Starting phenix.real_space_refine on Mon Mar 18 04:17:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tf2_41217/03_2024/8tf2_41217_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tf2_41217/03_2024/8tf2_41217.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tf2_41217/03_2024/8tf2_41217.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tf2_41217/03_2024/8tf2_41217.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tf2_41217/03_2024/8tf2_41217_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tf2_41217/03_2024/8tf2_41217_updated.pdb" } resolution = 2.57 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.056 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 136 5.16 5 C 13000 2.51 5 N 3260 2.21 5 O 3456 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 33": "NH1" <-> "NH2" Residue "A ARG 35": "NH1" <-> "NH2" Residue "A ARG 43": "NH1" <-> "NH2" Residue "A ARG 45": "NH1" <-> "NH2" Residue "A ARG 59": "NH1" <-> "NH2" Residue "A ARG 75": "NH1" <-> "NH2" Residue "A ARG 134": "NH1" <-> "NH2" Residue "A ARG 139": "NH1" <-> "NH2" Residue "A ARG 146": "NH1" <-> "NH2" Residue "A ARG 153": "NH1" <-> "NH2" Residue "A ARG 154": "NH1" <-> "NH2" Residue "A ARG 180": "NH1" <-> "NH2" Residue "A ARG 190": "NH1" <-> "NH2" Residue "A ARG 263": "NH1" <-> "NH2" Residue "A ARG 302": "NH1" <-> "NH2" Residue "A ARG 305": "NH1" <-> "NH2" Residue "A GLU 315": "OE1" <-> "OE2" Residue "A ARG 326": "NH1" <-> "NH2" Residue "A ARG 350": "NH1" <-> "NH2" Residue "A ARG 355": "NH1" <-> "NH2" Residue "A ARG 359": "NH1" <-> "NH2" Residue "A ARG 363": "NH1" <-> "NH2" Residue "A ARG 385": "NH1" <-> "NH2" Residue "A ARG 409": "NH1" <-> "NH2" Residue "A ARG 414": "NH1" <-> "NH2" Residue "A ARG 443": "NH1" <-> "NH2" Residue "A ARG 470": "NH1" <-> "NH2" Residue "A ARG 492": "NH1" <-> "NH2" Residue "A ARG 584": "NH1" <-> "NH2" Residue "A ARG 589": "NH1" <-> "NH2" Residue "A ARG 594": "NH1" <-> "NH2" Residue "A ARG 606": "NH1" <-> "NH2" Residue "A ARG 610": "NH1" <-> "NH2" Residue "A ARG 615": "NH1" <-> "NH2" Residue "A ARG 628": "NH1" <-> "NH2" Residue "A ARG 632": "NH1" <-> "NH2" Residue "B ARG 33": "NH1" <-> "NH2" Residue "B ARG 35": "NH1" <-> "NH2" Residue "B ARG 43": "NH1" <-> "NH2" Residue "B ARG 45": "NH1" <-> "NH2" Residue "B ARG 59": "NH1" <-> "NH2" Residue "B ARG 75": "NH1" <-> "NH2" Residue "B ARG 134": "NH1" <-> "NH2" Residue "B ARG 139": "NH1" <-> "NH2" Residue "B ARG 146": "NH1" <-> "NH2" Residue "B ARG 153": "NH1" <-> "NH2" Residue "B ARG 154": "NH1" <-> "NH2" Residue "B ARG 180": "NH1" <-> "NH2" Residue "B ARG 190": "NH1" <-> "NH2" Residue "B ARG 263": "NH1" <-> "NH2" Residue "B ARG 302": "NH1" <-> "NH2" Residue "B ARG 305": "NH1" <-> "NH2" Residue "B GLU 315": "OE1" <-> "OE2" Residue "B ARG 326": "NH1" <-> "NH2" Residue "B ARG 350": "NH1" <-> "NH2" Residue "B ARG 355": "NH1" <-> "NH2" Residue "B ARG 359": "NH1" <-> "NH2" Residue "B ARG 363": "NH1" <-> "NH2" Residue "B ARG 385": "NH1" <-> "NH2" Residue "B ARG 409": "NH1" <-> "NH2" Residue "B ARG 414": "NH1" <-> "NH2" Residue "B ARG 443": "NH1" <-> "NH2" Residue "B ARG 470": "NH1" <-> "NH2" Residue "B ARG 492": "NH1" <-> "NH2" Residue "B ARG 584": "NH1" <-> "NH2" Residue "B ARG 589": "NH1" <-> "NH2" Residue "B ARG 594": "NH1" <-> "NH2" Residue "B ARG 606": "NH1" <-> "NH2" Residue "B ARG 610": "NH1" <-> "NH2" Residue "B ARG 615": "NH1" <-> "NH2" Residue "B ARG 628": "NH1" <-> "NH2" Residue "B ARG 632": "NH1" <-> "NH2" Residue "C ARG 33": "NH1" <-> "NH2" Residue "C ARG 35": "NH1" <-> "NH2" Residue "C ARG 43": "NH1" <-> "NH2" Residue "C ARG 45": "NH1" <-> "NH2" Residue "C ARG 59": "NH1" <-> "NH2" Residue "C ARG 75": "NH1" <-> "NH2" Residue "C ARG 134": "NH1" <-> "NH2" Residue "C ARG 139": "NH1" <-> "NH2" Residue "C ARG 146": "NH1" <-> "NH2" Residue "C ARG 153": "NH1" <-> "NH2" Residue "C ARG 154": "NH1" <-> "NH2" Residue "C ARG 180": "NH1" <-> "NH2" Residue "C ARG 190": "NH1" <-> "NH2" Residue "C ARG 263": "NH1" <-> "NH2" Residue "C ARG 302": "NH1" <-> "NH2" Residue "C ARG 305": "NH1" <-> "NH2" Residue "C GLU 315": "OE1" <-> "OE2" Residue "C ARG 326": "NH1" <-> "NH2" Residue "C ARG 350": "NH1" <-> "NH2" Residue "C ARG 355": "NH1" <-> "NH2" Residue "C ARG 359": "NH1" <-> "NH2" Residue "C ARG 363": "NH1" <-> "NH2" Residue "C ARG 385": "NH1" <-> "NH2" Residue "C ARG 409": "NH1" <-> "NH2" Residue "C ARG 414": "NH1" <-> "NH2" Residue "C ARG 443": "NH1" <-> "NH2" Residue "C ARG 470": "NH1" <-> "NH2" Residue "C ARG 492": "NH1" <-> "NH2" Residue "C ARG 584": "NH1" <-> "NH2" Residue "C ARG 589": "NH1" <-> "NH2" Residue "C ARG 594": "NH1" <-> "NH2" Residue "C ARG 606": "NH1" <-> "NH2" Residue "C ARG 610": "NH1" <-> "NH2" Residue "C ARG 615": "NH1" <-> "NH2" Residue "C ARG 628": "NH1" <-> "NH2" Residue "C ARG 632": "NH1" <-> "NH2" Residue "D ARG 33": "NH1" <-> "NH2" Residue "D ARG 35": "NH1" <-> "NH2" Residue "D ARG 43": "NH1" <-> "NH2" Residue "D ARG 45": "NH1" <-> "NH2" Residue "D ARG 59": "NH1" <-> "NH2" Residue "D ARG 75": "NH1" <-> "NH2" Residue "D ARG 134": "NH1" <-> "NH2" Residue "D ARG 139": "NH1" <-> "NH2" Residue "D ARG 146": "NH1" <-> "NH2" Residue "D ARG 153": "NH1" <-> "NH2" Residue "D ARG 154": "NH1" <-> "NH2" Residue "D ARG 180": "NH1" <-> "NH2" Residue "D ARG 190": "NH1" <-> "NH2" Residue "D ARG 263": "NH1" <-> "NH2" Residue "D ARG 302": "NH1" <-> "NH2" Residue "D ARG 305": "NH1" <-> "NH2" Residue "D GLU 315": "OE1" <-> "OE2" Residue "D ARG 326": "NH1" <-> "NH2" Residue "D ARG 350": "NH1" <-> "NH2" Residue "D ARG 355": "NH1" <-> "NH2" Residue "D ARG 359": "NH1" <-> "NH2" Residue "D ARG 363": "NH1" <-> "NH2" Residue "D ARG 385": "NH1" <-> "NH2" Residue "D ARG 409": "NH1" <-> "NH2" Residue "D ARG 414": "NH1" <-> "NH2" Residue "D ARG 443": "NH1" <-> "NH2" Residue "D ARG 470": "NH1" <-> "NH2" Residue "D ARG 492": "NH1" <-> "NH2" Residue "D ARG 584": "NH1" <-> "NH2" Residue "D ARG 589": "NH1" <-> "NH2" Residue "D ARG 594": "NH1" <-> "NH2" Residue "D ARG 606": "NH1" <-> "NH2" Residue "D ARG 610": "NH1" <-> "NH2" Residue "D ARG 615": "NH1" <-> "NH2" Residue "D ARG 628": "NH1" <-> "NH2" Residue "D ARG 632": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 19856 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 602, 4822 Classifications: {'peptide': 602} Link IDs: {'PTRANS': 24, 'TRANS': 577} Chain breaks: 2 Chain: "B" Number of atoms: 4822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 602, 4822 Classifications: {'peptide': 602} Link IDs: {'PTRANS': 24, 'TRANS': 577} Chain breaks: 2 Chain: "C" Number of atoms: 4822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 602, 4822 Classifications: {'peptide': 602} Link IDs: {'PTRANS': 24, 'TRANS': 577} Chain breaks: 2 Chain: "D" Number of atoms: 4822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 602, 4822 Classifications: {'peptide': 602} Link IDs: {'PTRANS': 24, 'TRANS': 577} Chain breaks: 2 Chain: "A" Number of atoms: 171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 171 Unusual residues: {'CPL': 6, 'ERG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 199 Unresolved non-hydrogen angles: 244 Unresolved non-hydrogen dihedrals: 179 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'CPL:plan-4': 6, 'CPL:plan-3': 6, 'CPL:plan-2': 5, 'CPL:plan-1': 5} Unresolved non-hydrogen planarities: 78 Chain: "B" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 129 Unusual residues: {'CPL': 3, 'ERG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CPL:plan-4': 3, 'CPL:plan-3': 3, 'CPL:plan-2': 2, 'CPL:plan-1': 2} Unresolved non-hydrogen planarities: 36 Chain: "C" Number of atoms: 155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 155 Unusual residues: {'CPL': 5, 'ERG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 163 Unresolved non-hydrogen angles: 199 Unresolved non-hydrogen dihedrals: 147 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'CPL:plan-4': 5, 'CPL:plan-3': 5, 'CPL:plan-2': 4, 'CPL:plan-1': 4} Unresolved non-hydrogen planarities: 64 Chain: "D" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 113 Unusual residues: {'CPL': 2, 'ERG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'CPL:plan-4': 2, 'CPL:plan-3': 2, 'CPL:plan-2': 1, 'CPL:plan-1': 1} Unresolved non-hydrogen planarities: 22 Time building chain proxies: 10.28, per 1000 atoms: 0.52 Number of scatterers: 19856 At special positions: 0 Unit cell: (138.61, 138.61, 121.18, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 136 16.00 P 4 15.00 O 3456 8.00 N 3260 7.00 C 13000 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.40 Conformation dependent library (CDL) restraints added in 3.2 seconds 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4544 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 136 helices and 8 sheets defined 63.9% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.08 Creating SS restraints... Processing helix chain 'A' and resid 29 through 45 Processing helix chain 'A' and resid 48 through 55 Processing helix chain 'A' and resid 58 through 66 Processing helix chain 'A' and resid 82 through 88 Processing helix chain 'A' and resid 92 through 101 Processing helix chain 'A' and resid 103 through 107 Processing helix chain 'A' and resid 113 through 115 No H-bonds generated for 'chain 'A' and resid 113 through 115' Processing helix chain 'A' and resid 120 through 126 Processing helix chain 'A' and resid 130 through 139 removed outlier: 3.654A pdb=" N ARG A 139 " --> pdb=" O ALA A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 152 No H-bonds generated for 'chain 'A' and resid 150 through 152' Processing helix chain 'A' and resid 166 through 173 Processing helix chain 'A' and resid 176 through 184 Processing helix chain 'A' and resid 199 through 205 Processing helix chain 'A' and resid 209 through 222 removed outlier: 3.731A pdb=" N TYR A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 234 No H-bonds generated for 'chain 'A' and resid 232 through 234' Processing helix chain 'A' and resid 243 through 249 Processing helix chain 'A' and resid 253 through 262 removed outlier: 3.575A pdb=" N GLN A 261 " --> pdb=" O GLN A 257 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N LYS A 262 " --> pdb=" O HIS A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 284 No H-bonds generated for 'chain 'A' and resid 281 through 284' Processing helix chain 'A' and resid 292 through 297 Processing helix chain 'A' and resid 304 through 309 removed outlier: 4.097A pdb=" N LEU A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLU A 309 " --> pdb=" O ARG A 305 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 304 through 309' Processing helix chain 'A' and resid 311 through 323 Processing helix chain 'A' and resid 325 through 348 Processing helix chain 'A' and resid 373 through 376 No H-bonds generated for 'chain 'A' and resid 373 through 376' Processing helix chain 'A' and resid 380 through 410 Proline residue: A 405 - end of helix removed outlier: 3.516A pdb=" N PHE A 408 " --> pdb=" O ILE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 417 Processing helix chain 'A' and resid 423 through 444 Processing helix chain 'A' and resid 450 through 471 removed outlier: 3.631A pdb=" N VAL A 465 " --> pdb=" O GLY A 461 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N MET A 466 " --> pdb=" O TRP A 462 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N TYR A 467 " --> pdb=" O CYS A 463 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N PHE A 468 " --> pdb=" O SER A 464 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ALA A 469 " --> pdb=" O VAL A 465 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ARG A 470 " --> pdb=" O MET A 466 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N GLY A 471 " --> pdb=" O TYR A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 487 Proline residue: A 477 - end of helix Processing helix chain 'A' and resid 489 through 512 removed outlier: 3.503A pdb=" N LEU A 496 " --> pdb=" O ARG A 492 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL