Starting phenix.real_space_refine on Mon Jul 22 22:53:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tf2_41217/07_2024/8tf2_41217.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tf2_41217/07_2024/8tf2_41217.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tf2_41217/07_2024/8tf2_41217.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tf2_41217/07_2024/8tf2_41217.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tf2_41217/07_2024/8tf2_41217.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tf2_41217/07_2024/8tf2_41217.cif" } resolution = 2.57 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.056 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 136 5.16 5 C 13000 2.51 5 N 3260 2.21 5 O 3456 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 33": "NH1" <-> "NH2" Residue "A ARG 35": "NH1" <-> "NH2" Residue "A ARG 43": "NH1" <-> "NH2" Residue "A ARG 45": "NH1" <-> "NH2" Residue "A ARG 59": "NH1" <-> "NH2" Residue "A ARG 75": "NH1" <-> "NH2" Residue "A ARG 134": "NH1" <-> "NH2" Residue "A ARG 139": "NH1" <-> "NH2" Residue "A ARG 146": "NH1" <-> "NH2" Residue "A ARG 153": "NH1" <-> "NH2" Residue "A ARG 154": "NH1" <-> "NH2" Residue "A ARG 180": "NH1" <-> "NH2" Residue "A ARG 190": "NH1" <-> "NH2" Residue "A ARG 263": "NH1" <-> "NH2" Residue "A ARG 302": "NH1" <-> "NH2" Residue "A ARG 305": "NH1" <-> "NH2" Residue "A GLU 315": "OE1" <-> "OE2" Residue "A ARG 326": "NH1" <-> "NH2" Residue "A ARG 350": "NH1" <-> "NH2" Residue "A ARG 355": "NH1" <-> "NH2" Residue "A ARG 359": "NH1" <-> "NH2" Residue "A ARG 363": "NH1" <-> "NH2" Residue "A ARG 385": "NH1" <-> "NH2" Residue "A ARG 409": "NH1" <-> "NH2" Residue "A ARG 414": "NH1" <-> "NH2" Residue "A ARG 443": "NH1" <-> "NH2" Residue "A ARG 470": "NH1" <-> "NH2" Residue "A ARG 492": "NH1" <-> "NH2" Residue "A ARG 584": "NH1" <-> "NH2" Residue "A ARG 589": "NH1" <-> "NH2" Residue "A ARG 594": "NH1" <-> "NH2" Residue "A ARG 606": "NH1" <-> "NH2" Residue "A ARG 610": "NH1" <-> "NH2" Residue "A ARG 615": "NH1" <-> "NH2" Residue "A ARG 628": "NH1" <-> "NH2" Residue "A ARG 632": "NH1" <-> "NH2" Residue "B ARG 33": "NH1" <-> "NH2" Residue "B ARG 35": "NH1" <-> "NH2" Residue "B ARG 43": "NH1" <-> "NH2" Residue "B ARG 45": "NH1" <-> "NH2" Residue "B ARG 59": "NH1" <-> "NH2" Residue "B ARG 75": "NH1" <-> "NH2" Residue "B ARG 134": "NH1" <-> "NH2" Residue "B ARG 139": "NH1" <-> "NH2" Residue "B ARG 146": "NH1" <-> "NH2" Residue "B ARG 153": "NH1" <-> "NH2" Residue "B ARG 154": "NH1" <-> "NH2" Residue "B ARG 180": "NH1" <-> "NH2" Residue "B ARG 190": "NH1" <-> "NH2" Residue "B ARG 263": "NH1" <-> "NH2" Residue "B ARG 302": "NH1" <-> "NH2" Residue "B ARG 305": "NH1" <-> "NH2" Residue "B GLU 315": "OE1" <-> "OE2" Residue "B ARG 326": "NH1" <-> "NH2" Residue "B ARG 350": "NH1" <-> "NH2" Residue "B ARG 355": "NH1" <-> "NH2" Residue "B ARG 359": "NH1" <-> "NH2" Residue "B ARG 363": "NH1" <-> "NH2" Residue "B ARG 385": "NH1" <-> "NH2" Residue "B ARG 409": "NH1" <-> "NH2" Residue "B ARG 414": "NH1" <-> "NH2" Residue "B ARG 443": "NH1" <-> "NH2" Residue "B ARG 470": "NH1" <-> "NH2" Residue "B ARG 492": "NH1" <-> "NH2" Residue "B ARG 584": "NH1" <-> "NH2" Residue "B ARG 589": "NH1" <-> "NH2" Residue "B ARG 594": "NH1" <-> "NH2" Residue "B ARG 606": "NH1" <-> "NH2" Residue "B ARG 610": "NH1" <-> "NH2" Residue "B ARG 615": "NH1" <-> "NH2" Residue "B ARG 628": "NH1" <-> "NH2" Residue "B ARG 632": "NH1" <-> "NH2" Residue "C ARG 33": "NH1" <-> "NH2" Residue "C ARG 35": "NH1" <-> "NH2" Residue "C ARG 43": "NH1" <-> "NH2" Residue "C ARG 45": "NH1" <-> "NH2" Residue "C ARG 59": "NH1" <-> "NH2" Residue "C ARG 75": "NH1" <-> "NH2" Residue "C ARG 134": "NH1" <-> "NH2" Residue "C ARG 139": "NH1" <-> "NH2" Residue "C ARG 146": "NH1" <-> "NH2" Residue "C ARG 153": "NH1" <-> "NH2" Residue "C ARG 154": "NH1" <-> "NH2" Residue "C ARG 180": "NH1" <-> "NH2" Residue "C ARG 190": "NH1" <-> "NH2" Residue "C ARG 263": "NH1" <-> "NH2" Residue "C ARG 302": "NH1" <-> "NH2" Residue "C ARG 305": "NH1" <-> "NH2" Residue "C GLU 315": "OE1" <-> "OE2" Residue "C ARG 326": "NH1" <-> "NH2" Residue "C ARG 350": "NH1" <-> "NH2" Residue "C ARG 355": "NH1" <-> "NH2" Residue "C ARG 359": "NH1" <-> "NH2" Residue "C ARG 363": "NH1" <-> "NH2" Residue "C ARG 385": "NH1" <-> "NH2" Residue "C ARG 409": "NH1" <-> "NH2" Residue "C ARG 414": "NH1" <-> "NH2" Residue "C ARG 443": "NH1" <-> "NH2" Residue "C ARG 470": "NH1" <-> "NH2" Residue "C ARG 492": "NH1" <-> "NH2" Residue "C ARG 584": "NH1" <-> "NH2" Residue "C ARG 589": "NH1" <-> "NH2" Residue "C ARG 594": "NH1" <-> "NH2" Residue "C ARG 606": "NH1" <-> "NH2" Residue "C ARG 610": "NH1" <-> "NH2" Residue "C ARG 615": "NH1" <-> "NH2" Residue "C ARG 628": "NH1" <-> "NH2" Residue "C ARG 632": "NH1" <-> "NH2" Residue "D ARG 33": "NH1" <-> "NH2" Residue "D ARG 35": "NH1" <-> "NH2" Residue "D ARG 43": "NH1" <-> "NH2" Residue "D ARG 45": "NH1" <-> "NH2" Residue "D ARG 59": "NH1" <-> "NH2" Residue "D ARG 75": "NH1" <-> "NH2" Residue "D ARG 134": "NH1" <-> "NH2" Residue "D ARG 139": "NH1" <-> "NH2" Residue "D ARG 146": "NH1" <-> "NH2" Residue "D ARG 153": "NH1" <-> "NH2" Residue "D ARG 154": "NH1" <-> "NH2" Residue "D ARG 180": "NH1" <-> "NH2" Residue "D ARG 190": "NH1" <-> "NH2" Residue "D ARG 263": "NH1" <-> "NH2" Residue "D ARG 302": "NH1" <-> "NH2" Residue "D ARG 305": "NH1" <-> "NH2" Residue "D GLU 315": "OE1" <-> "OE2" Residue "D ARG 326": "NH1" <-> "NH2" Residue "D ARG 350": "NH1" <-> "NH2" Residue "D ARG 355": "NH1" <-> "NH2" Residue "D ARG 359": "NH1" <-> "NH2" Residue "D ARG 363": "NH1" <-> "NH2" Residue "D ARG 385": "NH1" <-> "NH2" Residue "D ARG 409": "NH1" <-> "NH2" Residue "D ARG 414": "NH1" <-> "NH2" Residue "D ARG 443": "NH1" <-> "NH2" Residue "D ARG 470": "NH1" <-> "NH2" Residue "D ARG 492": "NH1" <-> "NH2" Residue "D ARG 584": "NH1" <-> "NH2" Residue "D ARG 589": "NH1" <-> "NH2" Residue "D ARG 594": "NH1" <-> "NH2" Residue "D ARG 606": "NH1" <-> "NH2" Residue "D ARG 610": "NH1" <-> "NH2" Residue "D ARG 615": "NH1" <-> "NH2" Residue "D ARG 628": "NH1" <-> "NH2" Residue "D ARG 632": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 19856 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 602, 4822 Classifications: {'peptide': 602} Link IDs: {'PTRANS': 24, 'TRANS': 577} Chain breaks: 2 Chain: "B" Number of atoms: 4822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 602, 4822 Classifications: {'peptide': 602} Link IDs: {'PTRANS': 24, 'TRANS': 577} Chain breaks: 2 Chain: "C" Number of atoms: 4822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 602, 4822 Classifications: {'peptide': 602} Link IDs: {'PTRANS': 24, 'TRANS': 577} Chain breaks: 2 Chain: "D" Number of atoms: 4822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 602, 4822 Classifications: {'peptide': 602} Link IDs: {'PTRANS': 24, 'TRANS': 577} Chain breaks: 2 Chain: "A" Number of atoms: 171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 171 Unusual residues: {'CPL': 6, 'ERG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 199 Unresolved non-hydrogen angles: 244 Unresolved non-hydrogen dihedrals: 179 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'CPL:plan-4': 6, 'CPL:plan-3': 6, 'CPL:plan-2': 5, 'CPL:plan-1': 5} Unresolved non-hydrogen planarities: 78 Chain: "B" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 129 Unusual residues: {'CPL': 3, 'ERG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CPL:plan-4': 3, 'CPL:plan-3': 3, 'CPL:plan-2': 2, 'CPL:plan-1': 2} Unresolved non-hydrogen planarities: 36 Chain: "C" Number of atoms: 155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 155 Unusual residues: {'CPL': 5, 'ERG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 163 Unresolved non-hydrogen angles: 199 Unresolved non-hydrogen dihedrals: 147 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'CPL:plan-4': 5, 'CPL:plan-3': 5, 'CPL:plan-2': 4, 'CPL:plan-1': 4} Unresolved non-hydrogen planarities: 64 Chain: "D" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 113 Unusual residues: {'CPL': 2, 'ERG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'CPL:plan-4': 2, 'CPL:plan-3': 2, 'CPL:plan-2': 1, 'CPL:plan-1': 1} Unresolved non-hydrogen planarities: 22 Time building chain proxies: 10.70, per 1000 atoms: 0.54 Number of scatterers: 19856 At special positions: 0 Unit cell: (138.61, 138.61, 121.18, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 136 16.00 P 4 15.00 O 3456 8.00 N 3260 7.00 C 13000 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.53 Conformation dependent library (CDL) restraints added in 3.2 seconds 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4544 Finding SS restraints... Secondary structure from input PDB file: 140 helices and 8 sheets defined 72.3% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.87 Creating SS restraints... Processing helix chain 'A' and resid 28 through 46 Processing helix chain 'A' and resid 47 through 56 Processing helix chain 'A' and resid 57 through 67 removed outlier: 3.822A pdb=" N ASN A 67 " --> pdb=" O ILE A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 89 Processing helix chain 'A' and resid 91 through 102 Processing helix chain 'A' and resid 103 through 108 Processing helix chain 'A' and resid 112 through 116 removed outlier: 3.714A pdb=" N VAL A 116 " --> pdb=" O GLU A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 127 Processing helix chain 'A' and resid 129 through 138 Processing helix chain 'A' and resid 149 through 153 removed outlier: 3.620A pdb=" N ARG A 153 " --> pdb=" O ALA A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 174 Processing helix chain 'A' and resid 175 through 185 Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 208 through 221 Processing helix chain 'A' and resid 231 through 235 Processing helix chain 'A' and resid 242 through 250 Processing helix chain 'A' and resid 252 through 261 removed outlier: 3.575A pdb=" N GLN A 261 " --> pdb=" O GLN A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 285 Processing helix chain 'A' and resid 291 through 298 Processing helix chain 'A' and resid 303 through 308 removed outlier: 4.032A pdb=" N ILE A 307 " --> pdb=" O GLU A 303 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LEU A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 303 through 308' Processing helix chain 'A' and resid 310 through 324 Processing helix chain 'A' and resid 324 through 349 Processing helix chain 'A' and resid 372 through 377 removed outlier: 3.983A pdb=" N TYR A 377 " --> pdb=" O LEU A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 411 Proline residue: A 405 - end of helix removed outlier: 3.516A pdb=" N PHE A 408 " --> pdb=" O ILE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 418 Processing helix chain 'A' and resid 422 through 445 Processing helix chain 'A' and resid 450 through 465 removed outlier: 3.631A pdb=" N VAL A 465 " --> pdb=" O GLY A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 472 