Starting phenix.real_space_refine on Thu Feb 15 15:33:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5tr1_8454/02_2024/5tr1_8454.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5tr1_8454/02_2024/5tr1_8454.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5tr1_8454/02_2024/5tr1_8454.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5tr1_8454/02_2024/5tr1_8454.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5tr1_8454/02_2024/5tr1_8454.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5tr1_8454/02_2024/5tr1_8454.pdb" } resolution = 3.95 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= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 66 5.16 5 C 8296 2.51 5 N 2058 2.21 5 O 2258 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 73": "NH1" <-> "NH2" Residue "A GLU 125": "OE1" <-> "OE2" Residue "A GLU 136": "OE1" <-> "OE2" Residue "A ARG 182": "NH1" <-> "NH2" Residue "A GLU 225": "OE1" <-> "OE2" Residue "A ARG 251": "NH1" <-> "NH2" Residue "A PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 351": "NH1" <-> "NH2" Residue "A ARG 355": "NH1" <-> "NH2" Residue "A GLU 381": "OE1" <-> "OE2" Residue "A PHE 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 430": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 490": "OE1" <-> "OE2" Residue "A ARG 538": "NH1" <-> "NH2" Residue "A ARG 544": "NH1" <-> "NH2" Residue "A ARG 553": "NH1" <-> "NH2" Residue "H ARG 39": "NH1" <-> "NH2" Residue "H GLU 47": "OE1" <-> "OE2" Residue "H TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 73": "NH1" <-> "NH2" Residue "B GLU 125": "OE1" <-> "OE2" Residue "B GLU 136": "OE1" <-> "OE2" Residue "B ARG 182": "NH1" <-> "NH2" Residue "B GLU 225": "OE1" <-> "OE2" Residue "B ARG 251": "NH1" <-> "NH2" Residue "B PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 351": "NH1" <-> "NH2" Residue "B ARG 355": "NH1" <-> "NH2" Residue "B GLU 381": "OE1" <-> "OE2" Residue "B PHE 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 430": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 490": "OE1" <-> "OE2" Residue "B ARG 538": "NH1" <-> "NH2" Residue "B ARG 544": "NH1" <-> "NH2" Residue "B ARG 553": "NH1" <-> "NH2" Residue "I ARG 39": "NH1" <-> "NH2" Residue "I GLU 47": "OE1" <-> "OE2" Residue "I TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 12678 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4618 Classifications: {'peptide': 606} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 33, 'TRANS': 572} Chain breaks: 4 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 55 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 50 Chain: "H" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 862 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 106} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "L" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 831 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101} Chain: "B" Number of atoms: 4618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4618 Classifications: {'peptide': 606} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 33, 'TRANS': 572} Chain breaks: 4 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 55 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 50 Chain: "I" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 862 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 106} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "M" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 831 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'Y01': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'Y01:plan-2': 1, 'Y01:plan-1': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'Y01': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'Y01:plan-2': 1, 'Y01:plan-1': 1} Unresolved non-hydrogen planarities: 7 Time building chain proxies: 6.65, per 1000 atoms: 0.52 Number of scatterers: 12678 At special positions: 0 Unit cell: (107.9, 115.7, 141.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 66 16.00 O 2258 8.00 N 2058 7.00 C 8296 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.03 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: 4.90 Conformation dependent library (CDL) restraints added in 2.4 seconds 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3056 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 15 sheets defined 57.0% alpha, 11.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.55 Creating SS restraints... Processing helix chain 'A' and resid 36 through 85 removed outlier: 3.840A pdb=" N CYS A 45 " --> pdb=" O ARG A 41 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N VAL A 46 " --> pdb=" O LYS A 42 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL A 74 " --> pdb=" O THR A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 115 removed outlier: 3.554A pdb=" N ARG A 92 " --> pdb=" O SER A 88 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N TYR A 99 " --> pdb=" O SER A 95 " (cutoff:3.500A) Proline residue: A 100 - end of helix removed outlier: 4.204A pdb=" N ILE A 114 " --> pdb=" O PHE A 110 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N THR A 115 " --> pdb=" O SER A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 132 Processing helix chain 'A' and resid 140 through 142 No H-bonds generated for 'chain 'A' and resid 140 through 142' Processing helix chain 'A' and resid 143 through 158 removed outlier: 3.557A pdb=" N LYS A 147 " --> pdb=" O ASN A 143 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL A 149 " --> pdb=" O GLY A 145 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY A 150 " --> pdb=" O ALA A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 185 Processing helix chain 'A' and resid 194 through 214 Processing helix chain 'A' and resid 215 through 228 removed outlier: 3.603A pdb=" N GLY A 219 " --> pdb=" O ALA A 215 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL A 220 " --> pdb=" O PRO A 216 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LEU A 221 " --> pdb=" O PHE A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 253 removed outlier: 3.502A pdb=" N TYR A 236 " --> pdb=" O SER A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 256 No H-bonds generated for 'chain 'A' and resid 254 through 256' Processing helix chain 'A' and resid 278 through 313 removed outlier: 3.940A pdb=" N ILE A 282 " --> pdb=" O ASP A 278 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N PHE A 283 " --> pdb=" O LEU A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 323 Processing helix chain 'A' and resid 323 through 340 removed outlier: 3.539A pdb=" N VAL A 338 " --> pdb=" O VAL A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 349 Processing helix chain 'A' and resid 353 through 362 removed outlier: 3.608A pdb=" N LEU A 358 " --> pdb=" O MET A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 374 Processing helix chain 'A' and resid 386 through 392 removed outlier: 3.618A pdb=" N PHE A 389 " --> pdb=" O ASN A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 419 removed outlier: 3.661A pdb=" N ILE A 414 " --> pdb=" O PHE A 410 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N LEU A 415 " --> pdb=" O TRP A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 448 Processing helix chain 'A' and resid 462 through 480 removed outlier: 3.917A pdb=" N TYR A 466 " --> pdb=" O MET A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 493 removed outlier: 4.028A pdb=" N LEU A 486 " --> pdb=" O ILE