Starting phenix.real_space_refine on Wed Mar 4 19:13:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lbf_23253/03_2026/7lbf_23253.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lbf_23253/03_2026/7lbf_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 { model { file = "/net/cci-nas-00/data/ceres_data/7lbf_23253/03_2026/7lbf_23253.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lbf_23253/03_2026/7lbf_23253.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7lbf_23253/03_2026/7lbf_23253.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lbf_23253/03_2026/7lbf_23253.map" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 3.54, per 1000 atoms: 0.23 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: 1.49 Conformation dependent library (CDL) restraints added in 726.6 milliseconds 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: 0.67 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: 3.12 Time building geometry restraints manager: 1.99 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: 1.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 16.170 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 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:6.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.150 ------------------------------------------------------------------------------- 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 16050 Z= 0.154 Angle : 0.567 6.986 21881 Z= 0.280 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.011 0.000 ARG F 124 TYR 0.016 0.001 TYR H 136 PHE 0.027 0.001 PHE F 123 TRP 0.009 0.001 TRP C 330 HIS 0.003 0.001 HIS C 447 Details of bonding type rmsd covalent geometry : bond 0.00325 (16012) covalent geometry : angle 0.55671 (21783) SS BOND : bond 0.00277 ( 16) SS BOND : angle 1.16070 ( 32) hydrogen bonds : bond 0.17915 ( 622) hydrogen bonds : angle 7.16525 ( 1647) link_ALPHA1-2 : bond 0.00629 ( 1) link_ALPHA1-2 : angle 2.59617 ( 3) link_ALPHA1-3 : bond 0.00594 ( 2) link_ALPHA1-3 : angle 2.54971 ( 6) link_ALPHA1-6 : bond 0.00808 ( 1) link_ALPHA1-6 : angle 1.36467 ( 3) link_BETA1-4 : bond 0.00496 ( 4) link_BETA1-4 : angle 2.62463 ( 12) link_NAG-ASN : bond 0.00200 ( 14) link_NAG-ASN : angle 1.54641 ( 42) *********************** 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 to be fit. rotamer outliers: 0 poor density : 300 time to evaluate : 0.768 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: 0.7303 time to fit residues: 239.0866 Evaluate side-chains 235 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 234 time to evaluate : 0.619 ------------------------------------------------------------------------------- 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 98 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 115 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.114698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.095229 restraints weight = 26948.361| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.65 r_work: 0.3144 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.1365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 16050 Z= 0.156 Angle : 0.608 7.611 21881 Z= 0.314 Chirality : 0.044 0.184 2557 Planarity : 0.004 0.041 2735 Dihedral : 7.235 77.702 2709 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.81 % Allowed : 9.42 % Favored : 88.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.20), residues: 1887 helix: 1.40 (0.27), residues: 406 sheet: 0.72 (0.23), residues: 481 loop : 0.02 (0.20), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 41 TYR 0.020 0.001 TYR D 206 PHE 0.022 0.002 PHE H 52 TRP 0.010 0.001 TRP C 183 HIS 0.008 0.001 HIS D 162 Details of bonding type rmsd covalent geometry : bond 0.00364 (16012) covalent geometry : angle 0.60131 (21783) SS BOND : bond 0.00374 ( 16) SS BOND : angle 1.09308 ( 32) hydrogen bonds : bond 0.04081 ( 622) hydrogen bonds : angle 5.54384 ( 1647) link_ALPHA1-2 : bond 0.00010 ( 1) link_ALPHA1-2 : angle 1.95071 ( 3) link_ALPHA1-3 : bond 0.00723 ( 2) link_ALPHA1-3 : angle 1.53036 ( 6) link_ALPHA1-6 : bond 0.00894 ( 1) link_ALPHA1-6 : angle 1.14780 ( 3) link_BETA1-4 : bond 0.00227 ( 4) link_BETA1-4 : angle 2.13746 ( 12) link_NAG-ASN : bond 0.00207 ( 14) link_NAG-ASN : angle 1.55046 ( 42) *********************** 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 284 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 253 time to evaluate : 0.588 Fit side-chains revert: symmetry clash REVERT: A 285 GLN cc_start: 0.8997 (OUTLIER) cc_final: 0.8783 (tt0) REVERT: A 534 ARG cc_start: 0.7981 (mtp180) cc_final: 0.7605 (mtm180) REVERT: C 377 MET cc_start: 0.8579 (mmp) cc_final: 0.8235 (mmp) REVERT: D 33 ASN cc_start: 0.8509 (t0) cc_final: 0.8106 (t0) REVERT: D 48 ARG cc_start: 0.7512 (ptm-80) cc_final: 0.7197 (ptp90) REVERT: D 58 GLN cc_start: 0.8366 (tp40) cc_final: 0.7912 (tp40) REVERT: D 74 GLU cc_start: 0.6972 (tt0) cc_final: 0.6353 (tp30) REVERT: D 173 ASP cc_start: 0.8702 (t0) cc_final: 0.8335 (t70) REVERT: D 176 GLN cc_start: 0.8574 (mt0) cc_final: 0.8138 (mt0) REVERT: D 215 ASP cc_start: 0.7792 (p0) cc_final: 0.7508 (p0) REVERT: E 68 LYS cc_start: 0.8311 (ttpt) cc_final: 0.7843 (ttpt) REVERT: F 50 TYR cc_start: 0.8618 (p90) cc_final: 0.7732 (p90) REVERT: F 95 ARG cc_start: 0.8264 (ppt90) cc_final: 0.7892 (ppt-90) REVERT: F 104 MET cc_start: 0.8306 (tmm) cc_final: 0.7899 (tmm) REVERT: F 112 GLU cc_start: 0.8783 (pt0) cc_final: 0.8077 (pm20) REVERT: F 124 ARG cc_start: 0.8347 (mtt-85) cc_final: 0.7896 (mpt90) REVERT: G 70 GLN cc_start: 0.8405 (mt0) cc_final: 0.8161 (mt0) REVERT: G 121 GLN cc_start: 0.8206 (mt0) cc_final: 0.7898 (mp10) REVERT: H 25 GLU cc_start: 0.8396 (mp0) cc_final: 0.8000 (mp0) REVERT: H 96 ASP cc_start: 0.8473 (t70) cc_final: 0.8180 (t70) REVERT: H 112 GLU cc_start: 0.7767 (pm20) cc_final: 0.7498 (pm20) outliers start: 31 outliers final: 13 residues processed: 266 average time/residue: 0.6997 time to fit residues: 203.4226 Evaluate side-chains 238 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 224 time to evaluate : 0.484 ------------------------------------------------------------------------------- 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 285 GLN Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain G residue 102 LYS Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 51 THR Chi-restraints excluded: chain H residue 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 100 optimal weight: 2.9990 chunk 115 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 170 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 135 optimal weight: 0.9990 chunk 159 optimal weight: 0.7980 chunk 138 optimal weight: 2.9990 chunk 154 optimal weight: 0.2980 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN A 370 GLN A 480 HIS B 115 ASN D 116 HIS D 162 HIS F 24 GLN F 66 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.114213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.094688 restraints weight = 27144.356| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 2.67 r_work: 0.3129 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16050 Z= 0.163 Angle : 0.589 8.507 21881 Z= 0.300 Chirality : 0.044 0.183 2557 Planarity : 0.004 0.046 2735 Dihedral : 6.959 68.272 2707 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.46 % Allowed : 12.16 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.19), residues: 1887 helix: 1.39 (0.27), residues: 407 sheet: 0.57 (0.23), residues: 479 loop : -0.08 (0.20), residues: 1001 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 41 TYR 0.019 0.001 TYR D 206 PHE 0.015 0.002 PHE A 304 TRP 0.011 0.001 TRP C 330 HIS 0.004 0.001 HIS C 447 Details of bonding type rmsd covalent geometry : bond 0.00384 (16012) covalent geometry : angle 0.58243 (21783) SS BOND : bond 0.00372 ( 16) SS BOND : angle 0.85867 ( 32) hydrogen bonds : bond 0.03783 ( 622) hydrogen bonds : angle 5.20771 ( 1647) link_ALPHA1-2 : bond 0.00071 ( 1) link_ALPHA1-2 : angle 1.80345 ( 3) link_ALPHA1-3 : bond 0.00814 ( 2) link_ALPHA1-3 : angle 1.38242 ( 6) link_ALPHA1-6 : bond 0.00817 ( 1) link_ALPHA1-6 : angle 1.27298 ( 3) link_BETA1-4 : bond 0.00167 ( 4) link_BETA1-4 : angle 2.00680 ( 12) link_NAG-ASN : bond 0.00201 ( 14) link_NAG-ASN : angle 1.60324 ( 42) *********************** 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 284 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 242 time to evaluate : 0.641 Fit side-chains revert: symmetry clash REVERT: A 285 GLN cc_start: 0.8966 (OUTLIER) cc_final: 0.8731 (tt0) REVERT: A 529 ASP cc_start: 0.8229 (p0) cc_final: 0.7787 (p0) REVERT: A 534 ARG cc_start: 0.8046 (mtp180) cc_final: 0.7841 (mtm180) REVERT: A 619 ASP cc_start: 0.8074 (t0) cc_final: 0.7874 (t0) REVERT: B 54 CYS cc_start: 0.8871 (p) cc_final: 0.8499 (p) REVERT: B 64 LYS cc_start: 0.9365 (tmmm) cc_final: 0.9072 (tmmm) REVERT: C 147 MET cc_start: 0.9003 (mmm) cc_final: 0.8735 (mmm) REVERT: C 377 MET cc_start: 0.8540 (mmp) cc_final: 0.8284 (mmp) REVERT: D 29 SER cc_start: 0.7857 (t) cc_final: 0.7626 (p) REVERT: D 31 LEU cc_start: 0.9287 (tt) cc_final: 0.9080 (tp) REVERT: D 33 ASN cc_start: 0.8577 (t0) cc_final: 0.8174 (t0) REVERT: D 48 ARG cc_start: 0.7511 (OUTLIER) cc_final: 0.7198 (ptp90) REVERT: D 58 GLN cc_start: 0.8401 (tp40) cc_final: 0.7887 (tp40) REVERT: D 74 GLU cc_start: 0.7046 (tt0) cc_final: 0.6593 (tp30) REVERT: D 165 GLU cc_start: 0.8014 (mp0) cc_final: 0.6951 (mp0) REVERT: D 173 ASP cc_start: 0.8730 (t0) cc_final: 0.8336 (t70) REVERT: D 176 GLN cc_start: 0.8642 (mt0) cc_final: 0.8349 (mt0) REVERT: D 215 ASP cc_start: 0.7793 (p0) cc_final: 0.7461 (p0) REVERT: D 246 GLN cc_start: 0.8164 (mm-40) cc_final: 0.7532 (mm110) REVERT: E 68 LYS cc_start: 0.8317 (ttpt) cc_final: 0.7917 (ttpt) REVERT: F 50 TYR cc_start: 0.8624 (p90) cc_final: 0.7456 (p90) REVERT: F 104 MET cc_start: 0.8285 (tmm) cc_final: 0.8012 (tmm) REVERT: F 112 GLU cc_start: 0.8747 (pt0) cc_final: 0.8089 (pm20) REVERT: G 70 GLN cc_start: 0.8131 (mt0) cc_final: 0.7875 (mt0) REVERT: G 107 GLU cc_start: 0.6379 (OUTLIER) cc_final: 0.5735 (mm-30) REVERT: G 121 GLN cc_start: 0.8109 (mt0) cc_final: 0.7798 (mt0) REVERT: G 128 GLN cc_start: 0.8074 (pm20) cc_final: 0.7850 (pm20) REVERT: H 25 GLU cc_start: 0.8422 (mp0) cc_final: 0.8036 (mp0) REVERT: H 96 ASP cc_start: 0.8430 (t70) cc_final: 0.8080 (t70) REVERT: H 112 GLU cc_start: 0.7788 (pm20) cc_final: 0.7500 (pm20) REVERT: H 151 VAL cc_start: 0.8566 (t) cc_final: 0.8218 (m) outliers start: 42 outliers final: 21 residues processed: 265 average time/residue: 0.6723 time to fit residues: 195.4120 Evaluate side-chains 251 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 227 time to evaluate : 0.658 ------------------------------------------------------------------------------- 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 72 LEU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 48 ARG Chi-restraints excluded: chain D residue 133 MET 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 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 101 SER 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 3 optimal weight: 4.9990 chunk 75 optimal weight: 0.9990 chunk 104 optimal weight: 0.0370 chunk 111 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 134 optimal weight: 0.3980 chunk 139 optimal weight: 3.9990 chunk 174 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 overall best weight: 0.6660 ------------------------------------------------------------------------------- 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 H 97 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.115700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.095986 restraints weight = 27196.375| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 2.72 r_work: 0.3129 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16050 Z= 0.126 Angle : 0.554 6.778 21881 Z= 0.283 Chirality : 0.042 0.183 2557 Planarity : 0.004 0.039 2735 Dihedral : 6.469 58.000 2707 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.46 % Allowed : 13.51 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.19), residues: 1887 helix: 1.47 (0.26), residues: 407 