Starting phenix.real_space_refine on Wed Apr 10 15:48:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tf3_41218/04_2024/8tf3_41218_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tf3_41218/04_2024/8tf3_41218.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tf3_41218/04_2024/8tf3_41218.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tf3_41218/04_2024/8tf3_41218.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tf3_41218/04_2024/8tf3_41218_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tf3_41218/04_2024/8tf3_41218_neut_updated.pdb" } resolution = 2.94 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= 0.046 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: 6 Type Number sf(0) Gaussians P 4 5.49 5 S 136 5.16 5 Cl 12 4.86 5 C 13008 2.51 5 N 3268 2.21 5 O 3460 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 GLU 176": "OE1" <-> "OE2" Residue "A ARG 180": "NH1" <-> "NH2" Residue "A ARG 190": "NH1" <-> "NH2" Residue "A ARG 263": "NH1" <-> "NH2" Residue "A ARG 305": "NH1" <-> "NH2" 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 GLU 176": "OE1" <-> "OE2" Residue "B ARG 180": "NH1" <-> "NH2" Residue "B ARG 190": "NH1" <-> "NH2" Residue "B ARG 263": "NH1" <-> "NH2" Residue "B ARG 305": "NH1" <-> "NH2" 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 GLU 176": "OE1" <-> "OE2" Residue "C ARG 180": "NH1" <-> "NH2" Residue "C ARG 190": "NH1" <-> "NH2" Residue "C ARG 263": "NH1" <-> "NH2" Residue "C ARG 305": "NH1" <-> "NH2" 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 GLU 176": "OE1" <-> "OE2" Residue "D ARG 180": "NH1" <-> "NH2" Residue "D ARG 190": "NH1" <-> "NH2" Residue "D ARG 263": "NH1" <-> "NH2" Residue "D ARG 305": "NH1" <-> "NH2" 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: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 19888 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: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 150 Unusual residues: {'CPL': 2, 'ECN': 1, 'ERG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'CPL:plan-4': 1, 'CPL:plan-3': 1, 'CPL:plan-2': 1, 'CPL:plan-1': 1} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 150 Unusual residues: {'CPL': 2, 'ECN': 1, 'ERG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'CPL:plan-4': 1, 'CPL:plan-3': 1, 'CPL:plan-2': 1, 'CPL:plan-1': 1} Unresolved non-hydrogen planarities: 14 Chain: "C" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 150 Unusual residues: {'CPL': 2, 'ECN': 1, 'ERG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'CPL:plan-4': 1, 'CPL:plan-3': 1, 'CPL:plan-2': 1, 'CPL:plan-1': 1} Unresolved non-hydrogen planarities: 14 Chain: "D" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 150 Unusual residues: {'CPL': 2, 'ECN': 1, 'ERG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'CPL:plan-4': 1, 'CPL:plan-3': 1, 'CPL:plan-2': 1, 'CPL:plan-1': 1} Unresolved non-hydrogen planarities: 14 Time building chain proxies: 10.96, per 1000 atoms: 0.55 Number of scatterers: 19888 At special positions: 0 Unit cell: (136.95, 136.95, 122.01, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 12 17.00 S 136 16.00 P 4 15.00 O 3460 8.00 N 3268 7.00 C 13008 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: 7.37 Conformation dependent library (CDL) restraints added in 3.1 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 63.3% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.06 Creating SS restraints... Processing helix chain 'A' and resid 29 through 46 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 120 through 126 Processing helix chain 'A' and resid 130 through 139 removed outlier: 3.620A 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 172 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: 3.979A pdb=" N GLN A 214 " --> pdb=" O THR A 210 " (cutoff:3.500A) removed outlier: 3.963A 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: 4.095A 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 Processing helix chain 'A' and resid 311 through 323 removed outlier: 4.114A pdb=" N GLU A 315 " --> pdb=" O THR A 311 " (cutoff:3.500A) 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 removed outlier: 3.514A pdb=" N GLY A 388 " --> pdb=" O ILE A 384 " (cutoff:3.500A) Proline residue: A 405 - end of helix removed outlier: 3.612A 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: 3.650A pdb=" N VAL A 465 " --> pdb=" O GLY A 461 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N MET A 466 " --> pdb=" O TRP A 462 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N TYR A 467 " --> pdb=" O CYS A 463 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N PHE A 468 " --> pdb=" O SER A 464 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ALA A 469 " --> pdb=" O VAL A 465 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ARG A 470 " --> pdb=" O MET A 466 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N GLY A 471 " --> pdb=" O TYR A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 487 Processing helix chain 'A' and resid 489 through 512 removed outlier: 3.683A pdb=" N VAL A 499 " --> pdb=" O TRP A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 523 No H-bonds generated for 'chain 'A' and resid 521 through 523' Processing helix chain 'A' and resid 526 through 537 Processing helix chain 'A' and resid 553 through 565 Processing helix chain 'A' and resid 569 through 607 removed outlier: 3.797A pdb=" N ILE A 575 " --> pdb=" O LEU A 571 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TRP A 583 " --> pdb=" O GLY A 579 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG A 584 " --> pdb=" O ASP A 580 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N GLN A 587 " --> pdb=" O TRP A 583 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N GLU A 588 " --> pdb=" O ARG A 584 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASP A 590 " --> pdb=" O ALA A 586 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL A 598 " --> pdb=" O ARG A 594 " (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 621 through 623 No H-bonds generated for 'chain 'A' and resid 621 through 623' Processing helix chain 'B' and resid 29 through 46 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 120 through 126 Processing helix chain 'B' and resid 130 through 139 removed outlier: 3.620A 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 172 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: 3.980A pdb=" N GLN B 214 " --> pdb=" O THR B 210 " (cutoff:3.500A) removed outlier: 3.964A 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: 4.095A 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 Processing helix chain 'B' and resid 311 through 323 removed outlier: 4.115A pdb=" N GLU B 315 " --> pdb=" O THR B 311 " (cutoff:3.500A) 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 removed outlier: 3.514A pdb=" N GLY B 388 " --> pdb=" O ILE B 384 " (cutoff:3.500A) Proline residue: B 405 - end of helix removed outlier: 3.612A 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: 3.650A pdb=" N VAL B 465 " --> pdb=" O GLY B 461 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N MET B 466 " --> pdb=" O TRP B 462 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N TYR B 467 " --> pdb=" O CYS B 463 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N PHE B 468 " --> pdb=" O SER B 464 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ALA B 469 " --> pdb=" O VAL B 465 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ARG B 470 " --> pdb=" O MET B 466 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N GLY B 471 " --> pdb=" O TYR B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 487 Processing helix chain 'B' and resid 489 through 512 removed outlier: 3.682A pdb=" N VAL B 499 " --> pdb=" O TRP B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 523 No H-bonds generated for 'chain 'B' and resid 521 through 523' Processing helix chain 'B' and resid 526 through 537 Processing helix chain 'B' and resid 553 through 565 Processing helix chain 'B' and resid 569 through 607 removed outlier: 3.796A pdb=" N ILE B 575 " --> pdb=" O LEU B 571 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TRP B 583 " --> pdb=" O GLY B 579 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG B 584 " --> pdb=" O ASP B 580 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N GLN B 587 " --> pdb=" O TRP B 583 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N GLU B 588 " --> pdb=" O ARG B 584 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASP B 590 " --> pdb=" O ALA B 586 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL B 598 " --> pdb=" O ARG B 594 " (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 621 through 623 No H-bonds generated for 'chain 'B' and resid 621 through 623' Processing helix chain 'C' and resid 29 through 46 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 120 through 126 Processing helix chain 'C' and resid 130 through 139 removed outlier: 3.619A 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 172 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: 3.979A pdb=" N GLN C 214 " --> pdb=" O THR C 210 " (cutoff:3.500A) removed outlier: 3.963A 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: 4.094A 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 Processing helix chain 'C' and resid 311 through 323 removed outlier: 4.114A pdb=" N GLU C 315 " --> pdb=" O THR C 311 " (cutoff:3.500A) 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 removed outlier: 3.514A pdb=" N GLY C 388 " --> pdb=" O ILE C 384 " (cutoff:3.500A) Proline residue: C 405 - end of helix removed outlier: 3.612A 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: 3.650A 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: 4.473A pdb=" N TYR C 467 " --> pdb=" O CYS C 463 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N