A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 516 removed outlier: 3.776A pdb=" N VAL A 501 " --> pdb=" O HIS A 497 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU A 502 " --> pdb=" O ALA A 498 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N CYS A 515 " --> pdb=" O ILE A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 528 Processing helix chain 'A' and resid 546 through 551 removed outlier: 4.093A pdb=" N PHE A 550 " --> pdb=" O THR A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 575 Processing helix chain 'A' and resid 596 through 605 Processing helix chain 'A' and resid 619 through 625 Processing helix chain 'A' and resid 640 through 652 Processing helix chain 'A' and resid 670 through 682 Processing helix chain 'H' and resid 62 through 65 removed outlier: 3.833A pdb=" N LYS H 65 " --> pdb=" O PRO H 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 62 through 65' Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.905A pdb=" N LEU L 83 " --> pdb=" O SER L 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 85 removed outlier: 3.825A pdb=" N CYS B 45 " --> pdb=" O ARG B 41 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N VAL B 46 " --> pdb=" O LYS B 42 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL B 74 " --> pdb=" O THR B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 115 removed outlier: 3.556A pdb=" N ARG B 92 " --> pdb=" O SER B 88 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N TYR B 99 " --> pdb=" O SER B 95 " (cutoff:3.500A) Proline residue: B 100 - end of helix removed outlier: 4.204A pdb=" N ILE B 114 " --> pdb=" O PHE B 110 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N THR B 115 " --> pdb=" O SER B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 132 Processing helix chain 'B' and resid 140 through 142 No H-bonds generated for 'chain 'B' and resid 140 through 142' Processing helix chain 'B' and resid 143 through 158 removed outlier: 3.556A pdb=" N LYS B 147 " --> pdb=" O ASN B 143 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VAL B 149 " --> pdb=" O GLY B 145 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY B 150 " --> pdb=" O ALA B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 185 Processing helix chain 'B' and resid 194 through 214 Processing helix chain 'B' and resid 215 through 228 removed outlier: 3.603A pdb=" N GLY B 219 " --> pdb=" O ALA B 215 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL B 220 " --> pdb=" O PRO B 216 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N LEU B 221 " --> pdb=" O PHE B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 253 removed outlier: 3.501A pdb=" N TYR B 236 " --> pdb=" O SER B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 256 No H-bonds generated for 'chain 'B' and resid 254 through 256' Processing helix chain 'B' and resid 278 through 313 removed outlier: 3.941A pdb=" N ILE B 282 " --> pdb=" O ASP B 278 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N PHE B 283 " --> pdb=" O LEU B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 323 Processing helix chain 'B' and resid 323 through 340 removed outlier: 3.540A pdb=" N VAL B 338 " --> pdb=" O VAL B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 349 Processing helix chain 'B' and resid 353 through 362 removed outlier: 3.608A pdb=" N LEU B 358 " --> pdb=" O MET B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 374 Processing helix chain 'B' and resid 386 through 392 removed outlier: 3.616A pdb=" N PHE B 389 " --> pdb=" O ASN B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 419 removed outlier: 3.662A pdb=" N ILE B 414 " --> pdb=" O PHE B 410 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N LEU B 415 " --> pdb=" O TRP B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 448 Processing helix chain 'B' and resid 462 through 480 removed outlier: 3.918A pdb=" N TYR B 466 " --> pdb=" O MET B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 493 removed outlier: 4.026A pdb=" N LEU B 486 " --> pdb=" O ILE B 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 497 through 516 removed outlier: 3.776A pdb=" N VAL B 501 " --> pdb=" O HIS B 497 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU B 502 " --> pdb=" O ALA B 498 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N CYS B 515 " --> pdb=" O ILE B 511 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 528 Processing helix chain 'B' and resid 546 through 551 removed outlier: 4.093A pdb=" N PHE B 550 " --> pdb=" O THR B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 575 Processing helix chain 'B' and resid 596 through 605 Processing helix chain 'B' and resid 619 through 625 Processing helix chain 'B' and resid 640 through 652 Processing helix chain 'B' and resid 670 through 682 Processing helix chain 'I' and resid 62 through 65 removed outlier: 3.831A pdb=" N LYS I 65 " --> pdb=" O PRO I 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 62 through 65' Processing helix chain 'I' and resid 87 through 91 Processing helix chain 'M' and resid 79 through 83 removed outlier: 3.904A pdb=" N LEU M 83 " --> pdb=" O SER M 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 558 through 559 removed outlier: 3.626A pdb=" N VAL A 582 " --> pdb=" O LEU A 558 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N TYR A 579 " --> pdb=" O THR A 593 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N THR A 593 " --> pdb=" O TYR A 579 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N LEU A 581 " --> pdb=" O VAL A 591 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 633 through 635 Processing sheet with id=AA3, first strand: chain 'A' and resid 655 through 660 removed outlier: 3.731A pdb=" N GLY A 666 " --> pdb=" O VAL A 658 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N SER A 660 " --> pdb=" O ALA A 664 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N ALA A 664 " --> pdb=" O SER A 660 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.531A pdb=" N GLN H 78 " --> pdb=" O ASP H 73 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASP H 73 " --> pdb=" O GLN H 78 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 58 through 60 removed outlier: 6.683A pdb=" N TRP H 37 " --> pdb=" O MET H 49 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N TYR H 51 " --> pdb=" O TRP H 35 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N TRP H 35 " --> pdb=" O TYR H 51 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.689A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.112A pdb=" N MET L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'L' and resid 53 through 54 removed outlier: 4.066A pdb=" N TRP L 50 " --> pdb=" O TYR L 53 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N TYR L 49 " --> pdb=" O VAL L 33 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N VAL L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 558 through 559 removed outlier: 3.626A pdb=" N VAL B 582 " --> pdb=" O LEU B 558 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N TYR B 579 " --> pdb=" O THR B 593 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N THR B 593 " --> pdb=" O TYR B 579 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N LEU B 581 " --> pdb=" O VAL B 591 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 655 through 660 removed outlier: 3.731A pdb=" N GLY B 666 " --> pdb=" O VAL B 658 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N SER B 660 " --> pdb=" O ALA B 664 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N ALA B 664 " --> pdb=" O SER B 660 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 3 through 7 removed outlier: 3.532A pdb=" N GLN I 78 " --> pdb=" O ASP I 73 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASP I 73 " --> pdb=" O GLN I 78 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 58 through 60 removed outlier: 6.683A pdb=" N TRP I 37 " --> pdb=" O MET I 49 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N TYR I 51 " --> pdb=" O TRP I 35 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N TRP I 35 " --> pdb=" O TYR I 51 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'M' and resid 4 through 7 removed outlier: 3.687A pdb=" N ASP M 70 " --> pdb=" O SER M 67 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'M' and resid 10 through 13 removed outlier: 6.111A pdb=" N MET M 11 " --> pdb=" O GLU M 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'M' and resid 53 through 54 removed outlier: 4.066A pdb=" N TRP M 50 " --> pdb=" O TYR M 53 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N TRP M 35 " --> pdb=" O LEU M 47 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N TYR M 49 " --> pdb=" O VAL M 33 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N VAL M 33 " --> pdb=" O TYR M 49 " (cutoff:3.500A) 735 hydrogen bonds defined for protein. 2121 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: 4.34 Time building geometry restraints manager: 5.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1928 1.31 - 1.44: 3739 1.44 - 1.56: 7217 1.56 - 1.69: 30 1.69 - 1.81: 106 Bond restraints: 13020 Sorted by residual: bond pdb=" CA ILE B 123 " pdb=" CB ILE B 123 " ideal model delta sigma weight residual 1.537 1.564 -0.027 5.00e-03 4.00e+04 2.96e+01 bond pdb=" CA ILE A 123 " pdb=" CB ILE A 123 " ideal model delta sigma weight residual 1.537 1.563 -0.027 5.00e-03 4.00e+04 2.83e+01 bond pdb=" CA SER A 296 " pdb=" C SER A 296 " ideal model delta sigma weight residual 1.523 1.467 0.057 1.30e-02 5.92e+03 1.91e+01 bond pdb=" CA SER B 296 " pdb=" C SER B 296 " ideal model delta sigma weight residual 1.523 1.467 0.057 1.30e-02 5.92e+03 1.91e+01 bond pdb=" C SER B 64 " pdb=" O SER B 64 " ideal model delta sigma weight residual 1.237 1.288 -0.051 1.17e-02 7.31e+03 1.89e+01 ... (remaining 13015 not shown) Histogram of bond angle deviations from ideal: 99.64 - 106.53: 450 106.53 - 113.43: 6781 113.43 - 120.33: 4739 120.33 - 127.22: 5612 127.22 - 134.12: 174 Bond angle restraints: 17756 Sorted by residual: angle pdb=" O ILE B 123 " pdb=" C ILE B 123 " pdb=" N PRO B 124 " ideal model delta sigma weight residual 120.42 125.59 -5.17 6.40e-01 2.44e+00 6.54e+01 angle pdb=" O ILE A 123 " pdb=" C ILE A 123 " pdb=" N PRO A 124 " ideal model delta sigma weight residual 120.42 125.54 -5.12 6.40e-01 2.44e+00 6.40e+01 angle pdb=" O LEU A 499 " pdb=" C LEU A 499 " pdb=" N PRO A 500 " ideal model delta sigma weight residual 120.27 125.77 -5.50 6.90e-01 2.10e+00 6.35e+01 angle pdb=" O LEU B 499 " pdb=" C LEU B 499 " pdb=" N PRO B 500 " ideal model delta sigma weight residual 120.27 125.72 -5.45 6.90e-01 2.10e+00 6.24e+01 angle pdb=" N PHE A 44 " pdb=" CA PHE A 44 " pdb=" C PHE A 44 " ideal model delta sigma weight residual 111.11 119.86 -8.75 1.20e+00 6.94e-01 5.32e+01 ... (remaining 17751 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.49: 6954 16.49 - 32.97: 552 32.97 - 49.46: 120 49.46 - 65.95: 32 65.95 - 82.43: 2 Dihedral angle restraints: 7660 sinusoidal: 2908 harmonic: 4752 Sorted by residual: dihedral pdb=" C THR B 417 " pdb=" N THR B 417 " pdb=" CA THR B 417 " pdb=" CB THR B 417 " ideal model delta harmonic sigma weight residual -122.00 -138.55 16.55 0 2.50e+00 1.60e-01 4.38e+01 dihedral pdb=" C THR A 417 " pdb=" N THR A 417 " pdb=" CA THR A 417 " pdb=" CB THR A 417 " ideal model delta harmonic sigma weight residual -122.00 -138.47 16.47 0 2.50e+00 1.60e-01 4.34e+01 dihedral pdb=" C VAL B 174 " pdb=" N VAL B 174 " pdb=" CA VAL B 174 " pdb=" CB VAL B 174 " ideal model delta harmonic sigma weight residual -122.00 -136.99 14.99 0 2.50e+00 1.60e-01 3.60e+01 ... (remaining 7657 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.123: 1770 0.123 - 0.247: 224 0.247 - 0.370: 38 0.370 - 0.494: 22 0.494 - 0.617: 2 Chirality restraints: 2056 Sorted by residual: chirality pdb=" CA THR B 417 " pdb=" N THR B 417 " pdb=" C THR B 417 " pdb=" CB THR B 417 " both_signs ideal model delta sigma weight residual False 2.53 1.91 0.62 2.00e-01 2.50e+01 9.53e+00 chirality pdb=" CA THR A 417 " pdb=" N THR A 417 " pdb=" C THR A 417 " pdb=" CB THR A 417 " both_signs ideal model delta sigma weight residual False 2.53 1.91 0.61 2.00e-01 2.50e+01 9.40e+00 chirality pdb=" CA ILE A 511 " pdb=" N ILE A 511 " pdb=" C ILE A 511 " pdb=" CB ILE A 511 " both_signs ideal model delta sigma weight residual False 2.43 1.94 0.49 2.00e-01 2.50e+01 6.02e+00 ... (remaining 2053 not shown) Planarity restraints: 2188 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 618 " 0.017 2.00e-02 2.50e+03 3.51e-02 1.23e+01 pdb=" C LEU A 618 " -0.061 2.00e-02 2.50e+03 pdb=" O LEU A 618 " 0.023 2.00e-02 2.50e+03 pdb=" N GLN A 619 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 618 " -0.017 2.00e-02 2.50e+03 3.48e-02 1.21e+01 pdb=" C LEU B 618 " 0.060 2.00e-02 2.50e+03 pdb=" O LEU B 618 " -0.023 2.00e-02 2.50e+03 pdb=" N GLN B 619 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 166 " -0.014 2.00e-02 2.50e+03 2.99e-02 8.97e+00 pdb=" C VAL B 166 " 0.052 2.00e-02 2.50e+03 pdb=" O VAL B 166 " -0.020 2.00e-02 2.50e+03 pdb=" N GLY B 167 " -0.018 2.00e-02 2.50e+03 ... (remaining 2185 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 77 2.67 - 3.22: 12159 3.22 - 3.78: 20041 3.78 - 4.34: 25676 4.34 - 4.90: 43062 Nonbonded interactions: 101015 Sorted by model distance: nonbonded pdb=" O ALA B 471 " pdb=" OG SER B 475 " model vdw 2.107 2.440 nonbonded pdb=" O ALA A 471 " pdb=" OG SER A 475 " model vdw 2.107 2.440 nonbonded pdb=" O ALA B 368 " pdb=" OG1 THR B 371 " model vdw 2.363 2.440 nonbonded pdb=" O ALA A 368 " pdb=" OG1 THR A 371 " model vdw 2.364 2.440 nonbonded pdb=" O ILE A 398 " pdb=" OG1 THR A 401 " model vdw 2.401 2.440 ... (remaining 101010 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' selection = chain 'B' } ncs_group { reference = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'L' selection = chain 'M' } 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 group one per residue 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: 0.680 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: 3.720 Check model and map are aligned: 0.170 Set scattering table: 0.120 Process input model: 36.110 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.090 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:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7063 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 : 0.008 0.069 13020 Z= 0.545 Angle : 1.542 8.754 17756 Z= 1.163 Chirality : 0.095 0.617 2056 Planarity : 0.006 0.057 2188 Dihedral : 12.777 82.433 4592 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.57 % Favored : 95.19 % Rotamer: Outliers : 2.23 % Allowed : 7.22 % Favored : 90.55 % Cbeta Deviations : 2.88 % Peptide Plane: Cis-proline : 4.88 % 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: -0.26 (0.18), residues: 1620 helix: 1.78 (0.14), residues: 814 sheet: -1.22 (0.35), residues: 168 loop : -2.63 (0.20), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP A 50 HIS 0.006 0.002 HIS B 642 PHE 0.023 0.003 PHE B 410 TYR 0.026 0.002 TYR B 357 ARG 0.005 0.001 ARG I 98 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 278 time to evaluate : 1.514 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 60 MET cc_start: 0.8961 (mmm) cc_final: 0.8504 (mmm) REVERT: A 64 SER cc_start: 0.8926 (t) cc_final: 0.8689 (p) REVERT: A 89 HIS cc_start: 0.8006 (OUTLIER) cc_final: 0.7772 (p90) REVERT: A 96 TRP cc_start: 0.8797 (t-100) cc_final: 0.8489 (t-100) REVERT: A 292 CYS cc_start: 0.8937 (m) cc_final: 0.8629 (m) REVERT: A 297 CYS cc_start: 0.8807 (t) cc_final: 0.8523 (m) REVERT: A 348 MET cc_start: 0.9221 (ttm) cc_final: 0.8899 (ttt) REVERT: A 408 MET cc_start: 0.8766 (mmm) cc_final: 0.8422 (mmm) REVERT: A 411 TRP cc_start: 0.8888 (t60) cc_final: 0.8451 (t60) REVERT: A 412 MET cc_start: 0.9329 (mtp) cc_final: 0.8924 (mtp) REVERT: A 421 MET cc_start: 0.8913 (ptm) cc_final: 0.7584 (ttp) REVERT: H 46 LEU cc_start: 0.8884 (mt) cc_final: 0.8569 (mp) REVERT: H 47 GLU cc_start: 0.8455 (tt0) cc_final: 0.8127 (tm-30) REVERT: H 67 ARG cc_start: 0.8951 (ptp-170) cc_final: 0.8594 (ptp-170) REVERT: H 100 VAL cc_start: 0.8931 (p) cc_final: 0.8690 (p) REVERT: H 101 ASP cc_start: 0.8968 (m-30) cc_final: 0.8706 (m-30) REVERT: L 11 MET cc_start: 0.8935 (mmm) cc_final: 0.8394 (mpp) REVERT: L 55 TYR cc_start: 0.8674 (t80) cc_final: 0.7576 (t80) REVERT: L 77 ASN cc_start: 0.9067 (m-40) cc_final: 0.8831 (p0) REVERT: L 89 GLN cc_start: 0.9046 (tt0) cc_final: 0.8536 (tm-30) REVERT: L 90 GLN cc_start: 0.9197 (pt0) cc_final: 0.8501 (pp30) REVERT: L 96 LEU cc_start: 0.9498 (mt) cc_final: 0.9295 (mt) REVERT: L 104 LEU cc_start: 0.8540 (tp) cc_final: 0.7991 (tp) REVERT: L 105 GLU cc_start: 0.7883 (mt-10) cc_final: 0.7642 (tp30) REVERT: B 60 MET cc_start: 0.8973 (mmm) cc_final: 0.8546 (mmm) REVERT: B 64 SER cc_start: 0.8922 (t) cc_final: 0.8686 (p) REVERT: B 96 TRP cc_start: 0.8703 (t-100) cc_final: 0.8420 (t-100) REVERT: B 292 CYS cc_start: 0.8914 (m) cc_final: 0.8605 (m) REVERT: B 297 CYS cc_start: 0.8787 (t) cc_final: 0.8506 (m) REVERT: B 348 MET cc_start: 0.9224 (ttm) cc_final: 0.8907 (ttt) REVERT: B 408 MET cc_start: 0.8775 (mmm) cc_final: 0.8447 (mmm) REVERT: B 411 TRP cc_start: 0.8885 (t60) cc_final: 0.8463 (t60) REVERT: B 412 MET cc_start: 0.9326 (mtp) cc_final: 0.8927 (mtp) REVERT: B 421 MET cc_start: 0.8900 (ptm) cc_final: 0.7599 (ttp) REVERT: I 46 LEU cc_start: 0.8908 (mt) cc_final: 0.8613 (mp) REVERT: I 47 GLU cc_start: 0.8449 (tt0) cc_final: 0.8111 (tm-30) REVERT: I 49 MET cc_start: 0.9321 (mmm) cc_final: 0.9069 (mmm) REVERT: I 67 ARG cc_start: 0.8960 (ptp-170) cc_final: 0.8554 (ptp-170) REVERT: I 100 VAL cc_start: 0.8957 (p) cc_final: 0.8713 (p) REVERT: I 101 ASP cc_start: 0.8969 (m-30) cc_final: 0.8731 (m-30) REVERT: M 11 MET cc_start: 0.8936 (mmm) cc_final: 0.8400 (mpp) REVERT: M 55 TYR cc_start: 0.8689 (t80) cc_final: 0.7571 (t80) REVERT: M 77 ASN cc_start: 0.9064 (m-40) cc_final: 0.8832 (p0) REVERT: M 89 GLN cc_start: 0.9017 (tt0) cc_final: 0.8491 (tm-30) REVERT: M 90 GLN cc_start: 0.9213 (pt0) cc_final: 0.8523 (pp30) REVERT: M 96 LEU cc_start: 0.9505 (mt) cc_final: 0.9264 (mt) REVERT: M 104 LEU cc_start: 0.8546 (tp) cc_final: 0.7928 (tp) REVERT: M 105 GLU cc_start: 0.7882 (mt-10) cc_final: 0.7538 (tp30) outliers start: 30 outliers final: 8 residues processed: 302 average time/residue: 0.2692 time to fit residues: 114.8416 Evaluate side-chains 154 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 145 time to evaluate : 1.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 89 HIS Chi-restraints excluded: chain A residue 99 TYR Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 99 TYR Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain M residue 49 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 136 optimal weight: 4.9990 chunk 122 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 65 optimal weight: 0.0040 chunk 126 optimal weight: 0.9980 chunk 49 optimal weight: 9.9990 chunk 77 optimal weight: 0.9980 chunk 94 optimal weight: 0.8980 chunk 147 optimal weight: 9.9990 overall best weight: 0.7792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 GLN A 313 ASN A 386 ASN A 564 GLN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 GLN B 303 GLN B 313 ASN B 386 ASN ** I 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 27 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7121 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13020 Z= 0.209 Angle : 0.634 7.128 17756 Z= 0.322 Chirality : 0.041 0.234 2056 Planarity : 0.005 0.050 2188 Dihedral : 6.300 55.384 1898 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.49 % Allowed : 14.88 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: 1.67 (0.22), residues: 1620 helix: 3.59 (0.18), residues: 824 sheet: -0.92 (0.33), residues: 182 loop : -1.94 (0.22), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 50 HIS 0.004 0.001 HIS B 642 PHE 0.014 0.001 PHE I 79 TYR 0.018 0.001 TYR B 99 ARG 0.009 0.001 ARG A 238 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 159 time to evaluate : 1.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 MET cc_start: 0.8793 (mmm) cc_final: 0.8396 (mmm) REVERT: A 64 SER cc_start: 0.8992 (t) cc_final: 0.8725 (p) REVERT: A 96 TRP cc_start: 0.8799 (t-100) cc_final: 0.8443 (t-100) REVERT: A 212 VAL cc_start: 0.7971 (OUTLIER) cc_final: 0.7758 (m) REVERT: A 348 MET cc_start: 0.9492 (ttm) cc_final: 0.9264 (ttt) REVERT: A 354 MET cc_start: 0.8558 (mmt) cc_final: 0.8315 (tpt) REVERT: A 408 MET cc_start: 0.8752 (mmm) cc_final: 0.8458 (mmm) REVERT: A 411 TRP cc_start: 0.8685 (t60) cc_final: 0.8413 (t60) REVERT: A 412 MET cc_start: 0.9320 (mtp) cc_final: 0.8815 (mtp) REVERT: A 421 MET cc_start: 0.8753 (ptm) cc_final: 0.7582 (ttp) REVERT: H 4 LEU cc_start: 0.8355 (mt) cc_final: 0.8054 (mp) REVERT: H 38 ILE cc_start: 0.9244 (mt) cc_final: 0.8985 (tt) REVERT: H 67 ARG cc_start: 0.8970 (ptp-170) cc_final: 0.8650 (ptm160) REVERT: H 100 VAL cc_start: 0.8919 (p) cc_final: 0.8565 (p) REVERT: H 101 ASP cc_start: 0.9176 (m-30) cc_final: 0.8907 (m-30) REVERT: L 11 MET cc_start: 0.8859 (mmm) cc_final: 0.8414 (mpp) REVERT: L 45 LYS cc_start: 0.9374 (mtmp) cc_final: 0.9171 (mmtm) REVERT: L 55 TYR cc_start: 0.8596 (t80) cc_final: 0.7610 (t80) REVERT: L 89 GLN cc_start: 0.8937 (tt0) cc_final: 0.8330 (tm-30) REVERT: L 90 GLN cc_start: 0.8631 (pt0) cc_final: 0.8361 (pp30) REVERT: L 96 LEU cc_start: 0.9368 (mt) cc_final: 0.9060 (mt) REVERT: B 60 MET cc_start: 0.8794 (mmm) cc_final: 0.8403 (mmm) REVERT: B 64 SER cc_start: 0.8988 (t) cc_final: 0.8726 (p) REVERT: B 96 TRP cc_start: 0.8802 (t-100) cc_final: 0.8413 (t-100) REVERT: B 212 VAL cc_start: 0.7956 (OUTLIER) cc_final: 0.7737 (m) REVERT: B 348 MET cc_start: 0.9498 (ttm) cc_final: 0.9264 (ttt) REVERT: B 354 MET cc_start: 0.8561 (mmt) cc_final: 0.8244 (tpt) REVERT: B 408 MET cc_start: 0.8745 (mmm) cc_final: 0.8432 (mmm) REVERT: B 411 TRP cc_start: 0.8685 (t60) cc_final: 0.8410 (t60) REVERT: B 412 MET cc_start: 0.9325 (mtp) cc_final: 0.8856 (mtp) REVERT: B 421 MET cc_start: 0.8755 (ptm) cc_final: 0.7594 (ttp) REVERT: I 47 GLU cc_start: 0.8394 (tt0) cc_final: 0.8139 (tm-30) REVERT: I 67 ARG cc_start: 0.8862 (ptp-170) cc_final: 0.8621 (ptm160) REVERT: I 100 VAL cc_start: 0.8943 (p) cc_final: 0.8586 (p) REVERT: I 101 ASP cc_start: 0.9193 (m-30) cc_final: 0.8958 (m-30) REVERT: M 11 MET cc_start: 0.8859 (mmm) cc_final: 0.8431 (mpp) REVERT: M 55 TYR cc_start: 0.8596 (t80) cc_final: 0.7628 (t80) REVERT: M 89 GLN cc_start: 0.8908 (tt0) cc_final: 0.8279 (tm-30) REVERT: M 90 GLN cc_start: 0.8659 (pt0) cc_final: 0.8353 (pp30) REVERT: M 96 LEU cc_start: 0.9373 (mt) cc_final: 0.9011 (mt) outliers start: 20 outliers final: 13 residues processed: 173 average time/residue: 0.2516 time to fit residues: 64.1028 Evaluate side-chains 138 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 123 time to evaluate : 1.