Starting phenix.real_space_refine on Fri Sep 27 11:07:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lbf_23253/09_2024/7lbf_23253.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lbf_23253/09_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_23253/09_2024/7lbf_23253.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lbf_23253/09_2024/7lbf_23253.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lbf_23253/09_2024/7lbf_23253.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lbf_23253/09_2024/7lbf_23253.cif" } 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. Time to flip 4 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 9.36, per 1000 atoms: 0.60 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=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: 4.18 Conformation dependent library (CDL) restraints added in 2.0 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: 2.12 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: 5.50 Time building geometry restraints manager: 4.79 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: 0.00 - 1.40: 21149 1.40 - 2.79: 502 2.79 - 4.19: 110 4.19 - 5.59: 15 5.59 - 6.99: 7 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 3.120 nonbonded pdb=" NH1 ARG A 264 " pdb=" OE1 GLU A 276 " model vdw 2.144 3.120 nonbonded pdb=" O LEU A 626 " pdb=" OG1 THR A 627 " model vdw 2.217 3.040 nonbonded pdb=" O GLN G 29 " pdb=" NE2 GLN G 128 " model vdw 2.226 3.120 nonbonded pdb=" O PRO C 345 " pdb=" NH2 ARG C 349 " model vdw 2.229 3.120 ... (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 Time spend for trying shortcut: 0.00 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: 1.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.650 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 37.180 Find NCS groups from input model: 0.210 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: 0.000 Load rotamer database and sin/cos tables:10.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.190 ------------------------------------------------------------------------------- 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 : 1.665 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: 1.3628 time to fit residues: 449.5130 Evaluate side-chains 235 residues out of total 1711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 234 time to evaluate : 1.839 ------------------------------------------------------------------------------- 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: 3.9990 chunk 79 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 96 optimal weight: 0.8980 chunk 76 optimal weight: 0.6980 chunk 147 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 109 optimal weight: 0.6980 chunk 170 optimal weight: 1.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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: 0.8147 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 16012 Z= 0.337 Angle : 0.643 8.445 21783 Z= 0.333 Chirality : 0.046 0.183 2557 Planarity : 0.005 0.043 2735 Dihedral : 7.330 76.974 2709 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.11 % Allowed : 9.65 % Favored : 88.25 % 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: 0.55 (0.19), residues: 1887 helix: 1.31 (0.27), residues: 406 sheet: 0.62 (0.24), residues: 478 loop : -0.08 (0.20), residues: 1003 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 330 HIS 0.008 0.001 HIS D 162 PHE 0.027 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 282 residues out of total 1711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 246 time to evaluate : 1.719 Fit side-chains revert: symmetry clash REVERT: A 534 ARG cc_start: 0.7937 (mtp180) cc_final: 0.7683 (mtm180) REVERT: C 147 MET cc_start: 0.8847 (mmm) cc_final: 0.8557 (mmm) REVERT: C 377 MET cc_start: 0.8041 (mmp) cc_final: 0.7751 (mmp) REVERT: C 414 ASP cc_start: 0.8179 (m-30) cc_final: 0.7972 (m-30) REVERT: D 31 LEU cc_start: 0.9189 (tt) cc_final: 0.8979 (OUTLIER) REVERT: D 33 ASN cc_start: 0.8028 (t0) cc_final: 0.7616 (t0) REVERT: D 58 GLN cc_start: 0.8212 (tp40) cc_final: 0.7918 (tp40) REVERT: D 176 GLN cc_start: 0.8239 (mt0) cc_final: 0.8026 (mt0) REVERT: D 215 ASP cc_start: 0.7623 (p0) cc_final: 0.7372 (p0) REVERT: E 68 LYS cc_start: 0.8459 (ttpt) cc_final: 0.8049 (ttpt) REVERT: F 50 TYR cc_start: 0.8719 (p90) cc_final: 0.7915 (p90) REVERT: F 104 MET cc_start: 0.8487 (tmm) cc_final: 0.8075 (tmm) REVERT: G 70 GLN cc_start: 0.8261 (mt0) cc_final: 0.7995 (mt0) REVERT: H 25 GLU cc_start: 0.8157 (mp0) cc_final: 0.7793 (mp0) outliers start: 36 outliers final: 18 residues processed: 263 average time/residue: 1.3160 time to fit residues: 379.6314 Evaluate side-chains 236 residues out of total 1711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 219 time to evaluate : 1.350 ------------------------------------------------------------------------------- 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 42 LYS Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain D residue 39 VAL 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 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 51 THR 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: 1.9990 chunk 52 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 chunk 116 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 171 optimal weight: 0.4980 chunk 184 optimal weight: 1.9990 chunk 152 optimal weight: 0.6980 chunk 169 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 137 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 GLN A 480 HIS B 115 ASN D 116 HIS 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16012 Z= 0.208 Angle : 0.565 8.457 21783 Z= 0.292 Chirality : 0.043 0.182 2557 Planarity : 0.004 0.041 2735 Dihedral : 6.931 66.103 2709 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.22 % Allowed : 12.57 % Favored : 85.20 % 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: 0.53 (0.19), residues: 1887 helix: 1.38 (0.26), residues: 407 sheet: 0.56 (0.23), residues: 479 loop : -0.11 (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 0.017 0.001 PHE H 52 TYR 0.018 0.001 TYR D 206 ARG 0.009 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 287 residues out of total 1711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 249 time to evaluate : 1.804 Fit side-chains revert: symmetry clash REVERT: A 285 GLN cc_start: 0.8896 (OUTLIER) cc_final: 0.8627 (tt0) REVERT: A 529 ASP cc_start: 0.7999 (p0) cc_final: 0.7616 (p0) REVERT: A 534 ARG cc_start: 0.7968 (mtp180) cc_final: 0.7747 (mtm180) REVERT: B 54 CYS cc_start: 0.8230 (p) cc_final: 0.7931 (p) REVERT: B 64 LYS cc_start: 0.9382 (tmmm) cc_final: 0.9129 (tmmm) REVERT: B 112 LEU cc_start: 0.8906 (pp) cc_final: 0.8508 (pt) REVERT: C 215 GLN cc_start: 0.8840 (mt0) cc_final: 0.8473 (mt0) REVERT: D 33 ASN cc_start: 0.8016 (t0) cc_final: 0.7602 (t0) REVERT: D 58 GLN cc_start: 0.8214 (tp40) cc_final: 0.7872 (tp40) REVERT: D 104 HIS cc_start: 0.7896 (p90) cc_final: 0.7656 (p90) REVERT: D 165 GLU cc_start: 0.7637 (mp0) cc_final: 0.6571 (mp0) REVERT: D 176 GLN cc_start: 0.8231 (mt0) cc_final: 0.7939 (mt0) REVERT: D 215 ASP cc_start: 0.7595 (p0) cc_final: 0.7330 (p0) REVERT: D 246 GLN cc_start: 0.8032 (mm-40) cc_final: 0.7476 (mm110) REVERT: E 68 LYS cc_start: 0.8451 (ttpt) cc_final: 0.8117 (ttpt) REVERT: F 50 TYR cc_start: 0.8726 (p90) cc_final: 0.7903 (p90) REVERT: F 104 MET cc_start: 0.8415 (tmm) cc_final: 0.8061 (tmm) REVERT: F 121 ARG cc_start: 0.8738 (OUTLIER) cc_final: 0.8415 (ttp-170) REVERT: G 70 GLN cc_start: 0.8250 (mt0) cc_final: 0.7973 (mt0) REVERT: G 107 GLU cc_start: 0.6891 (OUTLIER) cc_final: 0.6463 (mm-30) REVERT: H 25 GLU cc_start: 0.8123 (mp0) cc_final: 0.7779 (mp0) REVERT: H 42 ARG cc_start: 0.7783 (OUTLIER) cc_final: 0.7013 (tmm-80) REVERT: H 96 ASP cc_start: 0.8439 (t70) cc_final: 0.7613 (t70) outliers start: 38 outliers final: 16 residues processed: 271 average time/residue: 1.2889 time to fit residues: 385.2783 Evaluate side-chains 243 residues out of total 1711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 223 time to evaluate : 1.801 ------------------------------------------------------------------------------- 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 184 VAL Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 411 THR 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 F residue 34 VAL Chi-restraints excluded: chain F residue 121 ARG 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 