A 499 " --> pdb=" O TRP A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 537 Processing helix chain 'A' and resid 553 through 566 Processing helix chain 'A' and resid 570 through 607 removed outlier: 3.740A pdb=" N ILE A 575 " --> pdb=" O LEU A 571 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TRP A 583 " --> pdb=" O GLY A 579 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ARG A 584 " --> pdb=" O ASP A 580 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N GLN A 587 " --> pdb=" O TRP A 583 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N GLU A 588 " --> pdb=" O ARG A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 612 No H-bonds generated for 'chain 'A' and resid 610 through 612' Processing helix chain 'A' and resid 620 through 623 Processing helix chain 'B' and resid 29 through 45 Processing helix chain 'B' and resid 48 through 55 Processing helix chain 'B' and resid 58 through 66 Processing helix chain 'B' and resid 82 through 88 Processing helix chain 'B' and resid 92 through 101 Processing helix chain 'B' and resid 103 through 107 Processing helix chain 'B' and resid 113 through 115 No H-bonds generated for 'chain 'B' and resid 113 through 115' Processing helix chain 'B' and resid 120 through 126 Processing helix chain 'B' and resid 130 through 139 removed outlier: 3.654A pdb=" N ARG B 139 " --> pdb=" O ALA B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 152 No H-bonds generated for 'chain 'B' and resid 150 through 152' Processing helix chain 'B' and resid 166 through 173 Processing helix chain 'B' and resid 176 through 184 Processing helix chain 'B' and resid 199 through 205 Processing helix chain 'B' and resid 209 through 222 removed outlier: 3.731A pdb=" N TYR B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 234 No H-bonds generated for 'chain 'B' and resid 232 through 234' Processing helix chain 'B' and resid 243 through 249 Processing helix chain 'B' and resid 253 through 262 removed outlier: 3.575A pdb=" N GLN B 261 " --> pdb=" O GLN B 257 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N LYS B 262 " --> pdb=" O HIS B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 284 No H-bonds generated for 'chain 'B' and resid 281 through 284' Processing helix chain 'B' and resid 292 through 297 Processing helix chain 'B' and resid 304 through 309 removed outlier: 4.097A pdb=" N LEU B 308 " --> pdb=" O ALA B 304 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLU B 309 " --> pdb=" O ARG B 305 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 304 through 309' Processing helix chain 'B' and resid 311 through 323 Processing helix chain 'B' and resid 325 through 348 Processing helix chain 'B' and resid 373 through 376 No H-bonds generated for 'chain 'B' and resid 373 through 376' Processing helix chain 'B' and resid 380 through 410 Proline residue: B 405 - end of helix removed outlier: 3.516A pdb=" N PHE B 408 " --> pdb=" O ILE B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 417 Processing helix chain 'B' and resid 423 through 444 Processing helix chain 'B' and resid 450 through 471 removed outlier: 3.631A pdb=" N VAL B 465 " --> pdb=" O GLY B 461 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N MET B 466 " --> pdb=" O TRP B 462 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N TYR B 467 " --> pdb=" O CYS B 463 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N PHE B 468 " --> pdb=" O SER B 464 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ALA B 469 " --> pdb=" O VAL B 465 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ARG B 470 " --> pdb=" O MET B 466 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N GLY B 471 " --> pdb=" O TYR B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 487 Proline residue: B 477 - end of helix Processing helix chain 'B' and resid 489 through 512 removed outlier: 3.503A pdb=" N LEU B 496 " --> pdb=" O ARG B 492 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL B 499 " --> pdb=" O TRP B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 537 Processing helix chain 'B' and resid 553 through 565 Processing helix chain 'B' and resid 570 through 607 removed outlier: 3.740A pdb=" N ILE B 575 " --> pdb=" O LEU B 571 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TRP B 583 " --> pdb=" O GLY B 579 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ARG B 584 " --> pdb=" O ASP B 580 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N GLN B 587 " --> pdb=" O TRP B 583 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N GLU B 588 " --> pdb=" O ARG B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 610 through 612 No H-bonds generated for 'chain 'B' and resid 610 through 612' Processing helix chain 'B' and resid 620 through 623 Processing helix chain 'C' and resid 29 through 45 Processing helix chain 'C' and resid 48 through 55 Processing helix chain 'C' and resid 58 through 66 Processing helix chain 'C' and resid 82 through 88 Processing helix chain 'C' and resid 92 through 101 Processing helix chain 'C' and resid 103 through 107 Processing helix chain 'C' and resid 113 through 115 No H-bonds generated for 'chain 'C' and resid 113 through 115' Processing helix chain 'C' and resid 120 through 126 Processing helix chain 'C' and resid 130 through 139 removed outlier: 3.654A pdb=" N ARG C 139 " --> pdb=" O ALA C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 152 No H-bonds generated for 'chain 'C' and resid 150 through 152' Processing helix chain 'C' and resid 166 through 173 Processing helix chain 'C' and resid 176 through 184 Processing helix chain 'C' and resid 199 through 205 Processing helix chain 'C' and resid 209 through 222 removed outlier: 3.731A pdb=" N TYR C 222 " --> pdb=" O LEU C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 234 No H-bonds generated for 'chain 'C' and resid 232 through 234' Processing helix chain 'C' and resid 243 through 249 Processing helix chain 'C' and resid 253 through 262 removed outlier: 3.576A pdb=" N GLN C 261 " --> pdb=" O GLN C 257 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N LYS C 262 " --> pdb=" O HIS C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 284 No H-bonds generated for 'chain 'C' and resid 281 through 284' Processing helix chain 'C' and resid 292 through 297 Processing helix chain 'C' and resid 304 through 309 removed outlier: 4.096A pdb=" N LEU C 308 " --> pdb=" O ALA C 304 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLU C 309 " --> pdb=" O ARG C 305 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 304 through 309' Processing helix chain 'C' and resid 311 through 323 Processing helix chain 'C' and resid 325 through 348 Processing helix chain 'C' and resid 373 through 376 No H-bonds generated for 'chain 'C' and resid 373 through 376' Processing helix chain 'C' and resid 380 through 410 Proline residue: C 405 - end of helix removed outlier: 3.516A pdb=" N PHE C 408 " --> pdb=" O ILE C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 417 Processing helix chain 'C' and resid 423 through 444 Processing helix chain 'C' and resid 450 through 471 removed outlier: 3.631A pdb=" N VAL C 465 " --> pdb=" O GLY C 461 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N MET C 466 " --> pdb=" O TRP C 462 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N TYR C 467 " --> pdb=" O CYS C 463 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N PHE C 468 " --> pdb=" O SER C 464 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ALA C 469 " --> pdb=" O VAL C 465 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ARG C 470 " --> pdb=" O MET C 466 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N GLY C 471 " --> pdb=" O TYR C 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 487 Proline residue: C 477 - end of helix Processing helix chain 'C' and resid 489 through 512 removed outlier: 3.503A pdb=" N LEU C 496 " --> pdb=" O ARG C 492 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL C 499 " --> pdb=" O TRP C 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 526 through 537 Processing helix chain 'C' and resid 553 through 565 Processing helix chain 'C' and resid 570 through 607 removed outlier: 3.740A pdb=" N ILE C 575 " --> pdb=" O LEU C 571 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TRP C 583 " --> pdb=" O GLY C 579 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ARG C 584 " --> pdb=" O ASP C 580 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N GLN C 587 " --> pdb=" O TRP C 583 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N GLU C 588 " --> pdb=" O ARG C 584 " (cutoff:3.500A) Processing helix chain 'C' and resid 610 through 612 No H-bonds generated for 'chain 'C' and resid 610 through 612' Processing helix chain 'C' and resid 620 through 623 Processing helix chain 'D' and resid 29 through 45 Processing helix chain 'D' and resid 48 through 55 Processing helix chain 'D' and resid 58 through 66 Processing helix chain 'D' and resid 82 through 88 Processing helix chain 'D' and resid 92 through 101 Processing helix chain 'D' and resid 103 through 107 Processing helix chain 'D' and resid 113 through 115 No H-bonds generated for 'chain 'D' and resid 113 through 115' Processing helix chain 'D' and resid 120 through 126 Processing helix chain 'D' and resid 130 through 139 removed outlier: 3.654A pdb=" N ARG D 139 " --> pdb=" O ALA D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 152 No H-bonds generated for 'chain 'D' and resid 150 through 152' Processing helix chain 'D' and resid 166 through 173 Processing helix chain 'D' and resid 176 through 184 Processing helix chain 'D' and resid 199 through 205 Processing helix chain 'D' and resid 209 through 222 removed outlier: 3.731A pdb=" N TYR D 222 " --> pdb=" O LEU D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 234 No H-bonds generated for 'chain 'D' and resid 232 through 234' Processing helix chain 'D' and resid 243 through 249 Processing helix chain 'D' and resid 253 through 262 removed outlier: 3.575A pdb=" N GLN D 261 " --> pdb=" O GLN D 257 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N LYS D 262 " --> pdb=" O HIS D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 284 No H-bonds generated for 'chain 'D' and resid 281 through 284' Processing helix chain 'D' and resid 292 through 297 Processing helix chain 'D' and resid 304 through 309 removed outlier: 4.097A pdb=" N LEU D 308 " --> pdb=" O ALA D 304 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLU D 309 " --> pdb=" O ARG D 305 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 304 through 309' Processing helix chain 'D' and resid 311 through 323 Processing helix chain 'D' and resid 325 through 348 Processing helix chain 'D' and resid 373 through 376 No H-bonds generated for 'chain 'D' and resid 373 through 376' Processing helix chain 'D' and resid 380 through 410 Proline residue: D 405 - end of helix removed outlier: 3.516A pdb=" N PHE D 408 " --> pdb=" O ILE D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 412 through 417 Processing helix chain 'D' and resid 423 through 444 Processing helix chain 'D' and resid 450 through 471 removed outlier: 3.631A pdb=" N VAL D 465 " --> pdb=" O GLY D 461 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N MET D 466 " --> pdb=" O TRP D 462 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N TYR D 467 " --> pdb=" O CYS D 463 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N PHE D 468 " --> pdb=" O SER D 464 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ALA D 469 " --> pdb=" O VAL D 465 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ARG D 470 " --> pdb=" O MET D 466 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N GLY D 471 " --> pdb=" O TYR D 467 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 487 Proline residue: D 477 - end of helix Processing helix chain 'D' and resid 489 through 512 removed outlier: 