Starting phenix.real_space_refine on Thu Feb 15 16:05:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dd7_30647/02_2024/7dd7_30647_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dd7_30647/02_2024/7dd7_30647.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dd7_30647/02_2024/7dd7_30647.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dd7_30647/02_2024/7dd7_30647.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dd7_30647/02_2024/7dd7_30647_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dd7_30647/02_2024/7dd7_30647_updated.pdb" } resolution = 3.2 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= -0.001 sd= 0.051 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 6 9.91 5 S 70 5.16 5 Cl 2 4.86 5 C 8262 2.51 5 N 2033 2.21 5 O 2364 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 79": "OE1" <-> "OE2" Residue "A GLU 109": "OE1" <-> "OE2" Residue "A ARG 220": "NH1" <-> "NH2" Residue "A GLU 224": "OE1" <-> "OE2" Residue "A GLU 229": "OE1" <-> "OE2" Residue "A GLU 231": "OE1" <-> "OE2" Residue "A GLU 249": "OE1" <-> "OE2" Residue "A ARG 286": "NH1" <-> "NH2" Residue "A GLU 297": "OE1" <-> "OE2" Residue "A ARG 331": "NH1" <-> "NH2" Residue "A GLU 506": "OE1" <-> "OE2" Residue "A GLU 535": "OE1" <-> "OE2" Residue "A ARG 550": "NH1" <-> "NH2" Residue "A PHE 813": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 56": "OE1" <-> "OE2" Residue "B GLU 59": "OE1" <-> "OE2" Residue "B ARG 220": "NH1" <-> "NH2" Residue "B ARG 227": "NH1" <-> "NH2" Residue "B GLU 228": "OE1" <-> "OE2" Residue "B GLU 229": "OE1" <-> "OE2" Residue "B GLU 241": "OE1" <-> "OE2" Residue "B ARG 285": "NH1" <-> "NH2" Residue "B ARG 286": "NH1" <-> "NH2" Residue "B GLU 297": "OE1" <-> "OE2" Residue "B ARG 331": "NH1" <-> "NH2" Residue "B GLU 354": "OE1" <-> "OE2" Residue "B ARG 543": "NH1" <-> "NH2" Residue "B ARG 550": "NH1" <-> "NH2" Residue "B GLU 555": "OE1" <-> "OE2" Residue "B PHE 813": "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: 12737 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 6212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 791, 6212 Classifications: {'peptide': 791} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 19} Link IDs: {'PTRANS': 34, 'TRANS': 756} Chain breaks: 3 Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 125 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'TYR:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 65 Chain: "B" Number of atoms: 6235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 792, 6235 Classifications: {'peptide': 792} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 17} Link IDs: {'PTRANS': 33, 'TRANS': 758} Chain breaks: 3 Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 4, 'ASN:plan1': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 49 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 88 Unusual residues: {' CA': 2, ' CL': 1, 'H43': 1, 'NAG': 3} Inner-chain residues flagged as termini: ['pdbres="TRP A1107 "'] Classifications: {'peptide': 1, 'undetermined': 7} Modifications used: {'COO': 1} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 90 Unusual residues: {' CA': 4, ' CL': 1, 'H43': 1, 'NAG': 3} Inner-chain residues flagged as termini: ['pdbres="TRP B1109 "'] Classifications: {'peptide': 1, 'undetermined': 9} Modifications used: {'COO': 1} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 7.29, per 1000 atoms: 0.57 Number of scatterers: 12737 At special positions: 0 Unit cell: (105.456, 96.33, 183.534, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 6 19.99 Cl 2 17.00 S 70 16.00 O 2364 8.00 N 2033 7.00 C 8262 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 101 " distance=2.73 Simple disulfide: pdb=" SG CYS A 236 " - pdb=" SG CYS A 560 " distance=2.03 Simple disulfide: pdb=" SG CYS A 358 " - pdb=" SG CYS A 394 " distance=2.03 Simple disulfide: pdb=" SG CYS A 436 " - pdb=" SG CYS A 448 " distance=2.24 Simple disulfide: pdb=" SG CYS A 541 " - pdb=" SG CYS A 561 " distance=2.02 Simple disulfide: pdb=" SG CYS A 545 " - pdb=" SG CYS A 564 " distance=2.04 Simple disulfide: pdb=" SG CYS A 567 " - pdb=" SG CYS A 581 " distance=2.03 Simple disulfide: pdb=" SG CYS A 584 " - pdb=" SG CYS A 597 " distance=2.13 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 101 " distance=2.03 Simple disulfide: pdb=" SG CYS B 236 " - pdb=" SG CYS B 560 " distance=2.03 Simple disulfide: pdb=" SG CYS B 358 " - pdb=" SG CYS B 394 " distance=2.03 Simple disulfide: pdb=" SG CYS B 436 " - pdb=" SG CYS B 448 " distance=2.03 Simple disulfide: pdb=" SG CYS B 541 " - pdb=" SG CYS B 561 " distance=2.66 Simple disulfide: pdb=" SG CYS B 567 " - pdb=" SG CYS B 581 " distance=2.03 Simple disulfide: pdb=" SG CYS B 584 " - pdb=" SG CYS B 597 " distance=1.99 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A1104 " - " ASN A 287 " " NAG A1105 " - " ASN A 399 " " NAG A1106 " - " ASN A 467 " " NAG B1106 " - " ASN B 287 " " NAG B1107 " - " ASN B 399 " " NAG B1108 " - " ASN B 467 " " NAG C 1 " - " ASN A 487 " " NAG D 1 " - " ASN A 540 " " NAG E 1 " - " ASN B 487 " " NAG F 1 " - " ASN B 540 " Time building additional restraints: 5.57 Conformation dependent library (CDL) restraints added in 2.4 seconds 3134 Ramachandran restraints generated. 1567 Oldfield, 0 Emsley, 1567 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2980 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 52 helices and 14 sheets defined 44.0% alpha, 10.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.14 Creating SS restraints... Processing helix chain 'A' and resid 65 through 83 Processing helix chain 'A' and resid 104 through 117 removed outlier: 5.583A pdb=" N GLN A 117 " --> pdb=" O SER A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 160 removed outlier: 3.713A pdb=" N LEU A 156 " --> pdb=" O ALA A 152 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LEU A 159 " --> pdb=" O ASN A 155 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N PHE A 160 " --> pdb=" O LEU A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 175 Processing helix chain 'A' and resid 191 through 203 Processing helix chain 'A' and resid 220 through 233 removed outlier: 3.594A pdb=" N ARG A 233 " --> pdb=" O GLU A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 260 Processing helix chain 'A' and resid 274 through 286 Proline residue: A 278 - end of helix Processing helix chain 'A' and resid 308 through 314 removed outlier: 4.387A pdb=" N VAL A 313 " --> pdb=" O GLU A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 336 removed outlier: 4.072A pdb=" N LYS A 336 " --> pdb=" O GLU A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 356 Processing helix chain 'A' and resid 400 through 402 No H-bonds generated for 'chain 'A' and resid 400 through 402' Processing helix chain 'A' and resid 415 through 434 Processing helix chain 'A' and resid 444 through 446 No H-bonds generated for 'chain 'A' and resid 444 through 446' Processing helix chain 'A' and resid 451 through 453 No H-bonds generated for 