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: 0.3980 chunk 128 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 81 optimal weight: 0.4980 chunk 114 optimal weight: 0.7980 chunk 171 optimal weight: 0.7980 chunk 181 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 chunk 162 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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** D 106 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16012 Z= 0.193 Angle : 0.554 7.359 21783 Z= 0.285 Chirality : 0.042 0.180 2557 Planarity : 0.004 0.041 2735 Dihedral : 6.564 58.662 2709 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.81 % Allowed : 14.27 % Favored : 82.92 % 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: 0.54 (0.19), residues: 1887 helix: 1.45 (0.26), residues: 407 sheet: 0.52 (0.23), residues: 480 loop : -0.10 (0.20), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 330 HIS 0.003 0.001 HIS A 511 PHE 0.014 0.001 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 286 residues out of total 1711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 238 time to evaluate : 1.892 Fit side-chains revert: symmetry clash REVERT: A 285 GLN cc_start: 0.8883 (OUTLIER) cc_final: 0.8636 (tt0) REVERT: B 54 CYS cc_start: 0.8121 (p) cc_final: 0.7891 (p) REVERT: C 215 GLN cc_start: 0.8827 (mt0) cc_final: 0.8438 (mt0) REVERT: C 370 THR cc_start: 0.9305 (m) cc_final: 0.8965 (m) REVERT: C 377 MET cc_start: 0.8230 (mmp) cc_final: 0.7920 (mmt) REVERT: D 33 ASN cc_start: 0.8027 (t0) cc_final: 0.7622 (t0) REVERT: D 58 GLN cc_start: 0.8208 (tp40) cc_final: 0.7847 (tp40) REVERT: D 176 GLN cc_start: 0.8257 (mt0) cc_final: 0.7983 (mt0) REVERT: D 215 ASP cc_start: 0.7588 (p0) cc_final: 0.7342 (p0) REVERT: E 68 LYS cc_start: 0.8453 (ttpt) cc_final: 0.8141 (ttpt) REVERT: F 50 TYR cc_start: 0.8713 (p90) cc_final: 0.7813 (p90) REVERT: F 104 MET cc_start: 0.8364 (tmm) cc_final: 0.8038 (tmm) REVERT: G 27 MET cc_start: 0.7889 (OUTLIER) cc_final: 0.7496 (mmm) REVERT: G 70 GLN cc_start: 0.8242 (mt0) cc_final: 0.7963 (mt0) REVERT: G 76 ILE cc_start: 0.8473 (OUTLIER) cc_final: 0.8269 (mp) REVERT: G 107 GLU cc_start: 0.6883 (OUTLIER) cc_final: 0.6465 (mm-30) REVERT: H 25 GLU cc_start: 0.8108 (mp0) cc_final: 0.7802 (mp0) REVERT: H 66 LYS cc_start: 0.7538 (mppt) cc_final: 0.7168 (mppt) outliers start: 48 outliers final: 21 residues processed: 269 average time/residue: 1.1972 time to fit residues: 358.0747 Evaluate side-chains 245 residues out of total 1711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 220 time to evaluate : 1.830 ------------------------------------------------------------------------------- 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 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 B residue 184 VAL Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 200 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 27 MET Chi-restraints excluded: chain G residue 76 ILE 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 101 SER 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: 0.8980 chunk 103 optimal weight: 2.9990 chunk 2 optimal weight: 8.9990 chunk 135 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 155 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 92 optimal weight: 0.6980 chunk 163 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 383 ASN D 33 ASN 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 16012 Z= 0.379 Angle : 0.630 8.294 21783 Z= 0.323 Chirality : 0.045 0.180 2557 Planarity : 0.004 0.041 2735 Dihedral : 6.842 62.918 2709 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.33 % Allowed : 15.26 % Favored : 81.40 % 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: 0.37 (0.19), residues: 1887 helix: 1.35 (0.27), residues: 407 sheet: 0.36 (0.23), residues: 484 loop : -0.20 (0.20), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 70 HIS 0.005 0.001 HIS C 447 PHE 0.021 0.002 PHE H 52 TYR 0.025 0.002 TYR D 206 ARG 0.010 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 292 residues out of total 1711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 235 time to evaluate : 1.847 Fit side-chains revert: symmetry clash REVERT: A 596 