Processing helix chain 'A' and resid 475 through 488 Processing helix chain 'A' and resid 488 through 513 removed outlier: 3.503A pdb=" N LEU A 496 " --> pdb=" O ARG A 492 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL A 499 " --> pdb=" O TRP A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 538 Processing helix chain 'A' and resid 552 through 566 removed outlier: 3.855A pdb=" N CYS A 556 " --> pdb=" O PRO A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 608 removed outlier: 3.740A pdb=" N ILE A 575 " --> pdb=" O LEU A 571 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TRP A 583 " --> pdb=" O GLY A 579 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ARG A 584 " --> pdb=" O ASP A 580 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N GLN A 587 " --> pdb=" O TRP A 583 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N GLU A 588 " --> pdb=" O ARG A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 613 Processing helix chain 'A' and resid 621 through 624 removed outlier: 3.677A pdb=" N GLY A 624 " --> pdb=" O TYR A 621 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 621 through 624' Processing helix chain 'B' and resid 29 through 46 Processing helix chain 'B' and resid 47 through 56 Processing helix chain 'B' and resid 57 through 67 removed outlier: 3.822A pdb=" N ASN B 67 " --> pdb=" O ILE B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 89 Processing helix chain 'B' and resid 91 through 102 Processing helix chain 'B' and resid 103 through 108 Processing helix chain 'B' and resid 112 through 116 removed outlier: 3.714A pdb=" N VAL B 116 " --> pdb=" O GLU B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 127 Processing helix chain 'B' and resid 129 through 138 Processing helix chain 'B' and resid 149 through 153 removed outlier: 3.620A pdb=" N ARG B 153 " --> pdb=" O ALA B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 174 Processing helix chain 'B' and resid 175 through 185 Processing helix chain 'B' and resid 198 through 205 Processing helix chain 'B' and resid 208 through 221 Processing helix chain 'B' and resid 231 through 235 Processing helix chain 'B' and resid 242 through 250 Processing helix chain 'B' and resid 252 through 261 removed outlier: 3.575A pdb=" N GLN B 261 " --> pdb=" O GLN B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 285 Processing helix chain 'B' and resid 291 through 298 Processing helix chain 'B' and resid 303 through 308 removed outlier: 4.032A pdb=" N ILE B 307 " --> pdb=" O GLU B 303 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LEU B 308 " --> pdb=" O ALA B 304 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 303 through 308' Processing helix chain 'B' and resid 310 through 324 Processing helix chain 'B' and resid 324 through 349 Processing helix chain 'B' and resid 372 through 377 removed outlier: 3.983A pdb=" N TYR B 377 " --> pdb=" O LEU B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 411 Proline residue: B 405 - end of helix removed outlier: 3.516A pdb=" N PHE B 408 " --> pdb=" O ILE B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 418 Processing helix chain 'B' and resid 422 through 445 Processing helix chain 'B' and resid 450 through 465 removed outlier: 3.631A pdb=" N VAL B 465 " --> pdb=" O GLY B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 472 Processing helix chain 'B' and resid 475 through 488 Processing helix chain 'B' and resid 488 through 513 removed outlier: 3.503A pdb=" N LEU B 496 " --> pdb=" O ARG B 492 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL B 499 " --> pdb=" O TRP B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 538 Processing helix chain 'B' and resid 552 through 566 removed outlier: 3.855A pdb=" N CYS B 556 " --> pdb=" O PRO B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 608 removed outlier: 3.740A pdb=" N ILE B 575 " --> pdb=" O LEU B 571 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TRP B 583 " --> pdb=" O GLY B 579 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ARG B 584 " --> pdb=" O ASP B 580 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N GLN B 587 " --> pdb=" O TRP B 583 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N GLU B 588 " --> pdb=" O ARG B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 609 through 613 Processing helix chain 'B' and resid 621 through 624 removed outlier: 3.677A pdb=" N GLY B 624 " --> pdb=" O TYR B 621 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 621 through 624' Processing helix chain 'C' and resid 29 through 46 Processing helix chain 'C' and resid 47 through 56 Processing helix chain 'C' and resid 57 through 67 removed outlier: 3.822A pdb=" N ASN C 67 " --> pdb=" O ILE C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 91 through 102 Processing helix chain 'C' and resid 103 through 108 Processing helix chain 'C' and resid 112 through 116 removed outlier: 3.714A pdb=" N VAL C 116 " --> pdb=" O GLU C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 127 Processing helix chain 'C' and resid 129 through 138 Processing helix chain 'C' and resid 149 through 153 removed outlier: 3.621A pdb=" N ARG C 153 " --> pdb=" O ALA C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 174 Processing helix chain 'C' and resid 175 through 185 Processing helix chain 'C' and resid 198 through 205 Processing helix chain 'C' and resid 208 through 221 Processing helix chain 'C' and resid 231 through 235 Processing helix chain 'C' and resid 242 through 250 Processing helix chain 'C' and resid 252 through 261 removed outlier: 3.576A pdb=" N GLN C 261 " --> pdb=" O GLN C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 285 Processing helix chain 'C' and resid 291 through 298 Processing helix chain 'C' and resid 303 through 308 removed outlier: 4.032A pdb=" N ILE C 307 " --> pdb=" O GLU C 303 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LEU C 308 " --> pdb=" O ALA C 304 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 303 through 308' Processing helix chain 'C' and resid 310 through 324 Processing helix chain 'C' and resid 324 through 349 Processing helix chain 'C' and resid 372 through 377 removed outlier: 3.983A pdb=" N TYR C 377 " --> pdb=" O LEU C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 411 Proline residue: C 405 - end of helix removed outlier: 3.516A pdb=" N PHE C 408 " --> pdb=" O ILE C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 418 Processing helix chain 'C' and resid 422 through 445 Processing helix chain 'C' and resid 450 through 465 removed outlier: 3.631A pdb=" N VAL C 465 " --> pdb=" O GLY C 461 " (cutoff:3.500A) Processing helix chain 'C' and resid 466 through 472 Processing helix chain 'C' and resid 475 through 488 Processing helix chain 'C' and resid 488 through 513 removed outlier: 3.503A pdb=" N LEU C 496 " --> pdb=" O ARG C 492 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL C 499 " --> pdb=" O TRP C 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 525 through 538 Processing helix chain 'C' and resid 552 through 566 removed outlier: 3.855A pdb=" N CYS C 556 " --> pdb=" O PRO C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 608 removed outlier: 3.740A pdb=" N ILE C 575 " --> pdb=" O LEU C 571 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TRP C 583 " --> pdb=" O GLY C 579 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ARG C 584 " --> pdb=" O ASP C 580 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N GLN C 587 " --> pdb=" O TRP C 583 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N GLU C 588 " --> pdb=" O ARG C 584 " (cutoff:3.500A) Processing helix chain 'C' and resid 609 through 613 Processing helix chain 'C' and resid 621 through 624 removed outlier: 3.677A pdb=" N GLY C 624 " --> pdb=" O TYR C 621 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 621 through 624' Processing helix chain 'D' and resid 29 through 46 Processing helix chain 'D' and resid 47 through 56 Processing helix chain 'D' and resid 57 through 67 removed outlier: 3.822A pdb=" N ASN D 67 " --> pdb=" O ILE D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 89 Processing helix chain 'D' and resid 91 through 102 Processing helix chain 'D' and resid 103 through 108 Processing helix chain 'D' and resid 112 through 116 removed outlier: 3.714A pdb=" N VAL D 116 " --> pdb=" O GLU D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 127 Processing helix chain 'D' and resid 129 through 138 Processing helix chain 'D' and resid 149 through 153 removed outlier: 3.619A pdb=" N ARG D 153 " --> pdb=" O ALA D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 174 Processing helix chain 'D' and resid 175 through 185 Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 208 through 221 Processing helix chain 'D' and resid 231 through 235 Processing helix chain 'D' and resid 242 through 250 Processing helix chain 'D' and resid 252 through 261 removed outlier: 3.575A pdb=" N GLN D 261 " --> pdb=" O GLN D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 285 Processing helix chain 'D' and resid 291 through 298 Processing helix chain 'D' and resid 303 through 308 removed outlier: 4.032A pdb=" N ILE D 307 " --> pdb=" O GLU D 303 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LEU D 308 " --> pdb=" O ALA D 304 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 303 through 308' Processing helix chain 'D' and resid 310 through 324 Processing helix chain 'D' and resid 324 through 349 Processing helix chain 'D' and resid 372 through 377 removed outlier: 3.983A pdb=" N TYR D 377 " --> pdb=" O LEU D 373 " (cutoff:3.500A) Processing helix chain 'D' and resid 379 through 411 Proline residue: D 405 - end of helix removed outlier: 3.516A pdb=" N PHE D 408 " --> pdb=" O ILE D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 418 Processing helix chain 'D' and resid 422 through 445 Processing helix chain 'D' and resid 450 through 465 removed outlier: 3.631A pdb=" N VAL D 465 " --> pdb=" O GLY D 461 " (cutoff:3.500A) Processing helix chain 'D' and resid 466 through 472 Processing helix chain 'D' and resid 475 through 488 Processing helix chain 'D' and resid 488 through 513 removed outlier: 3.503A pdb=" N LEU D 496 " --> pdb=" O ARG D 492 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL D 499 " --> pdb=" O TRP D 495 " (cutoff:3.500A) Processing helix chain 'D' and resid 525 through 538 Processing helix chain 'D' and resid 552 through 566 removed outlier: 3.855A pdb=" N CYS D 556 " --> pdb=" O PRO D 552 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 608 removed outlier: 3.740A pdb=" N ILE D 575 " --> pdb=" O LEU D 571 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TRP D 583 " --> pdb=" O GLY D 579 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ARG D 584 " --> pdb=" O ASP D 580 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N GLN D 587 " --> pdb=" O TRP D 583 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N