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 524 ILE Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain M residue 49 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 81 optimal weight: 7.9990 chunk 45 optimal weight: 3.9990 chunk 122 optimal weight: 10.0000 chunk 100 optimal weight: 4.9990 chunk 40 optimal weight: 8.9990 chunk 147 optimal weight: 3.9990 chunk 159 optimal weight: 8.9990 chunk 131 optimal weight: 8.9990 chunk 146 optimal weight: 9.9990 chunk 50 optimal weight: 5.9990 chunk 118 optimal weight: 2.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 497 HIS A 549 HIS ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 497 HIS B 549 HIS B 564 GLN ** I 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 moved from start: 0.3540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 13020 Z= 0.358 Angle : 0.682 5.941 17756 Z= 0.352 Chirality : 0.041 0.195 2056 Planarity : 0.005 0.033 2188 Dihedral : 5.518 46.289 1888 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 4.69 % Allowed : 14.51 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: 1.07 (0.21), residues: 1620 helix: 2.82 (0.18), residues: 830 sheet: -1.51 (0.31), residues: 222 loop : -1.68 (0.24), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP M 35 HIS 0.005 0.001 HIS A 549 PHE 0.015 0.002 PHE I 80 TYR 0.027 0.002 TYR H 33 ARG 0.010 0.001 ARG B 553 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 114 time to evaluate : 1.397 Fit side-chains revert: symmetry clash REVERT: A 64 SER cc_start: 0.9069 (t) cc_final: 0.8839 (p) REVERT: A 175 MET cc_start: 0.9207 (ttm) cc_final: 0.8679 (mtp) REVERT: A 212 VAL cc_start: 0.7737 (OUTLIER) cc_final: 0.7487 (m) REVERT: A 355 ARG cc_start: 0.8798 (ptt180) cc_final: 0.8541 (ptm160) REVERT: A 359 ASP cc_start: 0.8973 (m-30) cc_final: 0.8738 (m-30) REVERT: A 412 MET cc_start: 0.9266 (mtp) cc_final: 0.8957 (mtp) REVERT: A 421 MET cc_start: 0.8529 (ptm) cc_final: 0.7497 (ttp) REVERT: A 538 ARG cc_start: 0.7038 (OUTLIER) cc_final: 0.6682 (ttt180) REVERT: H 47 GLU cc_start: 0.8368 (tt0) cc_final: 0.7954 (pp20) REVERT: H 67 ARG cc_start: 0.8818 (ptp-170) cc_final: 0.8482 (ptm160) REVERT: H 100 VAL cc_start: 0.8878 (OUTLIER) cc_final: 0.8581 (p) REVERT: L 11 MET cc_start: 0.8909 (mmm) cc_final: 0.8431 (mpp) REVERT: L 55 TYR cc_start: 0.8494 (t80) cc_final: 0.7867 (t80) REVERT: L 89 GLN cc_start: 0.8859 (tt0) cc_final: 0.8275 (tm-30) REVERT: L 107 LYS cc_start: 0.7883 (OUTLIER) cc_final: 0.7466 (mmmt) REVERT: B 64 SER cc_start: 0.9064 (t) cc_final: 0.8836 (p) REVERT: B 175 MET cc_start: 0.9197 (ttm) cc_final: 0.8634 (mtp) REVERT: B 212 VAL cc_start: 0.7729 (OUTLIER) cc_final: 0.7479 (m) REVERT: B 355 ARG cc_start: 0.8789 (ptt180) cc_final: 0.8537 (ptm160) REVERT: B 359 ASP cc_start: 0.8975 (m-30) cc_final: 0.8741 (m-30) REVERT: B 412 MET cc_start: 0.9265 (mtp) cc_final: 0.8954 (mtp) REVERT: B 421 MET cc_start: 0.8532 (ptm) cc_final: 0.7499 (ttp) REVERT: B 538 ARG cc_start: 0.7037 (OUTLIER) cc_final: 0.6682 (ttt180) REVERT: I 47 GLU cc_start: 0.8529 (tt0) cc_final: 0.8163 (tt0) REVERT: I 49 MET cc_start: 0.9232 (mmm) cc_final: 0.8933 (mmm) REVERT: I 67 ARG cc_start: 0.8878 (ptp-170) cc_final: 0.8552 (ptm160) REVERT: I 84 LYS cc_start: 0.8854 (OUTLIER) cc_final: 0.8631 (mmtm) REVERT: M 11 MET cc_start: 0.8941 (mmm) cc_final: 0.8468 (mpp) REVERT: M 55 TYR cc_start: 0.8505 (t80) cc_final: 0.7851 (t80) outliers start: 63 outliers final: 25 residues processed: 162 average time/residue: 0.2344 time to fit residues: 56.4279 Evaluate side-chains 130 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 98 time to evaluate : 1.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 TYR Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 230 HIS Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 297 CYS Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 538 ARG Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 107 LYS Chi-restraints excluded: chain B residue 99 TYR Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 230 HIS Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 297 CYS Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 538 ARG Chi-restraints excluded: chain I residue 84 LYS Chi-restraints excluded: chain M residue 33 VAL Chi-restraints excluded: chain M residue 49 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 145 optimal weight: 4.9990 chunk 110 optimal weight: 0.0870 chunk 76 optimal weight: 8.9990 chunk 16 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 98 optimal weight: 6.9990 chunk 147 optimal weight: 1.9990 chunk 156 optimal weight: 6.9990 chunk 77 optimal weight: 4.9990 chunk 140 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 overall best weight: 2.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 3 GLN ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 moved from start: 0.3779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13020 Z= 0.224 Angle : 0.584 6.784 17756 Z= 0.293 Chirality : 0.039 0.214 2056 Planarity : 0.004 0.035 2188 Dihedral : 5.407 55.337 1886 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.27 % Allowed : 16.22 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: 1.24 (0.21), residues: 1620 helix: 2.88 (0.18), residues: 828 sheet: -1.18 (0.33), residues: 218 loop : -1.57 (0.24), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 48 HIS 0.003 0.001 HIS A 497 PHE 0.010 0.001 PHE B 162 TYR 0.016 0.001 TYR H 33 ARG 0.004 0.000 ARG A 182 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 122 time to evaluate : 1.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 SER cc_start: 0.9092 (t) cc_final: 0.8844 (p) REVERT: A 175 MET cc_start: 0.9183 (ttm) cc_final: 0.8612 (mtp) REVERT: A 212 VAL cc_start: 0.7603 (p) cc_final: 0.7344 (m) REVERT: A 348 MET cc_start: 0.9282 (ttt) cc_final: 0.9021 (ttt) REVERT: A 355 ARG cc_start: 0.8802 (ptt180) cc_final: 0.8518 (ptm160) REVERT: A 359 ASP cc_start: 0.8982 (m-30) cc_final: 0.8702 (m-30) REVERT: A 411 TRP cc_start: 0.8721 (t60) cc_final: 0.8490 (t60) REVERT: A 412 MET cc_start: 0.9343 (mtp) cc_final: 0.8925 (mtp) REVERT: A 421 MET cc_start: 0.8526 (ptm) cc_final: 0.7309 (ttp) REVERT: H 47 GLU cc_start: 0.8061 (tt0) cc_final: 0.7674 (pp20) REVERT: H 67 ARG cc_start: 0.8785 (ptp-170) cc_final: 0.8517 (ptm-80) REVERT: H 100 VAL cc_start: 0.8937 (OUTLIER) cc_final: 0.8701 (p) REVERT: L 11 MET cc_start: 0.8901 (mmm) cc_final: 0.8426 (mpp) REVERT: L 55 TYR cc_start: 0.8247 (t80) cc_final: 0.7777 (t80) REVERT: L 89 GLN cc_start: 0.8657 (tt0) cc_final: 0.8021 (tm-30) REVERT: L 90 GLN cc_start: 0.8822 (OUTLIER) cc_final: 0.8430 (pp30) REVERT: B 64 SER cc_start: 0.9089 (t) cc_final: 0.8845 (p) REVERT: B 175 MET cc_start: 0.9125 (ttm) cc_final: 0.8588 (mtp) REVERT: B 212 VAL cc_start: 0.7585 (p) cc_final: 0.7326 (m) REVERT: B 355 ARG cc_start: 0.8786 (ptt180) cc_final: 0.8502 (ptm160) REVERT: B 359 ASP cc_start: 0.8979 (m-30) cc_final: 0.8696 (m-30) REVERT: B 411 TRP cc_start: 0.8721 (t60) cc_final: 0.8488 (t60) REVERT: B 412 MET cc_start: 0.9346 (mtp) cc_final: 0.8925 (mtp) REVERT: B 421 MET cc_start: 0.8527 (ptm) cc_final: 0.7322 (ttp) REVERT: I 47 GLU cc_start: 0.8405 (tt0) cc_final: 0.8164 (tt0) REVERT: I 67 ARG cc_start: 0.8833 (ptp-170) cc_final: 0.8553 (ptm160) REVERT: M 11 MET cc_start: 0.8874 (mmm) cc_final: 0.8399 (mpp) REVERT: M 55 TYR cc_start: 0.8281 (t80) cc_final: 0.7828 (t80) REVERT: M 89 GLN cc_start: 0.8663 (tt0) cc_final: 0.8259 (tm-30) REVERT: M 90 GLN cc_start: 0.8660 (OUTLIER) cc_final: 0.8328 (pp30) REVERT: M 96 LEU cc_start: 0.9343 (OUTLIER) cc_final: 0.9127 (mp) outliers start: 44 outliers final: 28 residues processed: 157 average time/residue: 0.2585 time to fit residues: 58.7248 Evaluate side-chains 135 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 103 time to evaluate : 1.