Starting phenix.real_space_refine on Sun Feb 18 12:55:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xn3_22266/02_2024/6xn3_22266.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xn3_22266/02_2024/6xn3_22266.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xn3_22266/02_2024/6xn3_22266.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xn3_22266/02_2024/6xn3_22266.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xn3_22266/02_2024/6xn3_22266.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xn3_22266/02_2024/6xn3_22266.pdb" } resolution = 3.0 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= -0.002 sd= 1.543 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 70 5.49 5 S 52 5.16 5 C 13784 2.51 5 N 3747 2.21 5 O 4396 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 121": "NH1" <-> "NH2" Residue "A GLU 285": "OE1" <-> "OE2" Residue "A GLU 293": "OE1" <-> "OE2" Residue "A PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 365": "NH1" <-> "NH2" Residue "A GLU 387": "OE1" <-> "OE2" Residue "A GLU 413": "OE1" <-> "OE2" Residue "A GLU 502": "OE1" <-> "OE2" Residue "A PHE 598": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 694": "NH1" <-> "NH2" Residue "A ARG 740": "NH1" <-> "NH2" Residue "B GLU 38": "OE1" <-> "OE2" Residue "B GLU 167": "OE1" <-> "OE2" Residue "B GLU 235": "OE1" <-> "OE2" Residue "B PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 85": "OE1" <-> "OE2" Residue "F GLU 106": "OE1" <-> "OE2" Residue "G GLU 69": "OE1" <-> "OE2" Residue "G GLU 106": "OE1" <-> "OE2" Residue "I GLU 69": "OE1" <-> "OE2" Residue "I GLU 85": "OE1" <-> "OE2" Residue "I GLU 108": "OE1" <-> "OE2" Residue "I GLU 120": "OE1" <-> "OE2" Residue "J ARG 6": "NH1" <-> "NH2" Residue "J ARG 61": "NH1" <-> "NH2" Residue "J PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 123": "NH1" <-> "NH2" Residue "J GLU 189": "OE1" <-> "OE2" Residue "J ARG 288": "NH1" <-> "NH2" Residue "J ARG 304": "NH1" <-> "NH2" Residue "J ARG 311": "NH1" <-> "NH2" Residue "J ARG 346": "NH1" <-> "NH2" Residue "C ARG 35": "NH1" <-> "NH2" Residue "C ARG 70": "NH1" <-> "NH2" Residue "C GLU 78": "OE1" <-> "OE2" Residue "C ARG 110": "NH1" <-> "NH2" Residue "C ARG 124": "NH1" <-> "NH2" Residue "C ARG 126": "NH1" <-> "NH2" Residue "D ARG 35": "NH1" <-> "NH2" Residue "D GLU 49": "OE1" <-> "OE2" Residue "D GLU 62": "OE1" <-> "OE2" Residue "D ARG 70": "NH1" <-> "NH2" Residue "D ARG 100": "NH1" <-> "NH2" Residue "D ARG 110": "NH1" <-> "NH2" Residue "D ARG 124": "NH1" <-> "NH2" Residue "D ARG 126": "NH1" <-> "NH2" Residue "E ARG 35": "NH1" <-> "NH2" Residue "E ARG 70": "NH1" <-> "NH2" Residue "E GLU 81": "OE1" <-> "OE2" Residue "E ARG 110": "NH1" <-> "NH2" Residue "E ARG 124": "NH1" <-> "NH2" Residue "E ARG 126": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 22049 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 741, 5984 Classifications: {'peptide': 741} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 7, 'TRANS': 730} Chain breaks: 2 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 2232 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 276, 2230 Classifications: {'peptide': 276} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 9, 'TRANS': 265} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 276, 2230 Classifications: {'peptide': 276} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 9, 'TRANS': 265} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 2277 Chain: "F" Number of atoms: 1617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1617 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 4, 'TRANS': 202} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "H" Number of atoms: 1673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1673 Classifications: {'peptide': 214} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 207} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "G" Number of atoms: 1673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1673 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 5, 'TRANS': 208} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "I" Number of atoms: 1673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1673 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 5, 'TRANS': 208} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "J" Number of atoms: 2467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2467 Classifications: {'peptide': 303} Modifications used: {'COO': 1} Link IDs: {'CIS': 5, 'PTRANS': 11, 'TRANS': 286} Chain breaks: 3 Chain: "R" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 776 Classifications: {'RNA': 37} Modifications used: {'5*END': 1, 'rna2p_pur': 12, 'rna2p_pyr': 6, 'rna3p_pur': 5, 'rna3p_pyr': 14} Link IDs: {'rna2p': 18, 'rna3p': 18} Chain: "C" Number of atoms: 1115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1115 Classifications: {'peptide': 139} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 136} Chain: "D" Number of atoms: 1089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1089 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 2, 'TRANS': 132} Chain: "E" Number of atoms: 1016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1016 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 2, 'TRANS': 122} Chain breaks: 1 Chain: "T" Number of atoms: 734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 734 Classifications: {'RNA': 34} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 3, 'rna3p_pur': 19, 'rna3p_pyr': 9} Link IDs: {'rna2p': 6, 'rna3p': 27} Time building chain proxies: 12.89, per 1000 atoms: 0.58 Number of scatterers: 22049 At special positions: 0 Unit cell: (122.436, 126.732, 208.356, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 52 16.00 P 70 15.00 O 4396 8.00 N 3747 7.00 C 13784 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 405 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 405 " - pdb=" SG CYS A 421 " distance=2.01 Simple disulfide: pdb=" SG CYS A 418 " - pdb=" SG CYS A 421 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.35 Conformation dependent library (CDL) restraints added in 4.2 seconds 5060 Ramachandran restraints generated. 