GLU D 588 " --> pdb=" O ARG D 584 " (cutoff:3.500A) Processing helix chain 'D' and resid 609 through 613 Processing helix chain 'D' and resid 621 through 624 removed outlier: 3.677A pdb=" N GLY D 624 " --> pdb=" O TYR D 621 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 621 through 624' Processing sheet with id=AA1, first strand: chain 'A' and resid 264 through 270 removed outlier: 6.616A pdb=" N LYS A 264 " --> pdb=" O ASP A 279 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ASP A 279 " --> pdb=" O LYS A 264 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N VAL A 266 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LEU A 277 " --> pdb=" O VAL A 266 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 352 through 354 Processing sheet with id=AA3, first strand: chain 'B' and resid 264 through 270 removed outlier: 6.616A pdb=" N LYS B 264 " --> pdb=" O ASP B 279 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ASP B 279 " --> pdb=" O LYS B 264 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N VAL B 266 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LEU B 277 " --> pdb=" O VAL B 266 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 352 through 354 Processing sheet with id=AA5, first strand: chain 'C' and resid 264 through 270 removed outlier: 6.616A pdb=" N LYS C 264 " --> pdb=" O ASP C 279 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ASP C 279 " --> pdb=" O LYS C 264 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N VAL C 266 " --> pdb=" O LEU C 277 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N LEU C 277 " --> pdb=" O VAL C 266 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 352 through 354 Processing sheet with id=AA7, first strand: chain 'D' and resid 264 through 270 removed outlier: 6.617A pdb=" N LYS D 264 " --> pdb=" O ASP D 279 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ASP D 279 " --> pdb=" O LYS D 264 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N VAL D 266 " --> pdb=" O LEU D 277 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LEU D 277 " --> pdb=" O VAL D 266 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 352 through 354 1181 hydrogen bonds defined for protein. 3363 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.94 Time building geometry restraints manager: 8.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3691 1.32 - 1.45: 4765 1.45 - 1.57: 11608 1.57 - 1.70: 16 1.70 - 1.82: 224 Bond restraints: 20304 Sorted by residual: bond pdb=" N ARG D 263 " pdb=" CA ARG D 263 " ideal model delta sigma weight residual 1.457 1.498 -0.041 1.19e-02 7.06e+03 1.18e+01 bond pdb=" N ARG B 263 " pdb=" CA ARG B 263 " ideal model delta sigma weight residual 1.457 1.498 -0.041 1.19e-02 7.06e+03 1.18e+01 bond pdb=" N ARG C 263 " pdb=" CA ARG C 263 " ideal model delta sigma weight residual 1.457 1.498 -0.041 1.19e-02 7.06e+03 1.18e+01 bond pdb=" N ARG A 263 " pdb=" CA ARG A 263 " ideal model delta sigma weight residual 1.457 1.498 -0.041 1.19e-02 7.06e+03 1.18e+01 bond pdb=" C ARG D 326 " pdb=" O ARG D 326 " ideal model delta sigma weight residual 1.244 1.211 0.033 1.00e-02 1.00e+04 1.08e+01 ... (remaining 20299 not shown) Histogram of bond angle deviations from ideal: 97.62 - 105.09: 412 105.09 - 112.55: 9181 112.55 - 120.02: 9639 120.02 - 127.48: 8124 127.48 - 134.95: 164 Bond angle restraints: 27520 Sorted by residual: angle pdb=" CB HIS B 84 " pdb=" CG HIS B 84 " pdb=" CD2 HIS B 84 " ideal model delta sigma weight residual 131.20 124.46 6.74 1.30e+00 5.92e-01 2.69e+01 angle pdb=" CB HIS C 84 " pdb=" CG HIS C 84 " pdb=" CD2 HIS C 84 " ideal model delta sigma weight residual 131.20 124.49 6.71 1.30e+00 5.92e-01 2.66e+01 angle pdb=" CB HIS A 84 " pdb=" CG HIS A 84 " pdb=" CD2 HIS A 84 " ideal model delta sigma weight residual 131.20 124.49 6.71 1.30e+00 5.92e-01 2.66e+01 angle pdb=" CB HIS D 84 " pdb=" CG HIS D 84 " pdb=" CD2 HIS D 84 " ideal model delta sigma weight residual 131.20 124.56 6.64 1.30e+00 5.92e-01 2.61e+01 angle pdb=" CA ASP C 57 " pdb=" CB ASP C 57 " pdb=" CG ASP C 57 " ideal model delta sigma weight residual 112.60 117.61 -5.01 1.00e+00 1.00e+00 2.51e+01 ... (remaining 27515 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.18: 12282 35.18 - 70.36: 217 70.36 - 105.54: 25 105.54 - 140.71: 4 140.71 - 175.89: 12 Dihedral angle restraints: 12540 sinusoidal: 5512 harmonic: 7028 Sorted by residual: dihedral pdb=" CA CYS D 112 " pdb=" C CYS D 112 " pdb=" N GLU D 113 " pdb=" CA GLU D 113 " ideal model delta harmonic sigma weight residual -180.00 -152.20 -27.80 0 5.00e+00 4.00e-02 3.09e+01 dihedral pdb=" CA CYS C 112 " pdb=" C CYS C 112 " pdb=" N GLU C 113 " pdb=" CA GLU C 113 " ideal model delta harmonic sigma weight residual -180.00 -152.21 -27.79 0 5.00e+00 4.00e-02 3.09e+01 dihedral pdb=" CA CYS B 112 " pdb=" C CYS B 112 " pdb=" N GLU B 113 " pdb=" CA GLU B 113 " ideal model delta harmonic sigma weight residual 180.00 -152.24 -27.76 0 5.00e+00 4.00e-02 3.08e+01 ... (remaining 12537 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1639 0.058 - 0.115: 985 0.115 - 0.173: 355 0.173 - 0.230: 101 0.230 - 0.287: 44 Chirality restraints: 3124 Sorted by residual: chirality pdb=" CA THR B 567 " pdb=" N THR B 567 " pdb=" C THR B 567 " pdb=" CB THR B 567 " both_signs ideal model delta sigma weight residual False 2.53 2.24 0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" CA THR C 567 " pdb=" N THR C 567 " pdb=" C THR C 567 " pdb=" CB THR C 567 " both_signs ideal model delta sigma weight residual False 2.53 2.24 0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" CA THR A 567 " pdb=" N THR A 567 " pdb=" C THR A 567 " pdb=" CB THR A 567 " both_signs ideal model delta sigma weight residual False 2.53 2.24 0.28 2.00e-01 2.50e+01 2.00e+00 ... (remaining 3121 not shown) Planarity restraints: 3404 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 593 " 0.140 2.00e-02 2.50e+03 6.56e-02 1.08e+02 pdb=" CG TRP C 593 " -0.064 2.00e-02 2.50e+03 pdb=" CD1 TRP C 593 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 TRP C 593 " -0.073 2.00e-02 2.50e+03 pdb=" NE1 TRP C 593 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP C 593 " -0.014 2.00e-02 2.50e+03 pdb=" CE3 TRP C 593 " -0.074 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 593 " 0.057 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 593 " -0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP C 593 " 0.065 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 593 " -0.140 2.00e-02 2.50e+03 6.56e-02 1.08e+02 pdb=" CG TRP D 593 " 0.064 2.00e-02 2.50e+03 pdb=" CD1 TRP D 593 " 0.030 2.00e-02 2.50e+03 pdb=" CD2 TRP D 593 " 0.074 2.00e-02 2.50e+03 pdb=" NE1 TRP D 593 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP D 593 " 0.014 2.00e-02 2.50e+03 pdb=" CE3 TRP D 593 " 0.073 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 593 " -0.057 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 593 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP D 593 " -0.065 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 593 " -0.140 2.00e-02 2.50e+03 6.55e-02 1.07e+02 pdb=" CG TRP A 593 " 0.064 2.00e-02 2.50e+03 pdb=" CD1 TRP A 593 " 0.030 2.00e-02 2.50e+03 pdb=" CD2 TRP A 593 " 0.073 2.00e-02 2.50e+03 pdb=" NE1 TRP A 593 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 593 " 0.014 2.00e-02 2.50e+03 pdb=" CE3 TRP A 593 " 0.073 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 593 " -0.057 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 593 " 0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP A 593 " -0.065 2.00e-02 2.50e+03 ... (remaining 3401 not shown) Histogram of nonbonded interaction distances: 2.48 - 2.97: 8464 2.97 - 3.45: 21137 3.45 - 3.93: 35760 3.93 - 4.42: 39821 4.42 - 4.90: 65999 Nonbonded interactions: 171181 Sorted by model distance: nonbonded pdb=" OD1 ASP C 489 " pdb=" NH1 ARG C 492 " model vdw 2.484 2.520 nonbonded pdb=" OD1 ASP B 489 " pdb=" NH1 ARG B 492 " model vdw 2.484 2.520 nonbonded pdb=" OD1 ASP A 489 " pdb=" NH1 ARG A 492 " model vdw 2.484 2.520 nonbonded pdb=" OD1 ASP D 489 " pdb=" NH1 ARG D 492 " model vdw 2.484 2.520 nonbonded pdb=" O THR D 311 " pdb=" OE1 GLU D 315 " model vdw 2.513 3.040 ... (remaining 171176 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 28 through 637 or resid 802 or resid 804)) selection = (chain 'B' and (resid 28 through 637 or resid 802 or resid 804)) selection = (chain 'C' and (resid 28 through 637 or resid 802 or resid 804)) selection = (chain 'D' and (resid 28 through 637 or resid 802 or resid 804)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.810 Check model and map are aligned: 0.140 Set scattering table: 0.200 Process input model: 49.390 Find NCS groups from input model: 1.300 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.059 20304 Z= 0.770 Angle : 1.754 10.363 27520 Z= 1.197 Chirality : 0.086 0.287 3124 Planarity : 0.013 0.066 3404 Dihedral : 15.410 175.892 7996 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 0.38 % Allowed : 0.82 % Favored : 98.80 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.16), residues: 2384 helix: -0.12 (0.12), residues: 1480 sheet: 1.03 (0.54), residues: 76 loop : 1.13 (0.24), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.140 0.021 TRP C 593 HIS 0.010 0.004 HIS C 582 PHE 0.066 0.015 PHE B 256 TYR 0.110 0.024 TYR C 336 ARG 0.006 0.001 ARG D 492 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 419 time to evaluate : 2.