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 604 GLN Chi-restraints excluded: chain I residue 84 LYS Chi-restraints excluded: chain M residue 33 VAL Chi-restraints excluded: chain M residue 49 TYR Chi-restraints excluded: chain M residue 90 GLN Chi-restraints excluded: chain M residue 96 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 130 optimal weight: 3.9990 chunk 88 optimal weight: 0.0000 chunk 2 optimal weight: 10.0000 chunk 116 optimal weight: 6.9990 chunk 64 optimal weight: 2.9990 chunk 133 optimal weight: 0.0170 chunk 108 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 79 optimal weight: 20.0000 chunk 140 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 overall best weight: 0.9424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 ASN ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 32 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 moved from start: 0.3956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 13020 Z= 0.164 Angle : 0.556 9.445 17756 Z= 0.272 Chirality : 0.038 0.186 2056 Planarity : 0.004 0.034 2188 Dihedral : 5.105 55.537 1886 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.68 % Allowed : 17.19 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: 1.49 (0.21), residues: 1620 helix: 3.00 (0.18), residues: 818 sheet: -0.74 (0.35), residues: 198 loop : -1.36 (0.24), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 48 HIS 0.003 0.000 HIS B 497 PHE 0.008 0.001 PHE A 432 TYR 0.014 0.001 TYR A 99 ARG 0.003 0.000 ARG A 182 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 132 time to evaluate : 1.542 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 SER cc_start: 0.9089 (t) cc_final: 0.8834 (p) REVERT: A 175 MET cc_start: 0.9127 (ttm) cc_final: 0.8481 (mtp) REVERT: A 212 VAL cc_start: 0.7378 (OUTLIER) cc_final: 0.7090 (m) REVERT: A 328 SER cc_start: 0.9483 (OUTLIER) cc_final: 0.9255 (p) REVERT: A 355 ARG cc_start: 0.8834 (ptt180) cc_final: 0.8536 (ptm160) REVERT: A 359 ASP cc_start: 0.8983 (m-30) cc_final: 0.8648 (m-30) REVERT: A 411 TRP cc_start: 0.8714 (t60) cc_final: 0.8506 (t60) REVERT: A 412 MET cc_start: 0.9328 (mtp) cc_final: 0.8942 (mtp) REVERT: A 421 MET cc_start: 0.8626 (ptm) cc_final: 0.7438 (ttp) REVERT: H 100 VAL cc_start: 0.8812 (OUTLIER) cc_final: 0.8580 (p) REVERT: L 11 MET cc_start: 0.8876 (mmm) cc_final: 0.8376 (mpp) REVERT: L 55 TYR cc_start: 0.8195 (t80) cc_final: 0.7615 (t80) REVERT: L 89 GLN cc_start: 0.8650 (tt0) cc_final: 0.7965 (tm-30) REVERT: L 90 GLN cc_start: 0.8731 (OUTLIER) cc_final: 0.8260 (pp30) REVERT: L 96 LEU cc_start: 0.9328 (mt) cc_final: 0.9063 (mt) REVERT: B 64 SER cc_start: 0.9087 (t) cc_final: 0.8834 (p) REVERT: B 175 MET cc_start: 0.9120 (ttm) cc_final: 0.8497 (mtp) REVERT: B 212 VAL cc_start: 0.7367 (OUTLIER) cc_final: 0.7077 (m) REVERT: B 328 SER cc_start: 0.9479 (OUTLIER) cc_final: 0.9249 (p) REVERT: B 348 MET cc_start: 0.9303 (ttt) cc_final: 0.8733 (tpp) REVERT: B 355 ARG cc_start: 0.8824 (ptt180) cc_final: 0.8529 (ptm160) REVERT: B 359 ASP cc_start: 0.8978 (m-30) cc_final: 0.8637 (m-30) REVERT: B 411 TRP cc_start: 0.8716 (t60) cc_final: 0.8493 (t60) REVERT: B 412 MET cc_start: 0.9348 (mtp) cc_final: 0.9050 (mtp) REVERT: B 421 MET cc_start: 0.8625 (ptm) cc_final: 0.7441 (ttp) REVERT: I 84 LYS cc_start: 0.8946 (OUTLIER) cc_final: 0.8728 (mmtm) REVERT: M 11 MET cc_start: 0.8842 (mmm) cc_final: 0.8353 (mpp) REVERT: M 55 TYR cc_start: 0.8239 (t80) cc_final: 0.7642 (t80) REVERT: M 89 GLN cc_start: 0.8777 (tt0) cc_final: 0.8347 (tm-30) REVERT: M 90 GLN cc_start: 0.8562 (pt0) cc_final: 0.8285 (pp30) REVERT: M 96 LEU cc_start: 0.9309 (OUTLIER) cc_final: 0.8691 (mt) outliers start: 36 outliers final: 16 residues processed: 158 average time/residue: 0.2423 time to fit residues: 56.7260 Evaluate side-chains 132 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 108 time to evaluate : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 328 SER Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain I residue 84 LYS Chi-restraints excluded: chain M residue 33 VAL Chi-restraints excluded: chain M residue 49 TYR Chi-restraints excluded: chain M residue 96 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 52 optimal weight: 7.9990 chunk 141 optimal weight: 20.0000 chunk 30 optimal weight: 1.9990 chunk 91 optimal weight: 10.0000 chunk 38 optimal weight: 3.9990 chunk 156 optimal weight: 5.9990 chunk 130 optimal weight: 0.9980 chunk 72 optimal weight: 0.3980 chunk 13 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 moved from start: 0.4197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 13020 Z= 0.208 Angle : 0.572 8.120 17756 Z= 0.284 Chirality : 0.038 0.179 2056 Planarity : 0.004 0.034 2188 Dihedral : 5.079 55.458 1886 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.05 % Allowed : 17.63 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: 1.48 (0.21), residues: 1620 helix: 2.97 (0.18), residues: 818 sheet: -0.70 (0.35), residues: 218 loop : -1.35 (0.24), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP I 37 HIS 0.003 0.001 HIS A 497 PHE 0.010 0.001 PHE I 79 TYR 0.019 0.001 TYR H 33 ARG 0.003 0.000 ARG A 182 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 112 time to evaluate : 1.536 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 SER cc_start: 0.9096 (t) cc_final: 0.8844 (p) REVERT: A 175 MET cc_start: 0.9123 (ttm) cc_final: 0.8491 (mtp) REVERT: A 212 VAL cc_start: 0.7349 (OUTLIER) cc_final: 0.7100 (m) REVERT: A 328 SER cc_start: 0.9486 (OUTLIER) cc_final: 0.9263 (p) REVERT: A 355 ARG cc_start: 0.8822 (ptt180) cc_final: 0.8516 (ptm160) REVERT: A 359 ASP cc_start: 0.8987 (m-30) cc_final: 0.8669 (m-30) REVERT: A 412 MET cc_start: 0.9333 (mtp) cc_final: 0.8983 (mtp) REVERT: A 421 MET cc_start: 0.8541 (ptm) cc_final: 0.7280 (ttp) REVERT: H 100 VAL cc_start: 0.8804 (OUTLIER) cc_final: 0.8592 (p) REVERT: L 11 MET cc_start: 0.8908 (mmm) cc_final: 0.8436 (mpp) REVERT: L 55 TYR cc_start: 0.8186 (t80) cc_final: 0.7638 (t80) REVERT: L 89 GLN cc_start: 0.8640 (tt0) cc_final: 0.7985 (tm-30) REVERT: L 90 GLN cc_start: 0.8761 (OUTLIER) cc_final: 0.8386 (pp30) REVERT: B 64 SER cc_start: 0.9092 (t) cc_final: 0.8843 (p) REVERT: B 175 MET cc_start: 0.9120 (ttm) cc_final: 0.8527 (mtp) REVERT: B 212 VAL cc_start: 0.7324 (OUTLIER) cc_final: 0.7077 (m) REVERT: B 328 SER cc_start: 0.9483 (OUTLIER) cc_final: 0.9253 (p) REVERT: B 348 MET cc_start: 0.9325 (ttt) cc_final: 0.8821 (tpp) REVERT: B 355 ARG cc_start: 0.8829 (ptt180) cc_final: 0.8532 (ptm160) REVERT: B 359 ASP cc_start: 0.8983 (m-30) cc_final: 0.8661 (m-30) REVERT: B 411 TRP cc_start: 0.8680 (t60) cc_final: 0.8479 (t60) REVERT: B 412 MET cc_start: 0.9324 (mtp) cc_final: 0.8972 (mtp) REVERT: B 421 MET cc_start: 0.8551 (ptm) cc_final: 0.7275 (ttp) REVERT: M 11 MET cc_start: 0.8860 (mmm) cc_final: 0.8370 (mpp) REVERT: M 55 TYR cc_start: 0.8300 (t80) cc_final: 0.7749 (t80) REVERT: M 89 GLN cc_start: 0.8755 (tt0) cc_final: 0.8365 (tm-30) REVERT: M 90 GLN cc_start: 0.8587 (pt0) cc_final: 0.8370 (pp30) outliers start: 41 outliers final: 24 residues processed: 143 average time/residue: 0.2158 time to fit residues: 47.1958 Evaluate side-chains 133 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 103 time to evaluate : 1.