PHE C 468 " --> pdb=" O SER C 464 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ALA C 469 " --> pdb=" O VAL C 465 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ARG C 470 " --> pdb=" O MET C 466 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N GLY C 471 " --> pdb=" O TYR C 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 487 Processing helix chain 'C' and resid 489 through 512 removed outlier: 3.682A pdb=" N VAL C 499 " --> pdb=" O TRP C 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 521 through 523 No H-bonds generated for 'chain 'C' and resid 521 through 523' Processing helix chain 'C' and resid 526 through 537 Processing helix chain 'C' and resid 553 through 565 Processing helix chain 'C' and resid 569 through 607 removed outlier: 3.797A pdb=" N ILE C 575 " --> pdb=" O LEU C 571 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TRP C 583 " --> pdb=" O GLY C 579 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG C 584 " --> pdb=" O ASP C 580 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N GLN C 587 " --> pdb=" O TRP C 583 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N GLU C 588 " --> pdb=" O ARG C 584 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASP C 590 " --> pdb=" O ALA C 586 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL C 598 " --> pdb=" O ARG C 594 " (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 621 through 623 No H-bonds generated for 'chain 'C' and resid 621 through 623' Processing helix chain 'D' and resid 29 through 46 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 120 through 126 Processing helix chain 'D' and resid 130 through 139 removed outlier: 3.620A 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 172 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: 3.979A pdb=" N GLN D 214 " --> pdb=" O THR D 210 " (cutoff:3.500A) removed outlier: 3.963A 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: 4.095A 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 Processing helix chain 'D' and resid 311 through 323 removed outlier: 4.115A pdb=" N GLU D 315 " --> pdb=" O THR D 311 " (cutoff:3.500A) 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 removed outlier: 3.514A pdb=" N GLY D 388 " --> pdb=" O ILE D 384 " (cutoff:3.500A) Proline residue: D 405 - end of helix removed outlier: 3.611A 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: 3.650A pdb=" N VAL D 465 " --> pdb=" O GLY D 461 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N MET D 466 " --> pdb=" O TRP D 462 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N TYR D 467 " --> pdb=" O CYS D 463 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N PHE D 468 " --> pdb=" O SER D 464 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ALA D 469 " --> pdb=" O VAL D 465 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ARG D 470 " --> pdb=" O MET D 466 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N GLY D 471 " --> pdb=" O TYR D 467 " (cutoff:3.500A) Processing helix chain 'D' and resid 476 through 487 Processing helix chain 'D' and resid 489 through 512 removed outlier: 3.683A pdb=" N VAL D 499 " --> pdb=" O TRP D 495 " (cutoff:3.500A) Processing helix chain 'D' and resid 521 through 523 No H-bonds generated for 'chain 'D' and resid 521 through 523' Processing helix chain 'D' and resid 526 through 537 Processing helix chain 'D' and resid 553 through 565 Processing helix chain 'D' and resid 569 through 607 removed outlier: 3.796A pdb=" N ILE D 575 " --> pdb=" O LEU D 571 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TRP D 583 " --> pdb=" O GLY D 579 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG D 584 " --> pdb=" O ASP D 580 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N GLN D 587 " --> pdb=" O TRP D 583 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N GLU D 588 " --> pdb=" O ARG D 584 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASP D 590 " --> pdb=" O ALA D 586 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL D 598 " --> pdb=" O ARG D 594 " (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 621 through 623 No H-bonds generated for 'chain 'D' and resid 621 through 623' Processing sheet with id= A, first strand: chain 'A' and resid 630 through 636 removed outlier: 3.539A pdb=" N TRP A 268 " --> pdb=" O SER A 275 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LEU A 277 " --> pdb=" O VAL A 266 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N VAL A 266 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ASP A 279 " --> pdb=" O LYS A 264 " (cutoff:3.500A) removed outlier: 6.535A 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: 3.538A pdb=" N TRP B 268 " --> pdb=" O SER B 275 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LEU B 277 " --> pdb=" O VAL B 266 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N VAL B 266 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ASP B 279 " --> pdb=" O LYS B 264 " (cutoff:3.500A) removed outlier: 6.536A 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: 3.539A pdb=" N TRP C 268 " --> pdb=" O SER C 275 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LEU C 277 " --> pdb=" O VAL C 266 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N VAL C 266 " --> pdb=" O LEU C 277 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ASP C 279 " --> pdb=" O LYS C 264 " (cutoff:3.500A) removed outlier: 6.535A 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: 3.538A pdb=" N TRP D 268 " --> pdb=" O SER D 275 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LEU D 277 " --> pdb=" O VAL D 266 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N VAL D 266 " --> pdb=" O LEU D 277 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ASP D 279 " --> pdb=" O LYS D 264 " (cutoff:3.500A) removed outlier: 6.535A 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 354 952 hydrogen bonds defined for protein. 2784 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: 6.31 Time building geometry restraints manager: 8.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 3096 1.30 - 1.43: 5424 1.43 - 1.56: 11580 1.56 - 1.69: 16 1.69 - 1.82: 236 Bond restraints: 20352 Sorted by residual: bond pdb=" C PRO B 312 " pdb=" O PRO B 312 " ideal model delta sigma weight residual 1.237 1.172 0.066 1.20e-02 6.94e+03 3.00e+01 bond pdb=" C PRO C 312 " pdb=" O PRO C 312 " ideal model delta sigma weight residual 1.237 1.173 0.065 1.20e-02 6.94e+03 2.90e+01 bond pdb=" C PRO D 312 " pdb=" O PRO D 312 " ideal model delta sigma weight residual 1.237 1.173 0.065 1.20e-02 6.94e+03 2.90e+01 bond pdb=" C PRO A 312 " pdb=" O PRO A 312 " ideal model delta sigma weight residual 1.237 1.173 0.065 1.20e-02 6.94e+03 2.90e+01 bond pdb=" CA ALA D 545 " pdb=" CB ALA D 545 " ideal model delta sigma weight residual 1.530 1.461 0.069 1.69e-02 3.50e+03 1.69e+01 ... (remaining 20347 not shown) Histogram of bond angle deviations from ideal: 97.66 - 105.13: 473 105.13 - 112.60: 9308 112.60 - 120.07: 9908 120.07 - 127.54: 7768 127.54 - 135.01: 155 Bond angle restraints: 27612 Sorted by residual: angle pdb=" N PRO A 312 " pdb=" CA PRO A 312 " pdb=" C PRO A 312 " ideal model delta sigma weight residual 113.40 105.19 8.21 1.34e+00 5.57e-01 3.75e+01 angle pdb=" N PRO D 312 " pdb=" CA PRO D 312 " pdb=" C PRO D 312 " ideal model delta sigma weight residual 113.40 105.23 8.17 1.34e+00 5.57e-01 3.72e+01 angle pdb=" N PRO B 312 " pdb=" CA PRO B 312 " pdb=" C PRO B 312 " ideal model delta sigma weight residual 113.40 105.23 8.17 1.34e+00 5.57e-01 3.72e+01 angle pdb=" N PRO C 312 " pdb=" CA PRO C 312 " pdb=" C PRO C 312 " ideal model delta sigma weight residual 113.40 105.23 8.17 1.34e+00 5.57e-01 3.71e+01 angle pdb=" N ILE B 540 " pdb=" CA ILE B 540 " pdb=" C ILE B 540 " ideal model delta sigma weight residual 112.83 107.07 5.76 9.90e-01 1.02e+00 3.39e+01 ... (remaining 27607 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.57: 12032 25.57 - 51.14: 384 51.14 - 76.71: 84 76.71 - 102.28: 32 102.28 - 127.85: 4 Dihedral angle restraints: 12536 sinusoidal: 5508 harmonic: 7028 Sorted by residual: dihedral pdb=" C THR D 539 " pdb=" N THR D 539 " pdb=" CA THR D 539 " pdb=" CB THR D 539 " ideal model delta harmonic sigma weight residual -122.00 -133.51 11.51 0 2.50e+00 1.60e-01 2.12e+01 dihedral pdb=" C THR A 539 " pdb=" N THR A 539 " pdb=" CA THR A 539 " pdb=" CB THR A 539 " ideal model delta harmonic sigma weight residual -122.00 -133.47 11.47 0 2.50e+00 1.60e-01 2.10e+01 dihedral pdb=" C THR B 539 " pdb=" N THR B 539 " pdb=" CA THR B 539 " pdb=" CB THR B 539 " ideal model delta harmonic sigma weight residual -122.00 -133.46 11.46 0 2.50e+00 1.60e-01 2.10e+01 ... (remaining 12533 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1631 0.061 - 0.121: 978 0.121 - 0.182: 393 0.182 - 0.243: 100 0.243 - 0.303: 26 Chirality restraints: 3128 Sorted by residual: chirality pdb=" CA THR D 539 " pdb=" N THR D 539 " pdb=" C THR D 539 " pdb=" CB THR D 539 " both_signs ideal model delta sigma weight residual False 2.53 2.22 0.30 2.00e-01 2.50e+01 2.30e+00 chirality pdb=" CA THR A 539 " pdb=" N THR A 539 " pdb=" C THR A 539 " pdb=" CB THR A 539 " both_signs ideal model delta sigma weight residual False 2.53 2.22 0.30 2.00e-01 2.50e+01 2.28e+00 chirality pdb=" CA THR B 539 " pdb=" N THR B 539 " pdb=" C THR B 539 " pdb=" CB THR B 539 " both_signs ideal model delta sigma weight residual False 2.53 2.22 0.30 2.00e-01 2.50e+01 2.28e+00 ... (remaining 3125 not shown) Planarity restraints: 3424 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C38 CPL C 801 " -0.098 2.00e-02 2.50e+03 2.60e-01 6.76e+02 pdb=" C39 CPL C 801 " 0.344 2.00e-02 2.50e+03 pdb=" C40 CPL C 801 " -0.360 2.00e-02 2.50e+03 pdb=" C41 CPL C 801 " 0.114 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C38 CPL D 801 " 0.098 2.00e-02 2.50e+03 