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8783 (mm) REVERT: B 54 CYS cc_start: 0.8245 (p) cc_final: 0.8026 (p) REVERT: C 165 GLN cc_start: 0.8513 (OUTLIER) cc_final: 0.7952 (mt0) REVERT: C 215 GLN cc_start: 0.8830 (OUTLIER) cc_final: 0.8422 (mt0) REVERT: C 366 GLU cc_start: 0.8218 (mm-30) cc_final: 0.8001 (mm-30) REVERT: C 370 THR cc_start: 0.9379 (m) cc_final: 0.9019 (m) REVERT: C 377 MET cc_start: 0.8272 (mmp) cc_final: 0.7989 (mpt) REVERT: D 33 ASN cc_start: 0.8077 (t0) cc_final: 0.7677 (t0) REVERT: D 58 GLN cc_start: 0.8239 (tp40) cc_final: 0.7894 (tp40) REVERT: D 176 GLN cc_start: 0.8316 (mt0) cc_final: 0.8020 (mt0) REVERT: D 215 ASP cc_start: 0.7724 (p0) cc_final: 0.7442 (p0) REVERT: E 68 LYS cc_start: 0.8476 (ttpt) cc_final: 0.8075 (ttpt) REVERT: F 93 MET cc_start: 0.8595 (mtt) cc_final: 0.8366 (mtt) REVERT: G 27 MET cc_start: 0.8005 (OUTLIER) cc_final: 0.7383 (mmm) REVERT: G 53 LEU cc_start: 0.9272 (OUTLIER) cc_final: 0.9057 (tp) REVERT: G 76 ILE cc_start: 0.8480 (OUTLIER) cc_final: 0.8214 (mp) REVERT: G 107 GLU cc_start: 0.6877 (mm-30) cc_final: 0.6607 (mm-30) REVERT: H 25 GLU cc_start: 0.8150 (mp0) cc_final: 0.7818 (mp0) REVERT: H 66 LYS cc_start: 0.7576 (mppt) cc_final: 0.7243 (mppt) REVERT: H 96 ASP cc_start: 0.8509 (t70) cc_final: 0.7876 (t70) outliers start: 57 outliers final: 35 residues processed: 272 average time/residue: 1.2494 time to fit residues: 376.2516 Evaluate side-chains 263 residues out of total 1711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 222 time to evaluate : 1.838 ------------------------------------------------------------------------------- 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 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 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 411 THR 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 200 THR Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 241 GLU 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 27 MET Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 53 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 51 THR Chi-restraints excluded: chain H residue 101 SER 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: 0.5980 chunk 163 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 chunk 106 optimal weight: 0.7980 chunk 44 optimal weight: 0.5980 chunk 181 optimal weight: 0.9980 chunk 150 optimal weight: 0.0060 chunk 84 optimal weight: 0.9990 chunk 15 optimal weight: 0.0570 chunk 60 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 overall best weight: 0.3714 ------------------------------------------------------------------------------- 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** 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: 0.8106 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 16012 Z= 0.159 Angle : 0.546 7.919 21783 Z= 0.281 Chirality : 0.042 0.192 2557 Planarity : 0.004 0.038 2735 Dihedral : 6.238 54.462 2709 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.22 % Allowed : 16.73 % Favored : 81.05 % 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: 0.48 (0.19), residues: 1887 helix: 1.45 (0.26), residues: 407 sheet: 0.43 (0.23), residues: 481 loop : -0.13 (0.20), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 330 HIS 0.003 0.001 HIS A 511 PHE 0.013 0.001 PHE A 81 TYR 0.021 0.001 TYR A 682 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 288 residues out of total 1711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 250 time to evaluate : 1.863 Fit side-chains revert: symmetry clash REVERT: A 285 GLN cc_start: 0.8864 (OUTLIER) cc_final: 0.8649 (tt0) REVERT: A 529 ASP cc_start: 0.7955 (p0) cc_final: 0.7615 (p0) REVERT: A 596 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8775 (mm) REVERT: B 237 GLN cc_start: 0.8595 (mp10) cc_final: 0.8289 (mp10) REVERT: C 147 MET cc_start: 0.8851 (mmm) cc_final: 0.8471 (mmm) REVERT: C 197 ASP cc_start: 0.8510 (p0) cc_final: 0.8257 (p0) REVERT: C 215 GLN cc_start: 0.8866 (OUTLIER) cc_final: 0.8449 (mt0) REVERT: C 366 GLU cc_start: 0.8186 (mm-30) cc_final: 0.7933 (mm-30) REVERT: C 377 MET cc_start: 0.8300 (mmp) cc_final: 0.7928 (mpt) REVERT: D 33 ASN cc_start: 0.8013 (t0) cc_final: 0.7621 (t0) REVERT: D 58 GLN cc_start: 0.8175 (tp40) cc_final: 0.7799 (tp40) REVERT: D 61 MET cc_start: 0.6729 (mmm) cc_final: 0.6446 (mmp) REVERT: D 176 GLN cc_start: 0.8253 (mt0) cc_final: 0.7928 (mt0) REVERT: D 215 ASP cc_start: 0.7599 (p0) cc_final: 0.7356 (p0) REVERT: E 68 LYS cc_start: 0.8433 (ttpt) cc_final: 0.8123 (ttpt) REVERT: G 107 GLU cc_start: 0.6800 (OUTLIER) cc_final: 0.6493 (mm-30) REVERT: H 66 LYS cc_start: 0.7616 (mppt) cc_final: 0.7231 (mppt) outliers start: 38 outliers final: 18 residues processed: 271 average time/residue: 1.1662 time to fit residues: 351.9866 Evaluate side-chains 249 residues out of total 1711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 227 time to evaluate : 1.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 285 GLN Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain B residue 184 VAL 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 D residue 39 VAL Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain F residue 33 GLU Chi-restraints excluded: chain F residue 34 VAL 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 145 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 175 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 132 optimal weight: 0.9980 chunk 102 optimal weight: 0.9990 chunk 153 optimal weight: 0.9980 chunk 101 optimal weight: 0.9980 chunk 181 optimal weight: 1.9990 chunk 113 optimal weight: 0.6980 chunk 110 optimal weight: 0.4980 chunk 83 optimal weight: 0.3980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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** F 24 GLN F 66 GLN ** G 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 97 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16012 Z= 0.207 Angle : 0.563 8.567 21783 Z= 0.288 Chirality : 0.042 0.180 2557 Planarity : 0.004 0.043 2735 Dihedral : 6.123 54.876 2709 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.63 % Allowed : 17.43 % Favored : 79.94 % 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: 0.52 (0.19), residues: 1887 helix: 1.46 (0.26), residues: 407 sheet: 0.44 (0.23), residues: 491 loop : -0.09 (0.20), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 330 HIS 0.003 0.001 HIS F 58 PHE 0.018 0.001 PHE A 304 TYR 0.018 0.001 TYR C 92 ARG 0.013 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 277 residues out of total 1711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 232 time to evaluate : 1.806 Fit side-chains revert: symmetry clash REVERT: A 122 LEU cc_start: 0.8337 (mt) cc_final: 0.8052 (mm) REVERT: A 285 GLN cc_start: 0.8921 (OUTLIER) cc_final: 0.8672 (tt0) REVERT: A 596 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8788 (mm) REVERT: A 645 GLU cc_start: 0.7487 (mp0) cc_final: 0.7188 (mp0) REVERT: B 237 GLN cc_start: 0.8610 (mp10) cc_final: 0.8310 (mp10) REVERT: C 147 MET cc_start: 0.8931 (mmm) cc_final: 0.8530 (mmm) REVERT: C 197 ASP cc_start: 0.8530 (p0) cc_final: 0.8275 (p0) REVERT: C 215 GLN cc_start: 0.8895 (OUTLIER) cc_final: 0.8502 (mt0) REVERT: C 366 GLU cc_start: 0.8161 (mm-30) cc_final: 0.7931 (mm-30) REVERT: C 377 MET cc_start: 0.8270 (mmp) cc_final: 0.7924 (mmm) REVERT: D 33 ASN cc_start: 0.8041 (t0) cc_final: 0.7646 (t0) REVERT: D 58 GLN cc_start: 0.8181 (tp40) cc_final: 0.7797 (tp40) REVERT: D 61 MET cc_start: 0.6747 (mmm) cc_final: 0.6436 (mmp) REVERT: D 176 GLN cc_start: 0.8274 (mt0) cc_final: 0.7918 (mt0) REVERT: D 215 ASP cc_start: 0.7627 (p0) cc_final: 0.7380 (p0) REVERT: E 68 LYS cc_start: 0.8467 (ttpt) cc_final: 0.8172 (ttpt) REVERT: G 89 ARG cc_start: 0.8116 (ptt-90) cc_final: 0.7838 (ptt-90) REVERT: G 107 GLU cc_start: 0.6959 (mm-30) cc_final: 0.6568 (mm-30) REVERT: H 66 LYS cc_start: 0.7683 (mppt) cc_final: 0.7451 (mppt) REVERT: H 96 ASP cc_start: 0.8345 (t70) cc_final: 0.7846 (t70) outliers start: 45 outliers final: 28 residues processed: 263 average time/residue: 1.2290 time to fit residues: 359.3082 Evaluate side-chains 256 residues out of total 1711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 225 time to evaluate : 1.