'chain 'A' and resid 451 through 453' Processing helix chain 'A' and resid 456 through 464 Processing helix chain 'A' and resid 524 through 526 No H-bonds generated for 'chain 'A' and resid 524 through 526' Processing helix chain 'A' and resid 610 through 636 Processing helix chain 'A' and resid 640 through 643 No H-bonds generated for 'chain 'A' and resid 640 through 643' Processing helix chain 'A' and resid 647 through 666 removed outlier: 3.951A pdb=" N SER A 664 " --> pdb=" O CYS A 660 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N LEU A 665 " --> pdb=" O PHE A 661 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N PHE A 666 " --> pdb=" O SER A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 673 through 696 Proline residue: A 681 - end of helix Processing helix chain 'A' and resid 701 through 705 Processing helix chain 'A' and resid 720 through 743 removed outlier: 5.310A pdb=" N THR A 731 " --> pdb=" O PHE A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 792 Processing helix chain 'A' and resid 802 through 825 Proline residue: A 822 - end of helix Processing helix chain 'A' and resid 829 through 861 removed outlier: 5.461A pdb=" N ASN A 854 " --> pdb=" O CYS A 850 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N LYS A 855 " --> pdb=" O ILE A 851 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 83 Processing helix chain 'B' and resid 104 through 114 Processing helix chain 'B' and resid 116 through 119 No H-bonds generated for 'chain 'B' and resid 116 through 119' Processing helix chain 'B' and resid 147 through 157 removed outlier: 4.027A pdb=" N LEU B 156 " --> pdb=" O ALA B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 175 No H-bonds generated for 'chain 'B' and resid 173 through 175' Processing helix chain 'B' and resid 191 through 203 Processing helix chain 'B' and resid 219 through 233 Processing helix chain 'B' and resid 249 through 260 Processing helix chain 'B' and resid 274 through 286 Proline residue: B 278 - end of helix Processing helix chain 'B' and resid 297 through 300 No H-bonds generated for 'chain 'B' and resid 297 through 300' Processing helix chain 'B' and resid 308 through 312 removed outlier: 3.702A pdb=" N ARG B 312 " --> pdb=" O PRO B 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 308 through 312' Processing helix chain 'B' and resid 330 through 336 removed outlier: 3.784A pdb=" N LYS B 336 " --> pdb=" O GLU B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 356 Processing helix chain 'B' and resid 416 through 434 Processing helix chain 'B' and resid 444 through 446 No H-bonds generated for 'chain 'B' and resid 444 through 446' Processing helix chain 'B' and resid 451 through 453 No H-bonds generated for 'chain 'B' and resid 451 through 453' Processing helix chain 'B' and resid 456 through 464 Processing helix chain 'B' and resid 610 through 636 Processing helix chain 'B' and resid 640 through 643 No H-bonds generated for 'chain 'B' and resid 640 through 643' Processing helix chain 'B' and resid 647 through 666 removed outlier: 3.952A pdb=" N SER B 664 " --> pdb=" O CYS B 660 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N LEU B 665 " --> pdb=" O PHE B 661 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N PHE B 666 " --> pdb=" O SER B 662 " (cutoff:3.500A) Processing helix chain 'B' and resid 673 through 697 Proline residue: B 681 - end of helix Processing helix chain 'B' and resid 701 through 705 Processing helix chain 'B' and resid 720 through 743 removed outlier: 5.310A pdb=" N THR B 731 " --> pdb=" O PHE B 728 " (cutoff:3.500A) Processing helix chain 'B' and resid 769 through 792 Processing helix chain 'B' and resid 802 through 825 Proline residue: B 822 - end of helix Processing helix chain 'B' and resid 829 through 861 removed outlier: 5.461A pdb=" N ASN B 854 " --> pdb=" O CYS B 850 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N LYS B 855 " --> pdb=" O ILE B 851 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 26 through 28 removed outlier: 6.103A pdb=" N ILE A 32 " --> pdb=" O GLY A 94 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N ARG A 96 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LEU A 34 " --> pdb=" O ARG A 96 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N PHE A 98 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N GLY A 36 " --> pdb=" O PHE A 98 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ALA A 140 " --> pdb=" O GLY A 35 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N LEU A 37 " --> pdb=" O ALA A 140 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N VAL A 142 " --> pdb=" O LEU A 37 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 164 through 166 Processing sheet with id= C, first strand: chain 'A' and resid 240 through 243 removed outlier: 9.506A pdb=" N GLU A 241 " --> pdb=" O VAL A 209 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N THR A 211 " --> pdb=" O GLU A 241 " (cutoff:3.500A) removed outlier: 8.222A pdb=" N ILE A 243 " --> pdb=" O THR A 211 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ALA A 213 " --> pdb=" O ILE A 243 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N VAL A 266 " --> pdb=" O GLY A 210 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N ILE A 212 " --> pdb=" O VAL A 266 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N VAL A 268 " --> pdb=" O ILE A 212 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N ALA A 214 " --> pdb=" O VAL A 268 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N PHE A 270 " --> pdb=" O ALA A 214 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ILE A 292 " --> pdb=" O ILE A 267 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N VAL A 269 " --> pdb=" O ILE A 292 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU A 294 " --> pdb=" O VAL A 269 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N SER A 316 " --> pdb=" O TRP A 293 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N ALA A 295 " --> pdb=" O SER A 316 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ILE A 318 " --> pdb=" O ALA A 295 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N THR A 317 " --> pdb=" O TRP A 493 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ASN A 492 " --> pdb=" O GLU A 506 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N GLU A 506 " --> pdb=" O ASN A 492 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N HIS A 494 " --> pdb=" O PHE A 504 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N PHE A 504 " --> pdb=" O HIS A 494 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 468 through 470 Processing sheet with id= E, first strand: chain 'A' and resid 549 through 553 Processing sheet with id= F, first strand: chain 'A' and resid 588 through 590 Processing sheet with id= G, first strand: chain 'A' and resid 601 through 603 Processing sheet with id= H, first strand: chain 'B' and resid 26 through 28 removed outlier: 5.971A pdb=" N ILE B 32 " --> pdb=" O GLY B 94 