sheet: 0.54 (0.23), residues: 481 loop : -0.07 (0.20), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 41 TYR 0.019 0.001 TYR D 206 PHE 0.012 0.001 PHE A 191 TRP 0.011 0.001 TRP C 330 HIS 0.003 0.001 HIS F 58 Details of bonding type rmsd covalent geometry : bond 0.00292 (16012) covalent geometry : angle 0.54811 (21783) SS BOND : bond 0.00265 ( 16) SS BOND : angle 0.70246 ( 32) hydrogen bonds : bond 0.03333 ( 622) hydrogen bonds : angle 4.96339 ( 1647) link_ALPHA1-2 : bond 0.00009 ( 1) link_ALPHA1-2 : angle 1.71093 ( 3) link_ALPHA1-3 : bond 0.00867 ( 2) link_ALPHA1-3 : angle 1.36181 ( 6) link_ALPHA1-6 : bond 0.00614 ( 1) link_ALPHA1-6 : angle 1.28769 ( 3) link_BETA1-4 : bond 0.00232 ( 4) link_BETA1-4 : angle 1.89535 ( 12) link_NAG-ASN : bond 0.00169 ( 14) link_NAG-ASN : angle 1.51089 ( 42) *********************** 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 281 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 239 time to evaluate : 0.658 Fit side-chains revert: symmetry clash REVERT: A 117 ARG cc_start: 0.8385 (tpm-80) cc_final: 0.8152 (tpm-80) REVERT: A 285 GLN cc_start: 0.8848 (OUTLIER) cc_final: 0.8645 (tt0) REVERT: A 619 ASP cc_start: 0.8088 (t0) cc_final: 0.7829 (t0) REVERT: B 54 CYS cc_start: 0.8755 (p) cc_final: 0.8407 (p) REVERT: B 100 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8855 (tp) REVERT: C 370 THR cc_start: 0.9242 (m) cc_final: 0.8960 (m) REVERT: C 377 MET cc_start: 0.8428 (mmp) cc_final: 0.8222 (mmt) REVERT: D 29 SER cc_start: 0.7915 (t) cc_final: 0.7621 (p) REVERT: D 31 LEU cc_start: 0.9217 (tt) cc_final: 0.9004 (tp) REVERT: D 33 ASN cc_start: 0.8490 (t0) cc_final: 0.8080 (t0) REVERT: D 48 ARG cc_start: 0.7384 (ptm-80) cc_final: 0.7075 (ptp90) REVERT: D 58 GLN cc_start: 0.8261 (tp40) cc_final: 0.7684 (tp40) REVERT: D 74 GLU cc_start: 0.6690 (tt0) cc_final: 0.6125 (tp30) REVERT: D 144 ASP cc_start: 0.8482 (t0) cc_final: 0.8224 (t0) REVERT: D 173 ASP cc_start: 0.8520 (t0) cc_final: 0.8092 (t70) REVERT: D 176 GLN cc_start: 0.8551 (mt0) cc_final: 0.8194 (mt0) REVERT: D 215 ASP cc_start: 0.7675 (p0) cc_final: 0.7372 (p0) REVERT: E 68 LYS cc_start: 0.8222 (ttpt) cc_final: 0.7856 (ttpt) REVERT: F 42 LYS cc_start: 0.8721 (tttt) cc_final: 0.8521 (tptm) REVERT: F 93 MET cc_start: 0.8727 (mtt) cc_final: 0.8450 (mtt) REVERT: F 104 MET cc_start: 0.8156 (tmm) cc_final: 0.7762 (tmm) REVERT: F 112 GLU cc_start: 0.8594 (pt0) cc_final: 0.8027 (pm20) REVERT: G 27 MET cc_start: 0.8044 (OUTLIER) cc_final: 0.7391 (mmm) REVERT: G 70 GLN cc_start: 0.8063 (mt0) cc_final: 0.7786 (mt0) REVERT: G 107 GLU cc_start: 0.6280 (mm-30) cc_final: 0.5747 (mm-30) REVERT: G 121 GLN cc_start: 0.8050 (mt0) cc_final: 0.7732 (mp10) REVERT: H 25 GLU cc_start: 0.8347 (mp0) cc_final: 0.8006 (mp0) REVERT: H 66 LYS cc_start: 0.7272 (mppt) cc_final: 0.6830 (mppt) REVERT: H 96 ASP cc_start: 0.8364 (t70) cc_final: 0.7379 (t70) REVERT: H 99 GLU cc_start: 0.7848 (mt-10) cc_final: 0.7132 (mp0) REVERT: H 112 GLU cc_start: 0.7796 (pm20) cc_final: 0.7466 (pm20) REVERT: H 151 VAL cc_start: 0.8461 (t) cc_final: 0.8150 (m) outliers start: 42 outliers final: 18 residues processed: 264 average time/residue: 0.6364 time to fit residues: 185.3308 Evaluate side-chains 249 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 228 time to evaluate : 0.645 ------------------------------------------------------------------------------- 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 B residue 100 LEU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 225 LEU 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 G residue 27 MET 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 33 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 174 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 147 optimal weight: 2.9990 chunk 153 optimal weight: 0.5980 chunk 90 optimal weight: 0.6980 chunk 75 optimal weight: 2.9990 chunk 122 optimal weight: 5.9990 chunk 171 optimal weight: 0.2980 chunk 7 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.115824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.096291 restraints weight = 27295.446| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 2.69 r_work: 0.3139 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16050 Z= 0.121 Angle : 0.543 7.016 21881 Z= 0.276 Chirality : 0.042 0.182 2557 Planarity : 0.004 0.038 2735 Dihedral : 6.205 54.683 2707 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.16 % Allowed : 14.44 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.19), residues: 1887 helix: 1.49 (0.26), residues: 407 sheet: 0.58 (0.23), residues: 491 loop : -0.05 (0.20), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 41 TYR 0.019 0.001 TYR D 206 PHE 0.017 0.001 PHE A 304 TRP 0.010 0.001 TRP C 330 HIS 0.003 0.001 HIS A 511 Details of bonding type rmsd covalent geometry : bond 0.00282 (16012) covalent geometry : angle 0.53629 (21783) SS BOND : bond 0.00270 ( 16) SS BOND : angle 0.74306 ( 32) hydrogen bonds : bond 0.03224 ( 622) hydrogen bonds : angle 4.84767 ( 1647) link_ALPHA1-2 : bond 0.00068 ( 1) link_ALPHA1-2 : angle 1.70106 ( 3) link_ALPHA1-3 : bond 0.00859 ( 2) link_ALPHA1-3 : angle 1.33762 ( 6) link_ALPHA1-6 : bond 0.00551 ( 1) link_ALPHA1-6 : angle 1.33539 ( 3) link_BETA1-4 : bond 0.00192 ( 4) link_BETA1-4 : angle 1.79821 ( 12) link_NAG-ASN : bond 0.00167 ( 14) link_NAG-ASN : angle 1.51616 ( 42) *********************** 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 298 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 244 time to evaluate : 0.662 Fit side-chains revert: symmetry clash REVERT: A 285 GLN cc_start: 0.8789 (OUTLIER) cc_final: 0.8559 (tt0) REVERT: A 596 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8580 (mm) REVERT: A 619 ASP cc_start: 0.8083 (t0) cc_final: 0.7830 (t0) REVERT: B 54 CYS cc_start: 0.8723 (p) cc_final: 0.8412 (p) REVERT: C 147 MET cc_start: 0.8977 (mmm) cc_final: 0.8709 (mmm) REVERT: C 197 ASP cc_start: 0.8822 (p0) cc_final: 0.8399 (p0) REVERT: C 370 THR cc_start: 0.9288 (m) cc_final: 0.9019 (m) REVERT: C 377 MET cc_start: 0.8439 (mmp) cc_final: 