16012 Z= 0.226 Angle : 0.547 7.584 21783 Z= 0.281 Chirality : 0.043 0.181 2557 Planarity : 0.004 0.040 2735 Dihedral : 6.537 60.464 2707 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.10 % Allowed : 14.09 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.65 % 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: 0.50 (0.20), residues: 1887 helix: 1.47 (0.27), residues: 407 sheet: 0.50 (0.24), residues: 479 loop : -0.17 (0.20), residues: 1001 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 330 HIS 0.003 0.001 HIS G 54 PHE 0.016 0.002 PHE H 52 TYR 0.019 0.001 TYR D 206 ARG 0.010 0.000 ARG E 41 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 240 time to evaluate : 1.779 Fit side-chains revert: symmetry clash REVERT: B 54 CYS cc_start: 0.8266 (p) cc_final: 0.7996 (p) REVERT: B 64 LYS cc_start: 0.9350 (tmmm) cc_final: 0.9123 (tmmm) REVERT: C 215 GLN cc_start: 0.8730 (OUTLIER) cc_final: 0.8405 (mt0) REVERT: C 370 THR cc_start: 0.9328 (m) cc_final: 0.8991 (m) REVERT: C 377 MET cc_start: 0.8261 (mmp) cc_final: 0.7906 (mmt) REVERT: D 31 LEU cc_start: 0.9138 (tt) cc_final: 0.8917 (tp) REVERT: D 33 ASN cc_start: 0.8115 (t0) cc_final: 0.7714 (t0) REVERT: D 48 ARG cc_start: 0.7536 (OUTLIER) cc_final: 0.7232 (ptm-80) REVERT: D 58 GLN cc_start: 0.8186 (tp40) cc_final: 0.7820 (tp40) REVERT: D 165 GLU cc_start: 0.7640 (mp0) cc_final: 0.6704 (mp0) REVERT: D 176 GLN cc_start: 0.8298 (mt0) cc_final: 0.8072 (mt0) REVERT: E 68 LYS cc_start: 0.8467 (ttpt) cc_final: 0.8157 (ttpt) REVERT: F 93 MET cc_start: 0.8624 (mtt) cc_final: 0.8405 (mtt) REVERT: G 76 ILE cc_start: 0.8360 (OUTLIER) cc_final: 0.8129 (mp) REVERT: G 107 GLU cc_start: 0.6912 (mm-30) cc_final: 0.6604 (mm-30) REVERT: H 25 GLU cc_start: 0.8114 (mp0) cc_final: 0.7788 (mp0) REVERT: H 42 ARG cc_start: 0.7826 (OUTLIER) cc_final: 0.7050 (tmm-80) outliers start: 53 outliers final: 28 residues processed: 270 average time/residue: 1.2898 time to fit residues: 385.4633 Evaluate side-chains 259 residues out of total 1711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 227 time to evaluate : 1.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 215 GLN Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 414 ASP Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 48 ARG Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 133 MET Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 76 ILE Chi-restraints excluded: chain G residue 102 LYS Chi-restraints excluded: chain G residue 134 ILE Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 42 ARG Chi-restraints excluded: chain H residue 51 THR Chi-restraints excluded: chain H residue 77 ASP Chi-restraints excluded: chain H residue 145 GLN Chi-restraints excluded: chain H residue 147 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 151 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 2 optimal weight: 7.9990 chunk 135 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 155 optimal weight: 2.9990 chunk 125 optimal weight: 0.0010 chunk 0 optimal weight: 4.9990 chunk 92 optimal weight: 3.9990 chunk 163 optimal weight: 0.7980 chunk 45 optimal weight: 4.9990 overall best weight: 1.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 383 ASN D 33 ASN ** F 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 66 GLN ** G 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 97 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 16012 Z= 0.341 Angle : 0.596 8.328 21783 Z= 0.305 Chirality : 0.045 0.180 2557 Planarity : 0.004 0.041 2735 Dihedral : 6.705 61.990 2707 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.74 % Allowed : 15.15 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.65 % 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: 0.36 (0.20), residues: 1887 helix: 1.42 (0.27), residues: 407 sheet: 0.38 (0.24), residues: 482 loop : -0.27 (0.20), residues: 998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 330 HIS 0.004 0.001 HIS C 447 PHE 0.021 0.002 PHE H 52 TYR 0.025 0.002 TYR D 206 ARG 0.011 0.001 ARG E 41 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 231 time to evaluate : 1.826 