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N ARG B 96 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LEU B 34 " --> pdb=" O ARG B 96 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N PHE B 98 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N GLY B 36 " --> pdb=" O PHE B 98 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N GLY B 35 " --> pdb=" O ILE B 139 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N VAL B 141 " --> pdb=" O GLY B 35 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N LEU B 37 " --> pdb=" O VAL B 141 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 164 through 166 Processing sheet with id= J, first strand: chain 'B' and resid 240 through 243 removed outlier: 9.433A pdb=" N GLU B 241 " --> pdb=" O VAL B 209 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N THR B 211 " --> pdb=" O GLU B 241 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N ILE B 243 " --> pdb=" O THR B 211 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ALA B 213 " --> pdb=" O ILE B 243 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N VAL B 266 " --> pdb=" O GLY B 210 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N ILE B 212 " --> pdb=" O VAL B 266 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N VAL B 268 " --> pdb=" O ILE B 212 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N ALA B 214 " --> pdb=" O VAL B 268 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N PHE B 270 " --> pdb=" O ALA B 214 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ILE B 292 " --> pdb=" O ILE B 267 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N VAL B 269 " --> pdb=" O ILE B 292 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LEU B 294 " --> pdb=" O VAL B 269 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N PHE B 320 " --> pdb=" O ALA B 295 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N THR B 317 " --> pdb=" O TRP B 493 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ASN B 492 " --> pdb=" O GLU B 506 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N GLU B 506 " --> pdb=" O ASN B 492 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N HIS B 494 " --> pdb=" O PHE B 504 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N PHE B 504 " --> pdb=" O HIS B 494 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 467 through 469 Processing sheet with id= L, first strand: chain 'B' and resid 549 through 552 Processing sheet with id= M, first strand: chain 'B' and resid 588 through 590 Processing sheet with id= N, first strand: chain 'B' and resid 601 through 603 533 hydrogen bonds defined for protein. 1449 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: 4.42 Time building geometry restraints manager: 5.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2065 1.31 - 1.44: 3672 1.44 - 1.57: 7224 1.57 - 1.70: 9 1.70 - 1.83: 86 Bond restraints: 13056 Sorted by residual: bond pdb=" C10 H43 B1110 " pdb=" C11 H43 B1110 " ideal model delta sigma weight residual 1.528 1.341 0.187 2.00e-02 2.50e+03 8.78e+01 bond pdb=" C10 H43 A1108 " pdb=" C11 H43 A1108 " ideal model delta sigma weight residual 1.528 1.341 0.187 2.00e-02 2.50e+03 8.76e+01 bond pdb=" C25 H43 B1110 " pdb=" C26 H43 B1110 " ideal model delta sigma weight residual 1.524 1.340 0.184 2.00e-02 2.50e+03 8.49e+01 bond pdb=" C25 H43 A1108 " pdb=" C26 H43 A1108 " ideal model delta sigma weight residual 1.524 1.340 0.184 2.00e-02 2.50e+03 8.48e+01 bond pdb=" C26 H43 A1108 " pdb=" N9 H43 A1108 " ideal model delta sigma weight residual 1.449 1.585 -0.136 2.00e-02 2.50e+03 4.64e+01 ... (remaining 13051 not shown) Histogram of bond angle deviations from ideal: 100.24 - 107.03: 401 107.03 - 113.82: 7341 113.82 - 120.62: 5384 120.62 - 127.41: 4466 127.41 - 134.21: 139 Bond angle restraints: 17731 Sorted by residual: angle pdb=" N GLU A 603 " pdb=" CA GLU A 603 " pdb=" C GLU A 603 " ideal model delta sigma weight residual 109.25 122.61 -13.36 1.53e+00 4.27e-01 7.63e+01 angle pdb=" C ILE A 598 " pdb=" N PRO A 599 " pdb=" CA PRO A 599 " ideal model delta sigma weight residual 119.90 127.96 -8.06 1.02e+00 9.61e-01 6.24e+01 angle pdb=" N ILE A 598 " pdb=" CA ILE A 598 " pdb=" C ILE A 598 " ideal model delta sigma weight residual 109.02 102.43 6.59 9.30e-01 1.16e+00 5.03e+01 angle pdb=" C10 H43 B1110 " pdb=" N9 H43 B1110 " pdb=" C8 H43 B1110 " ideal model delta sigma weight residual 123.60 107.77 15.83 3.00e+00 1.11e-01 2.79e+01 angle pdb=" C10 H43 A1108 " pdb=" N9 H43 A1108 " pdb=" C8 H43 A1108 " ideal model delta sigma weight residual 123.60 107.78 15.82 3.00e+00 1.11e-01 2.78e+01 ... (remaining 17726 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.35: 7327 23.35 - 46.70: 429 46.70 - 70.06: 72 70.06 - 93.41: 26 93.41 - 116.76: 7 Dihedral angle restraints: 7861 sinusoidal: 3257 harmonic: 4604 Sorted by residual: dihedral pdb=" CB CYS B 436 " pdb=" SG CYS B 436 " pdb=" SG CYS B 448 " pdb=" CB CYS B 448 " ideal model delta sinusoidal sigma weight residual 93.00 -178.39 -88.61 1 1.00e+01 1.00e-02 9.37e+01 dihedral pdb=" CB CYS B 541 " pdb=" SG CYS B 541 " pdb=" SG CYS B 561 " pdb=" CB CYS B 561 " ideal model delta sinusoidal sigma weight residual 93.00 16.56 76.44 1 1.00e+01 1.00e-02 7.35e+01 dihedral pdb=" CB CYS A 545 " pdb=" SG CYS A 545 " pdb=" SG CYS A 564 " pdb=" CB CYS A 564 " ideal model delta sinusoidal sigma weight residual 93.00 158.85 -65.85 1 1.00e+01 1.00e-02 5.67e+01 ... (remaining 7858 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 1917 0.105 - 0.211: 82 0.211 - 0.316: 7 0.316 - 0.421: 2 0.421 - 0.526: 1 Chirality restraints: 2009 Sorted by residual: chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.34 -0.06 2.00e-02 2.50e+03 8.36e+00 chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN A 487 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.87 -0.53 2.00e-01 2.50e+01 6.93e+00 chirality pdb=" CA CYS B 597 " pdb=" N CYS B 597 " pdb=" C CYS B 597 " pdb=" CB CYS B 597 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.08e+00 ... (remaining 2006 not shown) Planarity restraints: 2246 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 696 " -0.028 2.00e-02 2.50e+03 5.54e-02 3.07e+01 pdb=" C VAL A 696 " 0.096 2.00e-02 2.50e+03 pdb=" O VAL A 696 " -0.036 2.00e-02 2.50e+03 pdb=" N LYS A 697 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 599 " 0.018 2.00e-02 2.50e+03 3.60e-02 1.30e+01 pdb=" C PRO A 599 " -0.062 2.00e-02 2.50e+03 pdb=" O PRO A 599 " 0.023 2.00e-02 2.50e+03 pdb=" N LYS A 600 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 696 " 0.017 2.00e-02 2.50e+03 3.49e-02 1.22e+01 pdb=" C VAL B 696 " -0.060 2.00e-02 2.50e+03 pdb=" O VAL B 696 " 0.023 2.00e-02 2.50e+03 pdb=" N LYS B 697 " 0.020 2.00e-02 2.50e+03 ... (remaining 2243 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.40: 66 2.40 - 3.02: 8734 3.02 - 3.65: 18547 3.65 - 4.27: 28237 4.27 - 4.90: 46037 Nonbonded interactions: 101621 Sorted by model distance: nonbonded pdb=" O GLN B 601 " pdb=" CG2 ILE B 759 " model vdw 1.770 3.460 nonbonded pdb=" CE2 