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 GLU cc_start: 0.6799 (mt-10) cc_final: 0.6434 (mm-30) REVERT: A 74 GLN cc_start: 0.7343 (mt0) cc_final: 0.7083 (mt0) REVERT: A 99 MET cc_start: 0.7200 (mtm) cc_final: 0.6779 (mtm) REVERT: A 104 GLU cc_start: 0.7429 (pm20) cc_final: 0.6315 (tm-30) REVERT: A 107 LYS cc_start: 0.7095 (mttt) cc_final: 0.6510 (mttp) REVERT: A 155 SER cc_start: 0.7753 (m) cc_final: 0.7490 (p) REVERT: A 176 GLU cc_start: 0.6993 (tt0) cc_final: 0.6463 (mt-10) REVERT: A 194 SER cc_start: 0.8516 (m) cc_final: 0.8209 (p) REVERT: A 257 GLN cc_start: 0.7456 (pt0) cc_final: 0.6604 (tp-100) REVERT: A 262 LYS cc_start: 0.8328 (mttt) cc_final: 0.7990 (mptt) REVERT: A 300 LYS cc_start: 0.8437 (mttt) cc_final: 0.8163 (mmtt) REVERT: A 302 ARG cc_start: 0.7283 (ptm160) cc_final: 0.7057 (mtp-110) REVERT: A 322 LYS cc_start: 0.7698 (mtpt) cc_final: 0.7390 (mppt) REVERT: A 473 GLN cc_start: 0.8664 (tt0) cc_final: 0.8238 (tp40) REVERT: A 491 MET cc_start: 0.8466 (mmm) cc_final: 0.7920 (tpp) REVERT: A 570 MET cc_start: 0.8466 (mtp) cc_final: 0.8241 (mmm) REVERT: A 605 GLU cc_start: 0.8474 (tt0) cc_final: 0.8145 (tt0) REVERT: A 621 TYR cc_start: 0.7848 (t80) cc_final: 0.7640 (t80) REVERT: B 55 GLU cc_start: 0.6792 (mt-10) cc_final: 0.6413 (mm-30) REVERT: B 74 GLN cc_start: 0.7365 (mt0) cc_final: 0.7104 (mt0) REVERT: B 99 MET cc_start: 0.7206 (mtm) cc_final: 0.6793 (mtm) REVERT: B 104 GLU cc_start: 0.7432 (pm20) cc_final: 0.6308 (tm-30) REVERT: B 107 LYS cc_start: 0.7090 (mttt) cc_final: 0.6519 (mttp) REVERT: B 155 SER cc_start: 0.7751 (m) cc_final: 0.7491 (p) REVERT: B 176 GLU cc_start: 0.6983 (tt0) cc_final: 0.6430 (mt-10) REVERT: B 194 SER cc_start: 0.8530 (m) cc_final: 0.8224 (p) REVERT: B 257 GLN cc_start: 0.7447 (pt0) cc_final: 0.6574 (tp-100) REVERT: B 262 LYS cc_start: 0.8338 (mttt) cc_final: 0.8030 (mptt) REVERT: B 300 LYS cc_start: 0.8437 (mttt) cc_final: 0.8163 (mmtt) REVERT: B 302 ARG cc_start: 0.7270 (ptm160) cc_final: 0.7053 (mtp-110) REVERT: B 322 LYS cc_start: 0.7755 (mtpt) cc_final: 0.7450 (mppt) REVERT: B 473 GLN cc_start: 0.8661 (tt0) cc_final: 0.8226 (tp40) REVERT: B 491 MET cc_start: 0.8463 (mmm) cc_final: 0.7920 (tpp) REVERT: B 570 MET cc_start: 0.8467 (mtp) cc_final: 0.8247 (mmm) REVERT: B 605 GLU cc_start: 0.8465 (tt0) cc_final: 0.8132 (tt0) REVERT: C 55 GLU cc_start: 0.6793 (mt-10) cc_final: 0.6413 (mm-30) REVERT: C 74 GLN cc_start: 0.7365 (mt0) cc_final: 0.7103 (mt0) REVERT: C 99 MET cc_start: 0.7203 (mtm) cc_final: 0.6791 (mtm) REVERT: C 104 GLU cc_start: 0.7431 (pm20) cc_final: 0.6306 (tm-30) REVERT: C 107 LYS cc_start: 0.7098 (mttt) cc_final: 0.6520 (mttp) REVERT: C 155 SER cc_start: 0.7764 (m) cc_final: 0.7508 (p) REVERT: C 176 GLU cc_start: 0.6989 (tt0) cc_final: 0.6431 (mt-10) REVERT: C 194 SER cc_start: 0.8525 (m) cc_final: 0.8206 (p) REVERT: C 257 GLN cc_start: 0.7449 (pt0) cc_final: 0.6572 (tp-100) REVERT: C 262 LYS cc_start: 0.8335 (mttt) cc_final: 0.8026 (mptt) REVERT: C 300 LYS cc_start: 0.8436 (mttt) cc_final: 0.8160 (mmtt) REVERT: C 302 ARG cc_start: 0.7271 (ptm160) cc_final: 0.7053 (mtp-110) REVERT: C 322 LYS cc_start: 0.7750 (mtpt) cc_final: 0.7446 (mppt) REVERT: C 473 GLN cc_start: 0.8670 (tt0) cc_final: 0.8239 (tp40) REVERT: C 491 MET cc_start: 0.8462 (mmm) cc_final: 0.7917 (tpp) REVERT: C 570 MET cc_start: 0.8468 (mtp) cc_final: 0.8240 (mmm) REVERT: D 43 ARG cc_start: 0.7209 (mmm-85) cc_final: 0.6972 (mmm160) REVERT: D 55 GLU cc_start: 0.6756 (mt-10) cc_final: 0.6376 (mm-30) REVERT: D 74 GLN cc_start: 0.7409 (mt0) cc_final: 0.7157 (mt0) REVERT: D 99 MET cc_start: 0.7209 (mtm) cc_final: 0.6802 (mtm) REVERT: D 104 GLU cc_start: 0.7442 (pm20) cc_final: 0.6317 (tm-30) REVERT: D 107 LYS cc_start: 0.7097 (mttt) cc_final: 0.6532 (mttp) REVERT: D 155 SER cc_start: 0.7766 (m) cc_final: 0.7515 (p) REVERT: D 176 GLU cc_start: 0.6991 (tt0) cc_final: 0.6440 (mt-10) REVERT: D 194 SER cc_start: 0.8520 (m) cc_final: 0.8191 (p) REVERT: D 257 GLN cc_start: 0.7425 (pt0) cc_final: 0.6596 (tp-100) REVERT: D 262 LYS cc_start: 0.8332 (mttt) cc_final: 0.7994 (mptt) REVERT: D 300 LYS cc_start: 0.8436 (mttt) cc_final: 0.8161 (mmtt) REVERT: D 302 ARG cc_start: 0.7275 (ptm160) cc_final: 0.7053 (mtp-110) REVERT: D 322 LYS cc_start: 0.7767 (mtpt) cc_final: 0.7456 (mppt) REVERT: D 473 GLN cc_start: 0.8664 (tt0) cc_final: 0.8231 (tp40) REVERT: D 491 MET cc_start: 0.8471 (mmm) cc_final: 0.7927 (tpp) REVERT: D 570 MET cc_start: 0.8460 (mtp) cc_final: 0.8250 (mmm) REVERT: D 621 TYR cc_start: 0.7842 (t80) cc_final: 0.7642 (t80) outliers start: 8 outliers final: 10 residues processed: 427 average time/residue: 1.5619 time to fit residues: 737.5635 Evaluate side-chains 312 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 302 time to evaluate : 2.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 627 ASP Chi-restraints excluded: chain D residue 315 GLU Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 627 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 0.7980 chunk 181 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 122 optimal weight: 0.9980 chunk 97 optimal weight: 0.6980 chunk 188 optimal weight: 6.9990 chunk 72 optimal weight: 7.9990 chunk 114 optimal weight: 1.9990 chunk 140 optimal weight: 0.9990 chunk 217 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN A 51 GLN A 217 ASN ** A 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 418 GLN A 483 GLN A 596 GLN B 40 GLN B 51 GLN B 217 ASN ** B 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 418 GLN B 483 GLN B 596 GLN C 40 GLN C 51 GLN C 217 ASN ** C 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 418 GLN C 483 GLN C 596 GLN D 40 GLN D 51 GLN D 217 ASN ** D 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 418 GLN D 483 GLN D 596 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20304 Z= 0.175 Angle : 0.519 5.693 27520 Z= 0.279 Chirality : 0.039 0.147 3124 Planarity : 0.004 0.042 3404 Dihedral : 13.224 176.188 3452 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Rotamer: Outliers : 1.92 % Allowed : 6.97 % Favored : 91.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.93 (0.17), residues: 2384 helix: 1.45 (0.13), residues: 1528 sheet: 0.85 (0.50), residues: 80 loop : 1.25 (0.24), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 593 HIS 0.004 0.001 HIS C 201 PHE 0.016 0.002 PHE C 456 TYR 0.016 0.002 TYR C 89 ARG 0.004 0.000 ARG B 139 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 327 time to evaluate : 2.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 GLN cc_start: 0.6734 (tt0) cc_final: 0.6449 (mt0) REVERT: A 99 MET cc_start: 0.7131 (mtm) cc_final: 0.6820 (mtm) REVERT: A 100 GLU cc_start: 0.7118 (mt-10) cc_final: 0.6824 (mt-10) REVERT: A 104 GLU cc_start: 0.7373 (pm20) cc_final: 0.6050 (tm-30) REVERT: A 107 LYS cc_start: 0.7076 (mttt) cc_final: 0.6660 (mttp) REVERT: A 176 GLU cc_start: 0.6960 (tt0) cc_final: 0.6453 (mt-10) REVERT: A 194 SER cc_start: 0.8416 (m) cc_final: 0.8109 (p) REVERT: A 257 GLN cc_start: 0.7219 (pt0) cc_final: 0.6609 (tp-100) REVERT: A 262 LYS cc_start: 0.8259 (mttt) cc_final: 0.7993 (mmtm) REVERT: A 302 ARG cc_start: 0.7250 (ptm160) cc_final: 0.6522 (tmt-80) REVERT: A 379 THR cc_start: 0.7579 (m) cc_final: 0.7368 (m) REVERT: A 381 GLN cc_start: 0.7331 (mp10) cc_final: 0.5644 (mm-40) REVERT: A 408 PHE cc_start: 0.7256 (m-10) cc_final: 0.6932 (m-10) REVERT: A 414 ARG cc_start: 0.7315 (tpp80) cc_final: 0.7066 (tpp80) REVERT: A 491 MET cc_start: 0.8259 (mmm) cc_final: 0.7759 (tpp) REVERT: B 40 GLN cc_start: 0.6730 (tt0) cc_final: 0.6453 (mt0) REVERT: B 60 LEU cc_start: 0.7314 (tp) cc_final: 0.6874 (tm) REVERT: B 99 MET cc_start: 0.7153 (mtm) cc_final: 0.6846 (mtm) REVERT: B 100 GLU cc_start: 0.7118 (mt-10) cc_final: 0.6818 (mt-10) REVERT: B 104 GLU cc_start: 0.7381 (pm20) cc_final: 0.6022 (tm-30) REVERT: B 107 LYS cc_start: 0.7080 (mttt) cc_final: 0.6662 (mttp) REVERT: B 176 GLU cc_start: 0.6948 (tt0) cc_final: 0.6418 (mt-10) REVERT: B 194 SER cc_start: 0.8430 (m) cc_final: 0.8123 (p) REVERT: B 257 GLN cc_start: 0.7222 (pt0) cc_final: 0.6609 (tp-100) REVERT: B 262 LYS cc_start: 0.8270 (mttt) cc_final: 0.8001 (mmtm) REVERT: B 302 ARG cc_start: 0.7251 (ptm160) cc_final: 0.6521 (tmt-80) REVERT: B 379 THR cc_start: 0.7560 (m) cc_final: 0.7348 (m) REVERT: B 381 GLN cc_start: 0.7292 (mp10) cc_final: 0.5627 (mm-40) REVERT: B 408 PHE cc_start: 0.7229 (m-10) cc_final: 0.6914 (m-10) REVERT: B 414 ARG cc_start: 0.7309 (tpp80) cc_final: 0.7058 (tpp80) REVERT: B 491 MET cc_start: 0.8253 (mmm) cc_final: 0.7753 (tpp) REVERT: C 40 GLN cc_start: 0.6731 (tt0) cc_final: 0.6453 (mt0) REVERT: C 60 LEU cc_start: 0.7311 (tp) cc_final: 0.6877 (tm) REVERT: C 99 MET cc_start: 0.7154 (mtm) cc_final: 0.6845 (mtm) REVERT: C 100 GLU cc_start: 0.7117 (mt-10) cc_final: 0.6815 (mt-10) REVERT: C 104 GLU cc_start: 0.7379 (pm20) cc_final: 0.6021 (tm-30) REVERT: C 107 LYS cc_start: 0.7075 (mttt) cc_final: 0.6663 (mttp) REVERT: C 146 ARG cc_start: 0.7988 (mtp180) cc_final: 0.7787 (mmm-85) REVERT: C 176 GLU cc_start: 0.6951 (tt0) cc_final: 0.6423 (mt-10) REVERT: C 194 SER cc_start: 0.8421 (m) cc_final: 0.8110 (p) REVERT: C 257 GLN cc_start: 0.7236 (pt0) cc_final: 0.6613 (tp-100) REVERT: C 262 LYS cc_start: 0.8271 (mttt) cc_final: 0.8002 (mmtm) REVERT: C 302 ARG cc_start: 0.7253 (ptm160) cc_final: 0.6524 (tmt-80) REVERT: C 379 THR cc_start: 0.7567 (m) cc_final: 0.7352 (m) REVERT: C 381 GLN cc_start: 0.7283 (mp10) cc_final: 0.5624 (mm-40) REVERT: C 408 PHE cc_start: 0.7227 (m-10) cc_final: 0.6980 (m-10) REVERT: C 414 ARG cc_start: 0.7318 (tpp80) cc_final: 0.7055 (tpp80) REVERT: C 491 MET cc_start: 0.8249 (mmm) cc_final: 0.7752 (tpp) REVERT: D 40 GLN cc_start: 0.6741 (tt0) cc_final: 0.6456 (mt0) REVERT: D 60 LEU cc_start: 0.7263 (tp) cc_final: 0.6841 (tm) REVERT: D 99 MET cc_start: 0.7172 (mtm) cc_final: 0.6959 (mtm) REVERT: D 100 GLU cc_start: 0.7112 (mt-10) cc_final: 0.6807 (mt-10) REVERT: D 104 GLU cc_start: 0.7379 (pm20) cc_final: 0.6016 (tm-30) REVERT: D 107 LYS cc_start: 0.7069 (mttt) cc_final: 0.6668 (mttp) REVERT: D 176 GLU cc_start: 0.6964 (tt0) cc_final: 0.6431 (mt-10) REVERT: D 194 SER cc_start: 0.8462 (m) cc_final: 0.8163 (p) REVERT: D 257 GLN cc_start: 0.7217 (pt0) cc_final: 0.6602 (tp-100) REVERT: D 262 LYS cc_start: 0.8261 (mttt) cc_final: 0.7996 (mmtm) REVERT: D 302 ARG cc_start: 0.7245 (ptm160) cc_final: 0.6565 (tmt-80) REVERT: D 379 THR cc_start: 0.7568 (m) cc_final: 0.7354 (m) REVERT: D 381 GLN cc_start: 0.7289 (mp10) cc_final: 0.5610 (mm-40) REVERT: D 408 PHE cc_start: 0.7226 (m-10) cc_final: 0.6978 (m-10) REVERT: D 414 ARG cc_start: 0.7306 (tpp80) cc_final: 0.7046 (tpp80) REVERT: D 491 MET cc_start: 0.8251 (mmm) cc_final: 0.7759 (tpp) outliers start: 40 outliers final: 8 residues processed: 343 average time/residue: 1.4753 time to fit residues: 562.7486 Evaluate side-chains 288 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 280 time to evaluate : 2.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain D residue 315 GLU Chi-restraints excluded: chain D residue 354 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 121 optimal weight: 4.9990 chunk 67 optimal weight: 7.9990 chunk 181 optimal weight: 8.9990 chunk 148 optimal weight: 1.9990 chunk 60 optimal weight: 10.0000 chunk 218 optimal weight: 7.9990 chunk 235 optimal weight: 1.9990 chunk 194 optimal weight: 3.9990 chunk 216 optimal weight: 5.9990 chunk 74 optimal weight: 0.9980 chunk 175 optimal weight: 0.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 418 GLN B 418 GLN B 483 GLN ** C 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 418 GLN D 418 GLN D 483 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 20304 Z= 0.259 Angle : 0.532 8.931 27520 Z= 0.281 Chirality : 0.041 0.152 3124 Planarity : 0.004 0.046 3404 Dihedral : 12.649 173.700 3444 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 3.41 % Allowed : 7.69 % Favored : 88.89 % 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: 1.92 (0.17), residues: 2384 helix: 1.71 (0.13), residues: 1496 sheet: -1.04 (0.43), residues: 108 loop : 1.00 (0.24), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 593 HIS 0.006 0.001 HIS C 201 PHE 0.014 0.002 PHE B 472 TYR 0.018 0.002 TYR C 89 ARG 0.005 0.000 ARG B 180 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 301 time to evaluate : 2.