0.8184 (mmt) REVERT: D 29 SER cc_start: 0.7975 (t) cc_final: 0.7692 (p) REVERT: D 33 ASN cc_start: 0.8542 (t0) cc_final: 0.8087 (t0) REVERT: D 40 GLN cc_start: 0.7592 (pp30) cc_final: 0.7279 (tm130) REVERT: D 58 GLN cc_start: 0.8268 (tp40) cc_final: 0.7661 (tp40) REVERT: D 74 GLU cc_start: 0.6712 (tt0) cc_final: 0.6306 (tp30) REVERT: D 173 ASP cc_start: 0.8437 (t0) cc_final: 0.8027 (t70) REVERT: D 176 GLN cc_start: 0.8571 (mt0) cc_final: 0.8250 (mt0) REVERT: D 196 LYS cc_start: 0.6416 (OUTLIER) cc_final: 0.6028 (mtmm) REVERT: D 215 ASP cc_start: 0.7677 (p0) cc_final: 0.7383 (p0) REVERT: E 68 LYS cc_start: 0.8259 (ttpt) cc_final: 0.7902 (ttpt) REVERT: F 42 LYS cc_start: 0.8731 (tttt) cc_final: 0.8515 (tptm) REVERT: F 88 GLN cc_start: 0.8658 (mm-40) cc_final: 0.8313 (mt0) REVERT: F 93 MET cc_start: 0.8691 (mtt) cc_final: 0.8412 (mtt) REVERT: F 104 MET cc_start: 0.8176 (tmm) cc_final: 0.7843 (tmm) REVERT: F 112 GLU cc_start: 0.8581 (pt0) cc_final: 0.8021 (pm20) REVERT: G 27 MET cc_start: 0.8101 (OUTLIER) cc_final: 0.7402 (mmm) REVERT: G 70 GLN cc_start: 0.8079 (mt0) cc_final: 0.7793 (mt0) REVERT: G 107 GLU cc_start: 0.6300 (OUTLIER) cc_final: 0.5731 (mm-30) REVERT: G 121 GLN cc_start: 0.8060 (mt0) cc_final: 0.7757 (mp10) REVERT: H 25 GLU cc_start: 0.8359 (mp0) cc_final: 0.7979 (mp0) REVERT: H 66 LYS cc_start: 0.7455 (mppt) cc_final: 0.7162 (mppt) REVERT: H 96 ASP cc_start: 0.8338 (t70) cc_final: 0.7417 (t70) REVERT: H 99 GLU cc_start: 0.7836 (mt-10) cc_final: 0.7136 (mp0) REVERT: H 112 GLU cc_start: 0.7754 (pm20) cc_final: 0.7482 (pm20) REVERT: H 151 VAL cc_start: 0.8444 (t) cc_final: 0.8097 (m) outliers start: 54 outliers final: 22 residues processed: 275 average time/residue: 0.6149 time to fit residues: 186.3969 Evaluate side-chains 254 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 227 time to evaluate : 0.556 ------------------------------------------------------------------------------- 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 361 VAL Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 225 LEU 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 196 LYS Chi-restraints excluded: chain D residue 223 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 34 VAL Chi-restraints excluded: chain G residue 27 MET 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 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 107 optimal weight: 0.0010 chunk 96 optimal weight: 2.9990 chunk 100 optimal weight: 0.7980 chunk 80 optimal weight: 0.9990 chunk 155 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 120 optimal weight: 6.9990 chunk 182 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 106 optimal weight: 0.5980 overall best weight: 0.8790 ------------------------------------------------------------------------------- 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 33 ASN D 106 GLN F 24 GLN F 66 GLN G 81 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.114457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.094928 restraints weight = 26989.695| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 2.67 r_work: 0.3136 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16050 Z= 0.146 Angle : 0.560 7.490 21881 Z= 0.284 Chirality : 0.043 0.189 2557 Planarity : 0.004 0.038 2735 Dihedral : 6.137 55.447 2707 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.81 % Allowed : 16.20 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.19), residues: 1887 helix: 1.50 (0.26), residues: 407 sheet: 0.52 (0.23), residues: 492 loop : -0.05 (0.20), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 41 TYR 0.020 0.001 TYR A 682 PHE 0.018 0.002 PHE A 304 TRP 0.010 0.001 TRP C 330 HIS 0.003 0.001 HIS G 54 Details of bonding type rmsd covalent geometry : bond 0.00343 (16012) covalent geometry : angle 0.55361 (21783) SS BOND : bond 0.00348 ( 16) SS BOND : angle 0.73854 ( 32) hydrogen bonds : bond 0.03320 ( 622) hydrogen bonds : angle 4.81928 ( 1647) link_ALPHA1-2 : bond 0.00039 ( 1) link_ALPHA1-2 : angle 1.78711 ( 3) link_ALPHA1-3 : bond 0.00935 ( 2) link_ALPHA1-3 : angle 1.39282 ( 6) link_ALPHA1-6 : bond 0.00406 ( 1) link_ALPHA1-6 : angle 1.37189 ( 3) link_BETA1-4 : bond 0.00199 ( 4) link_BETA1-4 : angle 1.81406 ( 12) link_NAG-ASN : bond 0.00192 ( 14) link_NAG-ASN : angle 1.56075 ( 42) *********************** 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 282 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 234 time to evaluate : 0.586 Fit side-chains revert: symmetry clash REVERT: A 117 ARG cc_start: 0.8371 (tpm-80) cc_final: 0.8139 (tpm-80) REVERT: A 285 GLN cc_start: 0.8896 (OUTLIER) cc_final: 0.8658 (tt0) REVERT: A 596 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8545 (mm) REVERT: A 619 ASP cc_start: 0.8164 (t0) cc_final: 0.7902 (t0) REVERT: A 645 GLU cc_start: 0.7423 (mp0) cc_final: 0.7130 (mp0) REVERT: B 54 CYS cc_start: 0.8851 (p) cc_final: 0.8561 (p) REVERT: C 147 MET cc_start: 0.8986 (mmm) cc_final: 0.8745 (mmm) REVERT: C 197 ASP cc_start: 0.8899 (p0) cc_final: 0.8506 (p0) REVERT: C 215 GLN cc_start: 0.8782 (OUTLIER) cc_final: 0.8304 (mt0) REVERT: C 366 GLU cc_start: 0.8221 (mm-30) cc_final: 0.7837 (mm-30) REVERT: C 370 THR cc_start: 0.9288 (OUTLIER) cc_final: 0.9042 (m) REVERT: C 377 MET cc_start: 0.8539 (mmp) cc_final: 0.8267 (mmt) REVERT: D 29 SER cc_start: 0.8053 (t) cc_final: 0.7779 (p) REVERT: D 33 ASN cc_start: 0.8477 (t0) cc_final: 0.8041 (t0) REVERT: D 40 GLN cc_start: 0.7717 (pp30) cc_final: 0.7291 (tm130) REVERT: D 58 GLN cc_start: 0.8410 (tp40) cc_final: 0.7808 (tp40) REVERT: D 74 GLU cc_start: 0.6908 (tt0) cc_final: 0.6449 (tp30) REVERT: D 173 ASP cc_start: 0.8517 (t0) cc_final: 0.8089 (t70) REVERT: D 176 GLN cc_start: 0.8662 (mt0) cc_final: 0.8367 (mt0) REVERT: D 196 LYS cc_start: 0.6578 (OUTLIER) cc_final: 0.6157 (mtmm) REVERT: D 215 ASP cc_start: 0.7792 (p0) cc_final: 0.7456 (p0) REVERT: E 68 LYS cc_start: 0.8328 (ttpt) cc_final: 0.7969 (ttpt) REVERT: F 42 LYS cc_start: 0.8730 (tttt) cc_final: 0.8495 (tptm) REVERT: F 88 GLN cc_start: 0.8704 (mm-40) cc_final: 0.8278 (mt0) REVERT: F 93 MET cc_start: 0.8714 (mtt) cc_final: 0.8456 (mtt) REVERT: F 104 MET cc_start: 0.8247 (tmm) cc_final: 0.7911 (tmm) REVERT: F 112 GLU cc_start: 0.8731 (pt0) cc_final: 0.8144 (pm20) REVERT: G 27 MET cc_start: 0.8235 (OUTLIER) cc_final: 0.7394 (mmm) REVERT: G 70 GLN cc_start: 0.8141 (mt0) cc_final: 0.7849 (mt0) REVERT: G 89 ARG cc_start: 0.8160 (ptt90) cc_final: 0.7603 (ptm-80) REVERT: G 107 GLU cc_start: 0.6206 (OUTLIER) cc_final: 0.5684 (mm-30) REVERT: G 128 GLN cc_start: 0.8134 (pm20) cc_final: 0.7874 (pm20) REVERT: H 66 LYS cc_start: 0.7417 (mppt) cc_final: 0.7110 (mppt) REVERT: H 96 ASP cc_start: 0.8385 (t70) cc_final: 0.7525 (t70) REVERT: H 99 GLU cc_start: 0.7930 (mt-10) cc_final: 0.7191 (mp0) REVERT: H 112 GLU cc_start: 0.7831 (pm20) cc_final: 0.7518 (pm20) outliers start: 48 outliers final: 25 residues processed: 260 average time/residue: 0.6213 time to fit residues: 178.2315 Evaluate side-chains 264 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 232 time to evaluate : 0.564 ------------------------------------------------------------------------------- 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 279 VAL Chi-restraints excluded: chain A residue 285 GLN Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 692 THR Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain C residue 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 370 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 72 ARG Chi-restraints excluded: chain D residue 133 MET Chi-restraints excluded: chain D residue 196 LYS 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 27 MET Chi-restraints excluded: chain G residue 28 THR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 80 optimal weight: 2.9990 chunk 172 optimal weight: 0.9990 chunk 179 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 148 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 185 optimal weight: 2.9990 chunk 177 optimal weight: 0.5980 chunk 89 optimal weight: 0.9990 chunk 143 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 GLN D 116 HIS F 24 GLN F 66 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.114178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.094681 restraints weight = 27079.826| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 2.67 r_work: 0.3135 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16050 Z= 0.146 Angle : 0.560 8.361 21881 Z= 0.284 Chirality : 0.043 0.179 2557 Planarity : 0.004 0.037 2735 Dihedral : 6.090 55.298 2707 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.16 % Allowed : 16.26 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.19), residues: 1887 helix: 1.50 (0.26), residues: 407 sheet: 0.47 (0.23), residues: 483 loop : -0.07 (0.20), residues: 997 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 41 TYR 0.019 0.001 TYR C 92 PHE 0.020 0.002 PHE A 304 TRP 0.010 0.001 TRP C 330 HIS 0.003 0.001 HIS F 58 Details of bonding type rmsd covalent geometry : bond 0.00345 (16012) covalent geometry : angle 0.55322 (21783) SS BOND : bond 0.00327 ( 16) SS BOND : angle 0.81180 ( 32) hydrogen bonds : bond 0.03301 ( 622) hydrogen bonds : angle 4.78705 ( 1647) link_ALPHA1-2 : bond 0.00040 ( 1) link_ALPHA1-2 : angle 1.79829 ( 3) link_ALPHA1-3 : bond 0.00868 ( 2) link_ALPHA1-3 : angle 1.36601 ( 6) link_ALPHA1-6 : bond 0.00367 ( 1) link_ALPHA1-6 : angle 1.36859 ( 3) link_BETA1-4 : bond 0.00154 ( 4) link_BETA1-4 : angle 1.81158 ( 12) link_NAG-ASN : bond 0.00197 ( 14) link_NAG-ASN : angle 1.56908 ( 42) *********************** 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 294 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 240 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 285 GLN cc_start: 0.8913 (OUTLIER) cc_final: 0.8683 (tt0) REVERT: A 380 MET cc_start: 0.8419 (mmm) cc_final: 0.8208 (mmm) REVERT: A 596 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8546 (mm) REVERT: A 619 ASP cc_start: 0.8161 (t0) cc_final: 0.7929 (t0) REVERT: A 645 GLU cc_start: 0.7445 (mp0) cc_final: 0.7087 (mp0) REVERT: B 54 CYS cc_start: 0.8878 (p) cc_final: 0.8589 (p) REVERT: B 237 GLN cc_start: 0.8790 (mp10) cc_final: 0.8430 (mp10) REVERT: C 197 ASP cc_start: 0.8907 (p0) cc_final: 0.8498 (p0) REVERT: C 215 GLN cc_start: 0.8790 (OUTLIER) cc_final: 0.8313 (mt0) REVERT: C 366 GLU cc_start: 0.8175 (mm-30) cc_final: 0.7914 (mm-30) REVERT: C 370 THR cc_start: 0.9288 (OUTLIER) cc_final: 0.9028 (m) REVERT: C 377 MET cc_start: 0.8529 (mmp) cc_final: 0.8231 (mmt) REVERT: C 435 GLN cc_start: 0.8397 (OUTLIER) cc_final: 0.8033 (tm-30) REVERT: D 29 SER cc_start: 0.8058 (t) cc_final: 0.7786 (p) REVERT: D 33 ASN cc_start: 0.8583 (t0) cc_final: 0.8149 (t0) REVERT: D 58 GLN cc_start: 0.8396 (tp40) cc_final: 0.7783 (tp40) REVERT: D 61 MET cc_start: 0.7239 (mmm) cc_final: 0.6903 (mmp) REVERT: D 74 GLU cc_start: 0.6861 (tt0) cc_final: 0.6588 (tp30) REVERT: D 165 GLU cc_start: 0.7940 (mp0) cc_final: 0.7540 (mp0) REVERT: D 173 ASP cc_start: 0.8519 (t0) cc_final: 0.8060 (t70) REVERT: D 176 GLN cc_start: 0.8659 (mt0) cc_final: 0.8302 (mt0) REVERT: D 196 LYS cc_start: 0.6584 (OUTLIER) cc_final: 0.6160 (mtmm) REVERT: D 215 ASP cc_start: 0.7791 (p0) cc_final: 0.7448 (p0) REVERT: D 306 THR cc_start: 0.8060 (OUTLIER) cc_final: 0.7712 (m) REVERT: E 68 LYS cc_start: 0.8330 (ttpt) cc_final: 0.7978 (ttpt) REVERT: F 42 LYS cc_start: 0.8743 (tttt) cc_final: 0.8444 (tptm) REVERT: F 88 GLN cc_start: 0.8688 (mm-40) cc_final: 0.8248 (mt0) REVERT: F 93 MET cc_start: 0.8700 (mtt) cc_final: 0.8423 (mtt) REVERT: F 104 MET cc_start: 0.8249 (tmm) cc_final: 0.7940 (tmm) REVERT: F 112 GLU cc_start: 0.8695 (pt0) cc_final: 0.8096 (pm20) REVERT: G 70 GLN cc_start: 0.8140 (mt0) cc_final: 0.7835 (mt0) REVERT: G 107 GLU cc_start: 0.6194 (OUTLIER) cc_final: 0.5751 (mm-30) REVERT: G 128 GLN cc_start: 0.8157 (pm20) cc_final: 0.7919 (pm20) REVERT: H 42 ARG cc_start: 0.7768 (OUTLIER) cc_final: 0.7135 (tmm-80) REVERT: H 66 LYS cc_start: 0.7420 (mppt) cc_final: 0.7126 (mppt) REVERT: H 96 ASP cc_start: 0.8355 (t70) cc_final: 0.7478 (t70) REVERT: H 99 GLU cc_start: 0.7925 (mt-10) cc_final: 0.7193 (mp0) REVERT: H 112 GLU cc_start: 0.7812 (pm20) cc_final: 0.7465 (pm20) outliers start: 54 outliers final: 30 residues processed: 268 average time/residue: 0.5962 time to fit residues: 177.0910 Evaluate side-chains 270 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 231 time to evaluate : 0.589 ------------------------------------------------------------------------------- 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 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 370 THR Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 435 GLN Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 72 ARG Chi-restraints excluded: chain D residue 133 MET Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 196 LYS Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 306 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 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 101 SER 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 12 optimal weight: 2.9990 chunk 73 optimal weight: 0.4980 chunk 67 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 chunk 138 optimal weight: 0.0270 chunk 135 optimal weight: 0.0020 chunk 3 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 overall best weight: 0.4446 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.116428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.096869 restraints weight = 27198.377| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 2.71 r_work: 0.3152 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 16050 Z= 0.110 Angle : 0.552 10.556 21881 Z= 0.280 Chirality : 0.042 0.233 2557 Planarity : 0.004 0.038 2735 Dihedral : 5.886 53.945 2707 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.87 % Allowed : 17.08 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.20), residues: 1887 helix: 1.57 (0.26), residues: 405 sheet: 0.61 (0.23), residues: 484 loop : -0.04 (0.20), residues: 998 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG E 41 TYR 0.022 0.001 TYR A 682 PHE 0.022 0.001 PHE A 304 TRP 0.010 0.001 TRP C 330 HIS 0.003 0.001 HIS A 511 Details of bonding type rmsd covalent geometry : bond 0.00254 (16012) covalent geometry : angle 0.54143 (21783) SS BOND : bond 0.00280 ( 16) SS BOND : angle 1.93376 ( 32) hydrogen bonds : bond 0.03113 ( 622) hydrogen bonds : angle 4.73737 ( 1647) link_ALPHA1-2 : bond 0.00118 ( 1) link_ALPHA1-2 : angle 1.67524 ( 3) link_ALPHA1-3 : bond 0.00979 ( 2) link_ALPHA1-3 : angle 1.29477 ( 6) link_ALPHA1-6 : bond 0.00562 ( 1) link_ALPHA1-6 : angle 1.34510 ( 3) link_BETA1-4 : bond 0.00212 ( 4) link_BETA1-4 : angle 1.71651 ( 12) link_NAG-ASN : bond 0.00152 ( 14) link_NAG-ASN : angle 1.48406 ( 42) *********************** 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 282 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 233 time to evaluate : 0.643 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 117 ARG cc_start: 0.8279 (tpm-80) cc_final: 0.8075 (tpm-80) REVERT: A 380 MET cc_start: 0.8302 (mmm) cc_final: 0.8083 (mmm) REVERT: A 596 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8573 (mm) REVERT: A 619 ASP cc_start: 0.8071 (t0) cc_final: 0.7849 (t0) REVERT: A 645 GLU cc_start: 0.7481 (mp0) cc_final: 0.7132 (mp0) REVERT: B 54 CYS cc_start: 0.8711 (p) cc_final: 0.8398 (p) REVERT: B 237 GLN cc_start: 0.8752 (mp10) cc_final: 0.8385 (mp10) REVERT: C 110 ASP cc_start: 0.8786 (t0) cc_final: 0.8271 (t0) REVERT: C 197 ASP cc_start: 0.8792 (p0) cc_final: 0.8400 (p0) REVERT: C 215 GLN cc_start: 0.8739 (OUTLIER) cc_final: 0.8281 (mt0) REVERT: C 366 GLU cc_start: 0.8128 (mm-30) cc_final: 0.7859 (mm-30) REVERT: C 370 THR cc_start: 0.9278 (OUTLIER) cc_final: 0.9044 (p) REVERT: C 377 MET cc_start: 0.8375 (mmp) cc_final: 0.8063 (mmt) REVERT: C 435 GLN cc_start: 0.8335 (OUTLIER) cc_final: 0.7952 (tm-30) REVERT: D 29 SER cc_start: 0.7993 (t) cc_final: 0.7765 (p) REVERT: D 33 ASN cc_start: 0.8533 (t0) cc_final: 0.8116 (t0) REVERT: D 58 GLN cc_start: 0.8267 (tp40) cc_final: 0.7617 (tp40) REVERT: D 61 MET cc_start: 0.7099 (mmm) cc_final: 0.6790 (mmp) REVERT: D 165 GLU cc_start: 0.7855 (mp0) cc_final: 0.7345 (mp0) REVERT: D 176 GLN cc_start: 0.8561 (mt0) cc_final: 0.8288 (mt0) REVERT: D 196 LYS cc_start: 0.6415 (OUTLIER) cc_final: 0.6012 (mtmm) REVERT: D 215 ASP cc_start: 0.7676 (p0) cc_final: 0.7342 (p0) REVERT: E 68 LYS cc_start: 0.8244 (ttpt) cc_final: 0.7872 (ttpt) REVERT: F 42 LYS cc_start: 0.8722 (tttt) cc_final: 0.8488 (tptm) REVERT: F 88 GLN cc_start: 0.8654 (mm-40) cc_final: 0.8270 (mt0) REVERT: F 93 MET cc_start: 0.8622 (mtt) cc_final: 0.8380 (mtt) REVERT: F 104 MET cc_start: 0.8156 (tmm) cc_final: 0.7861 (tmm) REVERT: F 112 GLU cc_start: 0.8560 (pt0) cc_final: 0.8046 (pm20) REVERT: G 70 GLN cc_start: 0.8108 (mt0) cc_final: 0.7801 (mt0) REVERT: G 81 ASN cc_start: 0.8224 (m110) cc_final: 0.7952 (m-40) REVERT: G 89 ARG cc_start: 0.8240 (ptt90) cc_final: 0.7750 (ptm-80) REVERT: G 107 GLU cc_start: 0.6130 (OUTLIER) cc_final: 0.5612 (mm-30) REVERT: H 66 LYS cc_start: 0.7384 (mppt) cc_final: 0.7108 (mppt) REVERT: H 96 ASP cc_start: 0.8366 (t70) cc_final: 0.7518 (t70) REVERT: H 99 GLU cc_start: 0.7808 (mt-10) cc_final: 0.7129 (mp0) REVERT: H 112 GLU cc_start: 0.7798 (pm20) cc_final: 0.7428 (pm20) outliers start: 49 outliers final: 27 residues processed: 260 average time/residue: 0.6213 time to fit residues: 178.6782 Evaluate side-chains 250 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 217 time to evaluate : 0.616 ------------------------------------------------------------------------------- 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 279 VAL 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 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 370 THR Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 435 GLN Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 72 ARG Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 196 LYS 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 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 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 