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 596 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8658 (mm) REVERT: B 54 CYS cc_start: 0.8259 (p) cc_final: 0.8033 (p) REVERT: B 64 LYS cc_start: 0.9357 (tmmm) cc_final: 0.9071 (tmmm) REVERT: C 165 GLN cc_start: 0.8588 (OUTLIER) cc_final: 0.7997 (mt0) REVERT: C 215 GLN cc_start: 0.8774 (OUTLIER) cc_final: 0.8297 (mm110) REVERT: C 370 THR cc_start: 0.9368 (m) cc_final: 0.8997 (m) REVERT: C 377 MET cc_start: 0.8298 (OUTLIER) cc_final: 0.8006 (mpt) REVERT: D 31 LEU cc_start: 0.9154 (tt) cc_final: 0.8916 (tp) REVERT: D 33 ASN cc_start: 0.8137 (t0) cc_final: 0.7732 (t0) REVERT: D 58 GLN cc_start: 0.8144 (tp40) cc_final: 0.7817 (tp40) REVERT: D 176 GLN cc_start: 0.8333 (mt0) cc_final: 0.8018 (mt0) REVERT: D 215 ASP cc_start: 0.7665 (p0) cc_final: 0.7364 (p0) REVERT: E 68 LYS cc_start: 0.8466 (ttpt) cc_final: 0.8163 (ttpt) REVERT: G 76 ILE cc_start: 0.8389 (OUTLIER) cc_final: 0.8145 (mp) REVERT: G 107 GLU cc_start: 0.6907 (mm-30) cc_final: 0.6652 (mm-30) REVERT: H 25 GLU cc_start: 0.8137 (mp0) cc_final: 0.7813 (mp0) REVERT: H 42 ARG cc_start: 0.7863 (OUTLIER) cc_final: 0.7079 (tmm-80) REVERT: H 123 ARG cc_start: 0.8191 (OUTLIER) cc_final: 0.4810 (ttm-80) outliers start: 64 outliers final: 39 residues processed: 269 average time/residue: 1.2967 time to fit residues: 386.7368 Evaluate side-chains 271 residues out of total 1711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 225 time to evaluate : 1.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 285 GLN Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 477 MET Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 692 THR Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 165 GLN Chi-restraints excluded: chain C residue 215 GLN Chi-restraints excluded: chain C residue 374 THR Chi-restraints excluded: chain C residue 377 MET Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 414 ASP Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 133 MET Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain E residue 99 LEU Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 76 ILE Chi-restraints excluded: chain G residue 102 LYS Chi-restraints excluded: chain G residue 134 ILE Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 42 ARG Chi-restraints excluded: chain H residue 51 THR Chi-restraints excluded: chain H residue 77 ASP Chi-restraints excluded: chain H residue 123 ARG Chi-restraints excluded: chain H residue 145 GLN Chi-restraints excluded: chain H residue 147 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 61 optimal weight: 1.9990 chunk 163 optimal weight: 0.3980 chunk 35 optimal weight: 3.9990 chunk 106 optimal weight: 0.9990 chunk 44 optimal weight: 0.1980 chunk 181 optimal weight: 1.9990 chunk 150 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 116 HIS F 24 GLN F 66 GLN ** G 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16012 Z= 0.224 Angle : 0.547 7.539 21783 Z= 0.280 Chirality : 0.043 0.178 2557 Planarity : 0.004 0.039 2735 Dihedral : 6.437 56.078 2707 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.27 % Allowed : 16.20 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.65 % 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: 0.43 (0.20), residues: 1887 helix: 1.58 (0.27), residues: 401 sheet: 0.41 (0.24), residues: 477 loop : -0.25 (0.20), residues: 1009 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 330 HIS 0.003 0.001 HIS G 54 PHE 0.014 0.001 PHE H 52 TYR 0.022 0.001 TYR D 206 ARG 0.011 0.000 ARG E 41 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 235 time to evaluate : 2.045 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 596 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8694 (mm) REVERT: B 54 CYS cc_start: 0.8283 (p) cc_final: 0.8063 (p) REVERT: B 64 LYS cc_start: 0.9349 (tmmm) cc_final: 0.9037 (tmmm) REVERT: C 165 GLN cc_start: 0.8564 (OUTLIER) cc_final: 0.8000 (mt0) REVERT: C 215 GLN cc_start: 0.8835 (OUTLIER) cc_final: 0.8427 (mm110) REVERT: C 370 THR cc_start: 0.9380 (OUTLIER) cc_final: 0.9033 (m) REVERT: C 377 MET cc_start: 0.8234 (mmp) cc_final: 