TYR B 572 " pdb=" SG CYS B 584 " model vdw 1.854 3.700 nonbonded pdb=" O LEU B 630 " pdb=" NH2 ARG B 637 " model vdw 1.979 2.520 nonbonded pdb=" O LEU A 630 " pdb=" NH2 ARG A 637 " model vdw 1.980 2.520 nonbonded pdb=" OG1 THR A 634 " pdb=" NH2 ARG A 637 " model vdw 2.061 2.520 ... (remaining 101616 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 22 through 119 or resid 136 through 698 or (resid 699 thro \ ugh 718 and (name N or name CA or name C or name O or name CB )) or resid 719 th \ rough 867 or resid 1103 or resid 1106 through 1108)) selection = (chain 'B' and (resid 22 through 119 or resid 136 through 358 or (resid 359 and \ (name N or name CA or name C or name O or name CB )) or resid 392 through 867 or \ resid 1103 or resid 1106 or resid 1109 through 1110)) } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.210 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: 6.280 Check model and map are aligned: 0.220 Set scattering table: 0.130 Process input model: 38.630 Find NCS groups from input model: 0.860 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 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 : 0.010 0.187 13056 Z= 0.675 Angle : 0.876 15.834 17731 Z= 0.495 Chirality : 0.053 0.526 2009 Planarity : 0.005 0.055 2236 Dihedral : 15.844 116.758 4836 Min Nonbonded Distance : 1.770 Molprobity Statistics. All-atom Clashscore : 39.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 0.30 % Allowed : 14.17 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.39 (0.17), residues: 1567 helix: -1.65 (0.16), residues: 703 sheet: -2.08 (0.38), residues: 151 loop : -2.89 (0.19), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 817 HIS 0.004 0.001 HIS A 462 PHE 0.025 0.002 PHE B 814 TYR 0.007 0.001 TYR A 203 ARG 0.002 0.000 ARG B 220 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3134 Ramachandran restraints generated. 1567 Oldfield, 0 Emsley, 1567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3134 Ramachandran restraints generated. 1567 Oldfield, 0 Emsley, 1567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 301 time to evaluate : 1.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 ILE cc_start: 0.7922 (mp) cc_final: 0.7669 (tp) REVERT: A 805 PHE cc_start: 0.7161 (m-80) cc_final: 0.6790 (m-80) REVERT: A 824 TYR cc_start: 0.5679 (OUTLIER) cc_final: 0.5418 (t80) REVERT: B 522 ILE cc_start: 0.8946 (mt) cc_final: 0.8743 (mt) REVERT: B 805 PHE cc_start: 0.8948 (m-80) cc_final: 0.8649 (m-80) outliers start: 4 outliers final: 0 residues processed: 305 average time/residue: 0.2995 time to fit residues: 124.3444 Evaluate side-chains 161 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 160 time to evaluate : 1.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 824 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 133 optimal weight: 10.0000 chunk 119 optimal weight: 0.9980 chunk 66 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 63 optimal weight: 0.0040 chunk 123 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 chunk 92 optimal weight: 0.9980 chunk 143 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 72 GLN A 83 ASN A 193 GLN A 335 GLN A 338 HIS ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 594 HIS ** A 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 23 ASN B 193 GLN B 260 GLN B 335 GLN B 475 GLN ** B 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13056 Z= 0.228 Angle : 0.722 11.015 17731 Z= 0.353 Chirality : 0.050 0.699 2009 Planarity : 0.004 0.048 2236 Dihedral : 10.837 108.839 2011 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.89 % Allowed : 17.80 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.19), residues: 1567 helix: -0.40 (0.19), residues: 702 sheet: -1.68 (0.39), residues: 156 loop : -2.25 (0.20), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A 817 HIS 0.004 0.001 HIS A 494 PHE 0.036 0.001 PHE B 683 TYR 0.015 0.001 TYR B 651 ARG 0.007 0.001 ARG B 751 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3134 Ramachandran restraints generated. 1567 Oldfield, 0 Emsley, 1567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3134 Ramachandran restraints generated. 1567 Oldfield, 0 Emsley, 1567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 183 time to evaluate : 1.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 HIS cc_start: 0.7476 (OUTLIER) cc_final: 0.7075 (t-90) REVERT: A 805 PHE cc_start: 0.7134 (m-80) cc_final: 0.6810 (m-80) REVERT: A 808 PHE cc_start: 0.5086 (OUTLIER) cc_final: 0.4344 (m-80) REVERT: B 805 PHE cc_start: 0.9092 (m-80) cc_final: 0.8647 (m-80) REVERT: B 810 MET cc_start: 0.6712 (mtm) cc_final: 0.6374 (mtm) REVERT: B 814 PHE cc_start: 0.8850 (m-80) cc_final: 0.8640 (m-80) outliers start: 39 outliers final: 20 residues processed: 214 average time/residue: 0.2364 time to fit residues: 74.4816 Evaluate side-chains 166 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 144 time to evaluate : 1.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ASP Chi-restraints excluded: chain A residue 54 ARG Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 181 LYS Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 338 HIS Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 472 MET Chi-restraints excluded: chain A residue 561 CYS Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 763 THR Chi-restraints excluded: chain A residue 808 PHE Chi-restraints excluded: chain A residue 814 PHE Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 694 ILE Chi-restraints excluded: chain B residue 832 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 79 optimal weight: 0.0060 chunk 44 optimal weight: 4.9990 chunk 119 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 143 optimal weight: 6.9990 chunk 155 optimal weight: 8.9990 chunk 128 optimal weight: 5.9990 chunk 142 optimal weight: 20.0000 chunk 49 optimal weight: 4.9990 chunk 115 optimal weight: 0.9990 overall best weight: 2.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 HIS ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 494 HIS ** A 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 752 ASN B 465 HIS B 492 ASN ** B 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.3659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 13056 Z= 0.453 Angle : 0.748 11.414 17731 Z= 0.377 Chirality : 0.052 0.727 2009 Planarity : 0.005 0.045 2236 Dihedral : 9.699 105.752 2009 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 4.75 % Allowed : 19.21 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.20), residues: 1567 helix: -0.01 (0.19), residues: 701 sheet: -1.65 (0.38), residues: 166 loop : -1.92 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 817 HIS 0.022 0.002 HIS A 338 PHE 0.025 0.002 PHE B 845 TYR 0.022 0.002 TYR A 420 ARG 0.006 0.001 ARG B 227 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3134 Ramachandran restraints generated. 1567 Oldfield, 0 Emsley, 1567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3134 Ramachandran restraints generated. 