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 555 LEU Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain B residue 183 LEU 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 D residue 39 VAL Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 133 MET Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain F residue 33 GLU Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 134 ILE Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 101 SER Chi-restraints excluded: chain H residue 119 CYS Chi-restraints excluded: chain H residue 145 GLN Chi-restraints excluded: chain H residue 147 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 112 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 chunk 108 optimal weight: 0.8980 chunk 54 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 115 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 142 optimal weight: 3.9990 chunk 164 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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** D 116 HIS E 29 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: 0.8125 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 16012 Z= 0.232 Angle : 0.590 9.825 21783 Z= 0.302 Chirality : 0.043 0.223 2557 Planarity : 0.004 0.037 2735 Dihedral : 6.156 55.210 2709 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.57 % Allowed : 18.25 % Favored : 79.18 % 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: 0.49 (0.19), residues: 1887 helix: 1.45 (0.26), residues: 405 sheet: 0.48 (0.23), residues: 481 loop : -0.16 (0.20), residues: 1001 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 330 HIS 0.003 0.001 HIS F 58 PHE 0.021 0.002 PHE A 304 TYR 0.021 0.001 TYR A 682 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 271 residues out of total 1711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 227 time to evaluate : 1.813 Fit side-chains revert: symmetry clash REVERT: A 88 TYR cc_start: 0.8698 (m-80) cc_final: 0.8484 (m-80) REVERT: A 285 GLN cc_start: 0.8942 (OUTLIER) cc_final: 0.8675 (tt0) REVERT: A 380 MET cc_start: 0.8604 (mmm) cc_final: 0.8139 (mmm) REVERT: A 529 ASP cc_start: 0.7981 (p0) cc_final: 0.7738 (p0) REVERT: A 596 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8789 (mm) REVERT: B 237 GLN cc_start: 0.8600 (mp10) cc_final: 0.8294 (mp10) REVERT: C 197 ASP cc_start: 0.8527 (p0) cc_final: 0.8276 (p0) REVERT: C 215 GLN cc_start: 0.8897 (OUTLIER) cc_final: 0.8456 (mt0) REVERT: C 366 GLU cc_start: 0.8219 (mm-30) cc_final: 0.7969 (mm-30) REVERT: C 377 MET cc_start: 0.8249 (mmp) cc_final: 0.7834 (mmm) REVERT: C 435 GLN cc_start: 0.8397 (OUTLIER) cc_final: 0.8063 (tm-30) REVERT: D 33 ASN cc_start: 0.8045 (t0) cc_final: 0.7654 (t0) REVERT: D 58 GLN cc_start: 0.8189 (tp40) cc_final: 0.7804 (tp40) REVERT: D 61 MET cc_start: 0.6754 (mmm) cc_final: 0.6445 (mmp) REVERT: D 165 GLU cc_start: 0.7789 (mp0) cc_final: 0.7302 (mp0) REVERT: D 176 GLN cc_start: 0.8283 (mt0) cc_final: 0.7922 (mt0) REVERT: D 196 LYS cc_start: 0.6270 (OUTLIER) cc_final: 0.5980 (mtmm) REVERT: D 215 ASP cc_start: 0.7636 (p0) cc_final: 0.7373 (p0) REVERT: E 68 LYS cc_start: 0.8469 (ttpt) cc_final: 0.8169 (ttpt) REVERT: G 89 ARG cc_start: 0.8103 (ptt-90) cc_final: 0.7752 (ptt-90) REVERT: G 107 GLU cc_start: 0.6949 (mm-30) cc_final: 0.6565 (mm-30) REVERT: H 66 LYS cc_start: 0.7642 (mppt) cc_final: 0.7315 (mppt) outliers start: 44 outliers final: 29 residues processed: 256 average time/residue: 1.1735 time to fit residues: 334.1809 Evaluate side-chains 253 residues out of total 1711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 219 time to evaluate : 1.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 555 LEU Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 692 THR Chi-restraints excluded: chain B residue 183 LEU 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 435 GLN Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 196 LYS Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain F residue 33 GLU Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 134 ILE Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 101 SER Chi-restraints excluded: chain H residue 119 CYS Chi-restraints excluded: chain H residue 145 GLN Chi-restraints excluded: chain H residue 147 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 173 optimal weight: 0.0370 chunk 158 optimal weight: 0.9990 chunk 168 optimal weight: 0.6980 chunk 101 