0.7861 (mpt) REVERT: D 33 ASN cc_start: 0.8092 (t0) cc_final: 0.7690 (t0) REVERT: D 58 GLN cc_start: 0.8186 (tp40) cc_final: 0.7855 (tp40) REVERT: D 176 GLN cc_start: 0.8308 (mt0) cc_final: 0.7992 (mt0) REVERT: E 68 LYS cc_start: 0.8462 (ttpt) cc_final: 0.8160 (ttpt) REVERT: G 76 ILE cc_start: 0.8310 (OUTLIER) cc_final: 0.8099 (mp) REVERT: G 107 GLU cc_start: 0.6854 (OUTLIER) cc_final: 0.6600 (mm-30) REVERT: H 42 ARG cc_start: 0.7859 (OUTLIER) cc_final: 0.7088 (tmm-80) REVERT: H 123 ARG cc_start: 0.8155 (OUTLIER) cc_final: 0.4792 (ttm-80) outliers start: 56 outliers final: 36 residues processed: 266 average time/residue: 1.2687 time to fit residues: 376.8330 Evaluate side-chains 270 residues out of total 1711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 226 time to evaluate : 1.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 285 GLN Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 477 MET Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 692 THR Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 165 GLN Chi-restraints excluded: chain C residue 215 GLN Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 414 ASP Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 76 ILE Chi-restraints excluded: chain G residue 102 LYS Chi-restraints excluded: chain G residue 107 GLU Chi-restraints excluded: chain G residue 134 ILE Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 42 ARG Chi-restraints excluded: chain H residue 51 THR Chi-restraints excluded: chain H residue 77 ASP Chi-restraints excluded: chain H residue 123 ARG Chi-restraints excluded: chain H residue 145 GLN Chi-restraints excluded: chain H residue 147 THR Chi-restraints excluded: chain H residue 152 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 175 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 132 optimal weight: 0.9980 chunk 102 optimal weight: 0.8980 chunk 153 optimal weight: 0.7980 chunk 101 optimal weight: 0.5980 chunk 181 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 110 optimal weight: 0.3980 chunk 83 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 116 HIS F 24 GLN F 66 GLN ** G 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16012 Z= 0.201 Angle : 0.551 10.588 21783 Z= 0.280 Chirality : 0.042 0.230 2557 Planarity : 0.004 0.039 2735 Dihedral : 6.250 54.725 2707 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.22 % Allowed : 16.61 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.65 % 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: 0.45 (0.20), residues: 1887 helix: 1.65 (0.27), residues: 399 sheet: 0.38 (0.24), residues: 480 loop : -0.23 (0.20), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 330 HIS 0.003 0.001 HIS C 447 PHE 0.016 0.001 PHE A 304 TYR 0.022 0.001 TYR B 169 ARG 0.012 0.000 ARG E 41 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 237 time to evaluate : 2.105 Fit side-chains revert: symmetry clash REVERT: A 108 GLN cc_start: 0.7976 (pm20) cc_final: 0.7742 (pm20) REVERT: A 596 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8669 (mm) REVERT: B 54 CYS cc_start: 0.8288 (p) cc_final: 0.8065 (p) REVERT: B 64 LYS cc_start: 0.9338 (tmmm) cc_final: 0.9036 (tmmm) REVERT: B 237 GLN cc_start: 0.8608 (mp10) cc_final: 0.8319 (mp10) REVERT: C 165 GLN cc_start: 0.8493 (OUTLIER) cc_final: 0.7957 (mt0) REVERT: C 215 GLN cc_start: 0.8901 (OUTLIER) cc_final: 0.8421 (mm110) REVERT: C 370 THR cc_start: 0.9349 (OUTLIER) cc_final: 0.9007 (m) REVERT: C 377 MET cc_start: 0.8161 (mmp) cc_final: 0.7807 (mpt) REVERT: C 435 GLN cc_start: 0.8342 (OUTLIER) cc_final: 0.7857 (tm-30) REVERT: D 33 ASN cc_start: 0.8072 (t0) cc_final: 0.7674 (t0) REVERT: D 58 GLN cc_start: 0.8180 (tp40) cc_final: 0.7797 (tp-100) REVERT: D 165 GLU cc_start: 0.7801 (mp0) cc_final: 0.7448 (mp0) REVERT: D 176 GLN cc_start: 0.8300 (mt0) cc_final: 0.7997 (mt0) REVERT: D 215 ASP cc_start: 0.7733 (p0) cc_final: 0.7412 (p0) REVERT: E 68 LYS cc_start: 0.8461 (ttpt) cc_final: 0.8167 (ttpt) REVERT: G 76 ILE cc_start: 0.8296 (OUTLIER) cc_final: 0.8092 (mp) REVERT: G 107 GLU cc_start: 0.6826 (OUTLIER) cc_final: 0.6561 (mm-30) REVERT: H 42 ARG cc_start: 0.7834 (OUTLIER) cc_final: 0.7088 (tmm-80) outliers start: 55 outliers final: 31 residues processed: 265 average time/residue: 1.2347 time to fit residues: 364.7907 Evaluate side-chains 266 residues out of total 1711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 227 time to evaluate : 1.