3.503A pdb=" N LEU D 496 " --> pdb=" O ARG D 492 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL D 499 " --> pdb=" O TRP D 495 " (cutoff:3.500A) Processing helix chain 'D' and resid 526 through 537 Processing helix chain 'D' and resid 553 through 566 Processing helix chain 'D' and resid 570 through 607 removed outlier: 3.740A pdb=" N ILE D 575 " --> pdb=" O LEU D 571 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TRP D 583 " --> pdb=" O GLY D 579 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ARG D 584 " --> pdb=" O ASP D 580 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N GLN D 587 " --> pdb=" O TRP D 583 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N GLU D 588 " --> pdb=" O ARG D 584 " (cutoff:3.500A) Processing helix chain 'D' and resid 610 through 612 No H-bonds generated for 'chain 'D' and resid 610 through 612' Processing helix chain 'D' and resid 620 through 623 Processing sheet with id= A, first strand: chain 'A' and resid 630 through 636 removed outlier: 6.553A pdb=" N LEU A 277 " --> pdb=" O VAL A 266 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N VAL A 266 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ASP A 279 " --> pdb=" O LYS A 264 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LYS A 264 " --> pdb=" O ASP A 279 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 352 through 354 Processing sheet with id= C, first strand: chain 'B' and resid 630 through 636 removed outlier: 6.553A pdb=" N LEU B 277 " --> pdb=" O VAL B 266 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N VAL B 266 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ASP B 279 " --> pdb=" O LYS B 264 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LYS B 264 " --> pdb=" O ASP B 279 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 352 through 354 Processing sheet with id= E, first strand: chain 'C' and resid 630 through 636 removed outlier: 6.554A pdb=" N LEU C 277 " --> pdb=" O VAL C 266 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N VAL C 266 " --> pdb=" O LEU C 277 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ASP C 279 " --> pdb=" O LYS C 264 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LYS C 264 " --> pdb=" O ASP C 279 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 352 through 354 Processing sheet with id= G, first strand: chain 'D' and resid 630 through 636 removed outlier: 6.553A pdb=" N LEU D 277 " --> pdb=" O VAL D 266 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N VAL D 266 " --> pdb=" O LEU D 277 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ASP D 279 " --> pdb=" O LYS D 264 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LYS D 264 " --> pdb=" O ASP D 279 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 352 through 354 958 hydrogen bonds defined for protein. 2826 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: 6.40 Time building geometry restraints manager: 8.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3691 1.32 - 1.45: 4765 1.45 - 1.57: 11608 1.57 - 1.70: 16 1.70 - 1.82: 224 Bond restraints: 20304 Sorted by residual: bond pdb=" N ARG D 263 " pdb=" CA ARG D 263 " ideal model delta sigma weight residual 1.457 1.498 -0.041 1.19e-02 7.06e+03 1.18e+01 bond pdb=" N ARG B 263 " pdb=" CA ARG B 263 " ideal model delta sigma weight residual 1.457 1.498 -0.041 1.19e-02 7.06e+03 1.18e+01 bond pdb=" N ARG C 263 " pdb=" CA ARG C 263 " ideal model delta sigma weight residual 1.457 1.498 -0.041 1.19e-02 7.06e+03 1.18e+01 bond pdb=" N ARG A 263 " pdb=" CA ARG A 263 " ideal model delta sigma weight residual 1.457 1.498 -0.041 1.19e-02 7.06e+03 1.18e+01 bond pdb=" C ARG D 326 " pdb=" O ARG D 326 " ideal model delta sigma weight residual 1.244 1.211 0.033 1.00e-02 1.00e+04 1.08e+01 ... (remaining 20299 not shown) Histogram of bond angle deviations from ideal: 97.62 - 105.09: 412 105.09 - 112.55: 9181 112.55 - 120.02: 9639 120.02 - 127.48: 8124 127.48 - 134.95: 164 Bond angle restraints: 27520 Sorted by residual: angle pdb=" CB HIS B 84 " pdb=" CG HIS B 84 " pdb=" CD2 HIS B 84 " ideal model delta sigma weight residual 131.20 124.46 6.74 1.30e+00 5.92e-01 2.69e+01 angle pdb=" CB HIS C 84 " pdb=" CG HIS C 84 " pdb=" CD2 HIS C 84 " ideal model delta sigma weight residual 131.20 124.49 6.71 1.30e+00 5.92e-01 2.66e+01 angle pdb=" CB HIS A 84 " pdb=" CG HIS A 84 " pdb=" CD2 HIS A 84 " ideal model delta sigma weight residual 131.20 124.49 6.71 1.30e+00 5.92e-01 2.66e+01 angle pdb=" CB HIS D 84 " pdb=" CG HIS D 84 " pdb=" CD2 HIS D 84 " ideal model delta sigma weight residual 131.20 124.56 6.64 1.30e+00 5.92e-01 2.61e+01 angle pdb=" CA ASP C 57 " pdb=" CB ASP C 57 " pdb=" CG ASP C 57 " ideal model delta sigma weight residual 112.60 117.61 -5.01 1.00e+00 1.00e+00 2.51e+01 ... (remaining 27515 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.18: 12282 35.18 - 70.36: 217 70.36 - 105.54: 25 105.54 - 140.71: 4 140.71 - 175.89: 12 Dihedral angle restraints: 12540 sinusoidal: 5512 harmonic: 7028 Sorted by residual: dihedral pdb=" CA CYS D 112 " pdb=" C CYS D 112 " pdb=" N GLU D 113 " pdb=" CA GLU D 113 " ideal model delta harmonic sigma weight residual -180.00 -152.20 -27.80 0 5.00e+00 4.00e-02 3.09e+01 dihedral pdb=" CA CYS C 112 " pdb=" C CYS C 112 " pdb=" N GLU C 113 " pdb=" CA GLU C 113 " ideal model delta harmonic sigma weight residual -180.00 -152.21 -27.79 0 5.00e+00 4.00e-02 3.09e+01 dihedral pdb=" CA CYS B 112 " pdb=" C CYS B 112 " pdb=" N GLU B 113 " pdb=" CA GLU B 113 " ideal model delta harmonic sigma weight residual 180.00 -152.24 -27.76 0 5.00e+00 4.00e-02 3.08e+01 ... (remaining 12537 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1639 0.058 - 0.115: 985 0.115 - 0.173: 355 0.173 - 0.230: 101 0.230 - 0.287: 44 Chirality restraints: 3124 Sorted by residual: chirality pdb=" CA THR B 567 " pdb=" N THR B 567 " pdb=" C THR B 567 " pdb=" CB THR B 567 " both_signs ideal model delta sigma weight residual False 2.53 2.24 0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" CA THR C 567 " pdb=" N THR C 567 " pdb=" C THR C 567 " pdb=" CB THR C 567 " both_signs ideal model delta sigma weight residual False 2.53 2.24 0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" CA THR A 567 " pdb=" N THR A 567 " pdb=" C THR A 567 " pdb=" CB THR A 567 " both_signs ideal model delta sigma weight residual False 2.53 2.24 0.28 2.00e-01 2.50e+01 2.00e+00 ... (remaining 3121 not shown) Planarity restraints: 3404 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 593 " 0.140 2.00e-02 2.50e+03 6.56e-02 1.08e+02 pdb=" CG TRP C 593 " -0.064 2.00e-02 2.50e+03 pdb=" CD1 TRP C 593 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 TRP C 593 " -0.073 2.00e-02 2.50e+03 pdb=" NE1 TRP C 593 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP C 593 " -0.014 2.00e-02 2.50e+03 pdb=" CE3 TRP C 593 " -0.074 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 593 " 0.057 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 593 " -0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP C 593 " 0.065 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 593 " -0.140 2.00e-02 2.50e+03 6.56e-02 1.08e+02 pdb=" CG TRP D 593 " 0.064 2.00e-02 2.50e+03 pdb=" CD1 TRP D 593 " 0.030 2.00e-02 2.50e+03 pdb=" CD2 TRP D 593 " 0.074 2.00e-02 2.50e+03 pdb=" NE1 TRP D 593 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP D 593 " 0.014 2.00e-02 2.50e+03 pdb=" CE3 TRP D 593 " 0.073 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 593 " -0.057 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 593 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP D 593 " -0.065 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 593 " -0.140 2.00e-02 2.50e+03 6.55e-02 1.07e+02 pdb=" CG TRP A 593 " 0.064 2.00e-02 2.50e+03 pdb=" CD1 TRP A 593 " 0.030 2.00e-02 2.50e+03 pdb=" CD2 TRP A 593 " 0.073 2.00e-02 2.50e+03 pdb=" NE1 TRP A 593 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 593 " 0.014 2.00e-02 2.50e+03 pdb=" CE3 TRP A 593 " 0.073 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 593 " -0.057 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 593 " 0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP A 593 " -0.065 2.00e-02 2.50e+03 ... (remaining 3401 not shown) Histogram of nonbonded interaction distances: 2.48 - 2.97: 8574 2.97 - 3.45: 21257 3.45 - 3.93: 36085 3.93 - 4.42: 40145 4.42 - 4.90: 66012 Nonbonded interactions: 172073 Sorted by model distance: nonbonded pdb=" OD1 ASP C 489 " pdb=" NH1 ARG C 492 " model vdw 2.484 2.520 nonbonded pdb=" OD1 ASP B 489 " pdb=" NH1 ARG B 492 " model vdw 2.484 2.520 nonbonded pdb=" OD1 ASP A 489 " pdb=" NH1 ARG A 492 " model vdw 2.484 2.520 nonbonded pdb=" OD1 ASP D 489 " pdb=" NH1 ARG D 492 " model vdw 2.484 2.520 nonbonded pdb=" O THR D 311 " pdb=" OE1 GLU D 315 " model vdw 2.513 3.040 ... (remaining 172068 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 28 through 637 or resid 802 or resid 804)) selection = (chain 'B' and (resid 28 through 637 or resid 802 or resid 804)) selection = (chain 'C' and (resid 28 through 637 or resid 802 or resid 804)) selection = (chain 'D' and (resid 28 through 637 or resid 802 or resid 804)) } 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: 1.090 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: 6.100 Check model and map are aligned: 0.280 Set scattering table: 0.180 Process input model: 51.930 Find NCS groups from input model: 1.880 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 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 : 0.012 0.059 20304 Z= 0.771 Angle : 1.754 10.363 27520 Z= 1.197 Chirality : 0.086 0.287 3124 Planarity : 0.013 0.066 3404 Dihedral : 15.410 175.892 7996 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 0.38 % Allowed : 0.82 % Favored : 98.80 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.16), residues: 2384 helix: -0.12 (0.12), residues: 1480 sheet: 1.03 (0.54), residues: 76 loop : 1.13 (0.24), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.140 0.021 TRP C 593 HIS 0.010 0.004 HIS C 582 PHE 0.066 0.015 PHE B 256 TYR 0.110 0.024 TYR C 336 ARG 0.006 0.001 ARG D 492 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 419 time to evaluate : 2.