2.60e-01 6.75e+02 pdb=" C39 CPL D 801 " -0.344 2.00e-02 2.50e+03 pdb=" C40 CPL D 801 " 0.359 2.00e-02 2.50e+03 pdb=" C41 CPL D 801 " -0.114 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C38 CPL A 805 " 0.099 2.00e-02 2.50e+03 2.60e-01 6.75e+02 pdb=" C39 CPL A 805 " -0.345 2.00e-02 2.50e+03 pdb=" C40 CPL A 805 " 0.358 2.00e-02 2.50e+03 pdb=" C41 CPL A 805 " -0.113 2.00e-02 2.50e+03 ... (remaining 3421 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.86: 6232 2.86 - 3.37: 20276 3.37 - 3.88: 35316 3.88 - 4.39: 41918 4.39 - 4.90: 69325 Nonbonded interactions: 173067 Sorted by model distance: nonbonded pdb=" O LEU A 368 " pdb=" OG1 THR D 514 " model vdw 2.356 2.440 nonbonded pdb=" OG1 THR C 514 " pdb=" O LEU D 368 " model vdw 2.361 2.440 nonbonded pdb=" OG1 THR B 514 " pdb=" O LEU C 368 " model vdw 2.362 2.440 nonbonded pdb=" OG1 THR A 514 " pdb=" O LEU B 368 " model vdw 2.366 2.440 nonbonded pdb=" O ALA D 563 " pdb=" OG1 THR D 567 " model vdw 2.388 2.440 ... (remaining 173062 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)) selection = (chain 'B' and (resid 28 through 637 or resid 802)) selection = (chain 'C' and (resid 28 through 637 or resid 802)) selection = (chain 'D' and (resid 28 through 637 or resid 802)) } 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: 1.310 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: 6.050 Check model and map are aligned: 0.310 Set scattering table: 0.180 Process input model: 52.910 Find NCS groups from input model: 1.490 Set up NCS constraints: 0.160 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:14.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 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 0.069 20352 Z= 0.777 Angle : 1.798 9.695 27612 Z= 1.223 Chirality : 0.088 0.303 3128 Planarity : 0.016 0.260 3424 Dihedral : 14.586 127.848 7992 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Cbeta Deviations : 0.18 % 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: -0.94 (0.16), residues: 2384 helix: -1.01 (0.11), residues: 1500 sheet: 0.88 (0.51), residues: 80 loop : 0.47 (0.24), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.147 0.021 TRP C 593 HIS 0.011 0.003 HIS A 238 PHE 0.058 0.011 PHE C 256 TYR 0.110 0.020 TYR B 432 ARG 0.009 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 414 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 414 time to evaluate : 2.237 Fit side-chains REVERT: A 33 ARG cc_start: 0.6544 (ttt90) cc_final: 0.6341 (ttp-170) REVERT: A 74 GLN cc_start: 0.7121 (mt0) cc_final: 0.6894 (mt0) REVERT: A 93 GLU cc_start: 0.7416 (mp0) cc_final: 0.7110 (mp0) REVERT: A 214 GLN cc_start: 0.7683 (mm-40) cc_final: 0.7245 (mt0) REVERT: A 301 LYS cc_start: 0.7837 (mmmt) cc_final: 0.7357 (mmmt) REVERT: A 306 GLN cc_start: 0.7612 (mt0) cc_final: 0.6833 (mp10) REVERT: A 380 HIS cc_start: 0.7138 (t-170) cc_final: 0.6854 (t-90) REVERT: A 381 GLN cc_start: 0.6758 (mp10) cc_final: 0.5816 (mm-40) REVERT: A 448 ASN cc_start: 0.7710 (t0) cc_final: 0.7438 (t0) REVERT: A 483 GLN cc_start: 0.7712 (tt0) cc_final: 0.7417 (tm-30) REVERT: A 491 MET cc_start: 0.7517 (mmm) cc_final: 0.6797 (mmp) REVERT: B 33 ARG cc_start: 0.6515 (ttt90) cc_final: 0.6296 (ttp-170) REVERT: B 93 GLU cc_start: 0.7468 (mp0) cc_final: 0.7042 (mp0) REVERT: B 214 GLN cc_start: 0.7672 (mm-40) cc_final: 0.7249 (mt0) REVERT: B 301 LYS cc_start: 0.7818 (mmmt) cc_final: 0.7335 (mmmt) REVERT: B 306 GLN cc_start: 0.7602 (mt0) cc_final: 0.6830 (mp10) REVERT: B 380 HIS cc_start: 0.7096 (t-170) cc_final: 0.6836 (t-90) REVERT: B 448 ASN cc_start: 0.7723 (t0) cc_final: 0.7454 (t0) REVERT: B 491 MET cc_start: 0.7523 (mmm) cc_final: 0.6811 (mmp) REVERT: C 33 ARG cc_start: 0.6511 (ttt90) cc_final: 0.6294 (ttp-170) REVERT: C 93 GLU cc_start: 0.7467 (mp0) cc_final: 0.7036 (mp0) REVERT: C 214 GLN cc_start: 0.7676 (mm-40) cc_final: 0.7243 (mt0) REVERT: C 301 LYS cc_start: 0.7836 (mmmt) cc_final: 0.7357 (mmmt) REVERT: C 306 GLN cc_start: 0.7608 (mt0) cc_final: 0.6835 (mp10) REVERT: C 380 HIS cc_start: 0.7115 (t-170) cc_final: 0.6855 (t-90) REVERT: C 448 ASN cc_start: 0.7721 (t0) cc_final: 0.7451 (t0) REVERT: C 491 MET cc_start: 0.7515 (mmm) cc_final: 0.6804 (mmp) REVERT: D 33 ARG cc_start: 0.6505 (ttt90) cc_final: 0.6285 (ttp-170) REVERT: D 74 GLN cc_start: 0.7214 (mt0) cc_final: 0.7004 (mt0) REVERT: D 93 GLU cc_start: 0.7441 (mp0) cc_final: 0.7100 (mp0) REVERT: D 214 GLN cc_start: 0.7675 (mm-40) cc_final: 0.7250 (mt0) REVERT: D 301 LYS cc_start: 0.7837 (mmmt) cc_final: 0.7359 (mmmt) REVERT: D 306 GLN cc_start: 0.7597 (mt0) cc_final: 0.6832 (mp10) REVERT: D 380 HIS cc_start: 0.7121 (t-170) cc_final: 0.6860 (t-90) REVERT: D 448 ASN cc_start: 0.7714 (t0) cc_final: 0.7442 (t0) REVERT: D 491 MET cc_start: 0.7516 (mmm) cc_final: 0.6804 (mmp) outliers start: 0 outliers final: 0 residues processed: 414 average time/residue: 1.4488 time to fit residues: 670.0411 Evaluate side-chains 300 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 300 time to evaluate : 2.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 0.7980 chunk 181 optimal weight: 0.9990 chunk 100 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 188 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 chunk 114 optimal weight: 0.9980 chunk 140 optimal weight: 1.9990 chunk 217 optimal weight: 6.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 261 GLN A 473 GLN A 483 GLN A 596 GLN B 261 GLN B 473 GLN B 483 GLN B 596 GLN C 261 GLN C 473 GLN C 483 GLN C 596 GLN D 261 GLN D 473 GLN D 483 GLN D 596 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20352 Z= 0.194 Angle : 0.552 5.915 27612 Z= 0.283 Chirality : 0.039 0.156 3128 Planarity : 0.004 0.027 3424 Dihedral : 10.712 95.282 3428 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 1.73 % Allowed : 6.73 % Favored : 91.54 % 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: 1.42 (0.17), residues: 2384 helix: 1.05 (0.13), residues: 1520 sheet: 1.31 (0.53), residues: 80 loop : 1.01 (0.25), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 593 HIS 0.003 0.001 HIS A 201 PHE 0.015 0.002 PHE D 456 TYR 0.013 0.001 TYR C 555 ARG 0.004 0.001 ARG A 355 *********************** 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 378 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 342 time to evaluate : 2.210 Fit side-chains REVERT: A 35 ARG cc_start: 0.7586 (ttt-90) cc_final: 0.7299 (ttt90) REVERT: A 93 GLU cc_start: 0.7513 (mp0) cc_final: 0.7143 (mp0) REVERT: A 184 GLU cc_start: 0.7590 (mt-10) cc_final: 0.7054 (tp30) REVERT: A 214 GLN cc_start: 0.7489 (mm-40) cc_final: 0.7129 (mt0) REVERT: A 301 LYS cc_start: 0.7804 (mmmt) cc_final: 0.7352 (mmmt) REVERT: A 302 ARG cc_start: 0.7488 (mtm110) cc_final: 0.7053 (ttp80) REVERT: A 306 GLN cc_start: 0.7468 (mt0) cc_final: 0.6656 (mp10) REVERT: A 381 GLN cc_start: 0.6623 (mp10) cc_final: 0.5716 (mm-40) REVERT: A 447 MET cc_start: 0.7702 (OUTLIER) cc_final: 0.7291 (mtp) REVERT: A 448 ASN cc_start: 0.7737 (t0) cc_final: 0.7524 (t0) REVERT: A 491 MET cc_start: 0.7281 (mmm) cc_final: 0.6617 (mmp) REVERT: B 33 ARG cc_start: 0.6471 (ttt90) cc_final: 0.6262 (ttp-170) REVERT: B 35 ARG cc_start: 0.7590 (ttt-90) cc_final: 0.7293 (ttt90) REVERT: B 93 GLU cc_start: 0.7538 (mp0) cc_final: 0.7169 (mp0) REVERT: B 173 VAL cc_start: 0.8438 (t) cc_final: 0.8022 (m) REVERT: B 184 GLU cc_start: 0.7662 (mt-10) cc_final: 0.7083 (tp30) REVERT: B 214 GLN cc_start: 0.7498 (mm-40) cc_final: 0.7114 (mt0) REVERT: B 301 LYS cc_start: 0.7817 (mmmt) cc_final: 0.7357 (mmmt) REVERT: B 302 ARG cc_start: 0.7489 (mtm110) cc_final: 0.7058 (ttp80) REVERT: B 306 GLN cc_start: 0.7450 (mt0) cc_final: 0.6572 (mm-40) REVERT: B 448 ASN cc_start: 0.7768 (t0) cc_final: 0.7557 (t0) REVERT: B 491 MET cc_start: 0.7270 (mmm) cc_final: 0.6610 (mmp) REVERT: C 33 ARG cc_start: 0.6470 (ttt90) cc_final: 0.6264 (ttp-170) REVERT: C 35 ARG cc_start: 0.7588 (ttt-90) cc_final: 0.7293 (ttt90) REVERT: C 93 GLU cc_start: 0.7539 (mp0) cc_final: 0.7170 (mp0) REVERT: C 184 GLU cc_start: 0.7665 (mt-10) cc_final: 0.7079 (tp30) REVERT: C 214 GLN cc_start: 0.7483 (mm-40) cc_final: 0.7108 (mt0) REVERT: C 301 LYS cc_start: 0.7816 (mmmt) cc_final: 0.7355 (mmmt) REVERT: C 302 ARG cc_start: 0.7493 (mtm110) cc_final: 0.7060 (ttp80) REVERT: C 306 GLN cc_start: 0.7447 (mt0) cc_final: 0.6567 (mm-40) REVERT: C 381 GLN cc_start: 0.6618 (mp10) cc_final: 0.5703 (mm-40) REVERT: C 448 ASN cc_start: 0.7764 (t0) cc_final: 0.7554 (t0) REVERT: C 491 MET cc_start: 0.7274 (mmm) cc_final: 0.6611 (mmp) REVERT: D 33 ARG cc_start: 0.6472 (ttt90) cc_final: 0.6267 (ttp-170) REVERT: D 35 ARG cc_start: 0.7592 (ttt-90) cc_final: 0.7292 (ttt90) REVERT: D 93 GLU cc_start: 0.7530 (mp0) cc_final: 0.7163 (mp0) REVERT: D 173 VAL cc_start: 0.8435 (t) cc_final: 0.8018 (m) REVERT: D 184 GLU cc_start: 0.7661 (mt-10) cc_final: 0.7084 (tp30) REVERT: D 214 GLN cc_start: 0.7496 (mm-40) cc_final: 0.7114 (mt0) REVERT: D 301 LYS cc_start: 0.7813 (mmmt) cc_final: 0.7356 (mmmt) REVERT: D 302 ARG cc_start: 0.7481 (mtm110) cc_final: 0.7054 (ttp80) REVERT: D 306 GLN cc_start: 0.7446 (mt0) cc_final: 0.6686 (mp10) REVERT: D 447 MET cc_start: 0.7708 (OUTLIER) cc_final: 0.7290 (mtp) REVERT: D 448 ASN cc_start: 0.7748 (t0) cc_final: 0.7537 (t0) REVERT: D 491 MET cc_start: 0.7282 (mmm) cc_final: 0.6619 (mmp) outliers start: 36 outliers final: 24 residues processed: 361 average time/residue: 1.3731 time to fit residues: 557.3968 Evaluate side-chains 328 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 302 time to evaluate : 2.