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 328 SER Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain I residue 38 ILE Chi-restraints excluded: chain M residue 33 VAL Chi-restraints excluded: chain M residue 49 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 151 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 89 optimal weight: 9.9990 chunk 114 optimal weight: 7.9990 chunk 88 optimal weight: 1.9990 chunk 131 optimal weight: 3.9990 chunk 87 optimal weight: 7.9990 chunk 156 optimal weight: 4.9990 chunk 97 optimal weight: 0.9990 chunk 95 optimal weight: 3.9990 chunk 72 optimal weight: 5.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.4437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13020 Z= 0.250 Angle : 0.581 6.968 17756 Z= 0.293 Chirality : 0.038 0.209 2056 Planarity : 0.004 0.035 2188 Dihedral : 5.168 55.998 1886 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.68 % Allowed : 18.30 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.21), residues: 1620 helix: 2.91 (0.18), residues: 814 sheet: -0.71 (0.34), residues: 222 loop : -1.28 (0.24), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP H 48 HIS 0.003 0.001 HIS B 497 PHE 0.011 0.001 PHE L 98 TYR 0.020 0.002 TYR I 33 ARG 0.003 0.001 ARG H 67 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 103 time to evaluate : 1.526 Fit side-chains REVERT: A 64 SER cc_start: 0.9111 (t) cc_final: 0.8865 (p) REVERT: A 175 MET cc_start: 0.9139 (ttm) cc_final: 0.8498 (mtp) REVERT: A 212 VAL cc_start: 0.7393 (OUTLIER) cc_final: 0.7143 (m) REVERT: A 328 SER cc_start: 0.9477 (OUTLIER) cc_final: 0.9249 (p) REVERT: A 355 ARG cc_start: 0.8833 (ptt180) cc_final: 0.8536 (ptm160) REVERT: A 359 ASP cc_start: 0.8988 (m-30) cc_final: 0.8676 (m-30) REVERT: A 421 MET cc_start: 0.8547 (ptm) cc_final: 0.7357 (ttp) REVERT: H 100 VAL cc_start: 0.8704 (OUTLIER) cc_final: 0.8423 (p) REVERT: L 11 MET cc_start: 0.8912 (mmm) cc_final: 0.8455 (mpp) REVERT: L 55 TYR cc_start: 0.8254 (t80) cc_final: 0.7743 (t80) REVERT: L 89 GLN cc_start: 0.8568 (tt0) cc_final: 0.7943 (tm-30) REVERT: L 90 GLN cc_start: 0.8985 (OUTLIER) cc_final: 0.8596 (pp30) REVERT: B 64 SER cc_start: 0.9107 (t) cc_final: 0.8861 (p) REVERT: B 175 MET cc_start: 0.9121 (ttm) cc_final: 0.8529 (mtp) REVERT: B 212 VAL cc_start: 0.7351 (OUTLIER) cc_final: 0.7100 (m) REVERT: B 328 SER cc_start: 0.9456 (OUTLIER) cc_final: 0.9227 (p) REVERT: B 348 MET cc_start: 0.9284 (ttt) cc_final: 0.8807 (tpp) REVERT: B 355 ARG cc_start: 0.8825 (ptt180) cc_final: 0.8533 (ptm160) REVERT: B 359 ASP cc_start: 0.8986 (m-30) cc_final: 0.8675 (m-30) REVERT: B 412 MET cc_start: 0.9306 (mtp) cc_final: 0.8972 (mtp) REVERT: B 421 MET cc_start: 0.8556 (ptm) cc_final: 0.7342 (ttp) REVERT: M 11 MET cc_start: 0.8890 (mmm) cc_final: 0.8432 (mpp) REVERT: M 55 TYR cc_start: 0.8269 (t80) cc_final: 0.7713 (t80) REVERT: M 89 GLN cc_start: 0.8644 (tt0) cc_final: 0.8223 (tm-30) outliers start: 36 outliers final: 23 residues processed: 129 average time/residue: 0.2209 time to fit residues: 43.7604 Evaluate side-chains 128 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 99 time to evaluate : 1.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 328 SER Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain I residue 38 ILE Chi-restraints excluded: chain M residue 33 VAL Chi-restraints excluded: chain M residue 49 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 96 optimal weight: 6.9990 chunk 62 optimal weight: 9.9990 chunk 93 optimal weight: 3.9990 chunk 47 optimal weight: 0.0270 chunk 30 optimal weight: 2.9990 chunk 99 optimal weight: 6.9990 chunk 106 optimal weight: 4.9990 chunk 77 optimal weight: 9.9990 chunk 14 optimal weight: 0.9980 chunk 122 optimal weight: 0.6980 chunk 142 optimal weight: 0.0770 overall best weight: 0.9598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 moved from start: 0.4514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13020 Z= 0.169 Angle : 0.588 9.806 17756 Z= 0.285 Chirality : 0.038 0.175 2056 Planarity : 0.004 0.037 2188 Dihedral : 4.976 55.330 1886 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.23 % Allowed : 18.90 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: 1.50 (0.21), residues: 1620 helix: 2.87 (0.18), residues: 818 sheet: -0.35 (0.36), residues: 212 loop : -1.28 (0.24), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 411 HIS 0.003 0.000 HIS B 497 PHE 0.009 0.001 PHE A 432 TYR 0.016 0.001 TYR H 33 ARG 0.003 0.000 ARG I 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 114 time to evaluate : 1.332 Fit side-chains REVERT: A 64 SER cc_start: 0.9104 (t) cc_final: 0.8847 (p) REVERT: A 175 MET cc_start: 0.9130 (ttm) cc_final: 0.8489 (mtp) REVERT: A 212 VAL cc_start: 0.7312 (OUTLIER) cc_final: 0.7070 (m) REVERT: A 328 SER cc_start: 0.9456 (OUTLIER) cc_final: 0.9233 (p) REVERT: A 355 ARG cc_start: 0.8839 (ptt180) cc_final: 0.8541 (ptm160) REVERT: A 359 ASP cc_start: 0.8991 (m-30) cc_final: 0.8664 (m-30) REVERT: A 421 MET cc_start: 0.8561 (ptm) cc_final: 0.7334 (ttp) REVERT: H 100 VAL cc_start: 0.8627 (OUTLIER) cc_final: 0.8379 (p) REVERT: L 11 MET cc_start: 0.8893 (mmm) cc_final: 0.8458 (mpp) REVERT: L 55 TYR cc_start: 0.8245 (t80) cc_final: 0.7723 (t80) REVERT: L 89 GLN cc_start: 0.8563 (tt0) cc_final: 0.7976 (tm-30) REVERT: L 90 GLN cc_start: 0.8953 (OUTLIER) cc_final: 0.8665 (pp30) REVERT: B 56 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8632 (tp) REVERT: B 64 SER cc_start: 0.9100 (t) cc_final: 0.8846 (p) REVERT: B 175 MET cc_start: 0.9112 (ttm) cc_final: 0.8519 (mtp) REVERT: B 212 VAL cc_start: 0.7195 (OUTLIER) cc_final: 0.6961 (m) REVERT: B 328 SER cc_start: 0.9450 (OUTLIER) cc_final: 0.9223 (p) REVERT: B 348 MET cc_start: 0.9165 (ttt) cc_final: 0.8727 (tpp) REVERT: B 355 ARG cc_start: 0.8829 (ptt180) cc_final: 0.8527 (ptm160) REVERT: B 359 ASP cc_start: 0.8989 (m-30) cc_final: 0.8664 (m-30) REVERT: B 421 MET cc_start: 0.8581 (ptm) cc_final: 0.7346 (ttp) REVERT: M 11 MET cc_start: 0.8857 (mmm) cc_final: 0.8415 (mpp) REVERT: M 55 TYR cc_start: 0.8255 (t80) cc_final: 0.7727 (t80) REVERT: M 89 GLN cc_start: 0.8622 (tt0) cc_final: 0.8220 (tm-30) outliers start: 30 outliers final: 21 residues processed: 134 average time/residue: 0.2107 time to fit residues: 43.4360 Evaluate side-chains 137 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 109 time to evaluate : 1.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain H residue 38 ILE Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 328 SER Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain M residue 33 VAL Chi-restraints excluded: chain M residue 49 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 149 optimal weight: 1.9990 chunk 136 optimal weight: 30.0000 chunk 145 optimal weight: 0.9990 chunk 87 optimal weight: 4.9990 chunk 63 optimal weight: 0.5980 chunk 114 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 131 optimal weight: 6.9990 chunk 137 optimal weight: 5.9990 chunk 144 optimal weight: 0.9990 chunk 95 optimal weight: 9.