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 132 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 152 optimal weight: 0.8980 chunk 159 optimal weight: 1.9990 chunk 110 optimal weight: 0.6980 chunk 178 optimal weight: 0.9980 overall best weight: 0.6658 ------------------------------------------------------------------------------- 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 119 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: 0.8114 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 16012 Z= 0.202 Angle : 0.574 8.690 21783 Z= 0.293 Chirality : 0.043 0.185 2557 Planarity : 0.004 0.040 2735 Dihedral : 6.008 54.498 2709 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.46 % Allowed : 18.54 % Favored : 79.01 % 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: 0.55 (0.19), residues: 1887 helix: 1.53 (0.26), residues: 399 sheet: 0.56 (0.23), residues: 485 loop : -0.15 (0.20), residues: 1003 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 330 HIS 0.003 0.001 HIS F 58 PHE 0.022 0.001 PHE A 304 TYR 0.017 0.001 TYR C 92 ARG 0.014 0.001 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 269 residues out of total 1711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 227 time to evaluate : 1.813 Fit side-chains revert: symmetry clash REVERT: A 88 TYR cc_start: 0.8648 (m-80) cc_final: 0.8349 (m-80) REVERT: A 285 GLN cc_start: 0.8913 (OUTLIER) cc_final: 0.8664 (tt0) REVERT: A 380 MET cc_start: 0.8641 (mmm) cc_final: 0.8217 (mmm) REVERT: A 529 ASP cc_start: 0.7941 (p0) cc_final: 0.7524 (p0) REVERT: A 596 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8764 (mm) REVERT: A 645 GLU cc_start: 0.7426 (mp0) cc_final: 0.7210 (mp0) REVERT: B 237 GLN cc_start: 0.8585 (mp10) cc_final: 0.8272 (mp10) REVERT: C 197 ASP cc_start: 0.8514 (p0) cc_final: 0.8275 (p0) REVERT: C 215 GLN cc_start: 0.8888 (OUTLIER) cc_final: 0.8423 (mm110) REVERT: C 366 GLU cc_start: 0.8229 (mm-30) cc_final: 0.7980 (mm-30) REVERT: C 377 MET cc_start: 0.8271 (OUTLIER) cc_final: 0.7838 (mmm) REVERT: C 435 GLN cc_start: 0.8486 (OUTLIER) cc_final: 0.8099 (tm-30) REVERT: D 33 ASN cc_start: 0.8048 (t0) cc_final: 0.7668 (t0) REVERT: D 58 GLN cc_start: 0.8189 (tp40) cc_final: 0.7800 (tp40) REVERT: D 61 MET cc_start: 0.6796 (mmm) cc_final: 0.6454 (mmp) REVERT: D 165 GLU cc_start: 0.7785 (mp0) cc_final: 0.7292 (mp0) REVERT: D 176 GLN cc_start: 0.8270 (mt0) cc_final: 0.7905 (mt0) REVERT: D 215 ASP cc_start: 0.7633 (p0) cc_final: 0.7354 (p0) REVERT: E 68 LYS cc_start: 0.8463 (ttpt) cc_final: 0.8139 (ttpt) REVERT: G 89 ARG cc_start: 0.8095 (ptt-90) cc_final: 0.7781 (ptt-90) REVERT: G 107 GLU cc_start: 0.6964 (mm-30) cc_final: 0.6622 (mm-30) REVERT: H 66 LYS cc_start: 0.7690 (mppt) cc_final: 0.7388 (mppt) REVERT: H 96 ASP cc_start: 0.8152 (t70) cc_final: 0.7719 (t70) outliers start: 42 outliers final: 29 residues processed: 253 average time/residue: 1.1828 time to fit residues: 332.6731 Evaluate side-chains 251 residues out of total 1711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 217 time to evaluate : 1.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 555 LEU Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 692 THR Chi-restraints excluded: chain B residue 183 LEU 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 377 MET 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 72 ARG Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain F residue 33 GLU Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 134 ILE Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 101 SER Chi-restraints excluded: chain H residue 119 CYS Chi-restraints excluded: chain H residue 145 GLN Chi-restraints excluded: chain H residue 147 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 108 optimal weight: 0.4980 chunk 84 optimal weight: 1.9990 chunk 124 optimal weight: 0.0970 chunk 187 optimal weight: 1.9990 chunk 172 optimal weight: 0.8980 chunk 149 optimal weight: 3.9990 chunk 15 optimal weight: 0.0770 chunk 115 optimal weight: 4.9990 chunk 91 optimal weight: 0.5980 chunk 118 optimal weight: 1.9990 chunk 158 optimal weight: 1.9990 overall best weight: 0.4336 ------------------------------------------------------------------------------- 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** F 