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 GLU cc_start: 0.6799 (mt-10) cc_final: 0.6434 (mm-30) REVERT: A 74 GLN cc_start: 0.7343 (mt0) cc_final: 0.7083 (mt0) REVERT: A 99 MET cc_start: 0.7200 (mtm) cc_final: 0.6779 (mtm) REVERT: A 104 GLU cc_start: 0.7429 (pm20) cc_final: 0.6315 (tm-30) REVERT: A 107 LYS cc_start: 0.7095 (mttt) cc_final: 0.6510 (mttp) REVERT: A 155 SER cc_start: 0.7753 (m) cc_final: 0.7490 (p) REVERT: A 176 GLU cc_start: 0.6993 (tt0) cc_final: 0.6463 (mt-10) REVERT: A 194 SER cc_start: 0.8516 (m) cc_final: 0.8209 (p) REVERT: A 257 GLN cc_start: 0.7456 (pt0) cc_final: 0.6604 (tp-100) REVERT: A 262 LYS cc_start: 0.8328 (mttt) cc_final: 0.7990 (mptt) REVERT: A 300 LYS cc_start: 0.8437 (mttt) cc_final: 0.8163 (mmtt) REVERT: A 302 ARG cc_start: 0.7283 (ptm160) cc_final: 0.7057 (mtp-110) REVERT: A 322 LYS cc_start: 0.7698 (mtpt) cc_final: 0.7390 (mppt) REVERT: A 473 GLN cc_start: 0.8664 (tt0) cc_final: 0.8238 (tp40) REVERT: A 491 MET cc_start: 0.8466 (mmm) cc_final: 0.7920 (tpp) REVERT: A 570 MET cc_start: 0.8466 (mtp) cc_final: 0.8241 (mmm) REVERT: A 605 GLU cc_start: 0.8474 (tt0) cc_final: 0.8145 (tt0) REVERT: A 621 TYR cc_start: 0.7848 (t80) cc_final: 0.7640 (t80) REVERT: B 55 GLU cc_start: 0.6792 (mt-10) cc_final: 0.6413 (mm-30) REVERT: B 74 GLN cc_start: 0.7365 (mt0) cc_final: 0.7104 (mt0) REVERT: B 99 MET cc_start: 0.7206 (mtm) cc_final: 0.6793 (mtm) REVERT: B 104 GLU cc_start: 0.7432 (pm20) cc_final: 0.6308 (tm-30) REVERT: B 107 LYS cc_start: 0.7090 (mttt) cc_final: 0.6519 (mttp) REVERT: B 155 SER cc_start: 0.7751 (m) cc_final: 0.7491 (p) REVERT: B 176 GLU cc_start: 0.6983 (tt0) cc_final: 0.6430 (mt-10) REVERT: B 194 SER cc_start: 0.8530 (m) cc_final: 0.8224 (p) REVERT: B 257 GLN cc_start: 0.7447 (pt0) cc_final: 0.6574 (tp-100) REVERT: B 262 LYS cc_start: 0.8338 (mttt) cc_final: 0.8030 (mptt) REVERT: B 300 LYS cc_start: 0.8437 (mttt) cc_final: 0.8163 (mmtt) REVERT: B 302 ARG cc_start: 0.7270 (ptm160) cc_final: 0.7053 (mtp-110) REVERT: B 322 LYS cc_start: 0.7755 (mtpt) cc_final: 0.7450 (mppt) REVERT: B 473 GLN cc_start: 0.8661 (tt0) cc_final: 0.8226 (tp40) REVERT: B 491 MET cc_start: 0.8463 (mmm) cc_final: 0.7920 (tpp) REVERT: B 570 MET cc_start: 0.8467 (mtp) cc_final: 0.8247 (mmm) REVERT: B 605 GLU cc_start: 0.8465 (tt0) cc_final: 0.8132 (tt0) REVERT: C 55 GLU cc_start: 0.6793 (mt-10) cc_final: 0.6413 (mm-30) REVERT: C 74 GLN cc_start: 0.7365 (mt0) cc_final: 0.7103 (mt0) REVERT: C 99 MET cc_start: 0.7203 (mtm) cc_final: 0.6791 (mtm) REVERT: C 104 GLU cc_start: 0.7431 (pm20) cc_final: 0.6306 (tm-30) REVERT: C 107 LYS cc_start: 0.7098 (mttt) cc_final: 0.6520 (mttp) REVERT: C 155 SER cc_start: 0.7764 (m) cc_final: 0.7508 (p) REVERT: C 176 GLU cc_start: 0.6989 (tt0) cc_final: 0.6431 (mt-10) REVERT: C 194 SER cc_start: 0.8525 (m) cc_final: 0.8206 (p) REVERT: C 257 GLN cc_start: 0.7449 (pt0) cc_final: 0.6572 (tp-100) REVERT: C 262 LYS cc_start: 0.8335 (mttt) cc_final: 0.8026 (mptt) REVERT: C 300 LYS cc_start: 0.8436 (mttt) cc_final: 0.8160 (mmtt) REVERT: C 302 ARG cc_start: 0.7271 (ptm160) cc_final: 0.7053 (mtp-110) REVERT: C 322 LYS cc_start: 0.7750 (mtpt) cc_final: 0.7446 (mppt) REVERT: C 473 GLN cc_start: 0.8670 (tt0) cc_final: 0.8239 (tp40) REVERT: C 491 MET cc_start: 0.8462 (mmm) cc_final: 0.7917 (tpp) REVERT: C 570 MET cc_start: 0.8468 (mtp) cc_final: 0.8240 (mmm) REVERT: D 43 ARG cc_start: 0.7209 (mmm-85) cc_final: 0.6972 (mmm160) REVERT: D 55 GLU cc_start: 0.6756 (mt-10) cc_final: 0.6376 (mm-30) REVERT: D 74 GLN cc_start: 0.7409 (mt0) cc_final: 0.7157 (mt0) REVERT: D 99 MET cc_start: 0.7209 (mtm) cc_final: 0.6802 (mtm) REVERT: D 104 GLU cc_start: 0.7442 (pm20) cc_final: 0.6317 (tm-30) REVERT: D 107 LYS cc_start: 0.7097 (mttt) cc_final: 0.6532 (mttp) REVERT: D 155 SER cc_start: 0.7766 (m) cc_final: 0.7515 (p) REVERT: D 176 GLU cc_start: 0.6991 (tt0) cc_final: 0.6440 (mt-10) REVERT: D 194 SER cc_start: 0.8520 (m) cc_final: 0.8191 (p) REVERT: D 257 GLN cc_start: 0.7425 (pt0) cc_final: 0.6596 (tp-100) REVERT: D 262 LYS cc_start: 0.8332 (mttt) cc_final: 0.7994 (mptt) REVERT: D 300 LYS cc_start: 0.8436 (mttt) cc_final: 0.8161 (mmtt) REVERT: D 302 ARG cc_start: 0.7275 (ptm160) cc_final: 0.7053 (mtp-110) REVERT: D 322 LYS cc_start: 0.7767 (mtpt) cc_final: 0.7456 (mppt) REVERT: D 473 GLN cc_start: 0.8664 (tt0) cc_final: 0.8231 (tp40) REVERT: D 491 MET cc_start: 0.8471 (mmm) cc_final: 0.7927 (tpp) REVERT: D 570 MET cc_start: 0.8460 (mtp) cc_final: 0.8250 (mmm) REVERT: D 621 TYR cc_start: 0.7842 (t80) cc_final: 0.7642 (t80) outliers start: 8 outliers final: 10 residues processed: 427 average time/residue: 1.5713 time to fit residues: 740.3903 Evaluate side-chains 312 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 302 time to evaluate : 2.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 627 ASP Chi-restraints excluded: chain D residue 315 GLU Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 627 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 0.9980 chunk 181 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 62 optimal weight: 6.9990 chunk 122 optimal weight: 0.9990 chunk 97 optimal weight: 0.8980 chunk 188 optimal weight: 7.9990 chunk 72 optimal weight: 6.9990 chunk 114 optimal weight: 1.9990 chunk 140 optimal weight: 2.9990 chunk 217 optimal weight: 0.8980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN A 51 GLN A 217 ASN ** A 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 418 GLN A 483 GLN A 518 ASN A 596 GLN B 40 GLN B 51 GLN B 217 ASN ** B 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 418 GLN B 483 GLN B 596 GLN C 51 GLN C 217 ASN C 418 GLN C 596 GLN D 51 GLN D 217 ASN D 418 GLN D 596 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20304 Z= 0.192 Angle : 0.509 5.862 27520 Z= 0.271 Chirality : 0.039 0.151 3124 Planarity : 0.004 0.043 3404 Dihedral : 13.193 176.120 3452 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Rotamer: Outliers : 1.73 % Allowed : 7.31 % Favored : 90.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.17), residues: 2384 helix: 1.51 (0.13), residues: 1476 sheet: 1.02 (0.51), residues: 88 loop : 1.05 (0.24), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 593 HIS 0.004 0.001 HIS B 201 PHE 0.015 0.002 PHE C 456 TYR 0.016 0.002 TYR A 89 ARG 0.005 0.000 ARG B 139 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 322 time to evaluate : 2.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 GLN cc_start: 0.6758 (tt0) cc_final: 0.6466 (mt0) REVERT: A 99 MET cc_start: 0.7130 (mtm) cc_final: 0.6853 (mtm) REVERT: A 100 GLU cc_start: 0.7062 (mt-10) cc_final: 0.6723 (mt-10) REVERT: A 104 GLU cc_start: 0.7390 (pm20) cc_final: 0.6196 (tm-30) REVERT: A 107 LYS cc_start: 0.7090 (mttt) cc_final: 0.6638 (mttp) REVERT: A 146 ARG cc_start: 0.7974 (mtp180) cc_final: 0.7766 (mmm-85) REVERT: A 176 GLU cc_start: 0.6914 (tt0) cc_final: 0.6404 (mt-10) REVERT: A 194 SER cc_start: 0.8425 (m) cc_final: 0.8102 (p) REVERT: A 257 GLN cc_start: 0.7254 (pt0) cc_final: 0.6625 (tp-100) REVERT: A 262 LYS cc_start: 0.8281 (mttt) cc_final: 0.8007 (mmtm) REVERT: A 300 LYS cc_start: 0.8346 (mttt) cc_final: 0.8138 (mmtt) REVERT: A 302 ARG cc_start: 0.7251 (ptm160) cc_final: 0.6553 (tmt-80) REVERT: A 379 THR cc_start: 0.7684 (m) cc_final: 0.7476 (m) REVERT: A 381 GLN cc_start: 0.7281 (mp10) cc_final: 0.5582 (mm-40) REVERT: A 408 PHE cc_start: 0.7287 (m-10) cc_final: 0.7017 (m-10) REVERT: A 491 MET cc_start: 0.8171 (mmm) cc_final: 0.7669 (tpp) REVERT: B 35 ARG cc_start: 0.7516 (OUTLIER) cc_final: 0.7316 (ttt90) REVERT: B 40 GLN cc_start: 0.6772 (tt0) cc_final: 0.6470 (mt0) REVERT: B 99 MET cc_start: 0.7134 (mtm) cc_final: 0.6852 (mtm) REVERT: B 100 GLU cc_start: 0.7065 (mt-10) cc_final: 0.6753 (mt-10) REVERT: B 104 GLU cc_start: 0.7401 (pm20) cc_final: 0.6149 (tm-30) REVERT: B 107 LYS cc_start: 0.7083 (mttt) cc_final: 0.6639 (mttp) REVERT: B 146 ARG cc_start: 0.7990 (mtp180) cc_final: 0.7784 (mmm-85) REVERT: B 176 GLU cc_start: 0.6913 (tt0) cc_final: 0.6403 (mt-10) REVERT: B 194 SER cc_start: 0.8426 (m) cc_final: 0.8102 (p) REVERT: B 257 GLN cc_start: 0.7270 (pt0) cc_final: 0.6634 (tp-100) REVERT: B 262 LYS cc_start: 0.8283 (mttt) cc_final: 0.8008 (mmtm) REVERT: B 300 LYS cc_start: 0.8346 (mttt) cc_final: 0.8138 (mmtt) REVERT: B 302 ARG cc_start: 0.7269 (ptm160) cc_final: 0.6591 (tmt-80) REVERT: B 379 THR cc_start: 0.7681 (m) cc_final: 0.7475 (m) REVERT: B 381 GLN cc_start: 0.7268 (mp10) cc_final: 0.5548 (mm-40) REVERT: B 408 PHE cc_start: 0.7285 (m-10) cc_final: 0.7006 (m-10) REVERT: B 491 MET cc_start: 0.8171 (mmm) cc_final: 0.7667 (tpp) REVERT: C 40 GLN cc_start: 0.6758 (tt0) cc_final: 0.6421 (mt0) REVERT: C 99 MET cc_start: 0.7130 (mtm) cc_final: 0.6851 (mtm) REVERT: C 100 GLU cc_start: 0.7064 (mt-10) cc_final: 0.6752 (mt-10) REVERT: C 104 GLU cc_start: 0.7400 (pm20) cc_final: 0.6146 (tm-30) REVERT: C 107 LYS cc_start: 0.7081 (mttt) cc_final: 0.6636 (mttp) REVERT: C 146 ARG cc_start: 0.7976 (mtp180) cc_final: 0.7766 (mmm-85) REVERT: C 176 GLU cc_start: 0.6915 (tt0) cc_final: 0.6403 (mt-10) REVERT: C 194 SER cc_start: 0.8430 (m) cc_final: 0.8103 (p) REVERT: C 257 GLN cc_start: 0.7270 (pt0) cc_final: 0.6633 (tp-100) REVERT: C 262 LYS cc_start: 0.8284 (mttt) cc_final: 0.8008 (mmtm) REVERT: C 302 ARG cc_start: 0.7272 (ptm160) cc_final: 0.6593 (tmt-80) REVERT: C 379 THR cc_start: 0.7697 (m) cc_final: 0.7489 (m) REVERT: C 381 GLN cc_start: 0.7274 (mp10) cc_final: 0.5569 (mm-40) REVERT: C 408 PHE cc_start: 0.7275 (m-10) cc_final: 0.7003 (m-10) REVERT: C 491 MET cc_start: 0.8171 (mmm) cc_final: 0.7669 (tpp) REVERT: D 40 GLN cc_start: 0.6760 (tt0) cc_final: 0.6480 (mt0) REVERT: D 100 GLU cc_start: 0.7070 (mt-10) cc_final: 0.6756 (mt-10) REVERT: D 104 GLU cc_start: 0.7411 (pm20) cc_final: 0.6157 (tm-30) REVERT: D 107 LYS cc_start: 0.7084 (mttt) cc_final: 0.6646 (mttp) REVERT: D 176 GLU cc_start: 0.6959 (tt0) cc_final: 0.6420 (mt-10) REVERT: D 194 SER cc_start: 0.8446 (m) cc_final: 0.8139 (p) REVERT: D 257 GLN cc_start: 0.7235 (pt0) cc_final: 0.6624 (tp-100) REVERT: D 262 LYS cc_start: 0.8283 (mttt) cc_final: 0.8007 (mmtm) REVERT: D 300 LYS cc_start: 0.8349 (mttt) cc_final: 0.8140 (mmtt) REVERT: D 302 ARG cc_start: 0.7273 (ptm160) cc_final: 0.6563 (tmt-80) REVERT: D 379 THR cc_start: 0.7692 (m) cc_final: 0.7483 (m) REVERT: D 381 GLN cc_start: 0.7264 (mp10) cc_final: 0.5544 (mm-40) REVERT: D 408 PHE cc_start: 0.7271 (m-10) cc_final: 0.7035 (m-10) REVERT: D 491 MET cc_start: 0.8170 (mmm) cc_final: 0.7666 (tpp) outliers start: 36 outliers final: 8 residues processed: 338 average time/residue: 1.5639 time to fit residues: 584.2318 Evaluate side-chains 281 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 272 time to evaluate : 2.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain B residue 35 ARG Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain D residue 315 GLU Chi-restraints excluded: chain D residue 354 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 121 optimal weight: 5.9990 chunk 67 optimal weight: 9.9990 chunk 181 optimal weight: 6.9990 chunk 148 optimal weight: 0.4980 chunk 60 optimal weight: 10.0000 chunk 218 optimal weight: 3.9990 chunk 235 optimal weight: 0.0980 chunk 194 optimal weight: 6.9990 chunk 216 optimal weight: 4.9990 chunk 74 optimal weight: 6.9990 chunk 175 optimal weight: 0.7980 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 GLN B 418 GLN C 418 GLN D 418 GLN D 483 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 20304 Z= 0.263 Angle : 0.511 5.906 27520 Z= 0.269 Chirality : 0.040 0.148 3124 Planarity : 0.004 0.046 3404 Dihedral : 12.708 174.111 3444 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 2.93 % Allowed : 8.27 % Favored : 88.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.17), residues: 2384 helix: 1.54 (0.13), residues: 1484 sheet: -0.63 (0.44), residues: 108 loop : 0.85 (0.23), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 593 HIS 0.006 0.001 HIS A 201 PHE 0.012 0.002 PHE D 512 TYR 0.016 0.002 TYR A 89 ARG 0.004 0.000 ARG B 180 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 287 time to evaluate : 2.