186 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 105 optimal weight: 0.3980 chunk 36 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 chunk 13 optimal weight: 0.7980 chunk 167 optimal weight: 4.9990 chunk 172 optimal weight: 0.4980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 285 GLN D 116 HIS 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.116393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.096814 restraints weight = 27024.918| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 2.71 r_work: 0.3146 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 16050 Z= 0.127 Angle : 0.570 10.200 21881 Z= 0.289 Chirality : 0.042 0.202 2557 Planarity : 0.004 0.042 2735 Dihedral : 5.872 54.600 2707 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.57 % Allowed : 17.54 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.19), residues: 1887 helix: 1.54 (0.26), residues: 405 sheet: 0.60 (0.23), residues: 487 loop : -0.07 (0.20), residues: 995 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG E 41 TYR 0.016 0.001 TYR C 92 PHE 0.023 0.001 PHE A 304 TRP 0.009 0.001 TRP C 330 HIS 0.003 0.001 HIS A 511 Details of bonding type rmsd covalent geometry : bond 0.00300 (16012) covalent geometry : angle 0.55963 (21783) SS BOND : bond 0.00370 ( 16) SS BOND : angle 2.04325 ( 32) hydrogen bonds : bond 0.03232 ( 622) hydrogen bonds : angle 4.73536 ( 1647) link_ALPHA1-2 : bond 0.00050 ( 1) link_ALPHA1-2 : angle 1.72905 ( 3) link_ALPHA1-3 : bond 0.00886 ( 2) link_ALPHA1-3 : angle 1.31646 ( 6) link_ALPHA1-6 : bond 0.00542 ( 1) link_ALPHA1-6 : angle 1.41103 ( 3) link_BETA1-4 : bond 0.00257 ( 4) link_BETA1-4 : angle 1.70671 ( 12) link_NAG-ASN : bond 0.00155 ( 14) link_NAG-ASN : angle 1.50387 ( 42) *********************** 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 270 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 226 time to evaluate : 0.595 Fit side-chains revert: symmetry clash REVERT: A 122 LEU cc_start: 0.7985 (mt) cc_final: 0.7740 (mm) REVERT: A 596 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8572 (mm) REVERT: A 619 ASP cc_start: 0.8087 (t0) cc_final: 0.7844 (t0) REVERT: A 645 GLU cc_start: 0.7493 (mp0) cc_final: 0.7139 (mp0) REVERT: B 237 GLN cc_start: 0.8756 (mp10) cc_final: 0.8389 (mp10) REVERT: C 197 ASP cc_start: 0.8802 (p0) cc_final: 0.8388 (p0) REVERT: C 215 GLN cc_start: 0.8749 (OUTLIER) cc_final: 0.8304 (mt0) REVERT: C 366 GLU cc_start: 0.8175 (mm-30) cc_final: 0.7888 (mm-30) REVERT: C 370 THR cc_start: 0.9290 (OUTLIER) cc_final: 0.9064 (p) REVERT: C 377 MET cc_start: 0.8490 (mmp) cc_final: 0.8195 (mmt) REVERT: C 435 GLN cc_start: 0.8174 (OUTLIER) cc_final: 0.7742 (tm-30) REVERT: D 29 SER cc_start: 0.8028 (t) cc_final: 0.7796 (p) REVERT: D 33 ASN cc_start: 0.8528 (t0) cc_final: 0.8089 (t0) REVERT: D 40 GLN cc_start: 0.7517 (pp30) cc_final: 0.7234 (pp30) REVERT: D 58 GLN cc_start: 0.8268 (tp40) cc_final: 0.7613 (tp40) REVERT: D 61 MET cc_start: 0.7148 (mmm) cc_final: 0.6824 (mmp) REVERT: D 165 GLU cc_start: 0.7881 (mp0) cc_final: 0.7383 (mp0) REVERT: D 173 ASP cc_start: 0.8584 (t0) cc_final: 0.8212 (t0) REVERT: D 196 LYS cc_start: 0.6479 (OUTLIER) cc_final: 0.6036 (mtmm) REVERT: D 215 ASP cc_start: 0.7714 (p0) cc_final: 0.7373 (p0) REVERT: D 306 THR cc_start: 0.7997 (OUTLIER) cc_final: 0.7698 (m) REVERT: E 68 LYS cc_start: 0.8252 (ttpt) cc_final: 0.7868 (ttpt) REVERT: F 42 LYS cc_start: 0.8701 (tttt) cc_final: 0.8412 (tptm) REVERT: F 93 MET cc_start: 0.8602 (mtt) cc_final: 0.8352 (mtt) REVERT: F 104 MET cc_start: 0.8147 (tmm) cc_final: 0.7844 (tmm) REVERT: F 112 GLU cc_start: 0.8508 (pt0) cc_final: 0.7986 (pm20) REVERT: G 70 GLN cc_start: 0.8107 (mt0) cc_final: 0.7800 (mt0) REVERT: G 81 ASN cc_start: 0.8243 (m110) cc_final: 0.7970 (m-40) REVERT: G 89 ARG cc_start: 0.8253 (ptt90) cc_final: 0.7715 (ptm-80) REVERT: G 107 GLU cc_start: 0.6203 (OUTLIER) cc_final: 0.5697 (mm-30) REVERT: H 66 LYS cc_start: 0.7392 (mppt) cc_final: 0.7115 (mppt) REVERT: H 96 ASP cc_start: 0.8283 (t70) cc_final: 0.7342 (t70) REVERT: H 99 GLU cc_start: 0.7799 (mt-10) cc_final: 0.7108 (mp0) REVERT: H 112 GLU cc_start: 0.7565 (pm20) cc_final: 0.7236 (pm20) outliers start: 44 outliers final: 31 residues processed: 251 average time/residue: 0.6402 time to fit residues: 177.2538 Evaluate side-chains 260 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 222 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 159 ILE 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 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 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 370 THR Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 435 GLN Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 72 ARG 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 D residue 302 MET Chi-restraints excluded: chain D residue 306 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 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 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 121 optimal weight: 0.5980 chunk 129 optimal weight: 4.9990 chunk 133 optimal weight: 1.9990 chunk 154 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 82 optimal weight: 0.6980 chunk 182 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 101 optimal weight: 0.6980 chunk 73 optimal weight: 0.0570 overall best weight: 0.5698 ------------------------------------------------------------------------------- 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 285 GLN C 435 GLN F 24 GLN F 66 GLN ** G 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.116925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.097398 restraints weight = 27169.458| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.69 r_work: 0.3159 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 16050 Z= 0.119 Angle : 0.561 8.148 21881 Z= 0.285 Chirality : 0.042 0.194 2557 Planarity : 0.004 0.042 2735 Dihedral : 5.765 54.289 2707 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.51 % Allowed : 17.95 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.19), residues: 