2530 Oldfield, 0 Emsley, 2530 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4806 Finding SS restraints... Secondary structure from input PDB file: 91 helices and 30 sheets defined 44.4% alpha, 14.5% beta 16 base pairs and 29 stacking pairs defined. Time for finding SS restraints: 7.20 Creating SS restraints... Processing helix chain 'A' and resid 3 through 12 Processing helix chain 'A' and resid 14 through 21 Processing helix chain 'A' and resid 28 through 38 removed outlier: 3.858A pdb=" N LEU A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LYS A 38 " --> pdb=" O GLY A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 removed outlier: 3.732A pdb=" N THR A 49 " --> pdb=" O ASN A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 63 Processing helix chain 'A' and resid 73 through 85 Processing helix chain 'A' and resid 109 through 113 removed outlier: 3.527A pdb=" N ASN A 112 " --> pdb=" O SER A 109 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL A 113 " --> pdb=" O VAL A 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 109 through 113' Processing helix chain 'A' and resid 115 through 120 removed outlier: 3.674A pdb=" N LYS A 119 " --> pdb=" O ASN A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 165 removed outlier: 3.550A pdb=" N TYR A 154 " --> pdb=" O THR A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 168 No H-bonds generated for 'chain 'A' and resid 166 through 168' Processing helix chain 'A' and resid 174 through 186 Processing helix chain 'A' and resid 202 through 225 removed outlier: 3.507A pdb=" N HIS A 206 " --> pdb=" O SER A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 235 Processing helix chain 'A' and resid 257 through 262 Processing helix chain 'A' and resid 268 through 295 removed outlier: 3.510A pdb=" N LEU A 273 " --> pdb=" O ALA A 269 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG A 274 " --> pdb=" O LEU A 270 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ASP A 281 " --> pdb=" O SER A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 300 No H-bonds generated for 'chain 'A' and resid 298 through 300' Processing helix chain 'A' and resid 317 through 339 Processing helix chain 'A' and resid 364 through 381 removed outlier: 3.514A pdb=" N ASN A 381 " --> pdb=" O ALA A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 394 Processing helix chain 'A' and resid 418 through 430 removed outlier: 4.383A pdb=" N GLN A 425 " --> pdb=" O CYS A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 465 removed outlier: 3.932A pdb=" N LEU A 464 " --> pdb=" O ALA A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 507 removed outlier: 3.890A pdb=" N VAL A 507 " --> pdb=" O MET A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 530 removed outlier: 3.744A pdb=" N ALA A 527 " --> pdb=" O ASN A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 564 removed outlier: 3.808A pdb=" N THR A 542 " --> pdb=" O SER A 538 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N LYS A 564 " --> pdb=" O LEU A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 602 removed outlier: 4.110A pdb=" N ILE A 592 " --> pdb=" O LEU A 588 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N VAL A 593 " --> pdb=" O ASP A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 638 Processing helix chain 'A' and resid 662 through 684 removed outlier: 3.807A pdb=" N LYS A 683 " --> pdb=" O LYS A 679 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU A 684 " --> pdb=" O ASN A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 702 Processing helix chain 'A' and resid 705 through 720 removed outlier: 3.848A pdb=" N ASN A 709 " --> pdb=" O ASN A 705 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE A 710 " --> pdb=" O GLN A 706 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 725 removed outlier: 3.513A pdb=" N GLY A 725 " --> pdb=" O GLU A 721 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 739 removed outlier: 3.632A pdb=" N ALA A 729 " --> pdb=" O GLY A 725 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLN A 730 " --> pdb=" O LYS A 726 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASN A 737 " --> pdb=" O TYR A 733 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 755 removed outlier: 4.051A pdb=" N LEU A 743 " --> pdb=" O ASP A 739 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE A 744 " --> pdb=" O ARG A 740 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N MET A 745 " --> pdb=" O LYS A 741 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 43 removed outlier: 3.504A pdb=" N LEU B 31 " --> pdb=" O SER B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 54 removed outlier: 3.717A pdb=" N ASN B 54 " --> pdb=" O GLN B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 107 Processing helix chain 'B' and resid 163 through 174 Processing helix chain 'B' and resid 199 through 205 removed outlier: 3.802A pdb=" N PHE B 203 " --> pdb=" O ILE B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 227 Processing helix chain 'F' and resid 45 through 61 Processing helix chain 'F' and resid 74 through 82 Processing helix chain 'F' and resid 103 through 110 Processing helix chain 'F' and resid 157 through 174 removed outlier: 3.754A pdb=" N PHE F 174 " --> pdb=" O ASP F 170 " (cutoff:3.500A) Processing helix chain 'F' and resid 180 through 184 Processing helix chain 'F' and resid 204 through 213 removed outlier: 3.803A pdb=" N LEU F 208 " --> pdb=" O LYS F 204 " (cutoff:3.500A) Processing helix chain 'H' and resid 45 through 61 Processing helix chain 'H' and resid 69 through 73 removed outlier: 3.854A pdb=" N ASP H 73 " --> pdb=" O PRO H 70 " (cutoff:3.500A) Processing helix chain 'H' and resid 74 through 82 Processing helix