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.6650 (OUTLIER) cc_final: 0.6219 (mp0) REVERT: A 40 GLN cc_start: 0.6720 (tt0) cc_final: 0.6462 (mt0) REVERT: A 47 SER cc_start: 0.7662 (OUTLIER) cc_final: 0.7081 (m) REVERT: A 51 GLN cc_start: 0.7459 (tp-100) cc_final: 0.7017 (mm-40) REVERT: A 55 GLU cc_start: 0.6839 (mt-10) cc_final: 0.6401 (mm-30) REVERT: A 99 MET cc_start: 0.7192 (mtm) cc_final: 0.6958 (mtm) REVERT: A 100 GLU cc_start: 0.7135 (mt-10) cc_final: 0.6804 (mt-10) REVERT: A 104 GLU cc_start: 0.7542 (pm20) cc_final: 0.6321 (tm-30) REVERT: A 107 LYS cc_start: 0.7127 (mttt) cc_final: 0.6610 (mttp) REVERT: A 176 GLU cc_start: 0.7006 (tt0) cc_final: 0.6508 (mt-10) REVERT: A 190 ARG cc_start: 0.7786 (OUTLIER) cc_final: 0.6388 (mtm180) REVERT: A 257 GLN cc_start: 0.7203 (pt0) cc_final: 0.6537 (tp-100) REVERT: A 262 LYS cc_start: 0.8238 (mttt) cc_final: 0.7991 (mmtm) REVERT: A 300 LYS cc_start: 0.8481 (mttt) cc_final: 0.8231 (mmtt) REVERT: A 302 ARG cc_start: 0.7251 (ptm160) cc_final: 0.6648 (tmt-80) REVERT: A 323 LYS cc_start: 0.8166 (OUTLIER) cc_final: 0.7916 (tttm) REVERT: A 381 GLN cc_start: 0.7332 (mp10) cc_final: 0.5647 (mm-40) REVERT: A 491 MET cc_start: 0.8168 (mmm) cc_final: 0.7884 (mtm) REVERT: B 30 GLU cc_start: 0.6648 (OUTLIER) cc_final: 0.6216 (mp0) REVERT: B 35 ARG cc_start: 0.7560 (OUTLIER) cc_final: 0.7357 (ttt90) REVERT: B 47 SER cc_start: 0.7663 (OUTLIER) cc_final: 0.7081 (m) REVERT: B 51 GLN cc_start: 0.7467 (tp-100) cc_final: 0.7017 (mm-40) REVERT: B 55 GLU cc_start: 0.6838 (mt-10) cc_final: 0.6402 (mm-30) REVERT: B 99 MET cc_start: 0.7190 (mtm) cc_final: 0.6955 (mtm) REVERT: B 100 GLU cc_start: 0.7136 (mt-10) cc_final: 0.6793 (mt-10) REVERT: B 104 GLU cc_start: 0.7523 (pm20) cc_final: 0.6229 (tm-30) REVERT: B 107 LYS cc_start: 0.7123 (mttt) cc_final: 0.6610 (mttp) REVERT: B 176 GLU cc_start: 0.7005 (tt0) cc_final: 0.6510 (mt-10) REVERT: B 190 ARG cc_start: 0.7775 (OUTLIER) cc_final: 0.6383 (mtm180) REVERT: B 257 GLN cc_start: 0.7211 (pt0) cc_final: 0.6549 (tp-100) REVERT: B 262 LYS cc_start: 0.8239 (mttt) cc_final: 0.7992 (mmtm) REVERT: B 300 LYS cc_start: 0.8481 (mttt) cc_final: 0.8230 (mmtt) REVERT: B 302 ARG cc_start: 0.7252 (ptm160) cc_final: 0.6647 (tmt-80) REVERT: B 323 LYS cc_start: 0.8167 (OUTLIER) cc_final: 0.7917 (tttm) REVERT: B 381 GLN cc_start: 0.7337 (mp10) cc_final: 0.5649 (mm-40) REVERT: B 408 PHE cc_start: 0.7299 (m-10) cc_final: 0.7030 (m-10) REVERT: B 491 MET cc_start: 0.8170 (mmm) cc_final: 0.7887 (mtm) REVERT: C 30 GLU cc_start: 0.6648 (OUTLIER) cc_final: 0.6217 (mp0) REVERT: C 40 GLN cc_start: 0.6760 (tt0) cc_final: 0.6427 (mt0) REVERT: C 51 GLN cc_start: 0.7465 (tp-100) cc_final: 0.7016 (mm-40) REVERT: C 55 GLU cc_start: 0.6841 (mt-10) cc_final: 0.6402 (mm-30) REVERT: C 99 MET cc_start: 0.7191 (mtm) cc_final: 0.6958 (mtm) REVERT: C 100 GLU cc_start: 0.7135 (mt-10) cc_final: 0.6792 (mt-10) REVERT: C 104 GLU cc_start: 0.7523 (pm20) cc_final: 0.6228 (tm-30) REVERT: C 107 LYS cc_start: 0.7124 (mttt) cc_final: 0.6619 (mttp) REVERT: C 176 GLU cc_start: 0.7004 (tt0) cc_final: 0.6536 (mt-10) REVERT: C 190 ARG cc_start: 0.7778 (OUTLIER) cc_final: 0.6394 (mtm180) REVERT: C 257 GLN cc_start: 0.7201 (pt0) cc_final: 0.6559 (tp-100) REVERT: C 262 LYS cc_start: 0.8239 (mttt) cc_final: 0.7992 (mmtm) REVERT: C 302 ARG cc_start: 0.7256 (ptm160) cc_final: 0.6649 (tmt-80) REVERT: C 323 LYS cc_start: 0.8168 (OUTLIER) cc_final: 0.7917 (tttm) REVERT: C 381 GLN cc_start: 0.7332 (mp10) cc_final: 0.5645 (mm-40) REVERT: C 408 PHE cc_start: 0.7303 (m-10) cc_final: 0.7026 (m-10) REVERT: C 491 MET cc_start: 0.8170 (mmm) cc_final: 0.7890 (mtm) REVERT: D 30 GLU cc_start: 0.6643 (OUTLIER) cc_final: 0.6217 (mp0) REVERT: D 40 GLN cc_start: 0.6760 (tt0) cc_final: 0.6422 (mt0) REVERT: D 51 GLN cc_start: 0.7470 (tp-100) cc_final: 0.7023 (mm-40) REVERT: D 55 GLU cc_start: 0.6843 (mt-10) cc_final: 0.6400 (mm-30) REVERT: D 100 GLU cc_start: 0.7167 (mt-10) cc_final: 0.6859 (mt-10) REVERT: D 104 GLU cc_start: 0.7532 (pm20) cc_final: 0.6286 (tm-30) REVERT: D 107 LYS cc_start: 0.7123 (mttt) cc_final: 0.6615 (mttp) REVERT: D 176 GLU cc_start: 0.7000 (tt0) cc_final: 0.6507 (mt-10) REVERT: D 190 ARG cc_start: 0.7773 (OUTLIER) cc_final: 0.6381 (mtm180) REVERT: D 257 GLN cc_start: 0.7197 (pt0) cc_final: 0.6572 (tp-100) REVERT: D 262 LYS cc_start: 0.8239 (mttt) cc_final: 0.7992 (mmtm) REVERT: D 300 LYS cc_start: 0.8482 (mttt) cc_final: 0.8231 (mmtt) REVERT: D 302 ARG cc_start: 0.7251 (ptm160) cc_final: 0.6647 (tmt-80) REVERT: D 323 LYS cc_start: 0.8171 (OUTLIER) cc_final: 0.7921 (tttm) REVERT: D 381 GLN cc_start: 0.7336 (mp10) cc_final: 0.5647 (mm-40) REVERT: D 408 PHE cc_start: 0.7309 (m-10) cc_final: 0.7032 (m-10) REVERT: D 491 MET cc_start: 0.8176 (mmm) cc_final: 0.7899 (mtm) REVERT: D 497 MET cc_start: 0.8708 (ttt) cc_final: 0.8437 (ttt) outliers start: 61 outliers final: 18 residues processed: 319 average time/residue: 1.5983 time to fit residues: 562.4723 Evaluate side-chains 313 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 280 time to evaluate : 2.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 323 LYS Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 524 SER Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 35 ARG Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 323 LYS Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 524 SER Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 47 SER Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 323 LYS Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 524 SER Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 190 ARG Chi-restraints excluded: chain D residue 323 LYS Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 355 ARG Chi-restraints excluded: chain D residue 524 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 215 optimal weight: 3.9990 chunk 164 optimal weight: 0.5980 chunk 113 optimal weight: 0.8980 chunk 24 optimal weight: 6.9990 chunk 104 optimal weight: 0.6980 chunk 146 optimal weight: 0.9990 chunk 219 optimal weight: 0.9990 chunk 231 optimal weight: 0.9980 chunk 114 optimal weight: 0.8980 chunk 207 optimal weight: 2.9990 chunk 62 optimal weight: 9.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 GLN A 483 GLN B 418 GLN B 483 GLN C 418 GLN D 418 GLN D 483 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 20304 Z= 0.144 Angle : 0.441 5.745 27520 Z= 0.230 Chirality : 0.036 0.139 3124 Planarity : 0.004 0.040 3404 Dihedral : 11.991 172.248 3432 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 1.83 % Allowed : 9.81 % Favored : 88.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.07 (0.17), residues: 2384 helix: 1.76 (0.13), residues: 1484 sheet: 1.66 (0.54), residues: 68 loop : 0.83 (0.23), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 593 HIS 0.003 0.001 HIS A 201 PHE 0.011 0.001 PHE D 456 TYR 0.011 0.001 TYR C 89 ARG 0.006 0.000 ARG C 180 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 289 time to evaluate : 2.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.6681 (mt-10) cc_final: 0.6296 (mp0) REVERT: A 40 GLN cc_start: 0.6682 (tt0) cc_final: 0.6406 (mt0) REVERT: A 47 SER cc_start: 0.7723 (t) cc_final: 0.7156 (m) REVERT: A 51 GLN cc_start: 0.7409 (tp-100) cc_final: 0.7054 (mm-40) REVERT: A 100 GLU cc_start: 0.7120 (mt-10) cc_final: 0.6788 (mt-10) REVERT: A 104 GLU cc_start: 0.7631 (pm20) cc_final: 0.6395 (tm-30) REVERT: A 107 LYS cc_start: 0.7193 (mttt) cc_final: 0.6695 (mttp) REVERT: A 176 GLU cc_start: 0.7057 (tt0) cc_final: 0.6555 (mt-10) REVERT: A 190 ARG cc_start: 0.7773 (OUTLIER) cc_final: 0.6330 (mtm180) REVERT: A 257 GLN cc_start: 0.7088 (pt0) cc_final: 0.6552 (tp-100) REVERT: A 262 LYS cc_start: 0.8267 (mttt) cc_final: 0.7988 (mptt) REVERT: A 300 LYS cc_start: 0.8431 (mttt) cc_final: 0.8175 (mmtt) REVERT: A 302 ARG cc_start: 0.7266 (ptm160) cc_final: 0.6662 (tmt-80) REVERT: A 381 GLN cc_start: 0.7054 (mp10) cc_final: 0.5503 (mm-40) REVERT: A 414 ARG cc_start: 0.7724 (tpp80) cc_final: 0.7258 (tpp80) REVERT: A 497 MET cc_start: 0.8607 (ttt) cc_final: 0.8361 (ttt) REVERT: B 30 GLU cc_start: 0.6681 (mt-10) cc_final: 0.6300 (mp0) REVERT: B 47 SER cc_start: 0.7716 (t) cc_final: 0.7142 (m) REVERT: B 51 GLN cc_start: 0.7406 (tp-100) cc_final: 0.7048 (mm-40) REVERT: B 100 GLU cc_start: 0.7013 (mt-10) cc_final: 0.6656 (mt-10) REVERT: B 104 GLU cc_start: 0.7633 (pm20) cc_final: 0.6393 (tm-30) REVERT: B 107 LYS cc_start: 0.7192 (mttt) cc_final: 0.6697 (mttp) REVERT: B 176 GLU cc_start: 0.7057 (tt0) cc_final: 0.6558 (mt-10) REVERT: B 190 ARG cc_start: 0.7773 (OUTLIER) cc_final: 0.6328 (mtm180) REVERT: B 257 GLN cc_start: 0.7089 (pt0) cc_final: 0.6553 (tp-100) REVERT: B 262 LYS cc_start: 0.8267 (mttt) cc_final: 0.7988 (mptt) REVERT: B 300 LYS cc_start: 0.8430 (mttt) cc_final: 0.8173 (mmtt) REVERT: B 302 ARG cc_start: 0.7266 (ptm160) cc_final: 0.6663 (tmt-80) REVERT: B 381 GLN cc_start: 0.7060 (mp10) cc_final: 0.5507 (mm-40) REVERT: B 414 ARG cc_start: 0.7718 (tpp80) cc_final: 0.7252 (tpp80) REVERT: B 497 MET cc_start: 0.8609 (ttt) cc_final: 0.8363 (ttt) REVERT: C 30 GLU cc_start: 0.6679 (mt-10) cc_final: 0.6295 (mp0) REVERT: C 40 GLN cc_start: 0.6717 (tt0) cc_final: 0.6405 (mt0) REVERT: C 47 SER cc_start: 0.7724 (t) cc_final: 0.7154 (m) REVERT: C 51 GLN cc_start: 0.7407 (tp-100) cc_final: 0.7051 (mm-40) REVERT: C 100 GLU cc_start: 0.7030 (mt-10) cc_final: 0.6665 (mt-10) REVERT: C 104 GLU cc_start: 0.7632 (pm20) cc_final: 0.6391 (tm-30) REVERT: C 107 LYS cc_start: 0.7192 (mttt) cc_final: 0.6696 (mttp) REVERT: C 176 GLU cc_start: 0.7060 (tt0) cc_final: 0.6559 (mt-10) REVERT: C 190 ARG cc_start: 0.7774 (OUTLIER) cc_final: 0.6333 (mtm180) REVERT: C 257 GLN cc_start: 0.7088 (pt0) cc_final: 0.6552 (tp-100) REVERT: C 262 LYS cc_start: 0.8238 (mttt) cc_final: 0.7957 (mptt) REVERT: C 302 ARG cc_start: 0.7281 (ptm160) cc_final: 0.6665 (tmt-80) REVERT: C 381 GLN cc_start: 0.7051 (mp10) cc_final: 0.5500 (mm-40) REVERT: C 414 ARG cc_start: 0.7693 (tpp80) cc_final: 0.7232 (tpp80) REVERT: C 497 MET cc_start: 0.8608 (ttt) cc_final: 0.8359 (ttt) REVERT: D 30 GLU cc_start: 0.6672 (mt-10) cc_final: 0.6291 (mp0) REVERT: D 40 GLN cc_start: 0.6715 (tt0) cc_final: 0.6401 (mt0) REVERT: D 47 SER cc_start: 0.7732 (t) cc_final: 0.7158 (m) REVERT: D 51 GLN cc_start: 0.7405 (tp-100) cc_final: 0.7045 (mm-40) REVERT: D 100 GLU cc_start: 0.7079 (mt-10) cc_final: 0.6719 (mt-10) REVERT: D 104 GLU cc_start: 0.7624 (pm20) cc_final: 0.6432 (tm-30) REVERT: D 107 LYS cc_start: 0.7202 (mttt) cc_final: 0.6707 (mttp) REVERT: D 176 GLU cc_start: 0.7053 (tt0) cc_final: 0.6557 (mt-10) REVERT: D 190 ARG cc_start: 0.7773 (OUTLIER) cc_final: 0.6329 (mtm180) REVERT: D 257 GLN cc_start: 0.7087 (pt0) cc_final: 0.6566 (tp-100) REVERT: D 262 LYS cc_start: 0.8266 (mttt) cc_final: 0.7988 (mptt) REVERT: D 300 LYS cc_start: 0.8431 (mttt) cc_final: 0.8174 (mmtt) REVERT: D 302 ARG cc_start: 0.7253 (ptm160) cc_final: 0.6656 (tmt-80) REVERT: D 381 GLN cc_start: 0.7055 (mp10) cc_final: 0.5502 (mm-40) REVERT: D 414 ARG cc_start: 0.7717 (tpp80) cc_final: 0.7251 (tpp80) REVERT: D 497 MET cc_start: 0.8596 (ttt) cc_final: 0.8337 (ttt) outliers start: 38 outliers final: 16 residues processed: 310 average time/residue: 1.5575 time to fit residues: 534.1800 Evaluate side-chains 289 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 269 time to evaluate : 2.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 190 ARG Chi-restraints excluded: chain D residue 315 GLU Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 567 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 193 optimal weight: 7.9990 chunk 131 optimal weight: 10.0000 chunk 3 optimal weight: 3.9990 chunk 172 optimal weight: 3.9990 chunk 95 optimal weight: 0.9990 chunk 197 optimal weight: 0.9990 chunk 160 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 118 optimal weight: 5.9990 chunk 208 optimal weight: 1.9990 chunk 58 optimal weight: 0.4980 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 GLN B 418 GLN C 418 GLN D 418 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20304 Z= 0.224 Angle : 0.483 6.137 27520 Z= 0.250 Chirality : 0.038 0.142 3124 Planarity : 0.004 0.042 3404 Dihedral : 12.013 170.378 3432 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 3.22 % Allowed : 10.00 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.17), residues: 2384 helix: 1.61 (0.13), residues: 1488 sheet: -0.87 (0.46), residues: 108 loop : 0.87 (0.24), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 593 HIS 0.004 0.001 HIS D 201 PHE 0.009 0.001 PHE B 472 TYR 0.012 0.002 TYR D 89 ARG 0.005 0.000 ARG D 180 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 285 time to evaluate : 2.