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 285 GLN Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 692 THR Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 165 GLN Chi-restraints excluded: chain C residue 215 GLN Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 414 ASP Chi-restraints excluded: chain C residue 435 GLN Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 76 ILE Chi-restraints excluded: chain G residue 102 LYS Chi-restraints excluded: chain G residue 107 GLU Chi-restraints excluded: chain G residue 134 ILE Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 42 ARG Chi-restraints excluded: chain H residue 51 THR Chi-restraints excluded: chain H residue 77 ASP Chi-restraints excluded: chain H residue 145 GLN Chi-restraints excluded: chain H residue 147 THR Chi-restraints excluded: chain H residue 152 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 112 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 115 optimal weight: 7.9990 chunk 123 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 chunk 164 optimal weight: 3.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 435 GLN D 106 GLN F 24 GLN F 66 GLN ** G 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.078 16012 Z= 0.466 Angle : 0.670 9.209 21783 Z= 0.340 Chirality : 0.047 0.182 2557 Planarity : 0.005 0.042 2735 Dihedral : 6.849 61.543 2707 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.86 % Allowed : 16.73 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.65 % 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: 0.21 (0.19), residues: 1887 helix: 1.45 (0.27), residues: 399 sheet: 0.30 (0.24), residues: 484 loop : -0.43 (0.19), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 70 HIS 0.006 0.001 HIS F 58 PHE 0.021 0.002 PHE H 52 TYR 0.021 0.002 TYR D 206 ARG 0.013 0.001 ARG E 41 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 225 time to evaluate : 1.699 Fit side-chains revert: symmetry clash REVERT: A 596 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8763 (mm) REVERT: B 64 LYS cc_start: 0.9337 (tmmm) cc_final: 0.9013 (tmmm) REVERT: B 237 GLN cc_start: 0.8602 (mp10) cc_final: 0.8373 (mp10) REVERT: C 165 GLN cc_start: 0.8542 (OUTLIER) cc_final: 0.7967 (mt0) REVERT: C 215 GLN cc_start: 0.8940 (OUTLIER) cc_final: 0.8557 (mm110) REVERT: C 370 THR cc_start: 0.9409 (OUTLIER) cc_final: 0.9057 (m) REVERT: C 377 MET cc_start: 0.8203 (OUTLIER) cc_final: 0.7923 (mpt) REVERT: D 33 ASN cc_start: 0.8111 (t0) cc_final: 0.7711 (t0) REVERT: D 58 GLN cc_start: 0.8174 (tp40) cc_final: 0.7788 (tp-100) REVERT: D 176 GLN cc_start: 0.8390 (mt0) cc_final: 0.8099 (mt0) REVERT: E 68 LYS cc_start: 0.8500 (ttpt) cc_final: 0.8168 (ttpt) REVERT: G 76 ILE cc_start: 0.8401 (OUTLIER) cc_final: 0.8165 (mp) REVERT: G 107 GLU cc_start: 0.6924 (OUTLIER) cc_final: 0.6662 (mm-30) REVERT: H 66 LYS cc_start: 0.7593 (mppt) cc_final: 0.7174 (mppt) REVERT: H 123 ARG cc_start: 0.8301 (OUTLIER) cc_final: 0.4855 (ttm-80) outliers start: 66 outliers final: 42 residues processed: 264 average time/residue: 1.2996 time to fit residues: 379.6707 Evaluate side-chains 266 residues out of total 1711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 216 time to evaluate : 1.