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.6711 (OUTLIER) cc_final: 0.6342 (mp0) REVERT: A 40 GLN cc_start: 0.6759 (tt0) cc_final: 0.6476 (mt0) REVERT: A 55 GLU cc_start: 0.6772 (mt-10) cc_final: 0.6415 (mm-30) REVERT: A 99 MET cc_start: 0.7187 (mtm) cc_final: 0.6909 (mtm) REVERT: A 104 GLU cc_start: 0.7490 (pm20) cc_final: 0.6153 (tm-30) REVERT: A 107 LYS cc_start: 0.7098 (mttt) cc_final: 0.6678 (mttp) REVERT: A 176 GLU cc_start: 0.7004 (tt0) cc_final: 0.6513 (mt-10) REVERT: A 190 ARG cc_start: 0.7789 (OUTLIER) cc_final: 0.6339 (mtm180) REVERT: A 262 LYS cc_start: 0.8238 (mttt) cc_final: 0.7968 (mmtm) REVERT: A 302 ARG cc_start: 0.7288 (ptm160) cc_final: 0.6680 (tmt-80) REVERT: A 323 LYS cc_start: 0.8065 (OUTLIER) cc_final: 0.7849 (tttm) REVERT: A 414 ARG cc_start: 0.7372 (tpp80) cc_final: 0.7019 (tpp80) REVERT: B 30 GLU cc_start: 0.6653 (OUTLIER) cc_final: 0.6219 (mp0) REVERT: B 40 GLN cc_start: 0.6753 (tt0) cc_final: 0.6472 (mt0) REVERT: B 51 GLN cc_start: 0.7477 (tp-100) cc_final: 0.7071 (mm-40) REVERT: B 55 GLU cc_start: 0.6786 (mt-10) cc_final: 0.6356 (mm-30) REVERT: B 99 MET cc_start: 0.7189 (mtm) cc_final: 0.6908 (mtm) REVERT: B 104 GLU cc_start: 0.7505 (pm20) cc_final: 0.6059 (tm-30) REVERT: B 107 LYS cc_start: 0.7099 (mttt) cc_final: 0.6679 (mttp) REVERT: B 176 GLU cc_start: 0.7005 (tt0) cc_final: 0.6514 (mt-10) REVERT: B 190 ARG cc_start: 0.7786 (OUTLIER) cc_final: 0.6362 (mtm180) REVERT: B 257 GLN cc_start: 0.7227 (pt0) cc_final: 0.6602 (tp-100) REVERT: B 262 LYS cc_start: 0.8239 (mttt) cc_final: 0.7968 (mmtm) REVERT: B 302 ARG cc_start: 0.7288 (ptm160) cc_final: 0.6678 (tmt-80) REVERT: B 323 LYS cc_start: 0.8068 (OUTLIER) cc_final: 0.7851 (tttm) REVERT: B 381 GLN cc_start: 0.7350 (mp10) cc_final: 0.6659 (mp-120) REVERT: B 414 ARG cc_start: 0.7367 (tpp80) cc_final: 0.7031 (tpp80) REVERT: C 30 GLU cc_start: 0.6657 (OUTLIER) cc_final: 0.6222 (mp0) REVERT: C 40 GLN cc_start: 0.6754 (tt0) cc_final: 0.6474 (mt0) REVERT: C 55 GLU cc_start: 0.6787 (mt-10) cc_final: 0.6401 (mm-30) REVERT: C 99 MET cc_start: 0.7187 (mtm) cc_final: 0.6905 (mtm) REVERT: C 104 GLU cc_start: 0.7487 (pm20) cc_final: 0.6049 (tm-30) REVERT: C 107 LYS cc_start: 0.7098 (mttt) cc_final: 0.6627 (mttp) REVERT: C 176 GLU cc_start: 0.7025 (tt0) cc_final: 0.6546 (mt-10) REVERT: C 190 ARG cc_start: 0.7780 (OUTLIER) cc_final: 0.6378 (mtm180) REVERT: C 262 LYS cc_start: 0.8238 (mttt) cc_final: 0.7967 (mmtm) REVERT: C 302 ARG cc_start: 0.7287 (ptm160) cc_final: 0.6681 (tmt-80) REVERT: C 323 LYS cc_start: 0.8068 (OUTLIER) cc_final: 0.7850 (tttm) REVERT: C 414 ARG cc_start: 0.7367 (tpp80) cc_final: 0.7004 (tpp80) REVERT: D 30 GLU cc_start: 0.6650 (OUTLIER) cc_final: 0.6218 (mp0) REVERT: D 40 GLN cc_start: 0.6783 (tt0) cc_final: 0.6504 (mt0) REVERT: D 51 GLN cc_start: 0.7478 (tp-100) cc_final: 0.7073 (mm-40) REVERT: D 55 GLU cc_start: 0.6758 (mt-10) cc_final: 0.6329 (mm-30) REVERT: D 99 MET cc_start: 0.7161 (mtm) cc_final: 0.6960 (mtm) REVERT: D 104 GLU cc_start: 0.7508 (pm20) cc_final: 0.6093 (tm-30) REVERT: D 107 LYS cc_start: 0.7098 (mttt) cc_final: 0.6676 (mttp) REVERT: D 176 GLU cc_start: 0.7038 (tt0) cc_final: 0.6555 (mt-10) REVERT: D 190 ARG cc_start: 0.7781 (OUTLIER) cc_final: 0.6346 (mtm180) REVERT: D 257 GLN cc_start: 0.7224 (pt0) cc_final: 0.6603 (tp-100) REVERT: D 262 LYS cc_start: 0.8235 (mttt) cc_final: 0.7993 (mmtm) REVERT: D 302 ARG cc_start: 0.7305 (ptm160) cc_final: 0.6675 (tmt-80) REVERT: D 323 LYS cc_start: 0.8068 (OUTLIER) cc_final: 0.7850 (tttm) REVERT: D 381 GLN cc_start: 0.7347 (mp10) cc_final: 0.6661 (mp-120) REVERT: D 414 ARG cc_start: 0.7342 (tpp80) cc_final: 0.6991 (tpp80) outliers start: 71 outliers final: 29 residues processed: 334 average time/residue: 1.4936 time to fit residues: 553.6864 Evaluate side-chains 325 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 284 time to evaluate : 2.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 323 LYS Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 524 SER Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 323 LYS Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 524 SER Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 47 SER Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 323 LYS Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 524 SER Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 190 ARG Chi-restraints excluded: chain D residue 315 GLU Chi-restraints excluded: chain D residue 323 LYS Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 355 ARG Chi-restraints excluded: chain D residue 524 SER Chi-restraints excluded: chain D residue 567 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 215 optimal weight: 3.9990 chunk 164 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 24 optimal weight: 8.9990 chunk 104 optimal weight: 3.9990 chunk 146 optimal weight: 0.4980 chunk 219 optimal weight: 2.9990 chunk 231 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 207 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 GLN B 418 GLN C 418 GLN D 418 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 20304 Z= 0.283 Angle : 0.531 7.594 27520 Z= 0.279 Chirality : 0.041 0.151 3124 Planarity : 0.004 0.044 3404 Dihedral : 12.653 173.498 3444 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 2.50 % Allowed : 9.62 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.17), residues: 2384 helix: 1.59 (0.12), residues: 1496 sheet: -1.24 (0.44), residues: 108 loop : 0.92 (0.24), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 593 HIS 0.005 0.001 HIS A 201 PHE 0.012 0.002 PHE D 472 TYR 0.016 0.002 TYR A 89 ARG 0.003 0.000 ARG A 180 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 283 time to evaluate : 2.301 Fit side-chains revert: symmetry clash REVERT: A 30 GLU cc_start: 0.6656 (OUTLIER) cc_final: 0.6280 (mp0) REVERT: A 40 GLN cc_start: 0.6744 (tt0) cc_final: 0.6520 (mt0) REVERT: A 51 GLN cc_start: 0.7415 (tp-100) cc_final: 0.7049 (mm-40) REVERT: A 99 MET cc_start: 0.7198 (mtm) cc_final: 0.6904 (mtm) REVERT: A 104 GLU cc_start: 0.7467 (pm20) cc_final: 0.6156 (tm-30) REVERT: A 107 LYS cc_start: 0.7162 (mttt) cc_final: 0.6658 (mttp) REVERT: A 176 GLU cc_start: 0.7102 (tt0) cc_final: 0.6614 (mt-10) REVERT: A 190 ARG cc_start: 0.7770 (OUTLIER) cc_final: 0.6410 (mtm180) REVERT: A 257 GLN cc_start: 0.7211 (pt0) cc_final: 0.6624 (tp-100) REVERT: A 262 LYS cc_start: 0.8236 (mttt) cc_final: 0.7974 (mptt) REVERT: A 302 ARG cc_start: 0.7287 (ptm160) cc_final: 0.6623 (tmt-80) REVERT: A 381 GLN cc_start: 0.7281 (mp10) cc_final: 0.6599 (mp-120) REVERT: A 414 ARG cc_start: 0.7500 (tpp80) cc_final: 0.6990 (tpp80) REVERT: B 30 GLU cc_start: 0.6650 (OUTLIER) cc_final: 0.6193 (mp0) REVERT: B 40 GLN cc_start: 0.6718 (tt0) cc_final: 0.6494 (mt0) REVERT: B 51 GLN cc_start: 0.7414 (tp-100) cc_final: 0.7047 (mm-40) REVERT: B 60 LEU cc_start: 0.7271 (tp) cc_final: 0.6923 (tm) REVERT: B 99 MET cc_start: 0.7198 (mtm) cc_final: 0.6906 (mtm) REVERT: B 104 GLU cc_start: 0.7469 (pm20) cc_final: 0.6151 (tm-30) REVERT: B 107 LYS cc_start: 0.7162 (mttt) cc_final: 0.6674 (mttp) REVERT: B 176 GLU cc_start: 0.7103 (tt0) cc_final: 0.6614 (mt-10) REVERT: B 190 ARG cc_start: 0.7769 (OUTLIER) cc_final: 0.6408 (mtm180) REVERT: B 257 GLN cc_start: 0.7212 (pt0) cc_final: 0.6624 (tp-100) REVERT: B 262 LYS cc_start: 0.8236 (mttt) cc_final: 0.7974 (mptt) REVERT: B 302 ARG cc_start: 0.7286 (ptm160) cc_final: 0.6621 (tmt-80) REVERT: B 381 GLN cc_start: 0.7286 (mp10) cc_final: 0.6695 (mp-120) REVERT: B 414 ARG cc_start: 0.7502 (tpp80) cc_final: 0.7005 (tpp80) REVERT: C 30 GLU cc_start: 0.6651 (OUTLIER) cc_final: 0.6194 (mp0) REVERT: C 40 GLN cc_start: 0.6719 (tt0) cc_final: 0.6494 (mt0) REVERT: C 51 GLN cc_start: 0.7410 (tp-100) cc_final: 0.7047 (mm-40) REVERT: C 60 LEU cc_start: 0.7273 (tp) cc_final: 0.6926 (tm) REVERT: C 99 MET cc_start: 0.7198 (mtm) cc_final: 0.6907 (mtm) REVERT: C 104 GLU cc_start: 0.7468 (pm20) cc_final: 0.6153 (tm-30) REVERT: C 107 LYS cc_start: 0.7162 (mttt) cc_final: 0.6665 (mttp) REVERT: C 176 GLU cc_start: 0.7155 (tt0) cc_final: 0.6675 (mt-10) REVERT: C 190 ARG cc_start: 0.7771 (OUTLIER) cc_final: 0.6408 (mtm180) REVERT: C 257 GLN cc_start: 0.7207 (pt0) cc_final: 0.6628 (tp-100) REVERT: C 262 LYS cc_start: 0.8236 (mttt) cc_final: 0.7975 (mptt) REVERT: C 302 ARG cc_start: 0.7296 (ptm160) cc_final: 0.6652 (tmt-80) REVERT: C 381 GLN cc_start: 0.7281 (mp10) cc_final: 0.6695 (mp-120) REVERT: C 414 ARG cc_start: 0.7490 (tpp80) cc_final: 0.6966 (tpp80) REVERT: D 30 GLU cc_start: 0.6643 (OUTLIER) cc_final: 0.6184 (mp0) REVERT: D 40 GLN cc_start: 0.6762 (tt0) cc_final: 0.6539 (mt0) REVERT: D 51 GLN cc_start: 0.7416 (tp-100) cc_final: 0.7051 (mm-40) REVERT: D 60 LEU cc_start: 0.7260 (tp) cc_final: 0.6908 (tm) REVERT: D 99 MET cc_start: 0.7208 (mtm) cc_final: 0.6995 (mtm) REVERT: D 104 GLU cc_start: 0.7472 (pm20) cc_final: 0.6154 (tm-30) REVERT: D 107 LYS cc_start: 0.7162 (mttt) cc_final: 0.6666 (mttp) REVERT: D 176 GLU cc_start: 0.7099 (tt0) cc_final: 0.6612 (mt-10) REVERT: D 190 ARG cc_start: 0.7781 (OUTLIER) cc_final: 0.6408 (mtm180) REVERT: D 257 GLN cc_start: 0.7213 (pt0) cc_final: 0.6625 (tp-100) REVERT: D 262 LYS cc_start: 0.8236 (mttt) cc_final: 0.7974 (mptt) REVERT: D 302 ARG cc_start: 0.7295 (ptm160) cc_final: 0.6651 (tmt-80) REVERT: D 381 GLN cc_start: 0.7286 (mp10) cc_final: 0.6694 (mp-120) REVERT: D 414 ARG cc_start: 0.7489 (tpp80) cc_final: 0.6994 (tpp80) outliers start: 52 outliers final: 21 residues processed: 305 average time/residue: 1.5145 time to fit residues: 512.7294 Evaluate side-chains 306 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 277 time to evaluate : 2.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 524 SER Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 524 SER Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 47 SER Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 524 SER Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 190 ARG Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 355 ARG Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 524 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 193 optimal weight: 0.9990 chunk 131 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 172 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 chunk 197 optimal weight: 1.9990 chunk 160 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 118 optimal weight: 0.9990 chunk 208 optimal weight: 0.8980 chunk 58 optimal weight: 8.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 GLN ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 418 GLN C 418 GLN D 418 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20304 Z= 0.182 Angle : 0.479 7.633 27520 Z= 0.251 Chirality : 0.038 0.152 3124 Planarity : 0.004 0.040 3404 Dihedral : 12.077 172.224 3432 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 2.98 % Allowed : 9.38 % Favored : 87.64 % 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: 1.64 (0.12), residues: 1528 sheet: -1.43 (0.46), residues: 100 loop : 0.95 (0.24), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 593 HIS 0.003 0.001 HIS A 201 PHE 0.009 0.001 PHE A 537 TYR 0.012 0.001 TYR B 89 ARG 0.003 0.000 ARG D 180 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 302 time to evaluate : 2.