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.6653 (OUTLIER) cc_final: 0.6190 (mp0) REVERT: A 40 GLN cc_start: 0.6726 (tt0) cc_final: 0.6467 (mt0) REVERT: A 47 SER cc_start: 0.7694 (t) cc_final: 0.7127 (m) REVERT: A 51 GLN cc_start: 0.7398 (tp-100) cc_final: 0.7031 (mm-40) REVERT: A 55 GLU cc_start: 0.6929 (mt-10) cc_final: 0.6489 (mm-30) REVERT: A 100 GLU cc_start: 0.7047 (mt-10) cc_final: 0.6689 (mt-10) REVERT: A 104 GLU cc_start: 0.7652 (pm20) cc_final: 0.6387 (tm-30) REVERT: A 107 LYS cc_start: 0.7239 (mttt) cc_final: 0.6708 (mttp) REVERT: A 176 GLU cc_start: 0.7116 (tt0) cc_final: 0.6636 (mt-10) REVERT: A 190 ARG cc_start: 0.7758 (OUTLIER) cc_final: 0.6360 (mtm180) REVERT: A 257 GLN cc_start: 0.7160 (pt0) cc_final: 0.6588 (tp-100) REVERT: A 262 LYS cc_start: 0.8198 (mttt) cc_final: 0.7931 (mptt) REVERT: A 302 ARG cc_start: 0.7286 (ptm160) cc_final: 0.6651 (tmt-80) REVERT: A 381 GLN cc_start: 0.7087 (mp10) cc_final: 0.6582 (mp10) REVERT: A 414 ARG cc_start: 0.7825 (tpp80) cc_final: 0.7344 (tpp80) REVERT: A 497 MET cc_start: 0.8688 (ttt) cc_final: 0.8431 (ttt) REVERT: B 30 GLU cc_start: 0.6656 (OUTLIER) cc_final: 0.6193 (mp0) REVERT: B 47 SER cc_start: 0.7709 (OUTLIER) cc_final: 0.7139 (m) REVERT: B 51 GLN cc_start: 0.7395 (tp-100) cc_final: 0.7030 (mm-40) REVERT: B 55 GLU cc_start: 0.6930 (mt-10) cc_final: 0.6497 (mm-30) REVERT: B 100 GLU cc_start: 0.7046 (mt-10) cc_final: 0.6687 (mt-10) REVERT: B 104 GLU cc_start: 0.7620 (pm20) cc_final: 0.6378 (tm-30) REVERT: B 107 LYS cc_start: 0.7240 (mttt) cc_final: 0.6714 (mttp) REVERT: B 176 GLU cc_start: 0.7068 (tt0) cc_final: 0.6569 (mt-10) REVERT: B 190 ARG cc_start: 0.7758 (OUTLIER) cc_final: 0.6360 (mtm180) REVERT: B 257 GLN cc_start: 0.7159 (pt0) cc_final: 0.6591 (tp-100) REVERT: B 262 LYS cc_start: 0.8198 (mttt) cc_final: 0.7932 (mptt) REVERT: B 302 ARG cc_start: 0.7288 (ptm160) cc_final: 0.6650 (tmt-80) REVERT: B 414 ARG cc_start: 0.7789 (tpp80) cc_final: 0.7316 (tpp80) REVERT: B 497 MET cc_start: 0.8687 (ttt) cc_final: 0.8433 (ttt) REVERT: C 30 GLU cc_start: 0.6654 (OUTLIER) cc_final: 0.6193 (mp0) REVERT: C 40 GLN cc_start: 0.6711 (tt0) cc_final: 0.6429 (mt0) REVERT: C 47 SER cc_start: 0.7700 (t) cc_final: 0.7129 (m) REVERT: C 51 GLN cc_start: 0.7391 (tp-100) cc_final: 0.7033 (mm-40) REVERT: C 55 GLU cc_start: 0.6927 (mt-10) cc_final: 0.6496 (mm-30) REVERT: C 100 GLU cc_start: 0.7047 (mt-10) cc_final: 0.6688 (mt-10) REVERT: C 104 GLU cc_start: 0.7619 (pm20) cc_final: 0.6377 (tm-30) REVERT: C 107 LYS cc_start: 0.7239 (mttt) cc_final: 0.6712 (mttp) REVERT: C 176 GLU cc_start: 0.7068 (tt0) cc_final: 0.6568 (mt-10) REVERT: C 190 ARG cc_start: 0.7758 (OUTLIER) cc_final: 0.6363 (mtm180) REVERT: C 257 GLN cc_start: 0.7157 (pt0) cc_final: 0.6573 (tp-100) REVERT: C 262 LYS cc_start: 0.8197 (mttt) cc_final: 0.7931 (mptt) REVERT: C 302 ARG cc_start: 0.7295 (ptm160) cc_final: 0.6662 (tmt-80) REVERT: C 381 GLN cc_start: 0.7088 (mp10) cc_final: 0.6583 (mp10) REVERT: C 414 ARG cc_start: 0.7750 (tpp80) cc_final: 0.7276 (tpp80) REVERT: C 497 MET cc_start: 0.8687 (ttt) cc_final: 0.8431 (ttt) REVERT: D 30 GLU cc_start: 0.6647 (OUTLIER) cc_final: 0.6186 (mp0) REVERT: D 40 GLN cc_start: 0.6712 (tt0) cc_final: 0.6464 (mt0) REVERT: D 47 SER cc_start: 0.7730 (OUTLIER) cc_final: 0.7162 (m) REVERT: D 51 GLN cc_start: 0.7396 (tp-100) cc_final: 0.7035 (mm-40) REVERT: D 55 GLU cc_start: 0.6905 (mt-10) cc_final: 0.6483 (mm-30) REVERT: D 100 GLU cc_start: 0.7081 (mt-10) cc_final: 0.6742 (mt-10) REVERT: D 104 GLU cc_start: 0.7638 (pm20) cc_final: 0.6436 (tm-30) REVERT: D 107 LYS cc_start: 0.7239 (mttt) cc_final: 0.6717 (mttp) REVERT: D 176 GLU cc_start: 0.7103 (tt0) cc_final: 0.6611 (mt-10) REVERT: D 190 ARG cc_start: 0.7757 (OUTLIER) cc_final: 0.6361 (mtm180) REVERT: D 257 GLN cc_start: 0.7158 (pt0) cc_final: 0.6590 (tp-100) REVERT: D 262 LYS cc_start: 0.8198 (mttt) cc_final: 0.7933 (mptt) REVERT: D 302 ARG cc_start: 0.7288 (ptm160) cc_final: 0.6652 (tmt-80) REVERT: D 381 GLN cc_start: 0.7090 (mp10) cc_final: 0.6583 (mp10) REVERT: D 414 ARG cc_start: 0.7788 (tpp80) cc_final: 0.7315 (tpp80) REVERT: D 497 MET cc_start: 0.8693 (ttt) cc_final: 0.8431 (ttt) outliers start: 67 outliers final: 31 residues processed: 317 average time/residue: 1.6287 time to fit residues: 568.4280 Evaluate side-chains 326 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 285 time to evaluate : 2.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 374 GLN Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 374 GLN Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 190 ARG Chi-restraints excluded: chain D residue 315 GLU Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 355 ARG Chi-restraints excluded: chain D residue 374 GLN Chi-restraints excluded: chain D residue 419 THR Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 567 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 78 optimal weight: 0.9980 chunk 208 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 chunk 136 optimal weight: 0.9980 chunk 57 optimal weight: 4.9990 chunk 232 optimal weight: 2.9990 chunk 192 optimal weight: 0.3980 chunk 107 optimal weight: 2.9990 chunk 19 optimal weight: 7.9990 chunk 76 optimal weight: 0.9980 chunk 121 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 GLN A 418 GLN B 418 GLN C 418 GLN D 418 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 20304 Z= 0.147 Angle : 0.439 5.669 27520 Z= 0.226 Chirality : 0.036 0.137 3124 Planarity : 0.004 0.038 3404 Dihedral : 11.733 168.342 3432 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 2.02 % Allowed : 11.11 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.17), residues: 2384 helix: 1.74 (0.13), residues: 1500 sheet: 1.63 (0.56), residues: 68 loop : 0.69 (0.23), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 593 HIS 0.003 0.001 HIS D 201 PHE 0.009 0.001 PHE A 456 TYR 0.009 0.001 TYR A 555 ARG 0.006 0.000 ARG D 180 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 281 time to evaluate : 2.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.6682 (mt-10) cc_final: 0.6126 (mp0) REVERT: A 38 MET cc_start: 0.8040 (mmm) cc_final: 0.7701 (mmm) REVERT: A 40 GLN cc_start: 0.6636 (tt0) cc_final: 0.6417 (mt0) REVERT: A 47 SER cc_start: 0.7674 (OUTLIER) cc_final: 0.7124 (m) REVERT: A 51 GLN cc_start: 0.7407 (tp-100) cc_final: 0.7041 (mm-40) REVERT: A 100 GLU cc_start: 0.6957 (mt-10) cc_final: 0.6595 (mt-10) REVERT: A 104 GLU cc_start: 0.7609 (pm20) cc_final: 0.6412 (tm-30) REVERT: A 107 LYS cc_start: 0.7270 (mttt) cc_final: 0.6748 (mttp) REVERT: A 176 GLU cc_start: 0.7111 (tt0) cc_final: 0.6629 (mt-10) REVERT: A 190 ARG cc_start: 0.7791 (OUTLIER) cc_final: 0.6342 (mtm180) REVERT: A 257 GLN cc_start: 0.7083 (pt0) cc_final: 0.6577 (tp-100) REVERT: A 262 LYS cc_start: 0.8197 (mttt) cc_final: 0.7938 (mptt) REVERT: A 302 ARG cc_start: 0.7258 (ptm160) cc_final: 0.6578 (tmt-80) REVERT: A 409 ARG cc_start: 0.7238 (mtp-110) cc_final: 0.6653 (ttt90) REVERT: A 414 ARG cc_start: 0.7767 (tpp80) cc_final: 0.7351 (tpp80) REVERT: A 442 MET cc_start: 0.7446 (mtp) cc_final: 0.7216 (mtp) REVERT: A 497 MET cc_start: 0.8618 (ttt) cc_final: 0.8370 (ttt) REVERT: B 30 GLU cc_start: 0.6679 (OUTLIER) cc_final: 0.6116 (mp0) REVERT: B 47 SER cc_start: 0.7660 (t) cc_final: 0.7101 (m) REVERT: B 51 GLN cc_start: 0.7405 (tp-100) cc_final: 0.7037 (mm-40) REVERT: B 100 GLU cc_start: 0.6954 (mt-10) cc_final: 0.6592 (mt-10) REVERT: B 104 GLU cc_start: 0.7613 (pm20) cc_final: 0.6410 (tm-30) REVERT: B 107 LYS cc_start: 0.7271 (mttt) cc_final: 0.6752 (mttp) REVERT: B 176 GLU cc_start: 0.7101 (tt0) cc_final: 0.6611 (mt-10) REVERT: B 190 ARG cc_start: 0.7793 (OUTLIER) cc_final: 0.6340 (mtm180) REVERT: B 257 GLN cc_start: 0.7083 (pt0) cc_final: 0.6576 (tp-100) REVERT: B 262 LYS cc_start: 0.8197 (mttt) cc_final: 0.7938 (mptt) REVERT: B 302 ARG cc_start: 0.7278 (ptm160) cc_final: 0.6610 (tmt-80) REVERT: B 381 GLN cc_start: 0.7191 (mp10) cc_final: 0.5507 (mm-40) REVERT: B 414 ARG cc_start: 0.7783 (tpp80) cc_final: 0.7392 (tpp80) REVERT: B 442 MET cc_start: 0.7445 (mtp) cc_final: 0.7214 (mtp) REVERT: B 497 MET cc_start: 0.8608 (ttt) cc_final: 0.8361 (ttt) REVERT: C 30 GLU cc_start: 0.6679 (mt-10) cc_final: 0.6121 (mp0) REVERT: C 40 GLN cc_start: 0.6701 (tt0) cc_final: 0.6406 (mt0) REVERT: C 47 SER cc_start: 0.7652 (OUTLIER) cc_final: 0.7096 (m) REVERT: C 51 GLN cc_start: 0.7404 (tp-100) cc_final: 0.7039 (mm-40) REVERT: C 100 GLU cc_start: 0.6957 (mt-10) cc_final: 0.6593 (mt-10) REVERT: C 104 GLU cc_start: 0.7610 (pm20) cc_final: 0.6408 (tm-30) REVERT: C 107 LYS cc_start: 0.7269 (mttt) cc_final: 0.6748 (mttp) REVERT: C 176 GLU cc_start: 0.7105 (tt0) cc_final: 0.6612 (mt-10) REVERT: C 190 ARG cc_start: 0.7792 (OUTLIER) cc_final: 0.6343 (mtm180) REVERT: C 257 GLN cc_start: 0.7082 (pt0) cc_final: 0.6577 (tp-100) REVERT: C 262 LYS cc_start: 0.8197 (mttt) cc_final: 0.7938 (mptt) REVERT: C 302 ARG cc_start: 0.7306 (ptm160) cc_final: 0.6615 (tmt-80) REVERT: C 414 ARG cc_start: 0.7796 (tpp80) cc_final: 0.7388 (tpp80) REVERT: C 442 MET cc_start: 0.7597 (mtp) cc_final: 0.7386 (mtp) REVERT: C 497 MET cc_start: 0.8613 (ttt) cc_final: 0.8368 (ttt) REVERT: D 30 GLU cc_start: 0.6671 (mt-10) cc_final: 0.6119 (mp0) REVERT: D 40 GLN cc_start: 0.6706 (tt0) cc_final: 0.6435 (mt0) REVERT: D 47 SER cc_start: 0.7685 (t) cc_final: 0.7137 (m) REVERT: D 51 GLN cc_start: 0.7415 (tp-100) cc_final: 0.7048 (mm-40) REVERT: D 100 GLU cc_start: 0.6989 (mt-10) cc_final: 0.6621 (mt-10) REVERT: D 104 GLU cc_start: 0.7601 (pm20) cc_final: 0.6469 (tm-30) REVERT: D 107 LYS cc_start: 0.7274 (mttt) cc_final: 0.6754 (mttp) REVERT: D 176 GLU cc_start: 0.7113 (tt0) cc_final: 0.6626 (mt-10) REVERT: D 190 ARG cc_start: 0.7779 (OUTLIER) cc_final: 0.6306 (mtm180) REVERT: D 257 GLN cc_start: 0.7080 (pt0) cc_final: 0.6579 (tp-100) REVERT: D 262 LYS cc_start: 0.8197 (mttt) cc_final: 0.7938 (mptt) REVERT: D 302 ARG cc_start: 0.7277 (ptm160) cc_final: 0.6613 (tmt-80) REVERT: D 414 ARG cc_start: 0.7782 (tpp80) cc_final: 0.7392 (tpp80) REVERT: D 442 MET cc_start: 0.7623 (mtp) cc_final: 0.7381 (mtp) REVERT: D 497 MET cc_start: 0.8604 (ttt) cc_final: 0.8349 (ttt) outliers start: 42 outliers final: 21 residues processed: 305 average time/residue: 1.6092 time to fit residues: 541.1710 Evaluate side-chains 305 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 277 time to evaluate : 2.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 323 LYS Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 323 LYS Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain C residue 47 SER Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 190 ARG Chi-restraints excluded: chain D residue 315 GLU Chi-restraints excluded: chain D residue 323 LYS Chi-restraints excluded: chain D residue 419 THR Chi-restraints excluded: chain D residue 499 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 223 optimal weight: 3.9990 chunk 26 optimal weight: 0.5980 chunk 132 optimal weight: 9.9990 chunk 169 optimal weight: 4.9990 chunk 131 optimal weight: 1.9990 chunk 195 optimal weight: 2.9990 chunk 129 optimal weight: 8.9990 chunk 231 optimal weight: 0.1980 chunk 144 optimal weight: 1.9990 chunk 141 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 GLN A 418 GLN B 230 GLN B 418 GLN C 418 GLN D 418 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20304 Z= 0.210 Angle : 0.474 5.781 27520 Z= 0.244 Chirality : 0.038 0.140 3124 Planarity : 0.004 0.040 3404 Dihedral : 11.766 166.777 3432 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 2.88 % Allowed : 10.67 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.17), residues: 2384 helix: 1.64 (0.13), residues: 1500 sheet: -0.88 (0.47), residues: 108 loop : 0.73 (0.23), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 593 HIS 0.004 0.001 HIS B 201 PHE 0.009 0.001 PHE D 504 TYR 0.012 0.002 TYR A 555 ARG 0.005 0.000 ARG C 180 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 276 time to evaluate : 2.