chain 'H' and resid 103 through 109 Processing helix chain 'H' and resid 157 through 173 Processing helix chain 'H' and resid 205 through 213 removed outlier: 3.631A pdb=" N ILE H 211 " --> pdb=" O THR H 207 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 61 removed outlier: 3.577A pdb=" N LEU G 49 " --> pdb=" O PRO G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 74 through 82 Processing helix chain 'G' and resid 103 through 110 Processing helix chain 'G' and resid 154 through 156 No H-bonds generated for 'chain 'G' and resid 154 through 156' Processing helix chain 'G' and resid 157 through 174 removed outlier: 3.901A pdb=" N PHE G 174 " --> pdb=" O ASP G 170 " (cutoff:3.500A) Processing helix chain 'G' and resid 204 through 213 removed outlier: 4.205A pdb=" N LEU G 208 " --> pdb=" O LYS G 204 " (cutoff:3.500A) Processing helix chain 'I' and resid 45 through 61 removed outlier: 3.538A pdb=" N LEU I 49 " --> pdb=" O PRO I 45 " (cutoff:3.500A) Processing helix chain 'I' and resid 69 through 73 removed outlier: 3.867A pdb=" N ASP I 73 " --> pdb=" O PRO I 70 " (cutoff:3.500A) Processing helix chain 'I' and resid 74 through 82 Processing helix chain 'I' and resid 103 through 111 Processing helix chain 'I' and resid 157 through 172 Processing helix chain 'I' and resid 205 through 213 removed outlier: 3.705A pdb=" N GLU I 210 " --> pdb=" O ASN I 206 " (cutoff:3.500A) Processing helix chain 'J' and resid 41 through 51 Processing helix chain 'J' and resid 53 through 65 Processing helix chain 'J' and resid 71 through 76 Processing helix chain 'J' and resid 127 through 140 removed outlier: 3.744A pdb=" N LEU J 131 " --> pdb=" O PRO J 127 " (cutoff:3.500A) Processing helix chain 'J' and resid 152 through 154 No H-bonds generated for 'chain 'J' and resid 152 through 154' Processing helix chain 'J' and resid 165 through 167 No H-bonds generated for 'chain 'J' and resid 165 through 167' Processing helix chain 'J' and resid 209 through 228 Processing helix chain 'J' and resid 228 through 235 Processing helix chain 'J' and resid 238 through 242 removed outlier: 3.912A pdb=" N GLY J 241 " --> pdb=" O LEU J 238 " (cutoff:3.500A) Processing helix chain 'J' and resid 275 through 280 Processing helix chain 'J' and resid 286 through 300 removed outlier: 4.152A pdb=" N GLN J 290 " --> pdb=" O LYS J 286 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA J 291 " --> pdb=" O ASN J 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 38 Processing helix chain 'C' and resid 53 through 72 removed outlier: 3.721A pdb=" N ILE C 57 " --> pdb=" O THR C 53 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N VAL C 67 " --> pdb=" O LEU C 63 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N ARG C 70 " --> pdb=" O LYS C 66 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE C 72 " --> pdb=" O TYR C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 101 Processing helix chain 'C' and resid 101 through 111 Processing helix chain 'C' and resid 113 through 123 Processing helix chain 'C' and resid 125 through 146 Processing helix chain 'D' and resid 25 through 38 Processing helix chain 'D' and resid 53 through 69 removed outlier: 3.813A pdb=" N ILE D 57 " --> pdb=" O THR D 53 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N VAL D 67 " --> pdb=" O LEU D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 101 removed outlier: 3.621A pdb=" N GLU D 101 " --> pdb=" O GLU D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 111 Processing helix chain 'D' and resid 112 through 123 removed outlier: 3.660A pdb=" N ALA D 116 " --> pdb=" O ALA D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 146 removed outlier: 3.701A pdb=" N PHE D 129 " --> pdb=" O THR D 125 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TYR D 146 " --> pdb=" O TYR D 142 " (cutoff:3.500A) Processing helix chain 'E' and resid 25 through 39 removed outlier: 3.505A pdb=" N HIS E 39 " --> pdb=" O ARG E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 73 removed outlier: 4.007A pdb=" N ARG E 70 " --> pdb=" O LYS E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 101 removed outlier: 3.534A pdb=" N GLU E 101 " --> pdb=" O GLU E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 101 through 111 Processing helix chain 'E' and resid 112 through 124 Processing helix chain 'E' and resid 125 through 146 Processing sheet with id=AA1, first strand: chain 'A' and resid 314 through 315 Processing sheet with id=AA2, first strand: chain 'A' and resid 254 through 255 removed outlier: 4.060A pdb=" N TYR A 344 " --> pdb=" O SER A 255 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 302 through 305 removed outlier: 3.656A pdb=" N TYR A 304 " --> pdb=" O TYR A 311 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 452 through 453 removed outlier: 3.522A pdb=" N GLN A 472 " --> pdb=" O ILE A 439 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 568 through 572 removed outlier: 7.035A pdb=" N PHE A 579 " --> pdb=" O ILE A 571 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR A 653 " --> pdb=" O ALA A 610 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 97 through 99 removed outlier: 11.721A pdb=" N ALA B 62 " --> pdb=" O PRO B 73 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N PHE B 59 " --> pdb=" O GLU B 160 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N GLU B 160 " --> pdb=" O PHE B 59 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N ASP B 61 " --> pdb=" O LEU B 158 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N LEU B 158 " --> pdb=" O ASP B 61 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE B 65 " --> pdb=" O GLY B 154 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N THR B 153 " --> pdb=" O PHE B 8 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N PHE B 8 " --> pdb=" O THR B 153 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE B 159 " --> pdb=" O LYS B 2 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 