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ASP cc_start: 0.5720 (OUTLIER) cc_final: 0.5102 (p0) REVERT: A 30 GLU cc_start: 0.6712 (OUTLIER) cc_final: 0.5994 (mp0) REVERT: A 40 GLN cc_start: 0.6617 (tt0) cc_final: 0.6399 (mt0) REVERT: A 51 GLN cc_start: 0.7423 (tp-100) cc_final: 0.7051 (mm-40) REVERT: A 99 MET cc_start: 0.7122 (mtm) cc_final: 0.6919 (mtm) REVERT: A 104 GLU cc_start: 0.7462 (pm20) cc_final: 0.6163 (tm-30) REVERT: A 107 LYS cc_start: 0.7207 (mttt) cc_final: 0.6716 (mttp) REVERT: A 176 GLU cc_start: 0.7075 (tt0) cc_final: 0.6635 (mt-10) REVERT: A 190 ARG cc_start: 0.7805 (OUTLIER) cc_final: 0.6487 (mtm180) REVERT: A 257 GLN cc_start: 0.7134 (pt0) cc_final: 0.6546 (tp-100) REVERT: A 262 LYS cc_start: 0.8201 (mttt) cc_final: 0.7941 (mptt) REVERT: A 302 ARG cc_start: 0.7326 (ptm160) cc_final: 0.6670 (tmt-80) REVERT: A 414 ARG cc_start: 0.7417 (tpp80) cc_final: 0.6906 (tpp80) REVERT: B 30 GLU cc_start: 0.6669 (mt-10) cc_final: 0.6208 (mp0) REVERT: B 40 GLN cc_start: 0.6600 (tt0) cc_final: 0.6371 (mt0) REVERT: B 51 GLN cc_start: 0.7428 (tp-100) cc_final: 0.7064 (mm-40) REVERT: B 99 MET cc_start: 0.7140 (mtm) cc_final: 0.6910 (mtm) REVERT: B 104 GLU cc_start: 0.7445 (pm20) cc_final: 0.6135 (tm-30) REVERT: B 107 LYS cc_start: 0.7206 (mttt) cc_final: 0.6718 (mttp) REVERT: B 176 GLU cc_start: 0.7074 (tt0) cc_final: 0.6634 (mt-10) REVERT: B 190 ARG cc_start: 0.7804 (OUTLIER) cc_final: 0.6486 (mtm180) REVERT: B 257 GLN cc_start: 0.7134 (pt0) cc_final: 0.6596 (tp-100) REVERT: B 262 LYS cc_start: 0.8201 (mttt) cc_final: 0.7940 (mptt) REVERT: B 302 ARG cc_start: 0.7324 (ptm160) cc_final: 0.6671 (tmt-80) REVERT: B 381 GLN cc_start: 0.7262 (mp10) cc_final: 0.6669 (mp-120) REVERT: B 414 ARG cc_start: 0.7326 (tpp80) cc_final: 0.6767 (tpp80) REVERT: C 30 GLU cc_start: 0.6670 (mt-10) cc_final: 0.6207 (mp0) REVERT: C 40 GLN cc_start: 0.6603 (tt0) cc_final: 0.6372 (mt0) REVERT: C 51 GLN cc_start: 0.7426 (tp-100) cc_final: 0.7061 (mm-40) REVERT: C 99 MET cc_start: 0.7142 (mtm) cc_final: 0.6909 (mtm) REVERT: C 104 GLU cc_start: 0.7444 (pm20) cc_final: 0.6136 (tm-30) REVERT: C 107 LYS cc_start: 0.7207 (mttt) cc_final: 0.6718 (mttp) REVERT: C 176 GLU cc_start: 0.7124 (tt0) cc_final: 0.6696 (mt-10) REVERT: C 190 ARG cc_start: 0.7806 (OUTLIER) cc_final: 0.6447 (mtm180) REVERT: C 257 GLN cc_start: 0.7134 (pt0) cc_final: 0.6551 (tp-100) REVERT: C 262 LYS cc_start: 0.8201 (mttt) cc_final: 0.7941 (mptt) REVERT: C 302 ARG cc_start: 0.7295 (ptm160) cc_final: 0.6657 (tmt-80) REVERT: C 381 GLN cc_start: 0.7262 (mp10) cc_final: 0.6673 (mp-120) REVERT: C 414 ARG cc_start: 0.7355 (tpp80) cc_final: 0.6878 (tpp80) REVERT: D 30 GLU cc_start: 0.6662 (mt-10) cc_final: 0.6203 (mp0) REVERT: D 40 GLN cc_start: 0.6635 (tt0) cc_final: 0.6420 (mt0) REVERT: D 51 GLN cc_start: 0.7430 (tp-100) cc_final: 0.7064 (mm-40) REVERT: D 104 GLU cc_start: 0.7442 (pm20) cc_final: 0.6121 (tm-30) REVERT: D 107 LYS cc_start: 0.7209 (mttt) cc_final: 0.6723 (mttp) REVERT: D 176 GLU cc_start: 0.7070 (tt0) cc_final: 0.6635 (mt-10) REVERT: D 190 ARG cc_start: 0.7807 (OUTLIER) cc_final: 0.6445 (mtm180) REVERT: D 257 GLN cc_start: 0.7110 (pt0) cc_final: 0.6566 (tp-100) REVERT: D 262 LYS cc_start: 0.8204 (mttt) cc_final: 0.7944 (mptt) REVERT: D 302 ARG cc_start: 0.7294 (ptm160) cc_final: 0.6659 (tmt-80) REVERT: D 381 GLN cc_start: 0.7275 (mp10) cc_final: 0.6676 (mp-120) REVERT: D 414 ARG cc_start: 0.7325 (tpp80) cc_final: 0.6776 (tpp80) outliers start: 62 outliers final: 27 residues processed: 336 average time/residue: 1.4951 time to fit residues: 560.6025 Evaluate side-chains 316 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 283 time to evaluate : 2.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain C residue 47 SER Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 190 ARG Chi-restraints excluded: chain D residue 315 GLU Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 567 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 78 optimal weight: 4.9990 chunk 208 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 chunk 136 optimal weight: 7.9990 chunk 57 optimal weight: 0.0870 chunk 232 optimal weight: 6.9990 chunk 192 optimal weight: 3.9990 chunk 107 optimal weight: 0.7980 chunk 19 optimal weight: 9.9990 chunk 76 optimal weight: 0.8980 chunk 121 optimal weight: 0.7980 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN A 418 GLN A 483 GLN B 418 GLN C 261 GLN C 418 GLN C 483 GLN D 418 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 20304 Z= 0.142 Angle : 0.467 8.881 27520 Z= 0.239 Chirality : 0.037 0.163 3124 Planarity : 0.004 0.038 3404 Dihedral : 11.698 168.047 3432 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 2.26 % Allowed : 11.49 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (0.17), residues: 2384 helix: 1.83 (0.12), residues: 1528 sheet: -1.51 (0.47), residues: 100 loop : 0.95 (0.25), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 593 HIS 0.003 0.001 HIS C 201 PHE 0.008 0.001 PHE D 537 TYR 0.010 0.001 TYR A 89 ARG 0.004 0.000 ARG A 180 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 300 time to evaluate : 2.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ASP cc_start: 0.5628 (OUTLIER) cc_final: 0.5093 (p0) REVERT: A 30 GLU cc_start: 0.6718 (OUTLIER) cc_final: 0.6030 (mp0) REVERT: A 51 GLN cc_start: 0.7436 (tp-100) cc_final: 0.7071 (mm-40) REVERT: A 104 GLU cc_start: 0.7448 (pm20) cc_final: 0.6040 (tm-30) REVERT: A 107 LYS cc_start: 0.7171 (mttt) cc_final: 0.6671 (mttp) REVERT: A 176 GLU cc_start: 0.7081 (tt0) cc_final: 0.6686 (mt-10) REVERT: A 190 ARG cc_start: 0.7746 (OUTLIER) cc_final: 0.6299 (mtm180) REVERT: A 257 GLN cc_start: 0.7105 (pt0) cc_final: 0.6598 (tp-100) REVERT: A 262 LYS cc_start: 0.8214 (mttt) cc_final: 0.7946 (mptt) REVERT: A 302 ARG cc_start: 0.7324 (ptm160) cc_final: 0.6612 (tmt-80) REVERT: A 350 ARG cc_start: 0.7761 (ttp80) cc_final: 0.7508 (ptm-80) REVERT: A 381 GLN cc_start: 0.7263 (mp10) cc_final: 0.5557 (mm-40) REVERT: A 414 ARG cc_start: 0.7264 (tpp80) cc_final: 0.6782 (tpp80) REVERT: A 491 MET cc_start: 0.8119 (mtp) cc_final: 0.7910 (mtp) REVERT: A 497 MET cc_start: 0.8606 (ttt) cc_final: 0.8346 (ttp) REVERT: B 30 GLU cc_start: 0.6680 (OUTLIER) cc_final: 0.6117 (mp0) REVERT: B 51 GLN cc_start: 0.7418 (tp-100) cc_final: 0.7047 (mm-40) REVERT: B 104 GLU cc_start: 0.7450 (pm20) cc_final: 0.6037 (tm-30) REVERT: B 107 LYS cc_start: 0.7172 (mttt) cc_final: 0.6672 (mttp) REVERT: B 176 GLU cc_start: 0.7082 (tt0) cc_final: 0.6685 (mt-10) REVERT: B 190 ARG cc_start: 0.7747 (OUTLIER) cc_final: 0.6298 (mtm180) REVERT: B 257 GLN cc_start: 0.7083 (pt0) cc_final: 0.6533 (tp-100) REVERT: B 262 LYS cc_start: 0.8219 (mttt) cc_final: 0.7952 (mptt) REVERT: B 302 ARG cc_start: 0.7323 (ptm160) cc_final: 0.6612 (tmt-80) REVERT: B 350 ARG cc_start: 0.7760 (ttp80) cc_final: 0.7501 (ptm-80) REVERT: B 381 GLN cc_start: 0.7138 (mp10) cc_final: 0.6573 (mp-120) REVERT: B 414 ARG cc_start: 0.7305 (tpp80) cc_final: 0.6847 (tpp80) REVERT: B 491 MET cc_start: 0.8131 (mtp) cc_final: 0.7916 (mtp) REVERT: B 497 MET cc_start: 0.8604 (ttt) cc_final: 0.8343 (ttp) REVERT: C 30 GLU cc_start: 0.6683 (OUTLIER) cc_final: 0.6119 (mp0) REVERT: C 51 GLN cc_start: 0.7415 (tp-100) cc_final: 0.7044 (mm-40) REVERT: C 104 GLU cc_start: 0.7449 (pm20) cc_final: 0.6037 (tm-30) REVERT: C 107 LYS cc_start: 0.7173 (mttt) cc_final: 0.6673 (mttp) REVERT: C 176 GLU cc_start: 0.7081 (tt0) cc_final: 0.6685 (mt-10) REVERT: C 190 ARG cc_start: 0.7787 (OUTLIER) cc_final: 0.6361 (mtm180) REVERT: C 257 GLN cc_start: 0.7094 (pt0) cc_final: 0.6610 (tp-100) REVERT: C 262 LYS cc_start: 0.8214 (mttt) cc_final: 0.7945 (mptt) REVERT: C 302 ARG cc_start: 0.7320 (ptm160) cc_final: 0.6615 (tmt-80) REVERT: C 414 ARG cc_start: 0.7273 (tpp80) cc_final: 0.6814 (tpp80) REVERT: C 442 MET cc_start: 0.7460 (mtp) cc_final: 0.7254 (mtp) REVERT: C 491 MET cc_start: 0.8121 (mtp) cc_final: 0.7911 (mtp) REVERT: C 497 MET cc_start: 0.8608 (ttt) cc_final: 0.8347 (ttp) REVERT: D 30 GLU cc_start: 0.6680 (OUTLIER) cc_final: 0.6121 (mp0) REVERT: D 51 GLN cc_start: 0.7419 (tp-100) cc_final: 0.7047 (mm-40) REVERT: D 104 GLU cc_start: 0.7453 (pm20) cc_final: 0.6034 (tm-30) REVERT: D 107 LYS cc_start: 0.7174 (mttt) cc_final: 0.6671 (mttp) REVERT: D 176 GLU cc_start: 0.7090 (tt0) cc_final: 0.6700 (mt-10) REVERT: D 190 ARG cc_start: 0.7775 (OUTLIER) cc_final: 0.6325 (mtm180) REVERT: D 257 GLN cc_start: 0.7083 (pt0) cc_final: 0.6531 (tp-100) REVERT: D 262 LYS cc_start: 0.8204 (mttt) cc_final: 0.7948 (mptt) REVERT: D 302 ARG cc_start: 0.7324 (ptm160) cc_final: 0.6619 (tmt-80) REVERT: D 381 GLN cc_start: 0.7196 (mp10) cc_final: 0.6630 (mp-120) REVERT: D 414 ARG cc_start: 0.7296 (tpp80) cc_final: 0.6834 (tpp80) REVERT: D 442 MET cc_start: 0.7459 (mtp) cc_final: 0.7257 (mtp) REVERT: D 491 MET cc_start: 0.8113 (mtp) cc_final: 0.7902 (mtp) REVERT: D 497 MET cc_start: 0.8607 (ttt) cc_final: 0.8346 (ttp) outliers start: 47 outliers final: 27 residues processed: 325 average time/residue: 1.5622 time to fit residues: 561.7429 Evaluate side-chains 315 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 279 time to evaluate : 2.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 47 SER Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 190 ARG Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 315 GLU Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 355 ARG Chi-restraints excluded: chain D residue 419 THR Chi-restraints excluded: chain D residue 499 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 223 optimal weight: 3.9990 chunk 26 optimal weight: 9.9990 chunk 132 optimal weight: 1.9990 chunk 169 optimal weight: 4.9990 chunk 131 optimal weight: 9.9990 chunk 195 optimal weight: 3.9990 chunk 129 optimal weight: 5.9990 chunk 231 optimal weight: 0.9990 chunk 144 optimal weight: 2.9990 chunk 141 optimal weight: 6.9990 chunk 106 optimal weight: 4.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 GLN B 261 GLN B 418 GLN C 418 GLN D 261 GLN D 418 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 20304 Z= 0.331 Angle : 0.560 8.780 27520 Z= 0.289 Chirality : 0.042 0.165 3124 Planarity : 0.005 0.042 3404 Dihedral : 12.098 167.318 3432 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 2.79 % Allowed : 11.35 % Favored : 85.87 % 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: 1.53 (0.12), residues: 1532 sheet: -1.50 (0.46), residues: 100 loop : 0.91 (0.24), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 593 HIS 0.006 0.001 HIS A 201 PHE 0.013 0.002 PHE D 472 TYR 0.015 0.002 TYR C 89 ARG 0.006 0.000 ARG D 180 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 279 time to evaluate : 2.