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 323 LYS Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 447 MET Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 323 LYS Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 323 LYS Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 603 MET Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 323 LYS Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 447 MET Chi-restraints excluded: chain D residue 603 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 121 optimal weight: 0.6980 chunk 67 optimal weight: 6.9990 chunk 181 optimal weight: 9.9990 chunk 148 optimal weight: 4.9990 chunk 60 optimal weight: 10.0000 chunk 218 optimal weight: 3.9990 chunk 235 optimal weight: 0.7980 chunk 194 optimal weight: 2.9990 chunk 216 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 175 optimal weight: 5.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN B 31 GLN B 261 GLN C 31 GLN C 261 GLN D 31 GLN D 261 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 20352 Z= 0.319 Angle : 0.564 5.999 27612 Z= 0.286 Chirality : 0.041 0.166 3128 Planarity : 0.004 0.031 3424 Dihedral : 10.257 85.493 3428 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 2.93 % Allowed : 7.55 % Favored : 89.52 % 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: 1.45 (0.17), residues: 2384 helix: 1.12 (0.13), residues: 1540 sheet: 0.55 (0.51), residues: 80 loop : 0.98 (0.25), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 593 HIS 0.007 0.001 HIS A 201 PHE 0.014 0.002 PHE C 211 TYR 0.015 0.002 TYR B 216 ARG 0.005 0.001 ARG B 139 *********************** 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 407 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 346 time to evaluate : 2.056 Fit side-chains REVERT: A 35 ARG cc_start: 0.7609 (ttt-90) cc_final: 0.7344 (ttt90) REVERT: A 93 GLU cc_start: 0.7541 (mp0) cc_final: 0.7144 (mp0) REVERT: A 139 ARG cc_start: 0.7548 (mtt-85) cc_final: 0.7335 (mtp180) REVERT: A 173 VAL cc_start: 0.8442 (t) cc_final: 0.8156 (m) REVERT: A 184 GLU cc_start: 0.7565 (mt-10) cc_final: 0.6997 (tp30) REVERT: A 190 ARG cc_start: 0.7839 (OUTLIER) cc_final: 0.7429 (mtm180) REVERT: A 214 GLN cc_start: 0.7492 (mm-40) cc_final: 0.7131 (mt0) REVERT: A 301 LYS cc_start: 0.7816 (mmmt) cc_final: 0.7586 (mmmm) REVERT: A 302 ARG cc_start: 0.7583 (mtm110) cc_final: 0.7320 (mtp-110) REVERT: A 306 GLN cc_start: 0.7614 (mt0) cc_final: 0.6800 (mp10) REVERT: A 381 GLN cc_start: 0.6676 (mp10) cc_final: 0.5714 (mm-40) REVERT: A 421 LEU cc_start: 0.8561 (mm) cc_final: 0.8207 (mp) REVERT: A 448 ASN cc_start: 0.7907 (t0) cc_final: 0.7693 (t0) REVERT: A 491 MET cc_start: 0.7320 (mmm) cc_final: 0.6607 (mmp) REVERT: B 33 ARG cc_start: 0.6496 (ttt90) cc_final: 0.6218 (ttp-170) REVERT: B 35 ARG cc_start: 0.7606 (ttt-90) cc_final: 0.7340 (ttt90) REVERT: B 93 GLU cc_start: 0.7562 (mp0) cc_final: 0.7250 (mp0) REVERT: B 190 ARG cc_start: 0.7848 (OUTLIER) cc_final: 0.7430 (mtm180) REVERT: B 214 GLN cc_start: 0.7482 (mm-40) cc_final: 0.7130 (mt0) REVERT: B 302 ARG cc_start: 0.7584 (mtm110) cc_final: 0.7223 (mtp-110) REVERT: B 306 GLN cc_start: 0.7575 (mt0) cc_final: 0.6775 (mp10) REVERT: B 381 GLN cc_start: 0.6653 (mp10) cc_final: 0.5765 (mm-40) REVERT: B 421 LEU cc_start: 0.8563 (mm) cc_final: 0.8204 (mp) REVERT: B 447 MET cc_start: 0.7741 (ttp) cc_final: 0.7472 (mtp) REVERT: B 448 ASN cc_start: 0.7903 (t0) cc_final: 0.7689 (t0) REVERT: B 491 MET cc_start: 0.7324 (mmm) cc_final: 0.6612 (mmp) REVERT: C 33 ARG cc_start: 0.6495 (ttt90) cc_final: 0.6221 (ttp-170) REVERT: C 35 ARG cc_start: 0.7609 (ttt-90) cc_final: 0.7339 (ttt90) REVERT: C 93 GLU cc_start: 0.7550 (mp0) cc_final: 0.7144 (mp0) REVERT: C 173 VAL cc_start: 0.8457 (t) cc_final: 0.8197 (m) REVERT: C 184 GLU cc_start: 0.7564 (mt-10) cc_final: 0.6951 (tp30) REVERT: C 190 ARG cc_start: 0.7846 (OUTLIER) cc_final: 0.7410 (mtm180) REVERT: C 214 GLN cc_start: 0.7483 (mm-40) cc_final: 0.7130 (mt0) REVERT: C 301 LYS cc_start: 0.7819 (mmmt) cc_final: 0.7590 (mmmm) REVERT: C 302 ARG cc_start: 0.7587 (mtm110) cc_final: 0.7226 (mtp-110) REVERT: C 306 GLN cc_start: 0.7572 (mt0) cc_final: 0.6770 (mp10) REVERT: C 381 GLN cc_start: 0.6649 (mp10) cc_final: 0.5707 (mm-40) REVERT: C 421 LEU cc_start: 0.8564 (mm) cc_final: 0.8205 (mp) REVERT: C 447 MET cc_start: 0.7744 (ttp) cc_final: 0.7471 (mtp) REVERT: C 448 ASN cc_start: 0.7909 (t0) cc_final: 0.7698 (t0) REVERT: C 491 MET cc_start: 0.7323 (mmm) cc_final: 0.6611 (mmp) REVERT: D 33 ARG cc_start: 0.6495 (ttt90) cc_final: 0.6222 (ttp-170) REVERT: D 35 ARG cc_start: 0.7607 (ttt-90) cc_final: 0.7338 (ttt90) REVERT: D 93 GLU cc_start: 0.7577 (mp0) cc_final: 0.7190 (mp0) REVERT: D 184 GLU cc_start: 0.7572 (mt-10) cc_final: 0.6956 (tp30) REVERT: D 190 ARG cc_start: 0.7850 (OUTLIER) cc_final: 0.7434 (mtm180) REVERT: D 214 GLN cc_start: 0.7481 (mm-40) cc_final: 0.7125 (mt0) REVERT: D 302 ARG cc_start: 0.7585 (mtm110) cc_final: 0.7224 (mtp-110) REVERT: D 306 GLN cc_start: 0.7570 (mt0) cc_final: 0.6770 (mp10) REVERT: D 381 GLN cc_start: 0.6672 (mp10) cc_final: 0.5774 (mm-40) REVERT: D 421 LEU cc_start: 0.8562 (mm) cc_final: 0.8204 (mp) REVERT: D 448 ASN cc_start: 0.7905 (t0) cc_final: 0.7694 (t0) REVERT: D 491 MET cc_start: 0.7321 (mmm) cc_final: 0.6609 (mmp) outliers start: 61 outliers final: 43 residues processed: 384 average time/residue: 1.3364 time to fit residues: 578.6641 Evaluate side-chains 363 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 316 time to evaluate : 2.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 323 LYS Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 294 GLU Chi-restraints excluded: chain B residue 318 SER Chi-restraints excluded: chain B residue 323 LYS Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 497 MET Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 294 GLU Chi-restraints excluded: chain C residue 318 SER Chi-restraints excluded: chain C residue 323 LYS Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 445 THR Chi-restraints excluded: chain C residue 497 MET Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 603 MET Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 190 ARG Chi-restraints excluded: chain D residue 294 GLU Chi-restraints excluded: chain D residue 318 SER Chi-restraints excluded: chain D residue 323 LYS Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 445 THR Chi-restraints excluded: chain D residue 497 MET Chi-restraints excluded: chain D residue 514 THR Chi-restraints excluded: chain D residue 603 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 215 optimal weight: 6.9990 chunk 164 optimal weight: 1.9990 chunk 113 optimal weight: 0.9980 chunk 24 optimal weight: 6.9990 chunk 104 optimal weight: 1.9990 chunk 146 optimal weight: 0.9980 chunk 219 optimal weight: 0.6980 chunk 231 optimal weight: 0.9990 chunk 114 optimal weight: 0.9980 chunk 207 optimal weight: 0.9990 chunk 62 optimal weight: 9.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN B 261 GLN C 261 GLN D 261 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 20352 Z= 0.172 Angle : 0.486 5.741 27612 Z= 0.247 Chirality : 0.037 0.145 3128 Planarity : 0.004 0.031 3424 Dihedral : 9.260 82.734 3428 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 2.26 % Allowed : 9.33 % Favored : 88.41 % 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: 1.40 (0.13), residues: 1536 sheet: 0.24 (0.49), residues: 80 loop : 1.06 (0.25), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 593 HIS 0.003 0.001 HIS B 201 PHE 0.007 0.001 PHE C 504 TYR 0.009 0.001 TYR A 555 ARG 0.005 0.000 ARG A 139 *********************** 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 383 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 336 time to evaluate : 2.290 Fit side-chains REVERT: A 93 GLU cc_start: 0.7609 (mp0) cc_final: 0.7238 (mp0) REVERT: A 184 GLU cc_start: 0.7507 (mt-10) cc_final: 0.6930 (tp30) REVERT: A 214 GLN cc_start: 0.7488 (mm-40) cc_final: 0.7136 (mt0) REVERT: A 215 MET cc_start: 0.8497 (mmm) cc_final: 0.8219 (mmt) REVERT: A 302 ARG cc_start: 0.7550 (mtm110) cc_final: 0.6903 (ttt-90) REVERT: A 306 GLN cc_start: 0.7558 (mt0) cc_final: 0.6759 (mp10) REVERT: A 381 GLN cc_start: 0.6615 (mp10) cc_final: 0.5729 (mm-40) REVERT: A 421 LEU cc_start: 0.8430 (mm) cc_final: 0.8058 (mp) REVERT: A 448 ASN cc_start: 0.7929 (t0) cc_final: 0.7712 (t0) REVERT: A 491 MET cc_start: 0.7256 (mmm) cc_final: 0.6529 (mmp) REVERT: B 33 ARG cc_start: 0.6418 (ttt90) cc_final: 0.6184 (ttp-170) REVERT: B 93 GLU cc_start: 0.7625 (mp0) cc_final: 0.7247 (mp0) REVERT: B 173 VAL cc_start: 0.8374 (t) cc_final: 0.8098 (m) REVERT: B 184 GLU cc_start: 0.7447 (mt-10) cc_final: 0.6901 (tp30) REVERT: B 214 GLN cc_start: 0.7484 (mm-40) cc_final: 0.7127 (mt0) REVERT: B 302 ARG cc_start: 0.7559 (mtm110) cc_final: 0.6914 (ttt-90) REVERT: B 306 GLN cc_start: 0.7518 (mt0) cc_final: 0.6729 (mp10) REVERT: B 381 GLN cc_start: 0.6582 (mp10) cc_final: 0.5705 (mm-40) REVERT: B 421 LEU cc_start: 0.8437 (mm) cc_final: 0.8063 (mp) REVERT: B 447 MET cc_start: 0.7709 (ttp) cc_final: 0.7446 (mtp) REVERT: B 448 ASN cc_start: 0.7940 (t0) cc_final: 0.7723 (t0) REVERT: B 491 MET cc_start: 0.7256 (mmm) cc_final: 0.6531 (mmp) REVERT: C 33 ARG cc_start: 0.6447 (ttt90) cc_final: 0.6203 (ttp-170) REVERT: C 93 GLU cc_start: 0.7628 (mp0) cc_final: 0.7252 (mp0) REVERT: C 184 GLU cc_start: 0.7530 (mt-10) cc_final: 0.6949 (tp30) REVERT: C 214 GLN cc_start: 0.7485 (mm-40) cc_final: 0.7128 (mt0) REVERT: C 215 MET cc_start: 0.8464 (mmm) cc_final: 0.8181 (mmt) REVERT: C 302 ARG cc_start: 0.7555 (mtm110) cc_final: 0.6917 (ttt-90) REVERT: C 306 GLN cc_start: 0.7518 (mt0) cc_final: 0.6730 (mp10) REVERT: C 381 GLN cc_start: 0.6594 (mp10) cc_final: 0.5729 (mm-40) REVERT: C 421 LEU cc_start: 0.8438 (mm) cc_final: 0.8063 (mp) REVERT: C 447 MET cc_start: 0.7708 (ttp) cc_final: 0.7453 (mtp) REVERT: C 448 ASN cc_start: 0.7937 (t0) cc_final: 0.7721 (t0) REVERT: C 491 MET cc_start: 0.7257 (mmm) cc_final: 0.6536 (mmp) REVERT: D 33 ARG cc_start: 0.6433 (ttt90) cc_final: 0.6217 (ttp-170) REVERT: D 93 GLU cc_start: 0.7613 (mp0) cc_final: 0.7252 (mp0) REVERT: D 173 VAL cc_start: 0.8362 (t) cc_final: 0.8082 (m) REVERT: D 184 GLU cc_start: 0.7531 (mt-10) cc_final: 0.6951 (tp30) REVERT: D 214 GLN cc_start: 0.7477 (mm-40) cc_final: 0.7119 (mt0) REVERT: D 302 ARG cc_start: 0.7556 (mtm110) cc_final: 0.6902 (ttt-90) REVERT: D 303 GLU cc_start: 0.7943 (mp0) cc_final: 0.7437 (mp0) REVERT: D 306 GLN cc_start: 0.7522 (mt0) cc_final: 0.6730 (mp10) REVERT: D 381 GLN cc_start: 0.6587 (mp10) cc_final: 0.5710 (mm-40) REVERT: D 421 LEU cc_start: 0.8436 (mm) cc_final: 0.8061 (mp) REVERT: D 448 ASN cc_start: 0.7931 (t0) cc_final: 0.7712 (t0) REVERT: D 491 MET cc_start: 0.7256 (mmm) cc_final: 0.6536 (mmp) outliers start: 47 outliers final: 17 residues processed: 359 average time/residue: 1.3781 time to fit residues: 557.3647 Evaluate side-chains 327 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 310 time to evaluate : 2.