124 through 132 removed outlier: 3.629A pdb=" N THR B 148 " --> pdb=" O LYS B 124 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 184 through 185 removed outlier: 4.495A pdb=" N GLY B 185 " --> pdb=" O PHE F 96 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASN F 97 " --> pdb=" O GLU F 147 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N GLU F 147 " --> pdb=" O ASN F 97 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N LYS F 2 " --> pdb=" O ALA F 198 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N THR F 8 " --> pdb=" O ASN F 192 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N ASN F 192 " --> pdb=" O THR F 8 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N VAL F 10 " --> pdb=" O PHE F 190 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N PHE F 190 " --> pdb=" O VAL F 10 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 264 through 265 Processing sheet with id=AB1, first strand: chain 'B' and resid 234 through 237 Processing sheet with id=AB2, first strand: chain 'B' and resid 272 through 277 removed outlier: 3.573A pdb=" N ASP B 272 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N VAL B 284 " --> pdb=" O VAL B 276 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 43 through 44 Processing sheet with id=AB4, first strand: chain 'F' and resid 83 through 84 removed outlier: 3.807A pdb=" N ARG F 90 " --> pdb=" O SER F 83 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 115 through 123 Processing sheet with id=AB6, first strand: chain 'H' and resid 94 through 95 removed outlier: 4.553A pdb=" N THR H 8 " --> pdb=" O ASN H 192 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N ASN H 192 " --> pdb=" O THR H 8 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL H 10 " --> pdb=" O PHE H 190 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N PHE H 190 " --> pdb=" O VAL H 10 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 35 through 36 removed outlier: 3.699A pdb=" N LEU H 41 " --> pdb=" O ASP H 36 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 115 through 123 Processing sheet with id=AB9, first strand: chain 'G' and resid 43 through 44 removed outlier: 4.663A pdb=" N LYS G 100 " --> pdb=" O ASP G 145 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ASP G 145 " --> pdb=" O LYS G 100 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 43 through 44 removed outlier: 4.663A pdb=" N LYS G 100 " --> pdb=" O ASP G 145 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ASP G 145 " --> pdb=" O LYS G 100 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N THR G 8 " --> pdb=" O ASN G 192 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N ASN G 192 " --> pdb=" O THR G 8 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N VAL G 10 " --> pdb=" O PHE G 190 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N PHE G 190 " --> pdb=" O VAL G 10 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 115 through 120 Processing sheet with id=AC3, first strand: chain 'I' and resid 143 through 151 Processing sheet with id=AC4, first strand: chain 'I' and resid 143 through 151 Processing sheet with id=AC5, first strand: chain 'I' and resid 43 through 44 Processing sheet with id=AC6, first strand: chain 'I' and resid 115 through 120 Processing sheet with id=AC7, first strand: chain 'J' and resid 156 through 158 removed outlier: 3.597A pdb=" N THR J 195 " --> pdb=" O ALA J 11 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 22 through 23 removed outlier: 7.422A pdb=" N ASN J 114 " --> pdb=" O GLU J 189 " (cutoff:3.500A) removed outlier: 8.854A pdb=" N LEU J 191 " --> pdb=" O ASN J 114 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N LEU J 184 " --> pdb=" O ASP J 176 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N ASP J 176 " --> pdb=" O LEU J 184 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N LEU J 186 " --> pdb=" O LYS J 174 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG J 188 " --> pdb=" O TYR J 172 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'J' and resid 29 through 31 removed outlier: 3.770A pdb=" N MET J 39 " --> pdb=" O TYR J 86 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N TYR J 86 " --> pdb=" O MET J 39 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 13 through 15 Processing sheet with id=AD2, first strand: chain 'D' and resid 14 through 15 Processing sheet with id=AD3, first strand: chain 'D' and resid 42 through 43 removed outlier: 3.704A pdb=" N PHE D 42 " --> pdb=" O GLN D 50 " (cutoff:3.500A) 931 hydrogen bonds defined for protein. 2700 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 40 hydrogen bonds 76 hydrogen bond angles 0 basepair planarities 16 basepair parallelities 29 stacking parallelities Total time for adding SS restraints: 7.62 Time building geometry restraints manager: 9.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.35: 7048 1.35 - 1.49: 6169 1.49 - 1.63: 9257 1.63 - 1.77: 9 1.77 - 1.91: 88 Bond restraints: 22571 Sorted by residual: bond pdb=" CB CYS A 418 " pdb=" SG CYS A 418 " ideal model delta sigma weight residual 1.808 1.908 -0.100 3.30e-02 9.18e+02 9.16e+00 bond pdb=" CG1 ILE D 140 " pdb=" CD1 ILE D 140 " ideal model delta sigma weight residual 1.513 1.405 0.108 3.90e-02 6.57e+02 7.71e+00 bond pdb=" N SER H 21 " pdb=" CA SER H 21 " ideal model delta sigma weight residual 1.458 1.500 -0.042 1.90e-02 2.77e+03 4.89e+00 bond pdb=" CG1 ILE A 213 " pdb=" CD1 ILE A 213 " ideal model delta sigma weight residual 1.513 1.430 0.083 3.90e-02 6.57e+02 4.51e+00 bond pdb=" N GLU A 414 " pdb=" CA GLU A 414 " ideal model delta sigma weight residual 1.457 1.484 -0.026 1.29e-02 6.01e+03 4.16e+00 ... (remaining 22566 not shown) Histogram of bond angle deviations from ideal: 95.79 - 104.15: 452 104.15 - 112.51: 11331 112.51 - 120.87: 12106 120.87 - 129.23: 6721 129.23 - 137.58: 115 Bond angle restraints: 30725 Sorted by residual: angle pdb=" C SER H 20 " pdb=" N SER H 21 " pdb=" CA SER H 21 " ideal model delta sigma weight residual 121.70 137.58 -15.88 1.80e+00 3.09e-01 7.79e+01 angle pdb=" CA CYS A 418 " pdb=" CB CYS A 418 " pdb=" SG CYS A 418 " ideal model delta sigma weight residual 114.40 134.28 -19.88 2.30e+00 1.89e-01 7.47e+01 angle pdb=" N GLY B 185 " pdb=" CA GLY B 185 " pdb=" C GLY B 185 " ideal model delta sigma weight residual 113.18 98.14 15.04 2.37e+00 1.78e-01 4.03e+01 angle pdb=" CA ARG I 40 " pdb=" CB ARG I 40 " pdb=" CG ARG I 40 " ideal model delta sigma weight residual 114.10 126.53 -12.43 2.00e+00 2.50e-01 3.86e+01 angle pdb=" C THR J 306 " pdb=" N TYR J 307 " pdb=" CA TYR J 307 " ideal model delta sigma weight residual 121.54 132.80 -11.26 1.91e+00 2.74e-01 3.47e+01 ... (remaining 30720 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.00: 13295 34.00 - 68.00: 360 68.00 - 102.00: 48 102.00 - 136.00: 3 136.00 - 170.00: 3 Dihedral angle restraints: 13709 sinusoidal: 6247 harmonic: 7462 Sorted by residual: dihedral pdb=" CA SER B 184 " pdb=" C SER B 184 " pdb=" N GLY B 185 " pdb=" CA GLY B 185 " ideal model delta harmonic sigma weight residual 180.00 45.81 134.19 0 5.00e+00 4.00e-02 7.20e+02 dihedral pdb=" O4' C T 35 " pdb=" C1' C T 35 " pdb=" N1 C T 35 " pdb=" C2 C T 35 " ideal model delta sinusoidal sigma weight residual 200.00 42.67 157.33 1 1.50e+01 4.44e-03 8.20e+01 dihedral pdb=" CB CYS A 418 " pdb=" SG CYS A 418 " pdb=" SG CYS A 421 " pdb=" CB CYS A 421 " ideal model delta sinusoidal sigma weight residual 93.00 22.24 70.76 1 1.00e+01 1.00e-02 6.44e+01 ... (remaining 13706 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 2877 0.077 - 0.153: 526 0.153 - 0.230: 72 0.230 - 0.306: 15 0.306 - 0.383: 5 Chirality restraints: 3495 Sorted by residual: chirality pdb=" CB VAL A 672 " pdb=" CA VAL A 672 " pdb=" CG1 VAL A 672 " pdb=" CG2 VAL A 672 " both_signs ideal model delta sigma weight residual False -2.63 -2.25 -0.38 2.00e-01 2.50e+01 3.66e+00 chirality pdb=" C1' A R 21 " pdb=" O4' A R 21 " pdb=" C2' A R 21 " pdb=" N9 A R 21 " both_signs ideal model delta sigma weight residual False 2.44 2.06 0.38 2.00e-01 2.50e+01 3.55e+00 chirality pdb=" C1' A R 25 " pdb=" O4' A R 25 " pdb=" C2' A R 25 " pdb=" N9 A R 25 " both_signs ideal model delta sigma weight residual False 2.44 2.06 0.37 2.00e-01 2.50e+01 3.51e+00 ... (remaining 3492 not shown) Planarity restraints: 3683 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 169 " -0.078 5.00e-02 4.00e+02 1.19e-01 2.27e+01 pdb=" N PRO A 170 " 0.206 5.00e-02 4.00e+02 pdb=" CA PRO A 170 " -0.065 5.00e-02 4.00e+02 pdb=" CD PRO A 170 " -0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 553 " -0.019 2.00e-02 2.50e+03 3.84e-02 1.48e+01 pdb=" C PHE A 553 " 0.066 2.00e-02 2.50e+03 pdb=" O PHE A 553 " -0.025 2.00e-02 2.50e+03 pdb=" N LYS A 554 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR J 306 " -0.015 2.00e-02 2.50e+03 3.15e-02 9.92e+00 pdb=" C THR J 306 " 0.054 2.00e-02 2.50e+03 pdb=" O THR J 306 " -0.021 2.00e-02 2.50e+03 pdb=" N TYR J 307 " -0.018 2.00e-02 2.50e+03 ... (remaining 3680 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2955 2.75 - 3.29: 20705 3.29 - 3.82: 37481 3.82 - 4.36: 43997 4.36 - 4.90: 75115 Nonbonded interactions: 180253 Sorted by model distance: nonbonded pdb=" OG SER J 295 " pdb=" OG1 THR J 306 " model vdw 2.211 2.440 nonbonded pdb=" O ILE I 26 " pdb=" O2' U T 11 " model vdw 2.254 2.440 nonbonded pdb=" O THR E 125 " pdb=" OG SER E 128 " model vdw 2.263 2.440 nonbonded pdb=" O PHE C 107 " pdb=" OG1 THR C 111 " model vdw 2.272 2.440 nonbonded pdb=" O THR A 317 " pdb=" OG1 THR A 320 " model vdw 2.276 2.440 ... (remaining 180248 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 'C' and (resid 16 through 43 or resid 50 through 146)) selection = (chain 'D' and (resid 16 through 43 or resid 50 through 146)) selection = chain 'E' } ncs_group { reference = chain 'F' selection = (chain 'G' and (resid 1 through 65 or resid 73 through 214)) selection = (chain 'H' and (resid 1 through 65 or resid 73 through 214)) selection = (chain 'I' and (resid 1 through 65 or resid 73 through 214)) } 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=0.50 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: 0.860 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: 5.040 Check model and map are aligned: 0.340 Set scattering table: 0.200 Process input model: 64.990 Find NCS groups from input model: 1.010 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: 0.010 Load rotamer database and sin/cos tables:12.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 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 : 0.007 0.108 22571 Z= 0.479 Angle : 1.146 19.884 30725 Z= 0.625 Chirality : 0.063 0.383 3495 Planarity : 0.006 0.119 3683 Dihedral : 16.024 170.000 8894 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 0.04 % Allowed : 0.81 % Favored : 99.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -3.29 (0.14), residues: 2530 helix: -1.85 (0.13), residues: 1048 sheet: -1.60 (0.26), residues: 352 loop : -2.64 (0.15), residues: 1130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP A 186 HIS 0.013 0.002 HIS G 180 PHE 0.049 0.003 PHE G 162 TYR 0.039 0.003 TYR I 176 ARG 0.029 0.002 ARG I 183 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5060 Ramachandran restraints generated. 2530 Oldfield, 0 Emsley, 2530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5060 Ramachandran restraints generated. 2530 Oldfield, 0 Emsley, 2530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 517 time to evaluate : 2.454 Fit side-chains revert: symmetry clash REVERT: A 86 MET cc_start: 0.5263 (pmm) cc_final: 0.5019 (pmm) REVERT: A 230 GLN cc_start: 0.5940 (pp30) cc_final: 0.5612 (pp30) REVERT: A 285 GLU cc_start: 0.7666 (mm-30) cc_final: 0.7399 (tp30) REVERT: A 488 ARG cc_start: 0.7364 (ttm-80) cc_final: 0.7019 (ttm-80) REVERT: A 545 PHE cc_start: 0.7309 (t80) cc_final: 0.6865 (t80) REVERT: A 558 ASN cc_start: 0.7306 (m110) cc_final: 0.6749 (m110) REVERT: A 637 ASP cc_start: 0.7441 (m-30) cc_final: 0.7159 (m-30) REVERT: J 22 LYS cc_start: 0.8515 (ttpt) cc_final: 0.8154 (ptmm) REVERT: D 97 GLU cc_start: 0.7577 (tt0) cc_final: 0.7366 (tt0) outliers start: 1 outliers final: 1 residues processed: 517 average time/residue: 1.1347 time to fit residues: 680.7406 Evaluate side-chains 381 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 380 time to evaluate : 2.