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 285 GLN Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 692 THR Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 165 GLN Chi-restraints excluded: chain C residue 215 GLN Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 374 THR Chi-restraints excluded: chain C residue 377 MET Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 414 ASP Chi-restraints excluded: chain C residue 435 GLN Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 133 MET Chi-restraints excluded: chain D residue 142 ASP Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 76 ILE Chi-restraints excluded: chain G residue 102 LYS Chi-restraints excluded: chain G residue 107 GLU Chi-restraints excluded: chain G residue 134 ILE Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 51 THR Chi-restraints excluded: chain H residue 77 ASP Chi-restraints excluded: chain H residue 123 ARG Chi-restraints excluded: chain H residue 145 GLN Chi-restraints excluded: chain H residue 147 THR Chi-restraints excluded: chain H residue 152 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 173 optimal weight: 0.4980 chunk 158 optimal weight: 1.9990 chunk 168 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 chunk 73 optimal weight: 0.5980 chunk 132 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 152 optimal weight: 0.2980 chunk 159 optimal weight: 0.5980 chunk 110 optimal weight: 0.5980 chunk 178 optimal weight: 0.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 435 GLN F 24 GLN F 66 GLN ** G 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 16012 Z= 0.177 Angle : 0.562 8.957 21783 Z= 0.285 Chirality : 0.042 0.183 2557 Planarity : 0.004 0.051 2735 Dihedral : 6.271 53.668 2707 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.75 % Allowed : 17.84 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.65 % 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: 0.34 (0.20), residues: 1887 helix: 1.56 (0.27), residues: 399 sheet: 0.31 (0.23), residues: 483 loop : -0.30 (0.20), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 330 HIS 0.002 0.001 HIS A 670 PHE 0.018 0.001 PHE A 304 TYR 0.020 0.001 TYR C 92 ARG 0.015 0.000 ARG E 41 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 231 time to evaluate : 1.739 Fit side-chains revert: symmetry clash REVERT: A 380 MET cc_start: 0.8537 (mmm) cc_final: 0.6427 (tmm) REVERT: A 596 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8659 (mm) REVERT: A 659 ASP cc_start: 0.6680 (OUTLIER) cc_final: 0.6418 (m-30) REVERT: B 64 LYS cc_start: 0.9326 (tmmm) cc_final: 0.9084 (tmmm) REVERT: B 237 GLN cc_start: 0.8573 (mp10) cc_final: 0.8261 (mp10) REVERT: C 165 GLN cc_start: 0.8483 (OUTLIER) cc_final: 0.7977 (mt0) REVERT: C 215 GLN cc_start: 0.8914 (OUTLIER) cc_final: 0.8454 (mm110) REVERT: C 370 THR cc_start: 0.9362 (OUTLIER) cc_final: 0.9014 (m) REVERT: C 377 MET cc_start: 0.8186 (mmp) cc_final: 0.7744 (mmm) REVERT: D 33 ASN cc_start: 0.8056 (t0) cc_final: 0.7654 (t0) REVERT: D 58 GLN cc_start: 0.8166 (tp40) cc_final: 0.7787 (tp40) REVERT: D 176 GLN cc_start: 0.8288 (mt0) cc_final: 0.7975 (mt0) REVERT: E 68 LYS cc_start: 0.8459 (ttpt) cc_final: 0.8141 (ttpt) REVERT: G 107 GLU cc_start: 0.6771 (OUTLIER) cc_final: 0.6489 (mm-30) outliers start: 47 outliers final: 28 residues processed: 262 average time/residue: 1.3026 time to fit residues: 383.6180 Evaluate side-chains 255 residues out of total 1711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 221 time to evaluate : 1.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 659 ASP Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 165 GLN Chi-restraints excluded: chain C residue 215 GLN Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 374 THR Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 435 GLN Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 102 LYS Chi-restraints excluded: chain G residue 107 GLU Chi-restraints excluded: chain G residue 134 ILE Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 77 ASP Chi-restraints excluded: chain H residue 145 GLN Chi-restraints excluded: chain H residue 147 THR Chi-restraints excluded: chain H residue 152 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 108 optimal weight: 0.7980 chunk 84 optimal weight: 0.0870 chunk 124 optimal weight: 5.9990 chunk 187 optimal weight: 3.9990 chunk 172 optimal weight: 1.9990 chunk 149 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 115 optimal weight: 0.0870 chunk 91 optimal weight: 0.6980 chunk 118 optimal weight: 2.9990 chunk 158 optimal weight: 1.9990 overall best weight: 0.4936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 511 