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.6652 (OUTLIER) cc_final: 0.6096 (mp0) REVERT: A 38 MET cc_start: 0.8013 (mmm) cc_final: 0.7660 (mmm) REVERT: A 40 GLN cc_start: 0.6708 (tt0) cc_final: 0.6443 (mt0) REVERT: A 47 SER cc_start: 0.7658 (OUTLIER) cc_final: 0.7107 (m) REVERT: A 51 GLN cc_start: 0.7407 (tp-100) cc_final: 0.7031 (mm-40) REVERT: A 55 GLU cc_start: 0.6961 (mt-10) cc_final: 0.6502 (mm-30) REVERT: A 100 GLU cc_start: 0.6990 (mt-10) cc_final: 0.6638 (mt-10) REVERT: A 104 GLU cc_start: 0.7603 (pm20) cc_final: 0.6450 (tm-30) REVERT: A 107 LYS cc_start: 0.7245 (mttt) cc_final: 0.6732 (mttp) REVERT: A 176 GLU cc_start: 0.7115 (tt0) cc_final: 0.6629 (mt-10) REVERT: A 190 ARG cc_start: 0.7835 (OUTLIER) cc_final: 0.6375 (mtm180) REVERT: A 257 GLN cc_start: 0.7130 (pt0) cc_final: 0.6602 (tp-100) REVERT: A 262 LYS cc_start: 0.8209 (mttt) cc_final: 0.7951 (mptt) REVERT: A 302 ARG cc_start: 0.7293 (ptm160) cc_final: 0.6624 (tmt-80) REVERT: A 381 GLN cc_start: 0.7247 (mp10) cc_final: 0.5571 (mm-40) REVERT: A 414 ARG cc_start: 0.7859 (tpp80) cc_final: 0.7509 (tpp80) REVERT: A 442 MET cc_start: 0.7558 (mtp) cc_final: 0.7250 (mtp) REVERT: A 497 MET cc_start: 0.8683 (ttt) cc_final: 0.8427 (ttt) REVERT: B 30 GLU cc_start: 0.6631 (OUTLIER) cc_final: 0.6074 (mp0) REVERT: B 47 SER cc_start: 0.7638 (OUTLIER) cc_final: 0.7083 (m) REVERT: B 51 GLN cc_start: 0.7406 (tp-100) cc_final: 0.7025 (mm-40) REVERT: B 100 GLU cc_start: 0.6945 (mt-10) cc_final: 0.6598 (mt-10) REVERT: B 104 GLU cc_start: 0.7615 (pm20) cc_final: 0.6417 (tm-30) REVERT: B 107 LYS cc_start: 0.7246 (mttt) cc_final: 0.6734 (mttp) REVERT: B 176 GLU cc_start: 0.7128 (tt0) cc_final: 0.6655 (mt-10) REVERT: B 190 ARG cc_start: 0.7835 (OUTLIER) cc_final: 0.6364 (mtm180) REVERT: B 257 GLN cc_start: 0.7129 (pt0) cc_final: 0.6602 (tp-100) REVERT: B 262 LYS cc_start: 0.8210 (mttt) cc_final: 0.7951 (mptt) REVERT: B 302 ARG cc_start: 0.7296 (ptm160) cc_final: 0.6625 (tmt-80) REVERT: B 414 ARG cc_start: 0.7859 (tpp80) cc_final: 0.7509 (tpp80) REVERT: B 442 MET cc_start: 0.7565 (mtp) cc_final: 0.7250 (mtp) REVERT: B 497 MET cc_start: 0.8682 (ttt) cc_final: 0.8427 (ttt) REVERT: C 30 GLU cc_start: 0.6654 (OUTLIER) cc_final: 0.6096 (mp0) REVERT: C 38 MET cc_start: 0.8054 (mmm) cc_final: 0.7737 (mmm) REVERT: C 40 GLN cc_start: 0.6708 (tt0) cc_final: 0.6423 (mt0) REVERT: C 47 SER cc_start: 0.7660 (OUTLIER) cc_final: 0.7106 (m) REVERT: C 51 GLN cc_start: 0.7404 (tp-100) cc_final: 0.7029 (mm-40) REVERT: C 55 GLU cc_start: 0.6950 (mt-10) cc_final: 0.6482 (mm-30) REVERT: C 100 GLU cc_start: 0.6943 (mt-10) cc_final: 0.6597 (mt-10) REVERT: C 104 GLU cc_start: 0.7612 (pm20) cc_final: 0.6406 (tm-30) REVERT: C 107 LYS cc_start: 0.7247 (mttt) cc_final: 0.6733 (mttp) REVERT: C 176 GLU cc_start: 0.7116 (tt0) cc_final: 0.6639 (mt-10) REVERT: C 190 ARG cc_start: 0.7834 (OUTLIER) cc_final: 0.6364 (mtm180) REVERT: C 257 GLN cc_start: 0.7130 (pt0) cc_final: 0.6588 (tp-100) REVERT: C 262 LYS cc_start: 0.8210 (mttt) cc_final: 0.7951 (mptt) REVERT: C 302 ARG cc_start: 0.7325 (ptm160) cc_final: 0.6656 (tmt-80) REVERT: C 381 GLN cc_start: 0.7245 (mp10) cc_final: 0.5568 (mm-40) REVERT: C 414 ARG cc_start: 0.7831 (tpp80) cc_final: 0.7434 (tpp80) REVERT: C 442 MET cc_start: 0.7754 (mtp) cc_final: 0.7526 (mtp) REVERT: C 497 MET cc_start: 0.8680 (ttt) cc_final: 0.8428 (ttt) REVERT: D 30 GLU cc_start: 0.6645 (OUTLIER) cc_final: 0.6088 (mp0) REVERT: D 40 GLN cc_start: 0.6718 (tt0) cc_final: 0.6396 (mt0) REVERT: D 47 SER cc_start: 0.7662 (OUTLIER) cc_final: 0.7104 (m) REVERT: D 51 GLN cc_start: 0.7408 (tp-100) cc_final: 0.7031 (mm-40) REVERT: D 55 GLU cc_start: 0.6947 (mt-10) cc_final: 0.6440 (mm-30) REVERT: D 100 GLU cc_start: 0.6974 (mt-10) cc_final: 0.6618 (mt-10) REVERT: D 104 GLU cc_start: 0.7602 (pm20) cc_final: 0.6464 (tm-30) REVERT: D 107 LYS cc_start: 0.7247 (mttt) cc_final: 0.6736 (mttp) REVERT: D 176 GLU cc_start: 0.7124 (tt0) cc_final: 0.6654 (mt-10) REVERT: D 190 ARG cc_start: 0.7835 (OUTLIER) cc_final: 0.6364 (mtm180) REVERT: D 257 GLN cc_start: 0.7129 (pt0) cc_final: 0.6605 (tp-100) REVERT: D 262 LYS cc_start: 0.8210 (mttt) cc_final: 0.7951 (mptt) REVERT: D 302 ARG cc_start: 0.7297 (ptm160) cc_final: 0.6625 (tmt-80) REVERT: D 381 GLN cc_start: 0.7237 (mp10) cc_final: 0.5545 (mm-40) REVERT: D 414 ARG cc_start: 0.7858 (tpp80) cc_final: 0.7507 (tpp80) REVERT: D 442 MET cc_start: 0.7753 (mtp) cc_final: 0.7497 (mtp) REVERT: D 497 MET cc_start: 0.8686 (ttt) cc_final: 0.8426 (ttt) outliers start: 60 outliers final: 36 residues processed: 310 average time/residue: 1.6528 time to fit residues: 565.8152 Evaluate side-chains 324 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 276 time to evaluate : 1.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 323 LYS Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 577 MET Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 323 LYS Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain B residue 577 MET Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 47 SER Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 323 LYS Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 577 MET Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 190 ARG Chi-restraints excluded: chain D residue 315 GLU Chi-restraints excluded: chain D residue 323 LYS Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 355 ARG Chi-restraints excluded: chain D residue 419 THR Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 577 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 143 optimal weight: 4.9990 chunk 92 optimal weight: 3.9990 chunk 138 optimal weight: 0.8980 chunk 69 optimal weight: 7.9990 chunk 45 optimal weight: 0.8980 chunk 44 optimal weight: 0.6980 chunk 147 optimal weight: 2.9990 chunk 157 optimal weight: 0.4980 chunk 114 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 181 optimal weight: 0.0570 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 GLN A 418 GLN B 230 GLN B 418 GLN C 418 GLN D 418 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 20304 Z= 0.131 Angle : 0.437 6.551 27520 Z= 0.222 Chirality : 0.036 0.151 3124 Planarity : 0.004 0.037 3404 Dihedral : 11.452 164.114 3432 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 2.12 % Allowed : 11.73 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.17), residues: 2384 helix: 1.82 (0.13), residues: 1496 sheet: -0.47 (0.48), residues: 104 loop : 0.66 (0.23), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 593 HIS 0.002 0.001 HIS B 201 PHE 0.010 0.001 PHE B 456 TYR 0.008 0.001 TYR C 555 ARG 0.006 0.000 ARG C 180 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 284 time to evaluate : 2.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.6651 (OUTLIER) cc_final: 0.5776 (mp0) REVERT: A 34 ASP cc_start: 0.6936 (m-30) cc_final: 0.6719 (m-30) REVERT: A 47 SER cc_start: 0.7632 (OUTLIER) cc_final: 0.7140 (m) REVERT: A 51 GLN cc_start: 0.7436 (tp-100) cc_final: 0.7064 (mm-40) REVERT: A 62 LYS cc_start: 0.7392 (mtmp) cc_final: 0.7120 (mtpp) REVERT: A 100 GLU cc_start: 0.6958 (mt-10) cc_final: 0.6616 (mt-10) REVERT: A 104 GLU cc_start: 0.7592 (pm20) cc_final: 0.6458 (tm-30) REVERT: A 107 LYS cc_start: 0.7255 (mttt) cc_final: 0.6749 (mttp) REVERT: A 176 GLU cc_start: 0.7127 (tt0) cc_final: 0.6659 (mt-10) REVERT: A 190 ARG cc_start: 0.7734 (OUTLIER) cc_final: 0.6234 (mtm180) REVERT: A 257 GLN cc_start: 0.7089 (pt0) cc_final: 0.6545 (tp-100) REVERT: A 262 LYS cc_start: 0.8199 (mttt) cc_final: 0.7954 (mmtm) REVERT: A 302 ARG cc_start: 0.7308 (ptm160) cc_final: 0.6616 (tmt-80) REVERT: A 381 GLN cc_start: 0.7204 (mp10) cc_final: 0.5489 (mm-40) REVERT: A 414 ARG cc_start: 0.7795 (tpp80) cc_final: 0.7490 (tpp80) REVERT: A 491 MET cc_start: 0.8222 (mtp) cc_final: 0.7817 (mtt) REVERT: A 497 MET cc_start: 0.8581 (ttt) cc_final: 0.8336 (ttt) REVERT: B 30 GLU cc_start: 0.6656 (mt-10) cc_final: 0.5810 (mp0) REVERT: B 47 SER cc_start: 0.7602 (t) cc_final: 0.7099 (m) REVERT: B 51 GLN cc_start: 0.7421 (tp-100) cc_final: 0.7048 (mm-40) REVERT: B 100 GLU cc_start: 0.6848 (mt-10) cc_final: 0.6521 (mt-10) REVERT: B 104 GLU cc_start: 0.7615 (pm20) cc_final: 0.6480 (tm-30) REVERT: B 107 LYS cc_start: 0.7277 (mttt) cc_final: 0.6776 (mttp) REVERT: B 176 GLU cc_start: 0.7111 (tt0) cc_final: 0.6644 (mt-10) REVERT: B 190 ARG cc_start: 0.7735 (OUTLIER) cc_final: 0.6234 (mtm180) REVERT: B 257 GLN cc_start: 0.7087 (pt0) cc_final: 0.6534 (tp-100) REVERT: B 262 LYS cc_start: 0.8199 (mttt) cc_final: 0.7954 (mmtm) REVERT: B 302 ARG cc_start: 0.7309 (ptm160) cc_final: 0.6617 (tmt-80) REVERT: B 381 GLN cc_start: 0.7246 (mp10) cc_final: 0.5455 (mm-40) REVERT: B 414 ARG cc_start: 0.7827 (tpp80) cc_final: 0.7524 (tpp80) REVERT: B 491 MET cc_start: 0.8213 (mtp) cc_final: 0.7785 (mtt) REVERT: B 497 MET cc_start: 0.8581 (ttt) cc_final: 0.8337 (ttt) REVERT: C 30 GLU cc_start: 0.6649 (OUTLIER) cc_final: 0.5782 (mp0) REVERT: C 34 ASP cc_start: 0.6932 (m-30) cc_final: 0.6729 (m-30) REVERT: C 40 GLN cc_start: 0.6693 (tt0) cc_final: 0.6418 (mt0) REVERT: C 47 SER cc_start: 0.7633 (OUTLIER) cc_final: 0.7140 (m) REVERT: C 51 GLN cc_start: 0.7423 (tp-100) cc_final: 0.7054 (mm-40) REVERT: C 62 LYS cc_start: 0.7391 (mtmp) cc_final: 0.7117 (mtpp) REVERT: C 100 GLU cc_start: 0.6852 (mt-10) cc_final: 0.6527 (mt-10) REVERT: C 104 GLU cc_start: 0.7593 (pm20) cc_final: 0.6456 (tm-30) REVERT: C 107 LYS cc_start: 0.7276 (mttt) cc_final: 0.6774 (mttp) REVERT: C 176 GLU cc_start: 0.7123 (tt0) cc_final: 0.6659 (mt-10) REVERT: C 190 ARG cc_start: 0.7735 (OUTLIER) cc_final: 0.6236 (mtm180) REVERT: C 257 GLN cc_start: 0.7086 (pt0) cc_final: 0.6559 (tp-100) REVERT: C 262 LYS cc_start: 0.8198 (mttt) cc_final: 0.7953 (mmtm) REVERT: C 302 ARG cc_start: 0.7310 (ptm160) cc_final: 0.6615 (tmt-80) REVERT: C 381 GLN cc_start: 0.7204 (mp10) cc_final: 0.5488 (mm-40) REVERT: C 414 ARG cc_start: 0.7825 (tpp80) cc_final: 0.7529 (tpp80) REVERT: C 491 MET cc_start: 0.8217 (mtp) cc_final: 0.7781 (mtt) REVERT: C 497 MET cc_start: 0.8590 (ttt) cc_final: 0.8349 (ttt) REVERT: D 30 GLU cc_start: 0.6651 (mt-10) cc_final: 0.5831 (mp0) REVERT: D 40 GLN cc_start: 0.6675 (tt0) cc_final: 0.6358 (mt0) REVERT: D 47 SER cc_start: 0.7610 (t) cc_final: 0.7098 (m) REVERT: D 51 GLN cc_start: 0.7429 (tp-100) cc_final: 0.7059 (mm-40) REVERT: D 100 GLU cc_start: 0.6919 (mt-10) cc_final: 0.6549 (mt-10) REVERT: D 104 GLU cc_start: 0.7616 (pm20) cc_final: 0.6482 (tm-30) REVERT: D 107 LYS cc_start: 0.7257 (mttt) cc_final: 0.6753 (mttp) REVERT: D 176 GLU cc_start: 0.7121 (tt0) cc_final: 0.6658 (mt-10) REVERT: D 190 ARG cc_start: 0.7734 (OUTLIER) cc_final: 0.6233 (mtm180) REVERT: D 257 GLN cc_start: 0.7088 (pt0) cc_final: 0.6548 (tp-100) REVERT: D 262 LYS cc_start: 0.8199 (mttt) cc_final: 0.7954 (mmtm) REVERT: D 302 ARG cc_start: 0.7309 (ptm160) cc_final: 0.6617 (tmt-80) REVERT: D 381 GLN cc_start: 0.7206 (mp10) cc_final: 0.5490 (mm-40) REVERT: D 414 ARG cc_start: 0.7825 (tpp80) cc_final: 0.7522 (tpp80) REVERT: D 491 MET cc_start: 0.8219 (mtp) cc_final: 0.7814 (mtt) REVERT: D 497 MET cc_start: 0.8587 (ttt) cc_final: 0.8336 (ttt) outliers start: 44 outliers final: 20 residues processed: 315 average time/residue: 1.5355 time to fit residues: 535.1184 Evaluate side-chains 311 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 283 time to evaluate : 2.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 47 SER Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 190 ARG Chi-restraints excluded: chain D residue 315 GLU Chi-restraints excluded: chain D residue 355 ARG Chi-restraints excluded: chain D residue 419 THR Chi-restraints excluded: chain D residue 499 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 210 optimal weight: 0.9990 chunk 221 optimal weight: 0.9990 chunk 202 optimal weight: 4.9990 chunk 215 optimal weight: 1.9990 chunk 129 optimal weight: 8.9990 chunk 93 optimal weight: 0.9990 chunk 169 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 194 optimal weight: 1.9990 chunk 203 optimal weight: 0.1980 chunk 214 optimal weight: 4.9990 overall best weight: 1.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN A 418 GLN B 261 GLN B 418 GLN C 261 GLN C 418 GLN D 261 GLN D 418 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20304 Z= 0.166 Angle : 0.459 10.589 27520 Z= 0.232 Chirality : 0.037 0.154 3124 Planarity : 0.004 0.037 3404 Dihedral : 11.309 161.125 3432 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 1.92 % Allowed : 11.83 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.17), residues: 2384 helix: 1.80 (0.13), residues: 1500 sheet: -0.55 (0.47), residues: 104 loop : 0.71 (0.24), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 593 HIS 0.004 0.001 HIS D 201 PHE 0.008 0.001 PHE C 504 TYR 0.010 0.001 TYR D 555 ARG 0.005 0.000 ARG B 180 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 274 time to evaluate : 2.