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 323 LYS Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 323 LYS Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 548 SER Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 323 LYS Chi-restraints excluded: chain C residue 445 THR Chi-restraints excluded: chain C residue 548 SER Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 323 LYS Chi-restraints excluded: chain D residue 548 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 193 optimal weight: 4.9990 chunk 131 optimal weight: 7.9990 chunk 3 optimal weight: 7.9990 chunk 172 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 chunk 197 optimal weight: 1.9990 chunk 160 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 118 optimal weight: 7.9990 chunk 208 optimal weight: 2.9990 chunk 58 optimal weight: 8.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN B 261 GLN C 261 GLN C 572 ASN D 261 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 20352 Z= 0.363 Angle : 0.575 6.043 27612 Z= 0.290 Chirality : 0.042 0.160 3128 Planarity : 0.005 0.044 3424 Dihedral : 9.614 85.748 3428 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 3.03 % Allowed : 8.46 % Favored : 88.51 % 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: 1.35 (0.17), residues: 2384 helix: 1.10 (0.13), residues: 1544 sheet: -0.32 (0.51), residues: 80 loop : 0.91 (0.24), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 593 HIS 0.007 0.001 HIS A 201 PHE 0.013 0.002 PHE D 504 TYR 0.014 0.002 TYR D 216 ARG 0.008 0.001 ARG D 409 *********************** 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 383 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 320 time to evaluate : 2.116 Fit side-chains REVERT: A 57 ASP cc_start: 0.8069 (p0) cc_final: 0.7866 (p0) REVERT: A 74 GLN cc_start: 0.7233 (mt0) cc_final: 0.6963 (mt0) REVERT: A 93 GLU cc_start: 0.7600 (mp0) cc_final: 0.7284 (mp0) REVERT: A 184 GLU cc_start: 0.7502 (mt-10) cc_final: 0.6949 (tp30) REVERT: A 214 GLN cc_start: 0.7500 (mm-40) cc_final: 0.7163 (mt0) REVERT: A 303 GLU cc_start: 0.7941 (mp0) cc_final: 0.7458 (mp0) REVERT: A 306 GLN cc_start: 0.7552 (mt0) cc_final: 0.6753 (mp10) REVERT: A 381 GLN cc_start: 0.6652 (mp10) cc_final: 0.5691 (mm-40) REVERT: A 421 LEU cc_start: 0.8582 (mm) cc_final: 0.8217 (mp) REVERT: A 448 ASN cc_start: 0.7929 (t0) cc_final: 0.7724 (t0) REVERT: A 491 MET cc_start: 0.7371 (mmm) cc_final: 0.6634 (mmp) REVERT: B 33 ARG cc_start: 0.6480 (ttt90) cc_final: 0.6175 (ttp-170) REVERT: B 74 GLN cc_start: 0.7209 (mt0) cc_final: 0.6976 (mt0) REVERT: B 93 GLU cc_start: 0.7645 (mp0) cc_final: 0.7296 (mp0) REVERT: B 139 ARG cc_start: 0.7672 (mtt-85) cc_final: 0.7435 (mtp180) REVERT: B 184 GLU cc_start: 0.7504 (mt-10) cc_final: 0.6981 (tp30) REVERT: B 214 GLN cc_start: 0.7505 (mm-40) cc_final: 0.7165 (mt0) REVERT: B 215 MET cc_start: 0.8465 (mmm) cc_final: 0.8180 (mmt) REVERT: B 303 GLU cc_start: 0.7929 (mp0) cc_final: 0.7386 (mp0) REVERT: B 306 GLN cc_start: 0.7550 (mt0) cc_final: 0.6754 (mp10) REVERT: B 381 GLN cc_start: 0.6617 (mp10) cc_final: 0.5697 (mm-40) REVERT: B 421 LEU cc_start: 0.8551 (mm) cc_final: 0.8183 (mp) REVERT: B 447 MET cc_start: 0.7713 (OUTLIER) cc_final: 0.7485 (mtp) REVERT: B 448 ASN cc_start: 0.7930 (t0) cc_final: 0.7721 (t0) REVERT: B 491 MET cc_start: 0.7373 (mmm) cc_final: 0.6634 (mmp) REVERT: C 33 ARG cc_start: 0.6482 (ttt90) cc_final: 0.6178 (ttp-170) REVERT: C 74 GLN cc_start: 0.7205 (mt0) cc_final: 0.6963 (mt0) REVERT: C 93 GLU cc_start: 0.7608 (mp0) cc_final: 0.7256 (mp0) REVERT: C 184 GLU cc_start: 0.7558 (mt-10) cc_final: 0.6986 (tp30) REVERT: C 214 GLN cc_start: 0.7505 (mm-40) cc_final: 0.7165 (mt0) REVERT: C 303 GLU cc_start: 0.7945 (mp0) cc_final: 0.7725 (mp0) REVERT: C 306 GLN cc_start: 0.7553 (mt0) cc_final: 0.6753 (mp10) REVERT: C 381 GLN cc_start: 0.6636 (mp10) cc_final: 0.5684 (mm-40) REVERT: C 421 LEU cc_start: 0.8584 (mm) cc_final: 0.8217 (mp) REVERT: C 447 MET cc_start: 0.7714 (OUTLIER) cc_final: 0.7485 (mtp) REVERT: C 448 ASN cc_start: 0.7926 (t0) cc_final: 0.7721 (t0) REVERT: C 491 MET cc_start: 0.7341 (mmm) cc_final: 0.6599 (mmp) REVERT: D 33 ARG cc_start: 0.6486 (ttt90) cc_final: 0.6185 (ttp-170) REVERT: D 74 GLN cc_start: 0.7228 (mt0) cc_final: 0.6980 (mt0) REVERT: D 93 GLU cc_start: 0.7627 (mp0) cc_final: 0.7275 (mp0) REVERT: D 184 GLU cc_start: 0.7589 (mt-10) cc_final: 0.7002 (tp30) REVERT: D 214 GLN cc_start: 0.7505 (mm-40) cc_final: 0.7165 (mt0) REVERT: D 215 MET cc_start: 0.8468 (mmm) cc_final: 0.8183 (mmt) REVERT: D 303 GLU cc_start: 0.7926 (mp0) cc_final: 0.7382 (mp0) REVERT: D 306 GLN cc_start: 0.7550 (mt0) cc_final: 0.6751 (mp10) REVERT: D 381 GLN cc_start: 0.6625 (mp10) cc_final: 0.5715 (mm-40) REVERT: D 421 LEU cc_start: 0.8550 (mm) cc_final: 0.8182 (mp) REVERT: D 448 ASN cc_start: 0.7929 (t0) cc_final: 0.7716 (t0) REVERT: D 491 MET cc_start: 0.7340 (mmm) cc_final: 0.6601 (mmp) outliers start: 63 outliers final: 35 residues processed: 352 average time/residue: 1.3807 time to fit residues: 546.3775 Evaluate side-chains 348 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 311 time to evaluate : 2.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 323 LYS Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 294 GLU Chi-restraints excluded: chain B residue 318 SER Chi-restraints excluded: chain B residue 323 LYS Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 447 MET Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 548 SER Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 294 GLU Chi-restraints excluded: chain C residue 318 SER Chi-restraints excluded: chain C residue 323 LYS Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 447 MET Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 548 SER Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 190 ARG Chi-restraints excluded: chain D residue 294 GLU Chi-restraints excluded: chain D residue 318 SER Chi-restraints excluded: chain D residue 323 LYS Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 514 THR Chi-restraints excluded: chain D residue 548 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 78 optimal weight: 4.9990 chunk 208 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 136 optimal weight: 7.9990 chunk 57 optimal weight: 2.9990 chunk 232 optimal weight: 0.9990 chunk 192 optimal weight: 0.6980 chunk 107 optimal weight: 0.6980 chunk 19 optimal weight: 5.9990 chunk 76 optimal weight: 0.9980 chunk 121 optimal weight: 4.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN B 261 GLN C 261 GLN D 261 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 20352 Z= 0.165 Angle : 0.493 5.938 27612 Z= 0.248 Chirality : 0.037 0.136 3128 Planarity : 0.004 0.046 3424 Dihedral : 9.082 82.336 3428 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 1.92 % Allowed : 9.47 % Favored : 88.61 % 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: 1.69 (0.17), residues: 2384 helix: 1.41 (0.13), residues: 1544 sheet: -0.46 (0.49), residues: 80 loop : 0.97 (0.24), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 593 HIS 0.003 0.001 HIS D 201 PHE 0.007 0.001 PHE B 504 TYR 0.009 0.001 TYR A 555 ARG 0.009 0.000 ARG B 409 *********************** 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 365 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 325 time to evaluate : 2.197 Fit side-chains REVERT: A 35 ARG cc_start: 0.7688 (ttt90) cc_final: 0.7417 (tpt-90) REVERT: A 74 GLN cc_start: 0.7178 (mt0) cc_final: 0.6926 (mt0) REVERT: A 93 GLU cc_start: 0.7613 (mp0) cc_final: 0.7309 (mp0) REVERT: A 184 GLU cc_start: 0.7471 (mt-10) cc_final: 0.6930 (tp30) REVERT: A 190 ARG cc_start: 0.7833 (OUTLIER) cc_final: 0.7485 (mtm180) REVERT: A 214 GLN cc_start: 0.7509 (mm-40) cc_final: 0.7155 (mt0) REVERT: A 294 GLU cc_start: 0.7245 (OUTLIER) cc_final: 0.6910 (tt0) REVERT: A 302 ARG cc_start: 0.7586 (mtm110) cc_final: 0.6892 (tmt-80) REVERT: A 303 GLU cc_start: 0.7907 (mp0) cc_final: 0.7636 (mp0) REVERT: A 306 GLN cc_start: 0.7518 (mt0) cc_final: 0.6716 (mp10) REVERT: A 318 SER cc_start: 0.8272 (t) cc_final: 0.7872 (m) REVERT: A 381 GLN cc_start: 0.6631 (mp10) cc_final: 0.5666 (mm-40) REVERT: A 421 LEU cc_start: 0.8495 (mm) cc_final: 0.8150 (mp) REVERT: A 448 ASN cc_start: 0.7914 (t0) cc_final: 0.7712 (t0) REVERT: A 491 MET cc_start: 0.7276 (mmm) cc_final: 0.6539 (mmp) REVERT: B 33 ARG cc_start: 0.6433 (ttt90) cc_final: 0.6197 (ttp-170) REVERT: B 35 ARG cc_start: 0.7725 (ttt90) cc_final: 0.7442 (tpt-90) REVERT: B 93 GLU cc_start: 0.7658 (mp0) cc_final: 0.7322 (mp0) REVERT: B 173 VAL cc_start: 0.8301 (t) cc_final: 0.8024 (m) REVERT: B 184 GLU cc_start: 0.7427 (mt-10) cc_final: 0.6837 (tp30) REVERT: B 190 ARG cc_start: 0.7863 (OUTLIER) cc_final: 0.7517 (mtm180) REVERT: B 214 GLN cc_start: 0.7520 (mm-40) cc_final: 0.7173 (mt0) REVERT: B 302 ARG cc_start: 0.7600 (mtm110) cc_final: 0.6889 (tmt-80) REVERT: B 303 GLU cc_start: 0.7946 (mp0) cc_final: 0.7664 (mp0) REVERT: B 306 GLN cc_start: 0.7520 (mt0) cc_final: 0.6712 (mp10) REVERT: B 381 GLN cc_start: 0.6593 (mp10) cc_final: 0.5715 (mm-40) REVERT: B 421 LEU cc_start: 0.8495 (mm) cc_final: 0.8141 (mp) REVERT: B 448 ASN cc_start: 0.7943 (t0) cc_final: 0.7733 (t0) REVERT: B 491 MET cc_start: 0.7277 (mmm) cc_final: 0.6541 (mmp) REVERT: C 33 ARG cc_start: 0.6441 (ttt90) cc_final: 0.6210 (ttp-170) REVERT: C 35 ARG cc_start: 0.7718 (ttt90) cc_final: 0.7441 (tpt-90) REVERT: C 93 GLU cc_start: 0.7616 (mp0) cc_final: 0.7309 (mp0) REVERT: C 184 GLU cc_start: 0.7478 (mt-10) cc_final: 0.6858 (tp30) REVERT: C 190 ARG cc_start: 0.7816 (OUTLIER) cc_final: 0.7462 (mtm180) REVERT: C 214 GLN cc_start: 0.7523 (mm-40) cc_final: 0.7172 (mt0) REVERT: C 302 ARG cc_start: 0.7598 (mtm110) cc_final: 0.6885 (tmt-80) REVERT: C 303 GLU cc_start: 0.7901 (mp0) cc_final: 0.7631 (mp0) REVERT: C 306 GLN cc_start: 0.7520 (mt0) cc_final: 0.6716 (mp10) REVERT: C 318 SER cc_start: 0.8278 (t) cc_final: 0.7877 (m) REVERT: C 381 GLN cc_start: 0.6621 (mp10) cc_final: 0.5717 (mm-40) REVERT: C 421 LEU cc_start: 0.8490 (mm) cc_final: 0.8138 (mp) REVERT: C 448 ASN cc_start: 0.7942 (t0) cc_final: 0.7731 (t0) REVERT: C 491 MET cc_start: 0.7306 (mmm) cc_final: 0.6545 (mmp) REVERT: D 33 ARG cc_start: 0.6446 (ttt90) cc_final: 0.6212 (ttp-170) REVERT: D 35 ARG cc_start: 0.7695 (ttt90) cc_final: 0.7416 (tpt-90) REVERT: D 74 GLN cc_start: 0.7247 (mt0) cc_final: 0.6997 (mt0) REVERT: D 93 GLU cc_start: 0.7611 (mp0) cc_final: 0.7296 (mp0) REVERT: D 173 VAL cc_start: 0.8301 (t) cc_final: 0.8025 (m) REVERT: D 184 GLU cc_start: 0.7491 (mt-10) cc_final: 0.6882 (tp30) REVERT: D 190 ARG cc_start: 0.7859 (OUTLIER) cc_final: 0.7516 (mtm180) REVERT: D 214 GLN cc_start: 0.7520 (mm-40) cc_final: 0.7174 (mt0) REVERT: D 302 ARG cc_start: 0.7601 (mtm110) cc_final: 0.6893 (tmt-80) REVERT: D 303 GLU cc_start: 0.7944 (mp0) cc_final: 0.7665 (mp0) REVERT: D 306 GLN cc_start: 0.7519 (mt0) cc_final: 0.6711 (mp10) REVERT: D 381 GLN cc_start: 0.6636 (mp10) cc_final: 0.5724 (mm-40) REVERT: D 421 LEU cc_start: 0.8497 (mm) cc_final: 0.8148 (mp) REVERT: D 448 ASN cc_start: 0.7938 (t0) cc_final: 0.7734 (t0) REVERT: D 491 MET cc_start: 0.7307 (mmm) cc_final: 0.6547 (mmp) outliers start: 40 outliers final: 21 residues processed: 355 average time/residue: 1.3634 time to fit residues: 545.2123 Evaluate side-chains 332 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 306 time to evaluate : 2.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 323 LYS Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 323 LYS Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 323 LYS Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 190 ARG Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 323 LYS Chi-restraints excluded: chain D residue 335 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 223 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 132 optimal weight: 0.6980 chunk 169 optimal weight: 0.5980 chunk 131 optimal weight: 5.9990 chunk 195 optimal weight: 7.9990 chunk 129 optimal weight: 8.9990 chunk 231 optimal weight: 0.4980 chunk 144 optimal weight: 6.9990 chunk 141 optimal weight: 4.9990 chunk 106 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN A 261 GLN A 418 GLN A 572 ASN B 40 GLN B 261 GLN C 40 GLN C 261 GLN D 40 GLN D 261 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 20352 Z= 0.177 Angle : 0.503 7.713 27612 Z= 0.252 Chirality : 0.038 0.149 3128 Planarity : 0.004 0.056 3424 Dihedral : 8.868 79.865 3428 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 1.92 % Allowed : 9.90 % Favored : 88.17 % 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: 1.82 (0.17), residues: 2384 helix: 1.59 (0.13), residues: 1524 sheet: -0.71 (0.48), residues: 80 loop : 0.88 (0.24), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 593 HIS 0.004 0.001 HIS D 201 PHE 0.009 0.001 PHE C 504 TYR 0.009 0.001 TYR C 216 ARG 0.013 0.001 ARG A 409 *********************** 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 364 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 324 time to evaluate : 2.254 Fit side-chains REVERT: A 35 ARG cc_start: 0.7665 (ttt90) cc_final: 0.7398 (tpt-90) REVERT: A 93 GLU cc_start: 0.7633 (mp0) cc_final: 0.7338 (mp0) REVERT: A 184 GLU cc_start: 0.7449 (mt-10) cc_final: 0.6854 (tp30) REVERT: A 190 ARG cc_start: 0.7815 (OUTLIER) cc_final: 0.7502 (mtm180) REVERT: A 214 GLN cc_start: 0.7513 (mm-40) cc_final: 0.7155 (mt0) REVERT: A 215 MET cc_start: 0.8506 (mmm) cc_final: 0.8280 (mmt) REVERT: A 294 GLU cc_start: 0.7250 (OUTLIER) cc_final: 0.6920 (tt0) REVERT: A 302 ARG cc_start: 0.7614 (mtm110) cc_final: 0.6884 (tmt-80) REVERT: A 303 GLU cc_start: 0.7909 (mp0) cc_final: 0.7643 (mp0) REVERT: A 306 GLN cc_start: 0.7514 (mt0) cc_final: 0.6710 (mp10) REVERT: A 318 SER cc_start: 0.8281 (t) cc_final: 0.7901 (m) REVERT: A 381 GLN cc_start: 0.6597 (mp10) cc_final: 0.5697 (mm-40) REVERT: A 421 LEU cc_start: 0.8495 (mm) cc_final: 0.8138 (mp) REVERT: A 448 ASN cc_start: 0.7930 (t0) cc_final: 0.7721 (t0) REVERT: A 491 MET cc_start: 0.7317 (mmm) cc_final: 0.6571 (mmp) REVERT: B 33 ARG cc_start: 0.6422 (ttt90) cc_final: 0.6170 (ttp-170) REVERT: B 35 ARG cc_start: 0.7679 (ttt90) cc_final: 0.7411 (tpt-90) REVERT: B 80 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7568 (pt0) REVERT: B 93 GLU cc_start: 0.7642 (mp0) cc_final: 0.7320 (mp0) REVERT: B 173 VAL cc_start: 0.8297 (t) cc_final: 0.8023 (m) REVERT: B 184 GLU cc_start: 0.7443 (mt-10) cc_final: 0.6885 (tp30) REVERT: B 190 ARG cc_start: 0.7801 (OUTLIER) cc_final: 0.7491 (mtm180) REVERT: B 214 GLN cc_start: 0.7511 (mm-40) cc_final: 0.7139 (mt0) REVERT: B 302 ARG cc_start: 0.7626 (mtm110) cc_final: 0.6883 (tmt-80) REVERT: B 303 GLU cc_start: 0.7958 (mp0) cc_final: 0.7685 (mp0) REVERT: B 306 GLN cc_start: 0.7516 (mt0) cc_final: 0.6714 (mp10) REVERT: B 318 SER cc_start: 0.8291 (OUTLIER) cc_final: 0.7915 (m) REVERT: B 381 GLN cc_start: 0.6577 (mp10) cc_final: 0.5703 (mm-40) REVERT: B 421 LEU cc_start: 0.8487 (mm) cc_final: 0.8136 (mp) REVERT: B 448 ASN cc_start: 0.7973 (t0) cc_final: 0.7746 (t0) REVERT: B 491 MET cc_start: 0.7334 (mmm) cc_final: 0.6593 (mmp) REVERT: C 33 ARG cc_start: 0.6422 (ttt90) cc_final: 0.6170 (ttp-170) REVERT: C 35 ARG cc_start: 0.7679 (ttt90) cc_final: 0.7413 (tpt-90) REVERT: C 93 GLU cc_start: 0.7628 (mp0) cc_final: 0.7250 (mp0) REVERT: C 184 GLU cc_start: 0.7486 (mt-10) cc_final: 0.6869 (tp30) REVERT: C 214 GLN cc_start: 0.7512 (mm-40) cc_final: 0.7155 (mt0) REVERT: C 302 ARG cc_start: 0.7620 (mtm110) cc_final: 0.6886 (tmt-80) REVERT: C 303 GLU cc_start: 0.7908 (mp0) cc_final: 0.7640 (mp0) REVERT: C 306 GLN cc_start: 0.7518 (mt0) cc_final: 0.6712 (mp10) REVERT: C 318 SER cc_start: 0.8297 (OUTLIER) cc_final: 0.7920 (m) REVERT: C 381 GLN cc_start: 0.6575 (mp10) cc_final: 0.5696 (mm-40) REVERT: C 421 LEU cc_start: 0.8488 (mm) cc_final: 0.8142 (mp) REVERT: C 448 ASN cc_start: 0.7972 (t0) cc_final: 0.7745 (t0) REVERT: C 491 MET cc_start: 0.7333 (mmm) cc_final: 0.6592 (mmp) REVERT: D 33 ARG cc_start: 0.6420 (ttt90) cc_final: 0.6172 (ttp-170) REVERT: D 35 ARG cc_start: 0.7649 (ttt90) cc_final: 0.7380 (tpt-90) REVERT: D 74 GLN cc_start: 0.7268 (mt0) cc_final: 0.7034 (mt0) REVERT: D 93 GLU cc_start: 0.7626 (mp0) cc_final: 0.7310 (mp0) REVERT: D 173 VAL cc_start: 0.8294 (t) cc_final: 0.8026 (m) REVERT: D 184 GLU cc_start: 0.7471 (mt-10) cc_final: 0.6853 (tp30) REVERT: D 190 ARG cc_start: 0.7837 (OUTLIER) cc_final: 0.7529 (mtm180) REVERT: D 214 GLN cc_start: 0.7515 (mm-40) cc_final: 0.7141 (mt0) REVERT: D 302 ARG cc_start: 0.7628 (mtm110) cc_final: 0.6886 (tmt-80) REVERT: D 303 GLU cc_start: 0.7956 (mp0) cc_final: 0.7685 (mp0) REVERT: D 306 GLN cc_start: 0.7511 (mt0) cc_final: 0.6712 (mp10) REVERT: D 318 SER cc_start: 0.8292 (t) cc_final: 0.7916 (m) REVERT: D 381 GLN cc_start: 0.6582 (mp10) cc_final: 0.5699 (mm-40) REVERT: D 421 LEU cc_start: 0.8489 (mm) cc_final: 0.8141 (mp) REVERT: D 448 ASN cc_start: 0.7965 (t0) cc_final: 0.7748 (t0) REVERT: D 491 MET cc_start: 0.7336 (mmm) cc_final: 0.6595 (mmp) outliers start: 40 outliers final: 25 residues processed: 355 average time/residue: 1.4292 time to fit residues: 568.8729 Evaluate side-chains 341 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 309 time to evaluate : 2.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 323 LYS Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 318 SER Chi-restraints excluded: chain B residue 323 LYS Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 548 SER Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 318 SER Chi-restraints excluded: chain C residue 323 LYS Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 548 SER Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 190 ARG Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 323 LYS Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 548 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 143 optimal weight: 0.7980 chunk 92 optimal weight: 4.9990 chunk 138 optimal weight: 0.9980 chunk 69 optimal weight: 7.9990 chunk 45 optimal weight: 4.9990 chunk 44 optimal weight: 0.5980 chunk 147 optimal weight: 0.9990 chunk 157 optimal weight: 6.9990 chunk 114 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 181 optimal weight: 5.