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 542 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 217 optimal weight: 0.0470 chunk 195 optimal weight: 0.9990 chunk 108 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 131 optimal weight: 5.9990 chunk 104 optimal weight: 4.9990 chunk 202 optimal weight: 8.9990 chunk 78 optimal weight: 5.9990 chunk 122 optimal weight: 7.9990 chunk 150 optimal weight: 0.0570 chunk 234 optimal weight: 3.9990 overall best weight: 0.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 63 ASN I 209 ASN J 114 ASN ** J 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 290 GLN ** C 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 109 GLN C 122 ASN D 69 ASN D 109 GLN E 18 ASN E 69 ASN ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 22571 Z= 0.162 Angle : 0.633 16.424 30725 Z= 0.335 Chirality : 0.043 0.479 3495 Planarity : 0.004 0.083 3683 Dihedral : 14.709 174.706 3845 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 1.89 % Allowed : 14.04 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.25 (0.15), residues: 2530 helix: -0.48 (0.15), residues: 1063 sheet: -1.51 (0.25), residues: 391 loop : -2.51 (0.16), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 186 HIS 0.005 0.001 HIS J 282 PHE 0.033 0.001 PHE J 30 TYR 0.019 0.001 TYR E 89 ARG 0.007 0.001 ARG H 35 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5060 Ramachandran restraints generated. 2530 Oldfield, 0 Emsley, 2530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5060 Ramachandran restraints generated. 2530 Oldfield, 0 Emsley, 2530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 492 time to evaluate : 2.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4917 (ttp) cc_final: 0.4598 (tpp) REVERT: A 230 GLN cc_start: 0.6034 (pp30) cc_final: 0.5708 (pp30) REVERT: A 253 ASP cc_start: 0.8322 (t0) cc_final: 0.8068 (t0) REVERT: A 358 MET cc_start: 0.6649 (OUTLIER) cc_final: 0.4956 (tmm) REVERT: A 558 ASN cc_start: 0.7068 (m110) cc_final: 0.6519 (m110) REVERT: A 637 ASP cc_start: 0.7192 (m-30) cc_final: 0.6924 (m-30) REVERT: F 15 MET cc_start: 0.8130 (tmm) cc_final: 0.7169 (tmm) REVERT: F 120 GLU cc_start: 0.6954 (tp30) cc_final: 0.6378 (mm-30) REVERT: F 183 ARG cc_start: 0.8254 (mpp80) cc_final: 0.7960 (mtm110) REVERT: J 21 GLU cc_start: 0.6699 (tp30) cc_final: 0.6409 (tp30) REVERT: J 47 LYS cc_start: 0.8108 (mmtt) cc_final: 0.7536 (pptt) REVERT: J 188 ARG cc_start: 0.8499 (ptp-170) cc_final: 0.8157 (mtt180) REVERT: J 227 LYS cc_start: 0.7434 (tptt) cc_final: 0.7219 (tptt) REVERT: C 118 THR cc_start: 0.7997 (p) cc_final: 0.7476 (p) REVERT: D 97 GLU cc_start: 0.7497 (tt0) cc_final: 0.7121 (tt0) REVERT: E 34 ILE cc_start: 0.8695 (mm) cc_final: 0.8390 (mp) outliers start: 42 outliers final: 11 residues processed: 505 average time/residue: 1.0526 time to fit residues: 624.6080 Evaluate side-chains 410 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 398 time to evaluate : 2.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 MET Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain G residue 48 SER Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain E residue 125 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 130 optimal weight: 10.0000 chunk 72 optimal weight: 0.2980 chunk 194 optimal weight: 7.9990 chunk 159 optimal weight: 7.9990 chunk 64 optimal weight: 0.0980 chunk 234 optimal weight: 5.9990 chunk 253 optimal weight: 6.9990 chunk 209 optimal weight: 9.9990 chunk 232 optimal weight: 6.9990 chunk 80 optimal weight: 0.9990 chunk 188 optimal weight: 4.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN ** A 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 62 ASN H 180 HIS G 63 ASN ** I 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 122 ASN C 123 GLN D 69 ASN D 109 GLN E 50 GLN E 69 ASN ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 22571 Z= 0.225 Angle : 0.637 16.405 30725 Z= 0.331 Chirality : 0.044 0.450 3495 Planarity : 0.004 0.043 3683 Dihedral : 14.575 173.031 3844 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 3.06 % Allowed : 18.17 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.36 % 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: -1.72 (0.16), residues: 2530 helix: 0.15 (0.16), residues: 1061 sheet: -1.32 (0.25), residues: 380 loop : -2.39 (0.16), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 663 HIS 0.005 0.001 HIS G 180 PHE 0.014 0.001 PHE A 73 TYR 0.021 0.001 TYR A 218 ARG 0.004 0.001 ARG H 90 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5060 Ramachandran restraints generated. 2530 Oldfield, 0 Emsley, 2530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5060 Ramachandran restraints generated. 2530 Oldfield, 0 Emsley, 2530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 428 time to evaluate : 2.