1567 Oldfield, 0 Emsley, 1567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 147 time to evaluate : 1.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7643 (tt) REVERT: A 139 ILE cc_start: 0.8560 (tp) cc_final: 0.8235 (tp) REVERT: A 205 ARG cc_start: 0.7961 (OUTLIER) cc_final: 0.7641 (mmt180) REVERT: A 228 GLU cc_start: 0.7918 (tm-30) cc_final: 0.7696 (tm-30) REVERT: A 805 PHE cc_start: 0.7416 (m-80) cc_final: 0.7044 (m-80) REVERT: A 808 PHE cc_start: 0.4734 (OUTLIER) cc_final: 0.3924 (m-80) REVERT: B 770 MET cc_start: 0.5817 (mtm) cc_final: 0.5426 (mpp) REVERT: B 786 CYS cc_start: 0.8761 (t) cc_final: 0.8205 (p) REVERT: B 805 PHE cc_start: 0.9117 (m-80) cc_final: 0.8488 (m-80) REVERT: B 814 PHE cc_start: 0.8863 (m-80) cc_final: 0.8587 (m-80) outliers start: 64 outliers final: 37 residues processed: 201 average time/residue: 0.2111 time to fit residues: 64.8960 Evaluate side-chains 174 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 134 time to evaluate : 1.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ARG Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 181 LYS Chi-restraints excluded: chain A residue 205 ARG Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 472 MET Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 579 SER Chi-restraints excluded: chain A residue 674 TRP Chi-restraints excluded: chain A residue 693 CYS Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 763 THR Chi-restraints excluded: chain A residue 808 PHE Chi-restraints excluded: chain A residue 814 PHE Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 118 ASN Chi-restraints excluded: chain B residue 171 SER Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 248 ASP Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 352 TRP Chi-restraints excluded: chain B residue 424 TYR Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 694 ILE Chi-restraints excluded: chain B residue 752 ASN Chi-restraints excluded: chain B residue 832 VAL Chi-restraints excluded: chain B residue 850 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 142 optimal weight: 8.9990 chunk 108 optimal weight: 0.6980 chunk 74 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 144 optimal weight: 5.9990 chunk 152 optimal weight: 6.9990 chunk 75 optimal weight: 8.9990 chunk 136 optimal weight: 10.0000 chunk 41 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 HIS ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 494 HIS ** A 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 253 GLN ** B 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.3957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 13056 Z= 0.245 Angle : 0.634 9.819 17731 Z= 0.316 Chirality : 0.048 0.691 2009 Planarity : 0.004 0.047 2236 Dihedral : 9.040 104.615 2009 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 4.15 % Allowed : 20.10 % Favored : 75.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.20), residues: 1567 helix: 0.37 (0.19), residues: 700 sheet: -1.60 (0.37), residues: 171 loop : -1.69 (0.22), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 817 HIS 0.002 0.001 HIS A 509 PHE 0.025 0.001 PHE B 845 TYR 0.012 0.001 TYR A 434 ARG 0.005 0.000 ARG B 227 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3134 Ramachandran restraints generated. 1567 Oldfield, 0 Emsley, 1567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3134 Ramachandran restraints generated. 1567 Oldfield, 0 Emsley, 1567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 149 time to evaluate : 1.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 ILE cc_start: 0.8599 (tp) cc_final: 0.8299 (tp) REVERT: A 228 GLU cc_start: 0.7932 (tm-30) cc_final: 0.7674 (tm-30) REVERT: A 338 HIS cc_start: 0.7615 (OUTLIER) cc_final: 0.7344 (t-90) REVERT: A 668 ILE cc_start: 0.6678 (OUTLIER) cc_final: 0.5487 (mp) REVERT: A 805 PHE cc_start: 0.7335 (m-80) cc_final: 0.6950 (m-80) REVERT: A 808 PHE cc_start: 0.4864 (OUTLIER) cc_final: 0.4170 (m-80) REVERT: B 770 MET cc_start: 0.6031 (mtm) cc_final: 0.5782 (mpp) REVERT: B 786 CYS cc_start: 0.8802 (t) cc_final: 0.8238 (p) REVERT: B 805 PHE cc_start: 0.9136 (m-80) cc_final: 0.8715 (m-80) REVERT: B 814 PHE cc_start: 0.8918 (m-80) cc_final: 0.8602 (m-80) outliers start: 56 outliers final: 37 residues processed: 191 average time/residue: 0.2158 time to fit residues: 63.3137 Evaluate side-chains 174 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 134 time to evaluate : 1.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ARG Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 338 HIS Chi-restraints excluded: chain A residue 424 TYR Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 472 MET Chi-restraints excluded: chain A residue 559 THR Chi-restraints excluded: chain A residue 579 SER Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 661 PHE Chi-restraints excluded: chain A residue 664 SER Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 763 THR Chi-restraints excluded: chain A residue 808 PHE Chi-restraints excluded: chain A residue 814 PHE Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 352 TRP Chi-restraints excluded: chain B residue 424 TYR Chi-restraints excluded: chain B residue 544 ASP Chi-restraints excluded: chain B residue 668 ILE Chi-restraints excluded: chain B residue 694 ILE Chi-restraints excluded: chain B residue 752 ASN Chi-restraints excluded: chain B residue 838 ILE Chi-restraints excluded: chain B residue 850 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 127 optimal weight: 8.9990 chunk 86 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 113 optimal weight: 0.7980 chunk 63 optimal weight: 20.0000 chunk 130 optimal weight: 5.9990 chunk 105 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 77 optimal weight: 3.9990 chunk 137 optimal weight: 6.9990 chunk 38 optimal weight: 0.1980 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 253 GLN ** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.4232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 13056 Z= 0.359 Angle : 0.662 10.018 17731 Z= 0.334 Chirality : 0.049 0.718 2009 Planarity : 0.004 0.046 2236 Dihedral : 8.967 103.427 2009 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 4.82 % Allowed : 21.22 % Favored : 73.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.20), residues: 1567 helix: 0.42 (0.19), residues: 697 sheet: -1.47 (0.38), residues: 165 loop : -1.61 (0.22), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 817 HIS 0.012 0.001 HIS A 338 PHE 0.021 0.001 PHE B 845 TYR 0.018 0.002 TYR A 434 ARG 0.004 0.000 ARG B 285 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3134 Ramachandran restraints generated. 1567 Oldfield, 0 Emsley, 1567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3134 Ramachandran restraints generated. 1567 Oldfield, 0 Emsley, 1567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 141 time to evaluate : 1.