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN A 261 GLN B 40 GLN B 261 GLN C 261 GLN C 418 GLN D 261 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20352 Z= 0.168 Angle : 0.497 6.699 27612 Z= 0.247 Chirality : 0.037 0.146 3128 Planarity : 0.004 0.053 3424 Dihedral : 8.733 77.963 3428 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.68 % Allowed : 10.38 % Favored : 87.93 % 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: 1.86 (0.17), residues: 2384 helix: 1.63 (0.13), residues: 1524 sheet: -0.77 (0.48), residues: 80 loop : 0.89 (0.24), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 593 HIS 0.003 0.001 HIS B 201 PHE 0.014 0.001 PHE A 611 TYR 0.009 0.001 TYR C 216 ARG 0.012 0.001 ARG B 409 *********************** 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 346 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 311 time to evaluate : 2.033 Fit side-chains REVERT: A 35 ARG cc_start: 0.7637 (ttt90) cc_final: 0.7383 (tpt-90) REVERT: A 93 GLU cc_start: 0.7590 (mp0) cc_final: 0.7238 (mp0) REVERT: A 184 GLU cc_start: 0.7423 (mt-10) cc_final: 0.6820 (tp30) REVERT: A 190 ARG cc_start: 0.7801 (OUTLIER) cc_final: 0.7451 (mtm180) REVERT: A 214 GLN cc_start: 0.7488 (mm-40) cc_final: 0.7124 (mt0) REVERT: A 215 MET cc_start: 0.8520 (mmm) cc_final: 0.8313 (mmt) REVERT: A 294 GLU cc_start: 0.7254 (OUTLIER) cc_final: 0.6909 (tt0) REVERT: A 302 ARG cc_start: 0.7604 (mtm110) cc_final: 0.6882 (tmt-80) REVERT: A 303 GLU cc_start: 0.7906 (mp0) cc_final: 0.7552 (mp0) REVERT: A 306 GLN cc_start: 0.7522 (mt0) cc_final: 0.6718 (mp10) REVERT: A 318 SER cc_start: 0.8278 (OUTLIER) cc_final: 0.7911 (m) REVERT: A 381 GLN cc_start: 0.6576 (mp10) cc_final: 0.5669 (mm-40) REVERT: A 421 LEU cc_start: 0.8486 (mm) cc_final: 0.8137 (mp) REVERT: A 448 ASN cc_start: 0.7972 (t0) cc_final: 0.7745 (t0) REVERT: A 491 MET cc_start: 0.7320 (mmm) cc_final: 0.6587 (mmp) REVERT: B 33 ARG cc_start: 0.6394 (ttt90) cc_final: 0.6152 (ttp-170) REVERT: B 35 ARG cc_start: 0.7682 (ttt90) cc_final: 0.7430 (tpt-90) REVERT: B 80 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7489 (pt0) REVERT: B 93 GLU cc_start: 0.7647 (mp0) cc_final: 0.7331 (mp0) REVERT: B 173 VAL cc_start: 0.8265 (t) cc_final: 0.8010 (m) REVERT: B 184 GLU cc_start: 0.7426 (mt-10) cc_final: 0.6872 (tp30) REVERT: B 190 ARG cc_start: 0.7784 (OUTLIER) cc_final: 0.7438 (mtm180) REVERT: B 214 GLN cc_start: 0.7521 (mm-40) cc_final: 0.7163 (mt0) REVERT: B 302 ARG cc_start: 0.7618 (mtm110) cc_final: 0.6891 (tmt-80) REVERT: B 303 GLU cc_start: 0.7931 (mp0) cc_final: 0.7670 (mp0) REVERT: B 306 GLN cc_start: 0.7528 (mt0) cc_final: 0.6723 (mp10) REVERT: B 318 SER cc_start: 0.8278 (OUTLIER) cc_final: 0.7911 (m) REVERT: B 381 GLN cc_start: 0.6566 (mp10) cc_final: 0.5689 (mm-40) REVERT: B 421 LEU cc_start: 0.8477 (mm) cc_final: 0.8131 (mp) REVERT: B 448 ASN cc_start: 0.8006 (t0) cc_final: 0.7781 (t0) REVERT: B 491 MET cc_start: 0.7320 (mmm) cc_final: 0.6588 (mmp) REVERT: C 33 ARG cc_start: 0.6396 (ttt90) cc_final: 0.6154 (ttp-170) REVERT: C 35 ARG cc_start: 0.7685 (ttt90) cc_final: 0.7430 (tpt-90) REVERT: C 93 GLU cc_start: 0.7612 (mp0) cc_final: 0.7307 (mp0) REVERT: C 184 GLU cc_start: 0.7467 (mt-10) cc_final: 0.6851 (tp30) REVERT: C 190 ARG cc_start: 0.7780 (OUTLIER) cc_final: 0.7425 (mtm180) REVERT: C 214 GLN cc_start: 0.7489 (mm-40) cc_final: 0.7128 (mt0) REVERT: C 302 ARG cc_start: 0.7607 (mtm110) cc_final: 0.6883 (tmt-80) REVERT: C 303 GLU cc_start: 0.7908 (mp0) cc_final: 0.7549 (mp0) REVERT: C 306 GLN cc_start: 0.7527 (mt0) cc_final: 0.6720 (mp10) REVERT: C 318 SER cc_start: 0.8282 (OUTLIER) cc_final: 0.7915 (m) REVERT: C 381 GLN cc_start: 0.6554 (mp10) cc_final: 0.5666 (mm-40) REVERT: C 421 LEU cc_start: 0.8488 (mm) cc_final: 0.8131 (mp) REVERT: C 448 ASN cc_start: 0.8006 (t0) cc_final: 0.7781 (t0) REVERT: C 491 MET cc_start: 0.7320 (mmm) cc_final: 0.6591 (mmp) REVERT: D 33 ARG cc_start: 0.6390 (ttt90) cc_final: 0.6154 (ttp-170) REVERT: D 35 ARG cc_start: 0.7638 (ttt90) cc_final: 0.7376 (tpt-90) REVERT: D 74 GLN cc_start: 0.7295 (mt0) cc_final: 0.7051 (mt0) REVERT: D 93 GLU cc_start: 0.7611 (mp0) cc_final: 0.7306 (mp0) REVERT: D 173 VAL cc_start: 0.8265 (t) cc_final: 0.8014 (m) REVERT: D 184 GLU cc_start: 0.7489 (mt-10) cc_final: 0.6901 (tp30) REVERT: D 190 ARG cc_start: 0.7816 (OUTLIER) cc_final: 0.7482 (mtm180) REVERT: D 214 GLN cc_start: 0.7517 (mm-40) cc_final: 0.7161 (mt0) REVERT: D 302 ARG cc_start: 0.7619 (mtm110) cc_final: 0.6894 (tmt-80) REVERT: D 303 GLU cc_start: 0.7929 (mp0) cc_final: 0.7669 (mp0) REVERT: D 306 GLN cc_start: 0.7526 (mt0) cc_final: 0.6721 (mp10) REVERT: D 318 SER cc_start: 0.8276 (OUTLIER) cc_final: 0.7910 (m) REVERT: D 381 GLN cc_start: 0.6567 (mp10) cc_final: 0.5679 (mm-40) REVERT: D 421 LEU cc_start: 0.8479 (mm) cc_final: 0.8135 (mp) REVERT: D 448 ASN cc_start: 0.7971 (t0) cc_final: 0.7745 (t0) REVERT: D 491 MET cc_start: 0.7323 (mmm) cc_final: 0.6594 (mmp) outliers start: 35 outliers final: 21 residues processed: 335 average time/residue: 1.4163 time to fit residues: 531.8841 Evaluate side-chains 343 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 312 time to evaluate : 2.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 323 LYS Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 318 SER Chi-restraints excluded: chain B residue 323 LYS Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 318 SER Chi-restraints excluded: chain C residue 323 LYS Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 190 ARG Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 318 SER Chi-restraints excluded: chain D residue 323 LYS Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 548 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 210 optimal weight: 0.6980 chunk 221 optimal weight: 0.6980 chunk 202 optimal weight: 0.9990 chunk 215 optimal weight: 2.9990 chunk 129 optimal weight: 9.9990 chunk 93 optimal weight: 0.9980 chunk 169 optimal weight: 0.5980 chunk 66 optimal weight: 10.0000 chunk 194 optimal weight: 6.9990 chunk 203 optimal weight: 0.5980 chunk 214 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN A 261 GLN B 40 GLN B 261 GLN C 261 GLN D 40 GLN D 261 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 20352 Z= 0.154 Angle : 0.495 8.919 27612 Z= 0.244 Chirality : 0.037 0.137 3128 Planarity : 0.004 0.057 3424 Dihedral : 8.549 75.690 3428 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.63 % Allowed : 10.29 % Favored : 88.08 % 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: 1.95 (0.17), residues: 2384 helix: 1.71 (0.13), residues: 1524 sheet: -0.76 (0.48), residues: 80 loop : 0.89 (0.24), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 593 HIS 0.003 0.001 HIS B 201 PHE 0.014 0.001 PHE A 611 TYR 0.008 0.001 TYR A 216 ARG 0.013 0.000 ARG B 409 *********************** 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 346 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 312 time to evaluate : 2.322 Fit side-chains REVERT: A 35 ARG cc_start: 0.7635 (ttt90) cc_final: 0.7401 (tpt-90) REVERT: A 93 GLU cc_start: 0.7610 (mp0) cc_final: 0.7326 (mp0) REVERT: A 184 GLU cc_start: 0.7482 (mt-10) cc_final: 0.6872 (tp30) REVERT: A 214 GLN cc_start: 0.7495 (mm-40) cc_final: 0.7114 (mt0) REVERT: A 294 GLU cc_start: 0.7249 (OUTLIER) cc_final: 0.6761 (tt0) REVERT: A 302 ARG cc_start: 0.7604 (mtm110) cc_final: 0.6844 (tmt-80) REVERT: A 303 GLU cc_start: 0.7856 (mp0) cc_final: 0.7502 (mp0) REVERT: A 306 GLN cc_start: 0.7508 (mt0) cc_final: 0.6705 (mp10) REVERT: A 318 SER cc_start: 0.8271 (OUTLIER) cc_final: 0.7917 (m) REVERT: A 381 GLN cc_start: 0.6529 (mp10) cc_final: 0.5662 (mm-40) REVERT: A 409 ARG cc_start: 0.6879 (mtp-110) cc_final: 0.6575 (ttm-80) REVERT: A 421 LEU cc_start: 0.8478 (mm) cc_final: 0.8142 (mp) REVERT: A 448 ASN cc_start: 0.8016 (t0) cc_final: 0.7789 (t0) REVERT: A 491 MET cc_start: 0.7315 (mmm) cc_final: 0.6590 (mmp) REVERT: B 33 ARG cc_start: 0.6389 (ttt90) cc_final: 0.6161 (ttp-170) REVERT: B 35 ARG cc_start: 0.7671 (ttt90) cc_final: 0.7432 (tpt-90) REVERT: B 80 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7434 (pt0) REVERT: B 93 GLU cc_start: 0.7636 (mp0) cc_final: 0.7324 (mp0) REVERT: B 173 VAL cc_start: 0.8245 (t) cc_final: 0.8001 (m) REVERT: B 180 ARG cc_start: 0.7889 (mtt90) cc_final: 0.7660 (mtt-85) REVERT: B 184 GLU cc_start: 0.7422 (mt-10) cc_final: 0.6819 (tp30) REVERT: B 214 GLN cc_start: 0.7482 (mm-40) cc_final: 0.7104 (mt0) REVERT: B 294 GLU cc_start: 0.7274 (OUTLIER) cc_final: 0.6931 (tt0) REVERT: B 302 ARG cc_start: 0.7610 (mtm110) cc_final: 0.6848 (tmt-80) REVERT: B 303 GLU cc_start: 0.7915 (mp0) cc_final: 0.7551 (mp0) REVERT: B 306 GLN cc_start: 0.7512 (mt0) cc_final: 0.6710 (mp10) REVERT: B 318 SER cc_start: 0.8272 (OUTLIER) cc_final: 0.7919 (m) REVERT: B 381 GLN cc_start: 0.6525 (mp10) cc_final: 0.5622 (mm-40) REVERT: B 421 LEU cc_start: 0.8472 (mm) cc_final: 0.8127 (mp) REVERT: B 448 ASN cc_start: 0.8034 (t0) cc_final: 0.7813 (t0) REVERT: B 491 MET cc_start: 0.7316 (mmm) cc_final: 0.6592 (mmp) REVERT: C 33 ARG cc_start: 0.6392 (ttt90) cc_final: 0.6155 (ttp-170) REVERT: C 35 ARG cc_start: 0.7672 (ttt90) cc_final: 0.7435 (tpt-90) REVERT: C 93 GLU cc_start: 0.7563 (mp0) cc_final: 0.7213 (mp0) REVERT: C 184 GLU cc_start: 0.7559 (mt-10) cc_final: 0.6879 (tp30) REVERT: C 214 GLN cc_start: 0.7496 (mm-40) cc_final: 0.7117 (mt0) REVERT: C 294 GLU cc_start: 0.7280 (OUTLIER) cc_final: 0.6925 (tt0) REVERT: C 302 ARG cc_start: 0.7592 (mtm110) cc_final: 0.6790 (tmt-80) REVERT: C 303 GLU cc_start: 0.7855 (mp0) cc_final: 0.7501 (mp0) REVERT: C 306 GLN cc_start: 0.7511 (mt0) cc_final: 0.6706 (mp10) REVERT: C 318 SER cc_start: 0.8275 (OUTLIER) cc_final: 0.7921 (m) REVERT: C 381 GLN cc_start: 0.6524 (mp10) cc_final: 0.5655 (mm-40) REVERT: C 421 LEU cc_start: 0.8480 (mm) cc_final: 0.8143 (mp) REVERT: C 448 ASN cc_start: 0.8034 (t0) cc_final: 0.7811 (t0) REVERT: C 491 MET cc_start: 0.7318 (mmm) cc_final: 0.6592 (mmp) REVERT: D 33 ARG cc_start: 0.6393 (ttt90) cc_final: 0.6154 (ttp-170) REVERT: D 35 ARG cc_start: 0.7647 (ttt90) cc_final: 0.7401 (tpt-90) REVERT: D 74 GLN cc_start: 0.7245 (mt0) cc_final: 0.7005 (mt0) REVERT: D 93 GLU cc_start: 0.7625 (mp0) cc_final: 0.7323 (mp0) REVERT: D 139 ARG cc_start: 0.7787 (mtp180) cc_final: 0.7498 (mtp85) REVERT: D 173 VAL cc_start: 0.8241 (t) cc_final: 0.8001 (m) REVERT: D 184 GLU cc_start: 0.7521 (mt-10) cc_final: 0.6892 (tp30) REVERT: D 214 GLN cc_start: 0.7483 (mm-40) cc_final: 0.7104 (mt0) REVERT: D 294 GLU cc_start: 0.7274 (OUTLIER) cc_final: 0.6937 (tt0) REVERT: D 302 ARG cc_start: 0.7611 (mtm110) cc_final: 0.6850 (tmt-80) REVERT: D 303 GLU cc_start: 0.7914 (mp0) cc_final: 0.7552 (mp0) REVERT: D 306 GLN cc_start: 0.7514 (mt0) cc_final: 0.6710 (mp10) REVERT: D 318 SER cc_start: 0.8270 (OUTLIER) cc_final: 0.7917 (m) REVERT: D 381 GLN cc_start: 0.6558 (mp10) cc_final: 0.5653 (mm-40) REVERT: D 421 LEU cc_start: 0.8474 (mm) cc_final: 0.8129 (mp) REVERT: D 448 ASN cc_start: 0.8013 (t0) cc_final: 0.7788 (t0) REVERT: D 491 MET cc_start: 0.7321 (mmm) cc_final: 0.6596 (mmp) outliers start: 34 outliers final: 20 residues processed: 337 average time/residue: 1.4923 time to fit residues: 563.4679 Evaluate side-chains 334 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 305 time to evaluate : 2.