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5133 (ttp) cc_final: 0.4789 (tpp) REVERT: A 230 GLN cc_start: 0.6025 (pp30) cc_final: 0.5821 (pp30) REVERT: A 253 ASP cc_start: 0.8402 (t0) cc_final: 0.8136 (t0) REVERT: A 358 MET cc_start: 0.6873 (OUTLIER) cc_final: 0.5114 (tmm) REVERT: A 464 LEU cc_start: 0.5474 (OUTLIER) cc_final: 0.4937 (tm) REVERT: A 486 MET cc_start: 0.4881 (mtp) cc_final: 0.4643 (mtp) REVERT: A 558 ASN cc_start: 0.7098 (m110) cc_final: 0.6542 (m110) REVERT: A 637 ASP cc_start: 0.7401 (m-30) cc_final: 0.7142 (m-30) REVERT: B 232 TYR cc_start: 0.7285 (p90) cc_final: 0.7034 (p90) REVERT: F 120 GLU cc_start: 0.7194 (tp30) cc_final: 0.6623 (mm-30) REVERT: H 86 LYS cc_start: 0.8039 (tppt) cc_final: 0.7827 (tptp) REVERT: J 21 GLU cc_start: 0.6829 (tp30) cc_final: 0.6401 (tp30) REVERT: J 30 PHE cc_start: 0.6592 (t80) cc_final: 0.5900 (t80) REVERT: J 47 LYS cc_start: 0.8275 (mmtt) cc_final: 0.7614 (pptt) REVERT: C 108 ILE cc_start: 0.8616 (OUTLIER) cc_final: 0.8400 (mm) REVERT: C 118 THR cc_start: 0.7981 (p) cc_final: 0.7569 (p) REVERT: D 22 ASN cc_start: 0.8617 (p0) cc_final: 0.8344 (p0) REVERT: D 25 ASN cc_start: 0.7027 (t0) cc_final: 0.6701 (t0) REVERT: D 97 GLU cc_start: 0.7607 (tt0) cc_final: 0.7388 (tt0) REVERT: E 34 ILE cc_start: 0.8665 (mm) cc_final: 0.8384 (mp) REVERT: E 105 LYS cc_start: 0.7740 (ttmm) cc_final: 0.7168 (mtpt) outliers start: 68 outliers final: 30 residues processed: 460 average time/residue: 1.0253 time to fit residues: 556.9060 Evaluate side-chains 421 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 388 time to evaluate : 2.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 TRP Chi-restraints excluded: chain A residue 358 MET Chi-restraints excluded: chain A residue 368 TYR Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 520 ASP Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain F residue 41 LEU Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 48 SER Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain G residue 194 SER Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain I residue 127 THR Chi-restraints excluded: chain I residue 207 THR Chi-restraints excluded: chain J residue 39 MET Chi-restraints excluded: chain J residue 58 PHE Chi-restraints excluded: chain J residue 123 ARG Chi-restraints excluded: chain J residue 163 THR Chi-restraints excluded: chain J residue 307 TYR Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 125 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 231 optimal weight: 9.9990 chunk 176 optimal weight: 9.9990 chunk 121 optimal weight: 0.6980 chunk 25 optimal weight: 4.9990 chunk 112 optimal weight: 6.9990 chunk 157 optimal weight: 8.9990 chunk 235 optimal weight: 9.9990 chunk 249 optimal weight: 0.5980 chunk 123 optimal weight: 5.9990 chunk 223 optimal weight: 9.9990 chunk 67 optimal weight: 0.8980 overall best weight: 2.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 398 ASN ** A 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 122 ASN D 69 ASN D 109 GLN E 50 GLN E 69 ASN ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 22571 Z= 0.228 Angle : 0.629 16.444 30725 Z= 0.326 Chirality : 0.044 0.439 3495 Planarity : 0.003 0.042 3683 Dihedral : 14.513 173.338 3844 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 3.96 % Allowed : 20.47 % Favored : 75.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.16), residues: 2530 helix: 0.34 (0.16), residues: 1077 sheet: -1.21 (0.26), residues: 369 loop : -2.32 (0.16), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 663 HIS 0.005 0.001 HIS G 180 PHE 0.027 0.001 PHE A 278 TYR 0.021 0.001 TYR A 218 ARG 0.004 0.000 ARG H 35 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5060 Ramachandran restraints generated. 2530 Oldfield, 0 Emsley, 2530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5060 Ramachandran restraints generated. 2530 Oldfield, 0 Emsley, 2530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 422 time to evaluate : 2.397 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5243 (ttp) cc_final: 0.4987 (tpp) REVERT: A 181 MET cc_start: 0.3348 (mmp) cc_final: 0.2922 (mmt) REVERT: A 230 GLN cc_start: 0.6072 (pp30) cc_final: 0.5838 (pp30) REVERT: A 253 ASP cc_start: 0.8471 (t0) cc_final: 0.8098 (t0) REVERT: A 464 LEU cc_start: 0.5506 (OUTLIER) cc_final: 0.5012 (tm) REVERT: A 473 ILE cc_start: 0.7906 (mm) cc_final: 0.7521 (tp) REVERT: A 558 ASN cc_start: 0.7243 (m110) cc_final: 0.6680 (m110) REVERT: A 637 ASP cc_start: 0.7472 (m-30) cc_final: 0.7099 (m-30) REVERT: B 232 TYR cc_start: 0.7378 (p90) cc_final: 0.7066 (p90) REVERT: F 120 GLU cc_start: 0.7039 (tp30) cc_final: 0.6477 (mm-30) REVERT: H 86 LYS cc_start: 0.8126 (tppt) cc_final: 0.7894 (tptp) REVERT: J 21 GLU cc_start: 0.6704 (tp30) cc_final: 0.6372 (tp30) REVERT: J 39 MET cc_start: 0.7928 (OUTLIER) cc_final: 0.7411 (mtt) REVERT: J 47 LYS cc_start: 0.8321 (mmtt) cc_final: 0.7552 (pptt) REVERT: J 92 GLN cc_start: 0.7173 (tp40) cc_final: 0.6072 (mm-40) REVERT: J 187 TYR cc_start: 0.6982 (m-80) cc_final: 0.6566 (m-80) REVERT: C 118 THR cc_start: 0.7972 (p) cc_final: 0.7576 (p) REVERT: D 22 ASN cc_start: 0.8575 (p0) cc_final: 0.8242 (p0) REVERT: D 25 ASN cc_start: 0.6875 (t0) cc_final: 0.6185 (t0) REVERT: D 28 ASP cc_start: 0.7703 (m-30) cc_final: 0.7502 (m-30) REVERT: D 97 GLU cc_start: 0.7581 (tt0) cc_final: 0.7328 (tt0) REVERT: E 34 ILE cc_start: 0.8610 (mm) cc_final: 0.8337 (mp) REVERT: E 105 LYS cc_start: 0.7906 (ttmm) cc_final: 0.7385 (mtpt) outliers start: 88 outliers final: 47 residues processed: 465 average time/residue: 0.9823 time to fit residues: 542.5561 Evaluate side-chains 447 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 398 time to evaluate : 2.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 186 TRP Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 368 TYR Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 520 ASP Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 135 ASP Chi-restraints excluded: chain B residue 183 ASN Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain F residue 41 LEU Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain H residue 127 THR Chi-restraints excluded: chain H residue 197 THR Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 48 SER Chi-restraints excluded: chain I residue 13 THR Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain I residue 53 MET Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain I residue 127 THR Chi-restraints excluded: chain I residue 175 ASP Chi-restraints excluded: chain I residue 207 THR Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 39 MET Chi-restraints excluded: chain J residue 58 PHE Chi-restraints excluded: chain J residue 163 THR Chi-restraints excluded: chain J residue 298 ILE Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 125 THR Chi-restraints excluded: chain E residue 140 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 207 optimal weight: 6.9990 chunk 141 optimal weight: 0.2980 chunk 3 optimal weight: 4.9990 chunk 185 optimal weight: 8.9990 chunk 102 optimal weight: 10.0000 chunk 212 optimal weight: 0.4980 chunk 172 optimal weight: 10.0000 chunk 0 optimal weight: 30.0000 chunk 127 optimal weight: 9.9990 chunk 223 optimal weight: 0.0020 chunk 62 optimal weight: 10.0000 overall best weight: 2.