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.6638 (OUTLIER) cc_final: 0.6082 (mp0) REVERT: A 47 SER cc_start: 0.7612 (OUTLIER) cc_final: 0.7104 (m) REVERT: A 51 GLN cc_start: 0.7423 (tp-100) cc_final: 0.7039 (mm-40) REVERT: A 100 GLU cc_start: 0.6855 (mt-10) cc_final: 0.6540 (mt-10) REVERT: A 104 GLU cc_start: 0.7619 (pm20) cc_final: 0.6490 (tm-30) REVERT: A 107 LYS cc_start: 0.7233 (mttt) cc_final: 0.6722 (mttp) REVERT: A 176 GLU cc_start: 0.7188 (tt0) cc_final: 0.6660 (mt-10) REVERT: A 190 ARG cc_start: 0.7773 (OUTLIER) cc_final: 0.6260 (mtm180) REVERT: A 257 GLN cc_start: 0.7075 (pt0) cc_final: 0.6598 (tp-100) REVERT: A 262 LYS cc_start: 0.8183 (mttt) cc_final: 0.7934 (mptt) REVERT: A 302 ARG cc_start: 0.7310 (ptm160) cc_final: 0.6620 (tmt-80) REVERT: A 381 GLN cc_start: 0.7213 (mp10) cc_final: 0.5503 (mm-40) REVERT: A 414 ARG cc_start: 0.7844 (tpp80) cc_final: 0.7561 (tpp80) REVERT: A 491 MET cc_start: 0.8268 (mtp) cc_final: 0.7863 (mtt) REVERT: A 497 MET cc_start: 0.8620 (ttt) cc_final: 0.8369 (ttt) REVERT: B 30 GLU cc_start: 0.6494 (mt-10) cc_final: 0.5903 (mp0) REVERT: B 47 SER cc_start: 0.7558 (t) cc_final: 0.7086 (m) REVERT: B 51 GLN cc_start: 0.7418 (tp-100) cc_final: 0.7044 (mm-40) REVERT: B 104 GLU cc_start: 0.7602 (pm20) cc_final: 0.6469 (tm-30) REVERT: B 107 LYS cc_start: 0.7235 (mttt) cc_final: 0.6724 (mttp) REVERT: B 176 GLU cc_start: 0.7106 (tt0) cc_final: 0.6669 (mt-10) REVERT: B 190 ARG cc_start: 0.7774 (OUTLIER) cc_final: 0.6262 (mtm180) REVERT: B 257 GLN cc_start: 0.7075 (pt0) cc_final: 0.6599 (tp-100) REVERT: B 262 LYS cc_start: 0.8182 (mttt) cc_final: 0.7934 (mptt) REVERT: B 302 ARG cc_start: 0.7315 (ptm160) cc_final: 0.6597 (tmt-80) REVERT: B 381 GLN cc_start: 0.7257 (mp10) cc_final: 0.5513 (mm-40) REVERT: B 414 ARG cc_start: 0.7869 (tpp80) cc_final: 0.7579 (tpp80) REVERT: B 491 MET cc_start: 0.8257 (mtp) cc_final: 0.7823 (mtt) REVERT: B 497 MET cc_start: 0.8618 (ttt) cc_final: 0.8369 (ttt) REVERT: C 30 GLU cc_start: 0.6637 (OUTLIER) cc_final: 0.6080 (mp0) REVERT: C 40 GLN cc_start: 0.6655 (tt0) cc_final: 0.6327 (mt0) REVERT: C 47 SER cc_start: 0.7615 (OUTLIER) cc_final: 0.7107 (m) REVERT: C 51 GLN cc_start: 0.7418 (tp-100) cc_final: 0.7037 (mm-40) REVERT: C 104 GLU cc_start: 0.7618 (pm20) cc_final: 0.6490 (tm-30) REVERT: C 107 LYS cc_start: 0.7235 (mttt) cc_final: 0.6724 (mttp) REVERT: C 176 GLU cc_start: 0.7106 (tt0) cc_final: 0.6669 (mt-10) REVERT: C 190 ARG cc_start: 0.7775 (OUTLIER) cc_final: 0.6263 (mtm180) REVERT: C 257 GLN cc_start: 0.7070 (pt0) cc_final: 0.6628 (tp-100) REVERT: C 262 LYS cc_start: 0.8183 (mttt) cc_final: 0.7934 (mptt) REVERT: C 302 ARG cc_start: 0.7315 (ptm160) cc_final: 0.6621 (tmt-80) REVERT: C 381 GLN cc_start: 0.7213 (mp10) cc_final: 0.5502 (mm-40) REVERT: C 414 ARG cc_start: 0.7824 (tpp80) cc_final: 0.7541 (tpp80) REVERT: C 474 MET cc_start: 0.8305 (ptm) cc_final: 0.8096 (ptm) REVERT: C 491 MET cc_start: 0.8261 (mtp) cc_final: 0.7841 (mtt) REVERT: C 497 MET cc_start: 0.8613 (ttt) cc_final: 0.8367 (ttt) REVERT: D 30 GLU cc_start: 0.6488 (OUTLIER) cc_final: 0.5877 (mp0) REVERT: D 40 GLN cc_start: 0.6662 (tt0) cc_final: 0.6355 (mt0) REVERT: D 47 SER cc_start: 0.7603 (t) cc_final: 0.7088 (m) REVERT: D 51 GLN cc_start: 0.7409 (tp-100) cc_final: 0.7031 (mm-40) REVERT: D 104 GLU cc_start: 0.7605 (pm20) cc_final: 0.6461 (tm-30) REVERT: D 107 LYS cc_start: 0.7237 (mttt) cc_final: 0.6726 (mttp) REVERT: D 176 GLU cc_start: 0.7103 (tt0) cc_final: 0.6670 (mt-10) REVERT: D 190 ARG cc_start: 0.7775 (OUTLIER) cc_final: 0.6263 (mtm180) REVERT: D 257 GLN cc_start: 0.7075 (pt0) cc_final: 0.6601 (tp-100) REVERT: D 262 LYS cc_start: 0.8185 (mttt) cc_final: 0.7936 (mptt) REVERT: D 302 ARG cc_start: 0.7315 (ptm160) cc_final: 0.6598 (tmt-80) REVERT: D 381 GLN cc_start: 0.7214 (mp10) cc_final: 0.5502 (mm-40) REVERT: D 414 ARG cc_start: 0.7867 (tpp80) cc_final: 0.7577 (tpp80) REVERT: D 491 MET cc_start: 0.8263 (mtp) cc_final: 0.7856 (mtt) REVERT: D 497 MET cc_start: 0.8621 (ttt) cc_final: 0.8365 (ttt) outliers start: 40 outliers final: 22 residues processed: 301 average time/residue: 1.5423 time to fit residues: 514.6411 Evaluate side-chains 305 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 274 time to evaluate : 2.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 47 SER Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 190 ARG Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 315 GLU Chi-restraints excluded: chain D residue 355 ARG Chi-restraints excluded: chain D residue 419 THR Chi-restraints excluded: chain D residue 499 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 141 optimal weight: 0.7980 chunk 227 optimal weight: 3.9990 chunk 139 optimal weight: 7.9990 chunk 108 optimal weight: 0.7980 chunk 158 optimal weight: 5.9990 chunk 239 optimal weight: 3.9990 chunk 220 optimal weight: 0.9990 chunk 190 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 147 optimal weight: 0.7980 chunk 116 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 GLN B 418 GLN C 418 GLN D 418 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.2680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20304 Z= 0.168 Angle : 0.461 10.844 27520 Z= 0.232 Chirality : 0.037 0.155 3124 Planarity : 0.004 0.037 3404 Dihedral : 11.068 158.285 3432 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 1.92 % Allowed : 11.97 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.17), residues: 2384 helix: 1.77 (0.13), residues: 1500 sheet: -0.55 (0.47), residues: 104 loop : 0.71 (0.24), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 593 HIS 0.003 0.001 HIS B 201 PHE 0.011 0.001 PHE B 456 TYR 0.010 0.001 TYR A 555 ARG 0.005 0.000 ARG C 180 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 283 time to evaluate : 2.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.6648 (OUTLIER) cc_final: 0.6112 (mp0) REVERT: A 47 SER cc_start: 0.7598 (OUTLIER) cc_final: 0.7110 (m) REVERT: A 51 GLN cc_start: 0.7427 (tp-100) cc_final: 0.7047 (mm-40) REVERT: A 104 GLU cc_start: 0.7591 (pm20) cc_final: 0.6496 (tm-30) REVERT: A 107 LYS cc_start: 0.7227 (mttt) cc_final: 0.6724 (mttp) REVERT: A 176 GLU cc_start: 0.7192 (tt0) cc_final: 0.6673 (mt-10) REVERT: A 190 ARG cc_start: 0.7774 (OUTLIER) cc_final: 0.6252 (mtm180) REVERT: A 257 GLN cc_start: 0.7052 (pt0) cc_final: 0.6552 (tp-100) REVERT: A 262 LYS cc_start: 0.8181 (mttt) cc_final: 0.7939 (mptt) REVERT: A 302 ARG cc_start: 0.7311 (ptm160) cc_final: 0.6657 (tmt-80) REVERT: A 381 GLN cc_start: 0.7199 (mp10) cc_final: 0.5517 (mm-40) REVERT: A 414 ARG cc_start: 0.7838 (tpp80) cc_final: 0.7553 (tpp80) REVERT: A 491 MET cc_start: 0.8261 (mtp) cc_final: 0.7864 (mtt) REVERT: A 497 MET cc_start: 0.8626 (ttt) cc_final: 0.8374 (ttt) REVERT: B 30 GLU cc_start: 0.6411 (OUTLIER) cc_final: 0.5914 (mp0) REVERT: B 47 SER cc_start: 0.7547 (t) cc_final: 0.7065 (m) REVERT: B 51 GLN cc_start: 0.7439 (tp-100) cc_final: 0.7067 (mm-40) REVERT: B 100 GLU cc_start: 0.7029 (mt-10) cc_final: 0.6823 (mt-10) REVERT: B 104 GLU cc_start: 0.7592 (pm20) cc_final: 0.6496 (tm-30) REVERT: B 107 LYS cc_start: 0.7228 (mttt) cc_final: 0.6724 (mttp) REVERT: B 176 GLU cc_start: 0.7116 (tt0) cc_final: 0.6671 (mt-10) REVERT: B 190 ARG cc_start: 0.7776 (OUTLIER) cc_final: 0.6254 (mtm180) REVERT: B 257 GLN cc_start: 0.7051 (pt0) cc_final: 0.6552 (tp-100) REVERT: B 262 LYS cc_start: 0.8196 (mttt) cc_final: 0.7964 (mptt) REVERT: B 302 ARG cc_start: 0.7315 (ptm160) cc_final: 0.6594 (tmt-80) REVERT: B 381 GLN cc_start: 0.7255 (mp10) cc_final: 0.5510 (mm-40) REVERT: B 414 ARG cc_start: 0.7857 (tpp80) cc_final: 0.7561 (tpp80) REVERT: B 491 MET cc_start: 0.8231 (mtp) cc_final: 0.7808 (mtt) REVERT: B 497 MET cc_start: 0.8622 (ttt) cc_final: 0.8372 (ttt) REVERT: C 30 GLU cc_start: 0.6633 (OUTLIER) cc_final: 0.6081 (mp0) REVERT: C 40 GLN cc_start: 0.6653 (tt0) cc_final: 0.6324 (mt0) REVERT: C 47 SER cc_start: 0.7558 (OUTLIER) cc_final: 0.7064 (m) REVERT: C 51 GLN cc_start: 0.7425 (tp-100) cc_final: 0.7048 (mm-40) REVERT: C 100 GLU cc_start: 0.7087 (mt-10) cc_final: 0.6803 (mt-10) REVERT: C 104 GLU cc_start: 0.7591 (pm20) cc_final: 0.6494 (tm-30) REVERT: C 107 LYS cc_start: 0.7227 (mttt) cc_final: 0.6722 (mttp) REVERT: C 176 GLU cc_start: 0.7117 (tt0) cc_final: 0.6668 (mt-10) REVERT: C 190 ARG cc_start: 0.7775 (OUTLIER) cc_final: 0.6255 (mtm180) REVERT: C 257 GLN cc_start: 0.7047 (pt0) cc_final: 0.6551 (tp-100) REVERT: C 262 LYS cc_start: 0.8181 (mttt) cc_final: 0.7939 (mptt) REVERT: C 302 ARG cc_start: 0.7315 (ptm160) cc_final: 0.6620 (tmt-80) REVERT: C 381 GLN cc_start: 0.7199 (mp10) cc_final: 0.5517 (mm-40) REVERT: C 414 ARG cc_start: 0.7859 (tpp80) cc_final: 0.7565 (tpp80) REVERT: C 474 MET cc_start: 0.8372 (ptm) cc_final: 0.8117 (ptm) REVERT: C 491 MET cc_start: 0.8193 (mtp) cc_final: 0.7797 (mtt) REVERT: C 497 MET cc_start: 0.8621 (ttt) cc_final: 0.8374 (ttt) REVERT: D 30 GLU cc_start: 0.6496 (OUTLIER) cc_final: 0.5955 (mp0) REVERT: D 40 GLN cc_start: 0.6661 (tt0) cc_final: 0.6332 (mt0) REVERT: D 47 SER cc_start: 0.7557 (t) cc_final: 0.7083 (m) REVERT: D 51 GLN cc_start: 0.7437 (tp-100) cc_final: 0.7063 (mm-40) REVERT: D 100 GLU cc_start: 0.7204 (mt-10) cc_final: 0.6996 (mt-10) REVERT: D 104 GLU cc_start: 0.7607 (pm20) cc_final: 0.6450 (tm-30) REVERT: D 107 LYS cc_start: 0.7229 (mttt) cc_final: 0.6727 (mttp) REVERT: D 176 GLU cc_start: 0.7116 (tt0) cc_final: 0.6669 (mt-10) REVERT: D 190 ARG cc_start: 0.7775 (OUTLIER) cc_final: 0.6256 (mtm180) REVERT: D 257 GLN cc_start: 0.7050 (pt0) cc_final: 0.6564 (tp-100) REVERT: D 262 LYS cc_start: 0.8198 (mttt) cc_final: 0.7965 (mptt) REVERT: D 302 ARG cc_start: 0.7314 (ptm160) cc_final: 0.6595 (tmt-80) REVERT: D 381 GLN cc_start: 0.7193 (mp10) cc_final: 0.5504 (mm-40) REVERT: D 414 ARG cc_start: 0.7865 (tpp80) cc_final: 0.7568 (tpp80) REVERT: D 491 MET cc_start: 0.8259 (mtp) cc_final: 0.7859 (mtt) REVERT: D 497 MET cc_start: 0.8621 (ttt) cc_final: 0.8365 (ttt) outliers start: 40 outliers final: 22 residues processed: 309 average time/residue: 1.5223 time to fit residues: 521.3403 Evaluate side-chains 310 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 278 time to evaluate : 2.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 47 SER Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 190 ARG Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 315 GLU Chi-restraints excluded: chain D residue 355 ARG Chi-restraints excluded: chain D residue 419 THR Chi-restraints excluded: chain D residue 499 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 151 optimal weight: 4.9990 chunk 202 optimal weight: 0.9980 chunk 58 optimal weight: 0.0030 chunk 175 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 190 optimal weight: 0.9990 chunk 79 optimal weight: 0.1980 chunk 195 optimal weight: 5.9990 chunk 24 optimal weight: 0.9980 chunk 35 optimal weight: 7.9990 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 GLN B 31 GLN B 418 GLN C 40 GLN C 418 GLN D 418 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.127189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.100680 restraints weight = 22571.876| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 1.43 r_work: 0.3006 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 20304 Z= 0.130 Angle : 0.442 10.723 27520 Z= 0.222 Chirality : 0.036 0.147 3124 Planarity : 0.004 0.036 3404 Dihedral : 10.775 153.970 3432 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 1.83 % Allowed : 11.97 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.17), residues: 2384 helix: 1.85 (0.13), residues: 1496 sheet: -0.39 (0.48), residues: 104 loop : 0.73 (0.24), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 593 HIS 0.003 0.001 HIS D 426 PHE 0.007 0.001 PHE A 537 TYR 0.008 0.001 TYR C 555 ARG 0.005 0.000 ARG C 180 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8581.85 seconds wall clock time: 151 minutes 34.96 seconds (9094.96 seconds total)