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.7737 (tt) REVERT: A 139 ILE cc_start: 0.8636 (tp) cc_final: 0.8376 (tp) REVERT: A 205 ARG cc_start: 0.7912 (OUTLIER) cc_final: 0.7681 (mmt180) REVERT: A 805 PHE cc_start: 0.7425 (m-80) cc_final: 0.7048 (m-80) REVERT: A 808 PHE cc_start: 0.4898 (OUTLIER) cc_final: 0.4232 (m-80) REVERT: A 814 PHE cc_start: 0.7946 (OUTLIER) cc_final: 0.7666 (m-80) REVERT: B 770 MET cc_start: 0.6078 (mtm) cc_final: 0.5868 (mpp) REVERT: B 786 CYS cc_start: 0.8875 (t) cc_final: 0.8524 (p) REVERT: B 805 PHE cc_start: 0.9146 (m-80) cc_final: 0.8594 (m-80) REVERT: B 814 PHE cc_start: 0.8938 (m-10) cc_final: 0.8651 (m-80) outliers start: 65 outliers final: 43 residues processed: 194 average time/residue: 0.2093 time to fit residues: 62.3294 Evaluate side-chains 186 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 139 time to evaluate : 1.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ARG Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 205 ARG Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 472 MET Chi-restraints excluded: chain A residue 541 CYS Chi-restraints excluded: chain A residue 579 SER Chi-restraints excluded: chain A residue 583 LYS Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 661 PHE Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 763 THR Chi-restraints excluded: chain A residue 808 PHE Chi-restraints excluded: chain A residue 814 PHE Chi-restraints excluded: chain A residue 831 PHE Chi-restraints excluded: chain B residue 118 ASN Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 171 SER Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 352 TRP Chi-restraints excluded: chain B residue 424 TYR Chi-restraints excluded: chain B residue 433 ILE Chi-restraints excluded: chain B residue 544 ASP Chi-restraints excluded: chain B residue 694 ILE Chi-restraints excluded: chain B residue 739 VAL Chi-restraints excluded: chain B residue 752 ASN Chi-restraints excluded: chain B residue 832 VAL Chi-restraints excluded: chain B residue 838 ILE Chi-restraints excluded: chain B residue 850 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 51 optimal weight: 5.9990 chunk 137 optimal weight: 5.9990 chunk 30 optimal weight: 0.5980 chunk 89 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 152 optimal weight: 1.9990 chunk 126 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 50 optimal weight: 9.9990 chunk 80 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 HIS ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.4386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13056 Z= 0.194 Angle : 0.610 10.098 17731 Z= 0.304 Chirality : 0.047 0.675 2009 Planarity : 0.004 0.045 2236 Dihedral : 8.708 102.753 2009 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.56 % Allowed : 23.15 % Favored : 73.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.21), residues: 1567 helix: 0.59 (0.19), residues: 695 sheet: -1.42 (0.38), residues: 171 loop : -1.46 (0.23), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 817 HIS 0.002 0.001 HIS A 338 PHE 0.018 0.001 PHE B 845 TYR 0.013 0.001 TYR A 434 ARG 0.003 0.000 ARG B 227 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3134 Ramachandran restraints generated. 1567 Oldfield, 0 Emsley, 1567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3134 Ramachandran restraints generated. 1567 Oldfield, 0 Emsley, 1567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 147 time to evaluate : 1.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 LEU cc_start: 0.8291 (OUTLIER) cc_final: 0.7707 (tt) REVERT: A 139 ILE cc_start: 0.8608 (OUTLIER) cc_final: 0.8354 (tp) REVERT: A 338 HIS cc_start: 0.7661 (OUTLIER) cc_final: 0.7427 (t-90) REVERT: A 588 TYR cc_start: 0.7754 (m-80) cc_final: 0.7397 (m-80) REVERT: A 805 PHE cc_start: 0.7442 (m-80) cc_final: 0.7076 (m-80) REVERT: A 808 PHE cc_start: 0.4905 (OUTLIER) cc_final: 0.4279 (m-80) REVERT: A 814 PHE cc_start: 0.7929 (OUTLIER) cc_final: 0.7616 (m-80) REVERT: B 545 CYS cc_start: 0.7338 (OUTLIER) cc_final: 0.7107 (m) REVERT: B 673 ASN cc_start: 0.8318 (m-40) cc_final: 0.8110 (t0) REVERT: B 805 PHE cc_start: 0.9145 (m-80) cc_final: 0.8701 (m-80) REVERT: B 810 MET cc_start: 0.7002 (mtm) cc_final: 0.6672 (mtm) REVERT: B 814 PHE cc_start: 0.8969 (m-10) cc_final: 0.8676 (m-80) outliers start: 48 outliers final: 27 residues processed: 182 average time/residue: 0.2196 time to fit residues: 62.4962 Evaluate side-chains 171 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 138 time to evaluate : 1.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ARG Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 338 HIS Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 472 MET Chi-restraints excluded: chain A residue 661 PHE Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 808 PHE Chi-restraints excluded: chain A residue 814 PHE Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 248 ASP Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 352 TRP Chi-restraints excluded: chain B residue 424 TYR Chi-restraints excluded: chain B residue 433 ILE Chi-restraints excluded: chain B residue 545 CYS Chi-restraints excluded: chain B residue 694 ILE Chi-restraints excluded: chain B residue 752 ASN Chi-restraints excluded: chain B residue 832 VAL Chi-restraints excluded: chain B residue 838 ILE Chi-restraints excluded: chain B residue 850 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 147 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 111 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 128 optimal weight: 0.1980 chunk 85 optimal weight: 0.7980 chunk 152 optimal weight: 0.6980 chunk 95 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 475 GLN ** A 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.4523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13056 Z= 0.206 Angle : 0.597 10.132 17731 Z= 0.298 Chirality : 0.047 0.663 2009 Planarity : 0.004 0.042 2236 Dihedral : 8.517 101.506 2009 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 4.08 % Allowed : 23.22 % Favored : 72.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.21), residues: 1567 helix: 0.67 (0.19), residues: 693 sheet: -1.27 (0.39), residues: 172 loop : -1.35 (0.23), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A 817 HIS 0.020 0.001 HIS A 338 PHE 0.022 0.001 PHE B 845 TYR 0.016 0.001 TYR A 434 ARG 0.004 0.000 ARG B 227 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3134 Ramachandran restraints generated. 1567 Oldfield, 0 Emsley, 1567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3134 Ramachandran restraints generated. 1567 Oldfield, 0 Emsley, 1567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 143 time to evaluate : 1.