24 GLN F 66 GLN ** G 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 16012 Z= 0.176 Angle : 0.571 10.901 21783 Z= 0.292 Chirality : 0.042 0.205 2557 Planarity : 0.004 0.045 2735 Dihedral : 5.839 53.977 2709 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.99 % Allowed : 19.24 % Favored : 78.77 % 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: 0.55 (0.20), residues: 1887 helix: 1.54 (0.26), residues: 399 sheet: 0.50 (0.23), residues: 500 loop : -0.12 (0.20), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 330 HIS 0.003 0.001 HIS A 511 PHE 0.024 0.001 PHE A 304 TYR 0.022 0.001 TYR A 682 ARG 0.015 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 262 residues out of total 1711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 228 time to evaluate : 1.707 Fit side-chains revert: symmetry clash REVERT: A 88 TYR cc_start: 0.8598 (m-80) cc_final: 0.8366 (m-80) REVERT: A 285 GLN cc_start: 0.8931 (OUTLIER) cc_final: 0.8715 (tt0) REVERT: A 380 MET cc_start: 0.8600 (mmm) cc_final: 0.8220 (mmm) REVERT: A 596 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8761 (mm) REVERT: A 645 GLU cc_start: 0.7552 (mp0) cc_final: 0.7335 (mp0) REVERT: B 237 GLN cc_start: 0.8576 (mp10) cc_final: 0.8264 (mp10) REVERT: C 110 ASP cc_start: 0.8941 (t0) cc_final: 0.8427 (t0) REVERT: C 197 ASP cc_start: 0.8499 (p0) cc_final: 0.8268 (p0) REVERT: C 215 GLN cc_start: 0.8910 (OUTLIER) cc_final: 0.8466 (mm110) REVERT: C 366 GLU cc_start: 0.8216 (mm-30) cc_final: 0.7969 (mm-30) REVERT: C 377 MET cc_start: 0.8247 (OUTLIER) cc_final: 0.7829 (mmm) REVERT: C 435 GLN cc_start: 0.8428 (OUTLIER) cc_final: 0.8030 (tm-30) REVERT: D 33 ASN cc_start: 0.8023 (t0) cc_final: 0.7648 (t0) REVERT: D 58 GLN cc_start: 0.8184 (tp40) cc_final: 0.7785 (tp40) REVERT: D 61 MET cc_start: 0.6748 (mmm) cc_final: 0.6385 (mmp) REVERT: D 165 GLU cc_start: 0.7763 (mp0) cc_final: 0.7248 (mp0) REVERT: D 176 GLN cc_start: 0.8225 (mt0) cc_final: 0.7914 (mt0) REVERT: D 215 ASP cc_start: 0.7643 (p0) cc_final: 0.7368 (p0) REVERT: E 68 LYS cc_start: 0.8457 (ttpt) cc_final: 0.8156 (ttpt) REVERT: G 107 GLU cc_start: 0.6763 (mm-30) cc_final: 0.6501 (mm-30) outliers start: 34 outliers final: 26 residues processed: 248 average time/residue: 1.2148 time to fit residues: 336.3907 Evaluate side-chains 255 residues out of total 1711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 224 time to evaluate : 1.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 555 LEU Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 692 THR Chi-restraints excluded: chain B residue 183 LEU 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 377 MET 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 168 VAL Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain F residue 33 GLU Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 134 ILE Chi-restraints excluded: chain H residue 101 SER Chi-restraints excluded: chain H residue 145 GLN Chi-restraints excluded: chain H residue 147 THR 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: 0.6980 chunk 22 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 153 optimal weight: 0.5980 chunk 18 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 24 GLN F 66 GLN ** G 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.114880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.095197 restraints weight = 26821.887| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.66 r_work: 0.3131 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 16012 Z= 0.252 Angle : 0.586 8.571 21783 Z= 0.301 Chirality : 0.043 0.192 2557 Planarity : 0.004 0.043 2735 Dihedral : 6.013 55.969 2709 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.22 % Allowed : 19.12 % Favored : 78.65 % 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: 0.53 (0.20), residues: 1887 helix: 1.54 (0.26), residues: 399 sheet: 0.46 (0.23), residues: 498 loop : -0.12 (0.20), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 330 HIS 0.004 0.001 HIS G 54 PHE 0.025 0.002 PHE A 304 TYR 0.017 0.001 TYR C 92 ARG 0.014 0.001 ARG E 41 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6306.47 seconds wall clock time: 112 minutes 52.85 seconds (6772.85 seconds total)