1887 helix: 1.52 (0.26), residues: 405 sheet: 0.62 (0.24), residues: 481 loop : -0.04 (0.20), residues: 1001 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG E 41 TYR 0.023 0.001 TYR A 682 PHE 0.025 0.001 PHE A 304 TRP 0.009 0.001 TRP C 330 HIS 0.003 0.001 HIS A 511 Details of bonding type rmsd covalent geometry : bond 0.00281 (16012) covalent geometry : angle 0.55234 (21783) SS BOND : bond 0.00342 ( 16) SS BOND : angle 1.59679 ( 32) hydrogen bonds : bond 0.03123 ( 622) hydrogen bonds : angle 4.70370 ( 1647) link_ALPHA1-2 : bond 0.00100 ( 1) link_ALPHA1-2 : angle 1.68766 ( 3) link_ALPHA1-3 : bond 0.00938 ( 2) link_ALPHA1-3 : angle 1.31303 ( 6) link_ALPHA1-6 : bond 0.00504 ( 1) link_ALPHA1-6 : angle 1.37798 ( 3) link_BETA1-4 : bond 0.00203 ( 4) link_BETA1-4 : angle 1.66055 ( 12) link_NAG-ASN : bond 0.00157 ( 14) link_NAG-ASN : angle 1.49647 ( 42) ********************** 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 273 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 230 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 LEU cc_start: 0.7977 (mt) cc_final: 0.7733 (mm) REVERT: A 285 GLN cc_start: 0.8814 (OUTLIER) cc_final: 0.8607 (tt0) REVERT: A 596 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8582 (mm) REVERT: A 619 ASP cc_start: 0.8095 (t0) cc_final: 0.7851 (t0) REVERT: A 645 GLU cc_start: 0.7464 (mp0) cc_final: 0.7105 (mp0) REVERT: B 237 GLN cc_start: 0.8753 (mp10) cc_final: 0.8386 (mp10) REVERT: C 197 ASP cc_start: 0.8803 (p0) cc_final: 0.8395 (p0) REVERT: C 215 GLN cc_start: 0.8744 (OUTLIER) cc_final: 0.8309 (mt0) REVERT: C 366 GLU cc_start: 0.8184 (mm-30) cc_final: 0.7896 (mm-30) REVERT: C 370 THR cc_start: 0.9295 (OUTLIER) cc_final: 0.9067 (p) REVERT: C 377 MET cc_start: 0.8486 (mmp) cc_final: 0.8175 (mmt) REVERT: D 29 SER cc_start: 0.8030 (t) cc_final: 0.7791 (p) REVERT: D 33 ASN cc_start: 0.8518 (t0) cc_final: 0.8117 (t0) REVERT: D 58 GLN cc_start: 0.8269 (tp40) cc_final: 0.7601 (tp40) REVERT: D 61 MET cc_start: 0.7172 (mmm) cc_final: 0.6849 (mmp) REVERT: D 165 GLU cc_start: 0.7880 (mp0) cc_final: 0.7380 (mp0) REVERT: D 173 ASP cc_start: 0.8475 (t0) cc_final: 0.8115 (t0) REVERT: D 215 ASP cc_start: 0.7720 (p0) cc_final: 0.7370 (p0) REVERT: D 306 THR cc_start: 0.8005 (OUTLIER) cc_final: 0.7719 (m) REVERT: E 68 LYS cc_start: 0.8243 (ttpt) cc_final: 0.7866 (ttpt) REVERT: F 42 LYS cc_start: 0.8693 (tttt) cc_final: 0.8411 (tptm) REVERT: F 88 GLN cc_start: 0.8679 (mm-40) cc_final: 0.8398 (mt0) REVERT: F 93 MET cc_start: 0.8600 (mtt) cc_final: 0.8353 (mtt) REVERT: F 104 MET cc_start: 0.8149 (tmm) cc_final: 0.7849 (tmm) REVERT: F 112 GLU cc_start: 0.8489 (pt0) cc_final: 0.7975 (pm20) REVERT: G 70 GLN cc_start: 0.8125 (mt0) cc_final: 0.7849 (mt0) REVERT: G 81 ASN cc_start: 0.8233 (m110) cc_final: 0.7960 (m-40) REVERT: G 89 ARG cc_start: 0.8172 (ptt90) cc_final: 0.7656 (ptm-80) REVERT: G 107 GLU cc_start: 0.6211 (OUTLIER) cc_final: 0.5670 (mm-30) REVERT: H 66 LYS cc_start: 0.7406 (mppt) cc_final: 0.7135 (mppt) REVERT: H 96 ASP cc_start: 0.8246 (t70) cc_final: 0.7346 (t70) REVERT: H 99 GLU cc_start: 0.7780 (mt-10) cc_final: 0.7099 (mp0) REVERT: H 112 GLU cc_start: 0.7528 (pm20) cc_final: 0.7193 (pm20) outliers start: 43 outliers final: 32 residues processed: 254 average time/residue: 0.6336 time to fit residues: 177.7807 Evaluate side-chains 263 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 225 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 159 ILE 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 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 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 370 THR Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 435 GLN Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 40 GLN 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 D residue 306 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 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 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 144 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 130 optimal weight: 0.6980 chunk 63 optimal weight: 4.9990 chunk 1 optimal weight: 0.5980 chunk 8 optimal weight: 3.9990 chunk 149 optimal weight: 0.9990 chunk 159 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 134 optimal weight: 0.0010 chunk 47 optimal weight: 3.9990 overall best weight: 0.6590 ------------------------------------------------------------------------------- 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 646 ASN ** D 106 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.116876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.097278 restraints weight = 26969.669| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 2.71 r_work: 0.3154 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.160 16050 Z= 0.165 Angle : 0.841 59.164 21881 Z= 0.479 Chirality : 0.043 0.381 2557 Planarity : 0.005 0.143 2735 Dihedral : 5.786 54.298 2707 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.28 % Allowed : 18.42 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.19), residues: 1887 helix: 1.52 (0.26), residues: 405 sheet: 0.62 (0.24), residues: 481 loop : -0.04 (0.20), residues: 1001 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG E 41 TYR 0.033 0.001 TYR A 88 PHE 0.024 0.001 PHE A 304 TRP 0.009 0.001 TRP C 330 HIS 0.003 0.001 HIS A 511 Details of bonding type rmsd covalent geometry : bond 0.00371 (16012) covalent geometry : angle 0.83642 (21783) SS BOND : bond 0.00334 ( 16) SS BOND : angle 1.54708 ( 32) hydrogen bonds : bond 0.03136 ( 622) hydrogen bonds : angle 4.70347 ( 1647) link_ALPHA1-2 : bond 0.00114 ( 1) link_ALPHA1-2 : angle 1.69512 ( 3) link_ALPHA1-3 : bond 0.01116 ( 2) link_ALPHA1-3 : angle 1.40291 ( 6) link_ALPHA1-6 : bond 0.00374 ( 1) link_ALPHA1-6 : angle 1.33360 ( 3) link_BETA1-4 : bond 0.00267 ( 4) link_BETA1-4 : angle 1.68511 ( 12) link_NAG-ASN : bond 0.00157 ( 14) link_NAG-ASN : angle 1.49761 ( 42) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5860.54 seconds wall clock time: 100 minutes 35.89 seconds (6035.89 seconds total)