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 323 LYS Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 294 GLU Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 318 SER Chi-restraints excluded: chain B residue 323 LYS Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 548 SER Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 294 GLU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 318 SER Chi-restraints excluded: chain C residue 323 LYS Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 548 SER Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 294 GLU Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 318 SER Chi-restraints excluded: chain D residue 323 LYS Chi-restraints excluded: chain D residue 335 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 141 optimal weight: 1.9990 chunk 227 optimal weight: 2.9990 chunk 139 optimal weight: 9.9990 chunk 108 optimal weight: 2.9990 chunk 158 optimal weight: 0.3980 chunk 239 optimal weight: 0.0170 chunk 220 optimal weight: 0.0570 chunk 190 optimal weight: 5.9990 chunk 19 optimal weight: 9.9990 chunk 147 optimal weight: 3.9990 chunk 116 optimal weight: 0.7980 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN A 261 GLN B 40 GLN B 261 GLN B 572 ASN C 40 GLN C 261 GLN D 40 GLN D 261 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.3067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 20352 Z= 0.151 Angle : 0.491 8.313 27612 Z= 0.242 Chirality : 0.037 0.155 3128 Planarity : 0.004 0.061 3424 Dihedral : 8.417 73.795 3428 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.49 % Allowed : 10.91 % Favored : 87.60 % 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: 1.98 (0.17), residues: 2384 helix: 1.74 (0.13), residues: 1520 sheet: -0.84 (0.48), residues: 80 loop : 0.90 (0.24), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 593 HIS 0.003 0.001 HIS B 380 PHE 0.016 0.001 PHE D 611 TYR 0.009 0.001 TYR C 216 ARG 0.015 0.001 ARG D 409 ********************** 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 351 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 320 time to evaluate : 2.199 Fit side-chains REVERT: A 35 ARG cc_start: 0.7628 (ttt90) cc_final: 0.7364 (tpt-90) REVERT: A 93 GLU cc_start: 0.7505 (mp0) cc_final: 0.7164 (mp0) REVERT: A 180 ARG cc_start: 0.7870 (mtt90) cc_final: 0.7640 (mtt-85) REVERT: A 184 GLU cc_start: 0.7426 (mt-10) cc_final: 0.6828 (tp30) REVERT: A 214 GLN cc_start: 0.7490 (mm-40) cc_final: 0.7092 (mt0) REVERT: A 221 SER cc_start: 0.8794 (t) cc_final: 0.8364 (p) REVERT: A 294 GLU cc_start: 0.7255 (OUTLIER) cc_final: 0.6779 (tt0) REVERT: A 302 ARG cc_start: 0.7585 (mtm110) cc_final: 0.6784 (tmt-80) REVERT: A 303 GLU cc_start: 0.7848 (mp0) cc_final: 0.7508 (mp0) REVERT: A 306 GLN cc_start: 0.7492 (mt0) cc_final: 0.6692 (mp10) REVERT: A 318 SER cc_start: 0.8268 (OUTLIER) cc_final: 0.7924 (m) REVERT: A 381 GLN cc_start: 0.6490 (mp10) cc_final: 0.5619 (mm-40) REVERT: A 409 ARG cc_start: 0.6824 (mtp-110) cc_final: 0.6568 (ttm-80) REVERT: A 421 LEU cc_start: 0.8473 (mm) cc_final: 0.8139 (mp) REVERT: A 448 ASN cc_start: 0.8022 (t0) cc_final: 0.7789 (t0) REVERT: A 491 MET cc_start: 0.7336 (mmm) cc_final: 0.6622 (mmp) REVERT: B 33 ARG cc_start: 0.6386 (ttt90) cc_final: 0.6165 (ttp-170) REVERT: B 35 ARG cc_start: 0.7668 (ttt90) cc_final: 0.7434 (tpt-90) REVERT: B 80 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7398 (pt0) REVERT: B 93 GLU cc_start: 0.7594 (mp0) cc_final: 0.7225 (mp0) REVERT: B 173 VAL cc_start: 0.8234 (t) cc_final: 0.8007 (m) REVERT: B 184 GLU cc_start: 0.7409 (mt-10) cc_final: 0.6795 (tp30) REVERT: B 214 GLN cc_start: 0.7509 (mm-40) cc_final: 0.7143 (mt0) REVERT: B 221 SER cc_start: 0.8780 (t) cc_final: 0.8334 (p) REVERT: B 294 GLU cc_start: 0.7258 (OUTLIER) cc_final: 0.6795 (tt0) REVERT: B 302 ARG cc_start: 0.7591 (mtm110) cc_final: 0.6794 (tmt-80) REVERT: B 303 GLU cc_start: 0.7874 (mp0) cc_final: 0.7523 (mp0) REVERT: B 306 GLN cc_start: 0.7510 (mt0) cc_final: 0.6708 (mp10) REVERT: B 318 SER cc_start: 0.8270 (OUTLIER) cc_final: 0.7927 (m) REVERT: B 381 GLN cc_start: 0.6468 (mp10) cc_final: 0.5642 (mm-40) REVERT: B 409 ARG cc_start: 0.6848 (mtp-110) cc_final: 0.6583 (ttm-80) REVERT: B 421 LEU cc_start: 0.8455 (mm) cc_final: 0.8111 (mp) REVERT: B 448 ASN cc_start: 0.8036 (t0) cc_final: 0.7805 (t0) REVERT: B 491 MET cc_start: 0.7338 (mmm) cc_final: 0.6629 (mmp) REVERT: C 33 ARG cc_start: 0.6380 (ttt90) cc_final: 0.6157 (ttp-170) REVERT: C 35 ARG cc_start: 0.7667 (ttt90) cc_final: 0.7435 (tpt-90) REVERT: C 93 GLU cc_start: 0.7521 (mp0) cc_final: 0.7182 (mp0) REVERT: C 184 GLU cc_start: 0.7476 (mt-10) cc_final: 0.6831 (tp30) REVERT: C 214 GLN cc_start: 0.7511 (mm-40) cc_final: 0.7138 (mt0) REVERT: C 221 SER cc_start: 0.8779 (t) cc_final: 0.8334 (p) REVERT: C 294 GLU cc_start: 0.7259 (OUTLIER) cc_final: 0.6909 (tt0) REVERT: C 302 ARG cc_start: 0.7587 (mtm110) cc_final: 0.6789 (tmt-80) REVERT: C 303 GLU cc_start: 0.7849 (mp0) cc_final: 0.7507 (mp0) REVERT: C 306 GLN cc_start: 0.7507 (mt0) cc_final: 0.6704 (mp10) REVERT: C 318 SER cc_start: 0.8273 (OUTLIER) cc_final: 0.7930 (m) REVERT: C 381 GLN cc_start: 0.6502 (mp10) cc_final: 0.5632 (mm-40) REVERT: C 421 LEU cc_start: 0.8475 (mm) cc_final: 0.8140 (mp) REVERT: C 448 ASN cc_start: 0.8043 (t0) cc_final: 0.7817 (t0) REVERT: C 491 MET cc_start: 0.7363 (mmm) cc_final: 0.6625 (mmp) REVERT: D 33 ARG cc_start: 0.6379 (ttt90) cc_final: 0.6150 (ttp-170) REVERT: D 35 ARG cc_start: 0.7642 (ttt90) cc_final: 0.7372 (tpt-90) REVERT: D 74 GLN cc_start: 0.7288 (mt0) cc_final: 0.7047 (mt0) REVERT: D 93 GLU cc_start: 0.7575 (mp0) cc_final: 0.7211 (mp0) REVERT: D 139 ARG cc_start: 0.7780 (mtp180) cc_final: 0.7490 (mtp85) REVERT: D 173 VAL cc_start: 0.8216 (t) cc_final: 0.8000 (m) REVERT: D 184 GLU cc_start: 0.7497 (mt-10) cc_final: 0.6856 (tp30) REVERT: D 214 GLN cc_start: 0.7516 (mm-40) cc_final: 0.7153 (mt0) REVERT: D 221 SER cc_start: 0.8754 (t) cc_final: 0.8319 (p) REVERT: D 294 GLU cc_start: 0.7259 (OUTLIER) cc_final: 0.6799 (tt0) REVERT: D 302 ARG cc_start: 0.7578 (mtm110) cc_final: 0.6779 (tmt-80) REVERT: D 303 GLU cc_start: 0.7876 (mp0) cc_final: 0.7525 (mp0) REVERT: D 306 GLN cc_start: 0.7510 (mt0) cc_final: 0.6708 (mp10) REVERT: D 318 SER cc_start: 0.8268 (OUTLIER) cc_final: 0.7925 (m) REVERT: D 381 GLN cc_start: 0.6494 (mp10) cc_final: 0.5630 (mm-40) REVERT: D 409 ARG cc_start: 0.6827 (mtp-110) cc_final: 0.6556 (ttm-80) REVERT: D 421 LEU cc_start: 0.8467 (mm) cc_final: 0.8129 (mp) REVERT: D 448 ASN cc_start: 0.8042 (t0) cc_final: 0.7821 (t0) REVERT: D 491 MET cc_start: 0.7367 (mmm) cc_final: 0.6628 (mmp) outliers start: 31 outliers final: 20 residues processed: 341 average time/residue: 1.4091 time to fit residues: 539.3523 Evaluate side-chains 336 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 307 time to evaluate : 2.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 323 LYS Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 294 GLU Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 318 SER Chi-restraints excluded: chain B residue 323 LYS Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 548 SER Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 294 GLU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 318 SER Chi-restraints excluded: chain C residue 323 LYS Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 548 SER Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 294 GLU Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 318 SER Chi-restraints excluded: chain D residue 323 LYS Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 548 SER 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: 2.9990 chunk 58 optimal weight: 2.9990 chunk 175 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 190 optimal weight: 7.9990 chunk 79 optimal weight: 10.0000 chunk 195 optimal weight: 0.9990 chunk 24 optimal weight: 4.9990 chunk 35 optimal weight: 0.7980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN A 261 GLN B 40 GLN B 261 GLN C 40 GLN C 261 GLN D 40 GLN D 261 GLN D 572 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.147948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.109167 restraints weight = 22010.629| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 1.60 r_work: 0.3022 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20352 Z= 0.214 Angle : 0.520 10.391 27612 Z= 0.257 Chirality : 0.038 0.168 3128 Planarity : 0.004 0.061 3424 Dihedral : 8.632 75.271 3428 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.44 % Allowed : 11.35 % Favored : 87.21 % 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: 1.83 (0.17), residues: 2384 helix: 1.62 (0.13), residues: 1520 sheet: -0.95 (0.48), residues: 80 loop : 0.86 (0.24), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 593 HIS 0.004 0.001 HIS D 201 PHE 0.016 0.001 PHE B 611 TYR 0.009 0.001 TYR A 89 ARG 0.013 0.001 ARG B 409 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8216.81 seconds wall clock time: 147 minutes 52.71 seconds (8872.71 seconds total)