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.7701 (tt) REVERT: A 139 ILE cc_start: 0.8633 (tp) cc_final: 0.8366 (tp) REVERT: A 543 ARG cc_start: 0.8105 (mmm160) cc_final: 0.7649 (mmm160) REVERT: A 588 TYR cc_start: 0.7788 (m-80) cc_final: 0.7389 (m-80) REVERT: A 805 PHE cc_start: 0.7464 (m-80) cc_final: 0.7094 (m-80) REVERT: A 808 PHE cc_start: 0.4878 (OUTLIER) cc_final: 0.4263 (m-80) REVERT: A 814 PHE cc_start: 0.7939 (OUTLIER) cc_final: 0.7547 (m-80) REVERT: B 786 CYS cc_start: 0.9175 (t) cc_final: 0.8689 (p) REVERT: B 805 PHE cc_start: 0.9223 (m-80) cc_final: 0.8746 (m-80) REVERT: B 810 MET cc_start: 0.7019 (mtm) cc_final: 0.6803 (mtm) REVERT: B 814 PHE cc_start: 0.9006 (m-10) cc_final: 0.8705 (m-80) outliers start: 55 outliers final: 40 residues processed: 187 average time/residue: 0.2119 time to fit residues: 60.6984 Evaluate side-chains 183 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 140 time to evaluate : 1.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ARG Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 91 MET Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 181 LYS Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 472 MET Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 579 SER Chi-restraints excluded: chain A residue 584 CYS Chi-restraints excluded: chain A residue 661 PHE Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 763 THR Chi-restraints excluded: chain A residue 808 PHE Chi-restraints excluded: chain A residue 814 PHE Chi-restraints excluded: chain A residue 831 PHE Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 248 ASP Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 352 TRP Chi-restraints excluded: chain B residue 424 TYR Chi-restraints excluded: chain B residue 433 ILE Chi-restraints excluded: chain B residue 544 ASP Chi-restraints excluded: chain B residue 694 ILE Chi-restraints excluded: chain B residue 832 VAL Chi-restraints excluded: chain B residue 850 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 94 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 29 optimal weight: 0.0370 chunk 96 optimal weight: 0.7980 chunk 103 optimal weight: 0.6980 chunk 75 optimal weight: 7.9990 chunk 14 optimal weight: 1.9990 chunk 119 optimal weight: 6.9990 chunk 138 optimal weight: 0.9980 overall best weight: 0.9060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 GLN ** A 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 593 ASN ** B 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 338 HIS ** B 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.4709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13056 Z= 0.200 Angle : 0.594 9.744 17731 Z= 0.296 Chirality : 0.047 0.653 2009 Planarity : 0.004 0.042 2236 Dihedral : 8.272 99.684 2009 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 4.30 % Allowed : 22.70 % Favored : 73.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.21), residues: 1567 helix: 0.74 (0.19), residues: 691 sheet: -1.17 (0.39), residues: 172 loop : -1.24 (0.23), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 817 HIS 0.002 0.000 HIS B 753 PHE 0.016 0.001 PHE B 813 TYR 0.017 0.001 TYR A 434 ARG 0.003 0.000 ARG B 227 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3134 Ramachandran restraints generated. 1567 Oldfield, 0 Emsley, 1567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3134 Ramachandran restraints generated. 1567 Oldfield, 0 Emsley, 1567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 147 time to evaluate : 1.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.7652 (tt) REVERT: A 139 ILE cc_start: 0.8615 (OUTLIER) cc_final: 0.8370 (tp) REVERT: A 202 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.7331 (mt-10) REVERT: A 499 ASP cc_start: 0.7965 (OUTLIER) cc_final: 0.7670 (m-30) REVERT: A 543 ARG cc_start: 0.8135 (mmm160) cc_final: 0.7681 (mmm160) REVERT: A 588 TYR cc_start: 0.7822 (m-80) cc_final: 0.7407 (m-80) REVERT: A 607 TRP cc_start: 0.7688 (m100) cc_final: 0.7321 (m-10) REVERT: A 655 PHE cc_start: 0.6680 (OUTLIER) cc_final: 0.6278 (t80) REVERT: A 805 PHE cc_start: 0.7472 (m-80) cc_final: 0.7117 (m-80) REVERT: A 808 PHE cc_start: 0.4899 (OUTLIER) cc_final: 0.4305 (m-80) REVERT: A 814 PHE cc_start: 0.7919 (OUTLIER) cc_final: 0.7467 (m-80) REVERT: B 786 CYS cc_start: 0.9208 (t) cc_final: 0.8704 (p) REVERT: B 805 PHE cc_start: 0.9223 (m-80) cc_final: 0.8785 (m-80) REVERT: B 810 MET cc_start: 0.7075 (mtm) cc_final: 0.6867 (mtm) REVERT: B 813 PHE cc_start: 0.7576 (t80) cc_final: 0.7352 (t80) REVERT: B 814 PHE cc_start: 0.9024 (m-10) cc_final: 0.8676 (m-80) REVERT: B 850 CYS cc_start: 0.6553 (OUTLIER) cc_final: 0.6104 (p) outliers start: 58 outliers final: 36 residues processed: 191 average time/residue: 0.2175 time to fit residues: 64.2095 Evaluate side-chains 186 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 142 time to evaluate : 1.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 472 MET Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 579 SER Chi-restraints excluded: chain A residue 584 CYS Chi-restraints excluded: chain A residue 655 PHE Chi-restraints excluded: chain A residue 661 PHE Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 763 THR Chi-restraints excluded: chain A residue 808 PHE Chi-restraints excluded: chain A residue 814 PHE Chi-restraints excluded: chain B residue 118 ASN Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 248 ASP Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 352 TRP Chi-restraints excluded: chain B residue 433 ILE Chi-restraints excluded: chain B residue 674 TRP Chi-restraints excluded: chain B residue 694 ILE Chi-restraints excluded: chain B residue 752 ASN Chi-restraints excluded: chain B residue 838 ILE Chi-restraints excluded: chain B residue 850 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 145 optimal weight: 1.9990 chunk 133 optimal weight: 7.9990 chunk 141 optimal weight: 6.9990 chunk 85 optimal weight: 0.9980 chunk 61 optimal weight: 4.9990 chunk 111 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 128 optimal weight: 0.0050 chunk 134 optimal weight: 10.0000 chunk 93 optimal weight: 2.9990 chunk 150 optimal weight: 0.9990 overall best weight: 1.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 HIS ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.4843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13056 Z= 0.213 Angle : 0.616 17.730 17731 Z= 0.304 Chirality : 0.048 0.655 2009 Planarity : 0.004 0.043 2236 Dihedral : 8.164 98.287 2009 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.64 % Allowed : 23.44 % Favored : 72.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.21), residues: 1567 helix: 0.66 (0.19), residues: 698 sheet: -1.16 (0.39), residues: 172 loop : -1.18 (0.23), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP A 817 HIS 0.002 0.000 HIS A 338 PHE 0.015 0.001 PHE B 813 TYR 0.017 0.001 TYR A 434 ARG 0.003 0.000 ARG A 285 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3134 Ramachandran restraints generated. 1567 Oldfield, 0 Emsley, 1567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3134 Ramachandran restraints generated. 1567 Oldfield, 0 Emsley, 1567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 140 time to evaluate : 1.