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 435 GLN D 162 HIS F 24 GLN F 66 GLN ** G 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 16012 Z= 0.175 Angle : 0.562 10.280 21783 Z= 0.285 Chirality : 0.042 0.180 2557 Planarity : 0.004 0.039 2735 Dihedral : 6.081 53.857 2707 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.22 % Allowed : 18.65 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.65 % 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: 0.38 (0.20), residues: 1887 helix: 1.55 (0.27), residues: 399 sheet: 0.28 (0.23), residues: 502 loop : -0.23 (0.20), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 330 HIS 0.008 0.001 HIS A 511 PHE 0.021 0.001 PHE A 304 TYR 0.020 0.001 TYR A 682 ARG 0.014 0.000 ARG E 41 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 232 time to evaluate : 1.812 Fit side-chains revert: symmetry clash REVERT: A 88 TYR cc_start: 0.8699 (m-80) cc_final: 0.8465 (m-80) REVERT: A 380 MET cc_start: 0.8526 (mmm) cc_final: 0.8050 (mmm) REVERT: A 596 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8660 (mm) REVERT: A 659 ASP cc_start: 0.6791 (OUTLIER) cc_final: 0.6513 (m-30) REVERT: B 64 LYS cc_start: 0.9336 (tmmm) cc_final: 0.9097 (tmmm) REVERT: B 237 GLN cc_start: 0.8577 (mp10) cc_final: 0.8269 (mp10) REVERT: C 84 MET cc_start: 0.8136 (OUTLIER) cc_final: 0.7190 (mmt) REVERT: C 215 GLN cc_start: 0.8926 (OUTLIER) cc_final: 0.8487 (mm110) REVERT: C 377 MET cc_start: 0.8169 (mmp) cc_final: 0.7738 (mmm) REVERT: D 33 ASN cc_start: 0.8052 (t0) cc_final: 0.7661 (t0) REVERT: D 48 ARG cc_start: 0.7499 (ptp90) cc_final: 0.7089 (mtp-110) REVERT: D 58 GLN cc_start: 0.8165 (tp40) cc_final: 0.7780 (tp40) REVERT: D 165 GLU cc_start: 0.7796 (mp0) cc_final: 0.7417 (mp0) REVERT: D 176 GLN cc_start: 0.8276 (mt0) cc_final: 0.7979 (mt0) REVERT: E 68 LYS cc_start: 0.8458 (ttpt) cc_final: 0.8145 (ttpt) REVERT: G 107 GLU cc_start: 0.6748 (OUTLIER) cc_final: 0.6446 (mm-30) REVERT: H 66 LYS cc_start: 0.7504 (mppt) cc_final: 0.7072 (mppt) outliers start: 38 outliers final: 23 residues processed: 252 average time/residue: 1.3465 time to fit residues: 375.0933 Evaluate side-chains 253 residues out of total 1711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 225 time to evaluate : 1.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 659 ASP Chi-restraints excluded: chain A residue 692 THR Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 215 GLN Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 435 GLN Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 107 GLU Chi-restraints excluded: chain G residue 134 ILE Chi-restraints excluded: chain H residue 77 ASP Chi-restraints excluded: chain H residue 145 GLN Chi-restraints excluded: chain H residue 147 THR Chi-restraints excluded: chain H residue 152 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 45 optimal weight: 4.9990 chunk 137 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 153 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 511 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 435 GLN D 116 HIS F 24 GLN F 66 GLN ** G 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.110977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.091601 restraints weight = 27554.346| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 2.61 r_work: 0.3087 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.063 16012 Z= 0.498 Angle : 0.686 9.679 21783 Z= 0.348 Chirality : 0.048 0.188 2557 Planarity : 0.005 0.041 2735 Dihedral : 6.757 59.639 2707 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.51 % Allowed : 18.42 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.65 % 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: 0.16 (0.19), residues: 1887 helix: 1.32 (0.27), residues: 399 sheet: 0.23 (0.23), residues: 491 loop : -0.41 (0.20), residues: 997 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 70 HIS 0.006 0.002 HIS C 447 PHE 0.023 0.002 PHE A 304 TYR 0.022 0.002 TYR F 50 ARG 0.015 0.001 ARG E 41 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6595.62 seconds wall clock time: 119 minutes 0.08 seconds (7140.08 seconds total)