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 HIS A 543 HIS ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 543 HIS I 3 GLN ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 moved from start: 0.4627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13020 Z= 0.179 Angle : 0.582 11.115 17756 Z= 0.283 Chirality : 0.038 0.171 2056 Planarity : 0.004 0.037 2188 Dihedral : 4.865 53.747 1886 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.46 % Allowed : 18.01 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: 1.46 (0.21), residues: 1620 helix: 2.82 (0.18), residues: 818 sheet: -0.52 (0.36), residues: 226 loop : -1.22 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 411 HIS 0.018 0.001 HIS A 230 PHE 0.008 0.001 PHE I 79 TYR 0.013 0.001 TYR I 33 ARG 0.002 0.000 ARG A 182 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 116 time to evaluate : 1.465 Fit side-chains revert: symmetry clash REVERT: A 64 SER cc_start: 0.9108 (t) cc_final: 0.8849 (p) REVERT: A 175 MET cc_start: 0.9169 (ttm) cc_final: 0.8533 (mtp) REVERT: A 212 VAL cc_start: 0.7239 (p) cc_final: 0.7007 (m) REVERT: A 328 SER cc_start: 0.9455 (OUTLIER) cc_final: 0.9233 (p) REVERT: A 355 ARG cc_start: 0.8836 (ptt180) cc_final: 0.8538 (ptm160) REVERT: A 359 ASP cc_start: 0.8985 (m-30) cc_final: 0.8664 (m-30) REVERT: A 421 MET cc_start: 0.8568 (ptm) cc_final: 0.7367 (ttp) REVERT: H 100 VAL cc_start: 0.8615 (OUTLIER) cc_final: 0.8355 (p) REVERT: L 11 MET cc_start: 0.8889 (mmm) cc_final: 0.8462 (mpp) REVERT: L 55 TYR cc_start: 0.8212 (t80) cc_final: 0.7781 (t80) REVERT: L 89 GLN cc_start: 0.8603 (tt0) cc_final: 0.7895 (tm-30) REVERT: L 90 GLN cc_start: 0.8841 (OUTLIER) cc_final: 0.8465 (pp30) REVERT: B 64 SER cc_start: 0.9107 (t) cc_final: 0.8850 (p) REVERT: B 175 MET cc_start: 0.9103 (ttm) cc_final: 0.8518 (mtp) REVERT: B 212 VAL cc_start: 0.7195 (p) cc_final: 0.6964 (m) REVERT: B 328 SER cc_start: 0.9453 (OUTLIER) cc_final: 0.9231 (p) REVERT: B 355 ARG cc_start: 0.8829 (ptt180) cc_final: 0.8525 (ptm160) REVERT: B 359 ASP cc_start: 0.8984 (m-30) cc_final: 0.8655 (m-30) REVERT: B 421 MET cc_start: 0.8593 (ptm) cc_final: 0.7364 (ttp) REVERT: M 11 MET cc_start: 0.8852 (mmm) cc_final: 0.8418 (mpp) REVERT: M 55 TYR cc_start: 0.8244 (t80) cc_final: 0.7723 (t80) REVERT: M 89 GLN cc_start: 0.8622 (tt0) cc_final: 0.8183 (tm-30) outliers start: 33 outliers final: 21 residues processed: 141 average time/residue: 0.2086 time to fit residues: 45.4173 Evaluate side-chains 138 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 113 time to evaluate : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 328 SER Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain M residue 33 VAL Chi-restraints excluded: chain M residue 49 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 153 optimal weight: 10.0000 chunk 93 optimal weight: 5.9990 chunk 72 optimal weight: 8.9990 chunk 106 optimal weight: 3.9990 chunk 161 optimal weight: 0.0070 chunk 148 optimal weight: 5.9990 chunk 128 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 102 optimal weight: 8.9990 overall best weight: 2.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 HIS ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7171 moved from start: 0.4754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13020 Z= 0.222 Angle : 0.616 11.964 17756 Z= 0.298 Chirality : 0.038 0.172 2056 Planarity : 0.004 0.035 2188 Dihedral : 4.872 53.356 1886 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.08 % Allowed : 18.60 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.21), residues: 1620 helix: 2.78 (0.18), residues: 818 sheet: -0.54 (0.36), residues: 226 loop : -1.17 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 411 HIS 0.023 0.001 HIS B 230 PHE 0.009 0.001 PHE A 432 TYR 0.015 0.001 TYR I 33 ARG 0.002 0.000 ARG A 182 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 113 time to evaluate : 1.524 Fit side-chains revert: symmetry clash REVERT: A 64 SER cc_start: 0.9150 (t) cc_final: 0.8907 (p) REVERT: A 175 MET cc_start: 0.9158 (ttm) cc_final: 0.8527 (mtp) REVERT: A 212 VAL cc_start: 0.7271 (OUTLIER) cc_final: 0.7035 (m) REVERT: A 328 SER cc_start: 0.9489 (OUTLIER) cc_final: 0.9257 (p) REVERT: A 355 ARG cc_start: 0.8779 (ptt180) cc_final: 0.8465 (ptm160) REVERT: A 359 ASP cc_start: 0.8980 (m-30) cc_final: 0.8666 (m-30) REVERT: A 421 MET cc_start: 0.8568 (ptm) cc_final: 0.7412 (ttp) REVERT: L 11 MET cc_start: 0.8884 (mmm) cc_final: 0.8461 (mpp) REVERT: L 55 TYR cc_start: 0.8239 (t80) cc_final: 0.7878 (t80) REVERT: B 64 SER cc_start: 0.9110 (t) cc_final: 0.8858 (p) REVERT: B 175 MET cc_start: 0.9034 (ttm) cc_final: 0.8438 (mtp) REVERT: B 212 VAL cc_start: 0.7229 (p) cc_final: 0.6994 (m) REVERT: B 328 SER cc_start: 0.9466 (OUTLIER) cc_final: 0.9233 (p) REVERT: B 355 ARG cc_start: 0.8826 (ptt180) cc_final: 0.8537 (ptm160) REVERT: B 359 ASP cc_start: 0.8979 (m-30) cc_final: 0.8666 (m-30) REVERT: B 421 MET cc_start: 0.8593 (ptm) cc_final: 0.7403 (ttp) REVERT: M 11 MET cc_start: 0.8851 (mmm) cc_final: 0.8417 (mpp) REVERT: M 55 TYR cc_start: 0.8266 (t80) cc_final: 0.7866 (t80) REVERT: M 89 GLN cc_start: 0.8682 (tt0) cc_final: 0.8220 (tm-30) outliers start: 28 outliers final: 19 residues processed: 132 average time/residue: 0.2099 time to fit residues: 43.0746 Evaluate side-chains 128 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 106 time to evaluate : 1.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 328 SER Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain M residue 33 VAL Chi-restraints excluded: chain M residue 49 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 136 optimal weight: 9.9990 chunk 39 optimal weight: 8.9990 chunk 118 optimal weight: 10.0000 chunk 18 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 chunk 128 optimal weight: 8.9990 chunk 53 optimal weight: 5.9990 chunk 132 optimal weight: 0.0570 chunk 16 optimal weight: 0.9990 chunk 23 optimal weight: 8.9990 chunk 113 optimal weight: 0.8980 overall best weight: 2.3904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.039889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2620 r_free = 0.2620 target = 0.033824 restraints weight = 91221.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2659 r_free = 0.2659 target = 0.034925 restraints weight = 46644.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.035647 restraints weight = 29040.207| |-----------------------------------------------------------------------------| r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.4862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13020 Z= 0.230 Angle : 0.623 16.473 17756 Z= 0.302 Chirality : 0.039 0.164 2056 Planarity : 0.004 0.035 2188 Dihedral : 4.925 51.299 1886 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.23 % Allowed : 18.53 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: 1.43 (0.21), residues: 1620 helix: 2.73 (0.18), residues: 816 sheet: -0.57 (0.36), residues: 226 loop : -1.09 (0.25), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 411 HIS 0.003 0.001 HIS A 497 PHE 0.012 0.001 PHE A 404 TYR 0.015 0.002 TYR I 33 ARG 0.002 0.000 ARG H 67 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2281.33 seconds wall clock time: 43 minutes 4.89 seconds (2584.89 seconds total)