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.7683 (tt) REVERT: A 139 ILE cc_start: 0.8620 (OUTLIER) cc_final: 0.8372 (tp) REVERT: A 202 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.7338 (mt-10) REVERT: A 499 ASP cc_start: 0.7966 (OUTLIER) cc_final: 0.7667 (m-30) REVERT: A 607 TRP cc_start: 0.7731 (m100) cc_final: 0.7390 (m-10) REVERT: A 805 PHE cc_start: 0.7504 (m-80) cc_final: 0.7122 (m-80) REVERT: A 808 PHE cc_start: 0.4921 (OUTLIER) cc_final: 0.4318 (m-80) REVERT: A 814 PHE cc_start: 0.7901 (OUTLIER) cc_final: 0.7499 (m-80) REVERT: B 754 GLU cc_start: 0.8600 (mp0) cc_final: 0.8147 (mp0) REVERT: B 786 CYS cc_start: 0.9228 (t) cc_final: 0.8788 (p) REVERT: B 805 PHE cc_start: 0.9231 (m-80) cc_final: 0.8786 (m-80) REVERT: B 810 MET cc_start: 0.7111 (mtm) cc_final: 0.6816 (mtm) REVERT: B 814 PHE cc_start: 0.9032 (m-10) cc_final: 0.8690 (m-80) REVERT: B 850 CYS cc_start: 0.6585 (OUTLIER) cc_final: 0.6171 (p) outliers start: 49 outliers final: 40 residues processed: 177 average time/residue: 0.2173 time to fit residues: 60.6779 Evaluate side-chains 184 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 137 time to evaluate : 1.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 91 MET Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 181 LYS Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 338 HIS Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 472 MET Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 579 SER Chi-restraints excluded: chain A residue 584 CYS Chi-restraints excluded: chain A residue 661 PHE Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 763 THR Chi-restraints excluded: chain A residue 808 PHE Chi-restraints excluded: chain A residue 814 PHE Chi-restraints excluded: chain B residue 118 ASN Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 248 ASP Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 352 TRP Chi-restraints excluded: chain B residue 433 ILE Chi-restraints excluded: chain B residue 674 TRP Chi-restraints excluded: chain B residue 694 ILE Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain B residue 752 ASN Chi-restraints excluded: chain B residue 848 LEU Chi-restraints excluded: chain B residue 850 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 91 optimal weight: 0.0670 chunk 71 optimal weight: 9.9990 chunk 104 optimal weight: 4.9990 chunk 157 optimal weight: 8.9990 chunk 144 optimal weight: 0.9980 chunk 125 optimal weight: 0.1980 chunk 13 optimal weight: 3.9990 chunk 96 optimal weight: 0.7980 chunk 76 optimal weight: 6.9990 chunk 99 optimal weight: 0.8980 chunk 133 optimal weight: 5.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 734 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.4921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13056 Z= 0.182 Angle : 0.610 14.138 17731 Z= 0.302 Chirality : 0.047 0.639 2009 Planarity : 0.004 0.042 2236 Dihedral : 8.043 96.924 2009 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.97 % Allowed : 24.18 % Favored : 72.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.21), residues: 1567 helix: 0.74 (0.20), residues: 694 sheet: -1.18 (0.39), residues: 172 loop : -1.15 (0.23), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A 817 HIS 0.015 0.001 HIS A 338 PHE 0.026 0.001 PHE B 604 TYR 0.016 0.001 TYR A 434 ARG 0.003 0.000 ARG B 227 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3134 Ramachandran restraints generated. 1567 Oldfield, 0 Emsley, 1567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3134 Ramachandran restraints generated. 1567 Oldfield, 0 Emsley, 1567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 142 time to evaluate : 1.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.8013 (tt) REVERT: A 139 ILE cc_start: 0.8596 (OUTLIER) cc_final: 0.8348 (tp) REVERT: A 499 ASP cc_start: 0.7944 (OUTLIER) cc_final: 0.7628 (m-30) REVERT: A 588 TYR cc_start: 0.7723 (m-80) cc_final: 0.7338 (m-80) REVERT: A 607 TRP cc_start: 0.7556 (m100) cc_final: 0.7311 (m-10) REVERT: A 805 PHE cc_start: 0.7499 (m-80) cc_final: 0.7097 (m-80) REVERT: A 808 PHE cc_start: 0.4950 (OUTLIER) cc_final: 0.4351 (m-80) REVERT: A 814 PHE cc_start: 0.7863 (OUTLIER) cc_final: 0.7461 (m-80) REVERT: B 224 GLU cc_start: 0.7264 (tm-30) cc_final: 0.7059 (tm-30) REVERT: B 754 GLU cc_start: 0.8561 (mp0) cc_final: 0.8118 (mp0) REVERT: B 786 CYS cc_start: 0.9243 (t) cc_final: 0.8702 (p) REVERT: B 805 PHE cc_start: 0.9226 (m-80) cc_final: 0.8758 (m-80) REVERT: B 810 MET cc_start: 0.7176 (mtm) cc_final: 0.6901 (mtm) REVERT: B 814 PHE cc_start: 0.9053 (m-10) cc_final: 0.8790 (m-80) outliers start: 40 outliers final: 32 residues processed: 169 average time/residue: 0.1981 time to fit residues: 52.4840 Evaluate side-chains 178 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 141 time to evaluate : 1.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 91 MET Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 181 LYS Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 472 MET Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 584 CYS Chi-restraints excluded: chain A residue 661 PHE Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 763 THR Chi-restraints excluded: chain A residue 808 PHE Chi-restraints excluded: chain A residue 814 PHE Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 248 ASP Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 352 TRP Chi-restraints excluded: chain B residue 433 ILE Chi-restraints excluded: chain B residue 674 TRP Chi-restraints excluded: chain B residue 694 ILE Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain B residue 848 LEU Chi-restraints excluded: chain B residue 850 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 38 optimal weight: 0.0970 chunk 115 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 34 optimal weight: 0.0670 chunk 125 optimal weight: 0.7980 chunk 52 optimal weight: 4.9990 chunk 128 optimal weight: 0.0270 chunk 15 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 110 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 overall best weight: 0.3774 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 475 GLN ** B 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.156359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.107461 restraints weight = 19094.433| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 3.46 r_work: 0.3225 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.5086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13056 Z= 0.173 Angle : 0.592 11.276 17731 Z= 0.294 Chirality : 0.046 0.615 2009 Planarity : 0.004 0.042 2236 Dihedral : 7.764 93.178 2009 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.89 % Allowed : 24.41 % Favored : 72.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.21), residues: 1567 helix: 0.80 (0.20), residues: 694 sheet: -1.12 (0.39), residues: 172 loop : -1.06 (0.23), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 817 HIS 0.005 0.000 HIS A 338 PHE 0.025 0.001 PHE B 604 TYR 0.016 0.001 TYR B 95 ARG 0.003 0.000 ARG B 227 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2843.81 seconds wall clock time: 52 minutes 20.16 seconds (3140.16 seconds total)