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ASP cc_start: 0.5585 (OUTLIER) cc_final: 0.4976 (p0) REVERT: A 30 GLU cc_start: 0.6685 (OUTLIER) cc_final: 0.5905 (mp0) REVERT: A 51 GLN cc_start: 0.7433 (tp-100) cc_final: 0.7063 (mm-40) REVERT: A 104 GLU cc_start: 0.7458 (pm20) cc_final: 0.6043 (tm-30) REVERT: A 107 LYS cc_start: 0.7173 (mttt) cc_final: 0.6667 (mttp) REVERT: A 176 GLU cc_start: 0.7088 (tt0) cc_final: 0.6672 (mt-10) REVERT: A 190 ARG cc_start: 0.7864 (OUTLIER) cc_final: 0.6422 (mtm180) REVERT: A 257 GLN cc_start: 0.7173 (pt0) cc_final: 0.6587 (tp-100) REVERT: A 262 LYS cc_start: 0.8210 (mttt) cc_final: 0.7937 (mptt) REVERT: A 302 ARG cc_start: 0.7342 (ptm160) cc_final: 0.6601 (tmt-80) REVERT: A 414 ARG cc_start: 0.7398 (ttp80) cc_final: 0.6834 (tpp80) REVERT: A 491 MET cc_start: 0.8160 (mtp) cc_final: 0.7936 (mtp) REVERT: B 30 GLU cc_start: 0.6618 (OUTLIER) cc_final: 0.6054 (mp0) REVERT: B 51 GLN cc_start: 0.7427 (tp-100) cc_final: 0.7039 (mm-40) REVERT: B 55 GLU cc_start: 0.7012 (mt-10) cc_final: 0.6481 (mm-30) REVERT: B 104 GLU cc_start: 0.7460 (pm20) cc_final: 0.6040 (tm-30) REVERT: B 107 LYS cc_start: 0.7182 (mttt) cc_final: 0.6679 (mttp) REVERT: B 176 GLU cc_start: 0.7088 (tt0) cc_final: 0.6673 (mt-10) REVERT: B 190 ARG cc_start: 0.7864 (OUTLIER) cc_final: 0.6422 (mtm180) REVERT: B 257 GLN cc_start: 0.7165 (pt0) cc_final: 0.6582 (tp-100) REVERT: B 262 LYS cc_start: 0.8199 (mttt) cc_final: 0.7934 (mptt) REVERT: B 302 ARG cc_start: 0.7348 (ptm160) cc_final: 0.6609 (tmt-80) REVERT: B 414 ARG cc_start: 0.7391 (ttp80) cc_final: 0.6872 (tpp80) REVERT: B 491 MET cc_start: 0.8171 (mtp) cc_final: 0.7945 (mtp) REVERT: C 30 GLU cc_start: 0.6622 (OUTLIER) cc_final: 0.6058 (mp0) REVERT: C 51 GLN cc_start: 0.7424 (tp-100) cc_final: 0.6989 (mm-40) REVERT: C 55 GLU cc_start: 0.7012 (mt-10) cc_final: 0.6458 (mt-10) REVERT: C 104 GLU cc_start: 0.7460 (pm20) cc_final: 0.6042 (tm-30) REVERT: C 107 LYS cc_start: 0.7174 (mttt) cc_final: 0.6669 (mttp) REVERT: C 176 GLU cc_start: 0.7086 (tt0) cc_final: 0.6672 (mt-10) REVERT: C 190 ARG cc_start: 0.7868 (OUTLIER) cc_final: 0.6394 (mtm180) REVERT: C 257 GLN cc_start: 0.7185 (pt0) cc_final: 0.6601 (tp-100) REVERT: C 262 LYS cc_start: 0.8208 (mttt) cc_final: 0.7937 (mptt) REVERT: C 302 ARG cc_start: 0.7343 (ptm160) cc_final: 0.6619 (tmt-80) REVERT: C 381 GLN cc_start: 0.7346 (mp10) cc_final: 0.6679 (mp-120) REVERT: C 414 ARG cc_start: 0.7408 (ttp80) cc_final: 0.6818 (tpp80) REVERT: C 491 MET cc_start: 0.8162 (mtp) cc_final: 0.7938 (mtp) REVERT: D 30 GLU cc_start: 0.6603 (OUTLIER) cc_final: 0.6156 (mp0) REVERT: D 51 GLN cc_start: 0.7428 (tp-100) cc_final: 0.7036 (mm-40) REVERT: D 55 GLU cc_start: 0.6991 (mt-10) cc_final: 0.6466 (mm-30) REVERT: D 104 GLU cc_start: 0.7462 (pm20) cc_final: 0.6045 (tm-30) REVERT: D 107 LYS cc_start: 0.7185 (mttt) cc_final: 0.6683 (mttp) REVERT: D 176 GLU cc_start: 0.7102 (tt0) cc_final: 0.6678 (mt-10) REVERT: D 190 ARG cc_start: 0.7869 (OUTLIER) cc_final: 0.6394 (mtm180) REVERT: D 257 GLN cc_start: 0.7164 (pt0) cc_final: 0.6579 (tp-100) REVERT: D 262 LYS cc_start: 0.8193 (mttt) cc_final: 0.7926 (mptt) REVERT: D 302 ARG cc_start: 0.7342 (ptm160) cc_final: 0.6621 (tmt-80) REVERT: D 350 ARG cc_start: 0.7972 (ttp80) cc_final: 0.7772 (ptm160) REVERT: D 414 ARG cc_start: 0.7415 (ttp80) cc_final: 0.6824 (tpp80) REVERT: D 491 MET cc_start: 0.8171 (mtp) cc_final: 0.7947 (mtp) outliers start: 58 outliers final: 39 residues processed: 314 average time/residue: 1.5646 time to fit residues: 542.8967 Evaluate side-chains 317 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 269 time to evaluate : 1.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 577 MET Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain B residue 577 MET Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 47 SER Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 577 MET Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 190 ARG Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 315 GLU Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 355 ARG Chi-restraints excluded: chain D residue 419 THR Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 577 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 143 optimal weight: 5.9990 chunk 92 optimal weight: 7.9990 chunk 138 optimal weight: 0.8980 chunk 69 optimal weight: 4.9990 chunk 45 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 chunk 147 optimal weight: 0.6980 chunk 157 optimal weight: 0.7980 chunk 114 optimal weight: 0.9990 chunk 21 optimal weight: 5.9990 chunk 181 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 GLN A 418 GLN B 230 GLN B 418 GLN B 509 HIS C 230 GLN C 418 GLN D 230 GLN D 418 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 20304 Z= 0.154 Angle : 0.490 8.922 27520 Z= 0.253 Chirality : 0.038 0.207 3124 Planarity : 0.004 0.039 3404 Dihedral : 11.695 165.728 3432 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 2.07 % Allowed : 12.16 % Favored : 85.77 % 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: 1.97 (0.17), residues: 2384 helix: 1.78 (0.12), residues: 1536 sheet: -1.57 (0.47), residues: 100 loop : 0.94 (0.24), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 593 HIS 0.003 0.001 HIS A 201 PHE 0.010 0.001 PHE D 456 TYR 0.010 0.001 TYR A 89 ARG 0.007 0.000 ARG B 180 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 285 time to evaluate : 2.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ASP cc_start: 0.5621 (OUTLIER) cc_final: 0.5051 (p0) REVERT: A 30 GLU cc_start: 0.6696 (OUTLIER) cc_final: 0.6003 (mp0) REVERT: A 51 GLN cc_start: 0.7462 (tp-100) cc_final: 0.7097 (mm-40) REVERT: A 104 GLU cc_start: 0.7563 (pm20) cc_final: 0.6153 (tm-30) REVERT: A 107 LYS cc_start: 0.7134 (mttt) cc_final: 0.6622 (mttp) REVERT: A 176 GLU cc_start: 0.7082 (tt0) cc_final: 0.6685 (mt-10) REVERT: A 190 ARG cc_start: 0.7819 (OUTLIER) cc_final: 0.6364 (mtm180) REVERT: A 257 GLN cc_start: 0.7083 (pt0) cc_final: 0.6591 (tp-100) REVERT: A 262 LYS cc_start: 0.8193 (mttt) cc_final: 0.7928 (mptt) REVERT: A 302 ARG cc_start: 0.7368 (ptm160) cc_final: 0.6634 (tmt-80) REVERT: A 381 GLN cc_start: 0.7303 (mp10) cc_final: 0.5503 (mm-40) REVERT: A 414 ARG cc_start: 0.7288 (ttp80) cc_final: 0.6777 (tpp80) REVERT: A 491 MET cc_start: 0.8099 (mtp) cc_final: 0.7892 (mtp) REVERT: A 497 MET cc_start: 0.8674 (ttt) cc_final: 0.8415 (ttp) REVERT: B 30 GLU cc_start: 0.6648 (OUTLIER) cc_final: 0.6085 (mp0) REVERT: B 51 GLN cc_start: 0.7444 (tp-100) cc_final: 0.7069 (mm-40) REVERT: B 104 GLU cc_start: 0.7475 (pm20) cc_final: 0.6029 (tm-30) REVERT: B 107 LYS cc_start: 0.7134 (mttt) cc_final: 0.6622 (mttp) REVERT: B 176 GLU cc_start: 0.7072 (tt0) cc_final: 0.6676 (mt-10) REVERT: B 190 ARG cc_start: 0.7833 (OUTLIER) cc_final: 0.6368 (mtm180) REVERT: B 257 GLN cc_start: 0.7072 (pt0) cc_final: 0.6599 (tp-100) REVERT: B 262 LYS cc_start: 0.8190 (mttt) cc_final: 0.7930 (mptt) REVERT: B 302 ARG cc_start: 0.7356 (ptm160) cc_final: 0.6623 (tmt-80) REVERT: B 381 GLN cc_start: 0.7286 (mp10) cc_final: 0.5587 (mm-40) REVERT: B 414 ARG cc_start: 0.7294 (ttp80) cc_final: 0.6829 (tpp80) REVERT: B 491 MET cc_start: 0.8097 (mtp) cc_final: 0.7889 (mtp) REVERT: B 497 MET cc_start: 0.8659 (ttt) cc_final: 0.8400 (ttp) REVERT: C 30 GLU cc_start: 0.6652 (OUTLIER) cc_final: 0.6087 (mp0) REVERT: C 51 GLN cc_start: 0.7443 (tp-100) cc_final: 0.7070 (mm-40) REVERT: C 104 GLU cc_start: 0.7473 (pm20) cc_final: 0.6028 (tm-30) REVERT: C 107 LYS cc_start: 0.7135 (mttt) cc_final: 0.6623 (mttp) REVERT: C 176 GLU cc_start: 0.7072 (tt0) cc_final: 0.6673 (mt-10) REVERT: C 190 ARG cc_start: 0.7838 (OUTLIER) cc_final: 0.6370 (mtm180) REVERT: C 257 GLN cc_start: 0.7082 (pt0) cc_final: 0.6575 (tp-100) REVERT: C 262 LYS cc_start: 0.8191 (mttt) cc_final: 0.7927 (mptt) REVERT: C 302 ARG cc_start: 0.7334 (ptm160) cc_final: 0.6651 (tmt-80) REVERT: C 381 GLN cc_start: 0.7274 (mp10) cc_final: 0.5571 (mm-40) REVERT: C 414 ARG cc_start: 0.7320 (ttp80) cc_final: 0.6747 (tpp80) REVERT: C 442 MET cc_start: 0.7366 (mtp) cc_final: 0.7099 (mtp) REVERT: C 491 MET cc_start: 0.8099 (mtp) cc_final: 0.7894 (mtp) REVERT: C 497 MET cc_start: 0.8671 (ttt) cc_final: 0.8415 (ttp) REVERT: D 30 GLU cc_start: 0.6647 (OUTLIER) cc_final: 0.6086 (mp0) REVERT: D 51 GLN cc_start: 0.7449 (tp-100) cc_final: 0.7072 (mm-40) REVERT: D 104 GLU cc_start: 0.7470 (pm20) cc_final: 0.6041 (tm-30) REVERT: D 107 LYS cc_start: 0.7154 (mttt) cc_final: 0.6686 (mttp) REVERT: D 176 GLU cc_start: 0.7081 (tt0) cc_final: 0.6685 (mt-10) REVERT: D 190 ARG cc_start: 0.7837 (OUTLIER) cc_final: 0.6368 (mtm180) REVERT: D 257 GLN cc_start: 0.7069 (pt0) cc_final: 0.6606 (tp-100) REVERT: D 262 LYS cc_start: 0.8204 (mttt) cc_final: 0.7961 (mmtm) REVERT: D 302 ARG cc_start: 0.7333 (ptm160) cc_final: 0.6656 (tmt-80) REVERT: D 381 GLN cc_start: 0.7289 (mp10) cc_final: 0.5578 (mm-40) REVERT: D 414 ARG cc_start: 0.7355 (ttp80) cc_final: 0.6823 (tpp80) REVERT: D 442 MET cc_start: 0.7362 (mtp) cc_final: 0.7099 (mtp) REVERT: D 491 MET cc_start: 0.8097 (mtp) cc_final: 0.7891 (mtp) REVERT: D 497 MET cc_start: 0.8672 (ttt) cc_final: 0.8414 (ttp) outliers start: 43 outliers final: 26 residues processed: 311 average time/residue: 1.4914 time to fit residues: 515.9106 Evaluate side-chains 311 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 276 time to evaluate : 2.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 47 SER Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 190 ARG Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 315 GLU Chi-restraints excluded: chain D residue 419 THR Chi-restraints excluded: chain D residue 499 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 210 optimal weight: 4.9990 chunk 221 optimal weight: 0.9990 chunk 202 optimal weight: 5.9990 chunk 215 optimal weight: 3.9990 chunk 129 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 169 optimal weight: 3.9990 chunk 66 optimal weight: 10.0000 chunk 194 optimal weight: 6.9990 chunk 203 optimal weight: 0.0470 chunk 214 optimal weight: 0.8980 overall best weight: 1.5884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 GLN A 509 HIS B 418 GLN C 418 GLN D 418 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.2658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20304 Z= 0.221 Angle : 0.517 8.861 27520 Z= 0.267 Chirality : 0.039 0.185 3124 Planarity : 0.004 0.039 3404 Dihedral : 11.650 163.061 3432 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 2.12 % Allowed : 12.98 % Favored : 84.90 % 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: 1.87 (0.17), residues: 2384 helix: 1.74 (0.13), residues: 1508 sheet: -1.58 (0.47), residues: 100 loop : 0.83 (0.24), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 593 HIS 0.004 0.001 HIS B 201 PHE 0.009 0.001 PHE B 537 TYR 0.012 0.001 TYR C 89 ARG 0.007 0.000 ARG D 180 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 266 time to evaluate : 2.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ASP cc_start: 0.5654 (OUTLIER) cc_final: 0.5075 (p0) REVERT: A 30 GLU cc_start: 0.6698 (OUTLIER) cc_final: 0.5944 (mp0) REVERT: A 51 GLN cc_start: 0.7446 (tp-100) cc_final: 0.7074 (mm-40) REVERT: A 104 GLU cc_start: 0.7496 (pm20) cc_final: 0.6069 (tm-30) REVERT: A 107 LYS cc_start: 0.7112 (mttt) cc_final: 0.6591 (mttp) REVERT: A 176 GLU cc_start: 0.7083 (tt0) cc_final: 0.6683 (mt-10) REVERT: A 190 ARG cc_start: 0.7854 (OUTLIER) cc_final: 0.6424 (mtm180) REVERT: A 257 GLN cc_start: 0.7111 (pt0) cc_final: 0.6635 (tp-100) REVERT: A 262 LYS cc_start: 0.8202 (mttt) cc_final: 0.7932 (mptt) REVERT: A 302 ARG cc_start: 0.7374 (ptm160) cc_final: 0.6613 (tmt-80) REVERT: A 381 GLN cc_start: 0.7274 (mp10) cc_final: 0.5524 (mm-40) REVERT: A 414 ARG cc_start: 0.7316 (ttp80) cc_final: 0.6828 (tpp80) REVERT: A 491 MET cc_start: 0.8135 (mtp) cc_final: 0.7930 (mtp) REVERT: A 497 MET cc_start: 0.8686 (ttt) cc_final: 0.8425 (ttt) REVERT: B 30 GLU cc_start: 0.6629 (OUTLIER) cc_final: 0.6067 (mp0) REVERT: B 51 GLN cc_start: 0.7446 (tp-100) cc_final: 0.7068 (mm-40) REVERT: B 104 GLU cc_start: 0.7498 (pm20) cc_final: 0.6068 (tm-30) REVERT: B 107 LYS cc_start: 0.7111 (mttt) cc_final: 0.6591 (mttp) REVERT: B 176 GLU cc_start: 0.7067 (tt0) cc_final: 0.6678 (mt-10) REVERT: B 190 ARG cc_start: 0.7869 (OUTLIER) cc_final: 0.6434 (mtm180) REVERT: B 257 GLN cc_start: 0.7102 (pt0) cc_final: 0.6623 (tp-100) REVERT: B 262 LYS cc_start: 0.8206 (mttt) cc_final: 0.7938 (mptt) REVERT: B 302 ARG cc_start: 0.7364 (ptm160) cc_final: 0.6619 (tmt-80) REVERT: B 414 ARG cc_start: 0.7318 (ttp80) cc_final: 0.6870 (tpp80) REVERT: B 491 MET cc_start: 0.8158 (mtp) cc_final: 0.7940 (mtp) REVERT: C 30 GLU cc_start: 0.6632 (OUTLIER) cc_final: 0.6069 (mp0) REVERT: C 51 GLN cc_start: 0.7445 (tp-100) cc_final: 0.7069 (mm-40) REVERT: C 104 GLU cc_start: 0.7498 (pm20) cc_final: 0.6069 (tm-30) REVERT: C 107 LYS cc_start: 0.7112 (mttt) cc_final: 0.6591 (mttp) REVERT: C 176 GLU cc_start: 0.7067 (tt0) cc_final: 0.6671 (mt-10) REVERT: C 190 ARG cc_start: 0.7860 (OUTLIER) cc_final: 0.6387 (mtm180) REVERT: C 257 GLN cc_start: 0.7110 (pt0) cc_final: 0.6633 (tp-100) REVERT: C 262 LYS cc_start: 0.8199 (mttt) cc_final: 0.7930 (mptt) REVERT: C 302 ARG cc_start: 0.7367 (ptm160) cc_final: 0.6634 (tmt-80) REVERT: C 381 GLN cc_start: 0.7237 (mp10) cc_final: 0.5527 (mm-40) REVERT: C 414 ARG cc_start: 0.7331 (ttp80) cc_final: 0.6867 (tpp80) REVERT: C 491 MET cc_start: 0.8124 (mtp) cc_final: 0.7905 (mtp) REVERT: D 30 GLU cc_start: 0.6630 (OUTLIER) cc_final: 0.6073 (mp0) REVERT: D 51 GLN cc_start: 0.7450 (tp-100) cc_final: 0.7071 (mm-40) REVERT: D 104 GLU cc_start: 0.7497 (pm20) cc_final: 0.6072 (tm-30) REVERT: D 107 LYS cc_start: 0.7113 (mttt) cc_final: 0.6601 (mttp) REVERT: D 176 GLU cc_start: 0.7080 (tt0) cc_final: 0.6682 (mt-10) REVERT: D 190 ARG cc_start: 0.7858 (OUTLIER) cc_final: 0.6386 (mtm180) REVERT: D 257 GLN cc_start: 0.7103 (pt0) cc_final: 0.6622 (tp-100) REVERT: D 262 LYS cc_start: 0.8223 (mttt) cc_final: 0.7980 (mptt) REVERT: D 302 ARG cc_start: 0.7367 (ptm160) cc_final: 0.6635 (tmt-80) REVERT: D 381 GLN cc_start: 0.7237 (mp10) cc_final: 0.5587 (mm-40) REVERT: D 414 ARG cc_start: 0.7335 (ttp80) cc_final: 0.6834 (tpp80) REVERT: D 491 MET cc_start: 0.8157 (mtp) cc_final: 0.7942 (mtp) REVERT: D 497 MET cc_start: 0.8687 (ttt) cc_final: 0.8427 (ttt) outliers start: 44 outliers final: 28 residues processed: 293 average time/residue: 1.5097 time to fit residues: 491.6250 Evaluate side-chains 303 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 266 time to evaluate : 2.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 577 MET Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 47 SER Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 190 ARG Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 315 GLU Chi-restraints excluded: chain D residue 355 ARG Chi-restraints excluded: chain D residue 419 THR Chi-restraints excluded: chain D residue 499 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 141 optimal weight: 4.9990 chunk 227 optimal weight: 0.0000 chunk 139 optimal weight: 9.9990 chunk 108 optimal weight: 1.9990 chunk 158 optimal weight: 0.9990 chunk 239 optimal weight: 0.0970 chunk 220 optimal weight: 1.9990 chunk 190 optimal weight: 0.9990 chunk 19 optimal weight: 8.9990 chunk 147 optimal weight: 0.9990 chunk 116 optimal weight: 0.9980 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 GLN B 418 GLN C 418 GLN D 418 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 20304 Z= 0.144 Angle : 0.485 8.842 27520 Z= 0.251 Chirality : 0.037 0.199 3124 Planarity : 0.004 0.038 3404 Dihedral : 11.145 159.205 3432 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 1.97 % Allowed : 13.17 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.08 (0.17), residues: 2384 helix: 1.88 (0.13), residues: 1536 sheet: -1.60 (0.47), residues: 100 loop : 0.95 (0.24), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 593 HIS 0.003 0.001 HIS A 122 PHE 0.010 0.001 PHE D 456 TYR 0.010 0.001 TYR B 89 ARG 0.007 0.000 ARG B 180 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 284 time to evaluate : 2.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ASP cc_start: 0.5592 (OUTLIER) cc_final: 0.5040 (p0) REVERT: A 30 GLU cc_start: 0.6723 (OUTLIER) cc_final: 0.6038 (mp0) REVERT: A 51 GLN cc_start: 0.7469 (tp-100) cc_final: 0.7099 (mm-40) REVERT: A 104 GLU cc_start: 0.7581 (pm20) cc_final: 0.6191 (tm-30) REVERT: A 107 LYS cc_start: 0.7130 (mttt) cc_final: 0.6618 (mttp) REVERT: A 176 GLU cc_start: 0.7061 (tt0) cc_final: 0.6664 (mt-10) REVERT: A 190 ARG cc_start: 0.7788 (OUTLIER) cc_final: 0.6287 (mtm180) REVERT: A 257 GLN cc_start: 0.7077 (pt0) cc_final: 0.6664 (tp-100) REVERT: A 262 LYS cc_start: 0.8209 (mttt) cc_final: 0.7969 (mmtm) REVERT: A 302 ARG cc_start: 0.7364 (ptm160) cc_final: 0.6603 (tmt-80) REVERT: A 381 GLN cc_start: 0.7265 (mp10) cc_final: 0.5470 (mm-40) REVERT: A 414 ARG cc_start: 0.7196 (ttp80) cc_final: 0.6593 (tpp80) REVERT: A 442 MET cc_start: 0.7548 (mtp) cc_final: 0.7348 (mtp) REVERT: A 491 MET cc_start: 0.8048 (mtp) cc_final: 0.7845 (mtp) REVERT: A 497 MET cc_start: 0.8611 (ttt) cc_final: 0.8347 (ttp) REVERT: B 30 GLU cc_start: 0.6665 (OUTLIER) cc_final: 0.5792 (mp0) REVERT: B 34 ASP cc_start: 0.6943 (m-30) cc_final: 0.6734 (m-30) REVERT: B 51 GLN cc_start: 0.7456 (tp-100) cc_final: 0.7081 (mm-40) REVERT: B 104 GLU cc_start: 0.7556 (pm20) cc_final: 0.6151 (tm-30) REVERT: B 107 LYS cc_start: 0.7139 (mttt) cc_final: 0.6635 (mttp) REVERT: B 176 GLU cc_start: 0.7065 (tt0) cc_final: 0.6665 (mt-10) REVERT: B 190 ARG cc_start: 0.7789 (OUTLIER) cc_final: 0.6286 (mtm180) REVERT: B 257 GLN cc_start: 0.7062 (pt0) cc_final: 0.6643 (tp-100) REVERT: B 262 LYS cc_start: 0.8196 (mttt) cc_final: 0.7940 (mptt) REVERT: B 302 ARG cc_start: 0.7386 (ptm160) cc_final: 0.6588 (tmt-80) REVERT: B 381 GLN cc_start: 0.7242 (mp10) cc_final: 0.5463 (mm-40) REVERT: B 414 ARG cc_start: 0.7252 (ttp80) cc_final: 0.6858 (tpp80) REVERT: B 442 MET cc_start: 0.7547 (mtp) cc_final: 0.7340 (mtp) REVERT: B 491 MET cc_start: 0.8044 (mtp) cc_final: 0.7833 (mtp) REVERT: B 497 MET cc_start: 0.8611 (ttt) cc_final: 0.8352 (ttp) REVERT: C 30 GLU cc_start: 0.6667 (OUTLIER) cc_final: 0.5803 (mp0) REVERT: C 51 GLN cc_start: 0.7455 (tp-100) cc_final: 0.7083 (mm-40) REVERT: C 104 GLU cc_start: 0.7546 (pm20) cc_final: 0.6142 (tm-30) REVERT: C 107 LYS cc_start: 0.7130 (mttt) cc_final: 0.6621 (mttp) REVERT: C 176 GLU cc_start: 0.7041 (tt0) cc_final: 0.6648 (mt-10) REVERT: C 190 ARG cc_start: 0.7758 (OUTLIER) cc_final: 0.6298 (mtm180) REVERT: C 257 GLN cc_start: 0.7096 (pt0) cc_final: 0.6647 (tp-100) REVERT: C 262 LYS cc_start: 0.8208 (mttt) cc_final: 0.7968 (mmtm) REVERT: C 302 ARG cc_start: 0.7349 (ptm160) cc_final: 0.6594 (tmt-80) REVERT: C 381 GLN cc_start: 0.7191 (mp10) cc_final: 0.5525 (mm-40) REVERT: C 414 ARG cc_start: 0.7221 (ttp80) cc_final: 0.6573 (tpp80) REVERT: C 442 MET cc_start: 0.7312 (mtp) cc_final: 0.7099 (mtp) REVERT: C 491 MET cc_start: 0.8042 (mtp) cc_final: 0.7823 (mtp) REVERT: C 497 MET cc_start: 0.8613 (ttt) cc_final: 0.8354 (ttp) REVERT: D 30 GLU cc_start: 0.6663 (OUTLIER) cc_final: 0.5794 (mp0) REVERT: D 34 ASP cc_start: 0.6943 (m-30) cc_final: 0.6733 (m-30) REVERT: D 51 GLN cc_start: 0.7458 (tp-100) cc_final: 0.7083 (mm-40) REVERT: D 104 GLU cc_start: 0.7556 (pm20) cc_final: 0.6151 (tm-30) REVERT: D 107 LYS cc_start: 0.7137 (mttt) cc_final: 0.6627 (mttp) REVERT: D 176 GLU cc_start: 0.7060 (tt0) cc_final: 0.6664 (mt-10) REVERT: D 190 ARG cc_start: 0.7744 (OUTLIER) cc_final: 0.6284 (mtm180) REVERT: D 257 GLN cc_start: 0.7064 (pt0) cc_final: 0.6648 (tp-100) REVERT: D 262 LYS cc_start: 0.8294 (mttt) cc_final: 0.8070 (mmtm) REVERT: D 302 ARG cc_start: 0.7348 (ptm160) cc_final: 0.6594 (tmt-80) REVERT: D 381 GLN cc_start: 0.7165 (mp10) cc_final: 0.5517 (mm-40) REVERT: D 414 ARG cc_start: 0.7215 (ttp80) cc_final: 0.6596 (tpp80) REVERT: D 442 MET cc_start: 0.7315 (mtp) cc_final: 0.7102 (mtp) REVERT: D 491 MET cc_start: 0.8059 (mtp) cc_final: 0.7851 (mtp) REVERT: D 497 MET cc_start: 0.8614 (ttt) cc_final: 0.8353 (ttp) outliers start: 41 outliers final: 26 residues processed: 311 average time/residue: 1.4727 time to fit residues: 510.8352 Evaluate side-chains 311 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 276 time to evaluate : 2.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 47 SER Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 190 ARG Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 315 GLU Chi-restraints excluded: chain D residue 355 ARG Chi-restraints excluded: chain D residue 419 THR Chi-restraints excluded: chain D residue 499 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 151 optimal weight: 0.4980 chunk 202 optimal weight: 1.9990 chunk 58 optimal weight: 0.0970 chunk 175 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 190 optimal weight: 5.9990 chunk 79 optimal weight: 0.3980 chunk 195 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 GLN B 418 GLN C 418 GLN D 418 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.126492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.099624 restraints weight = 22686.246| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 1.44 r_work: 0.2995 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.2836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 20304 Z= 0.155 Angle : 0.486 8.667 27520 Z= 0.250 Chirality : 0.037 0.184 3124 Planarity : 0.004 0.038 3404 Dihedral : 11.002 155.565 3432 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 1.88 % Allowed : 13.41 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.12 (0.17), residues: 2384 helix: 1.93 (0.13), residues: 1532 sheet: -1.57 (0.47), residues: 100 loop : 0.93 (0.24), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 593 HIS 0.003 0.001 HIS C 201 PHE 0.008 0.001 PHE D 537 TYR 0.010 0.001 TYR B 89 ARG 0.007 0.000 ARG D 180 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8663.86 seconds wall clock time: 151 minutes 25.31 seconds (9085.31 seconds total)