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 62 ASN ** H 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 134 GLN C 122 ASN D 69 ASN D 109 GLN E 69 ASN ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 22571 Z= 0.226 Angle : 0.631 16.405 30725 Z= 0.327 Chirality : 0.044 0.431 3495 Planarity : 0.003 0.042 3683 Dihedral : 14.482 172.917 3844 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 4.50 % Allowed : 20.92 % Favored : 74.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.36 % 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: -1.37 (0.16), residues: 2530 helix: 0.47 (0.16), residues: 1081 sheet: -1.11 (0.25), residues: 381 loop : -2.31 (0.17), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 663 HIS 0.005 0.001 HIS G 180 PHE 0.015 0.001 PHE A 278 TYR 0.024 0.001 TYR A 218 ARG 0.003 0.000 ARG H 35 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5060 Ramachandran restraints generated. 2530 Oldfield, 0 Emsley, 2530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5060 Ramachandran restraints generated. 2530 Oldfield, 0 Emsley, 2530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 411 time to evaluate : 2.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5370 (ttp) cc_final: 0.5013 (tpp) REVERT: A 181 MET cc_start: 0.3200 (mmp) cc_final: 0.2824 (mmt) REVERT: A 230 GLN cc_start: 0.6007 (pp30) cc_final: 0.5745 (pp30) REVERT: A 253 ASP cc_start: 0.8510 (t0) cc_final: 0.8126 (t0) REVERT: A 464 LEU cc_start: 0.5522 (OUTLIER) cc_final: 0.5024 (tm) REVERT: A 558 ASN cc_start: 0.7192 (m110) cc_final: 0.6581 (m110) REVERT: A 637 ASP cc_start: 0.7501 (m-30) cc_final: 0.7088 (m-30) REVERT: A 719 ARG cc_start: 0.7654 (OUTLIER) cc_final: 0.7447 (ttm110) REVERT: F 120 GLU cc_start: 0.7031 (OUTLIER) cc_final: 0.6441 (mm-30) REVERT: J 21 GLU cc_start: 0.6733 (tp30) cc_final: 0.6394 (tp30) REVERT: J 39 MET cc_start: 0.8018 (OUTLIER) cc_final: 0.7587 (mtt) REVERT: J 47 LYS cc_start: 0.8389 (mmtt) cc_final: 0.7613 (pptt) REVERT: J 188 ARG cc_start: 0.8439 (ptp-170) cc_final: 0.8123 (ptt180) REVERT: J 315 ASP cc_start: 0.6984 (t0) cc_final: 0.6651 (t0) REVERT: C 118 THR cc_start: 0.8035 (p) cc_final: 0.7704 (p) REVERT: D 97 GLU cc_start: 0.7511 (tt0) cc_final: 0.7216 (tt0) REVERT: E 70 ARG cc_start: 0.8119 (OUTLIER) cc_final: 0.7641 (ttt-90) outliers start: 100 outliers final: 54 residues processed: 459 average time/residue: 0.9671 time to fit residues: 528.4140 Evaluate side-chains 455 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 396 time to evaluate : 2.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 186 TRP Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 218 TYR Chi-restraints excluded: chain A residue 335 PHE Chi-restraints excluded: chain A residue 368 TYR Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 520 ASP Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 719 ARG Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 183 ASN Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 41 LEU Chi-restraints excluded: chain F residue 120 GLU Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain H residue 127 THR Chi-restraints excluded: chain H residue 197 THR Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 48 SER Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain I residue 13 THR Chi-restraints excluded: chain I residue 17 ILE Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain I residue 53 MET Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain I residue 127 THR Chi-restraints excluded: chain I residue 207 THR Chi-restraints excluded: chain J residue 39 MET Chi-restraints excluded: chain J residue 58 PHE Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 157 GLN Chi-restraints excluded: chain J residue 163 THR Chi-restraints excluded: chain J residue 349 LEU Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain E residue 70 ARG Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 125 THR Chi-restraints excluded: chain E residue 140 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 83 optimal weight: 10.0000 chunk 224 optimal weight: 0.9990 chunk 49 optimal weight: 8.9990 chunk 146 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 249 optimal weight: 6.9990 chunk 207 optimal weight: 3.9990 chunk 115 optimal weight: 3.9990 chunk 20 optimal weight: 9.9990 chunk 82 optimal weight: 8.9990 chunk 131 optimal weight: 6.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 109 GLN E 50 GLN E 69 ASN ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 22571 Z= 0.251 Angle : 0.643 16.355 30725 Z= 0.333 Chirality : 0.045 0.438 3495 Planarity : 0.003 0.042 3683 Dihedral : 14.492 172.429 3844 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 4.50 % Allowed : 22.72 % Favored : 72.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.36 % 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: -1.31 (0.16), residues: 2530 helix: 0.52 (0.16), residues: 1081 sheet: -1.11 (0.25), residues: 382 loop : -2.26 (0.17), residues: 1067 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 334 HIS 0.005 0.001 HIS G 180 PHE 0.016 0.001 PHE A 73 TYR 0.017 0.001 TYR E 89 ARG 0.003 0.000 ARG H 35 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5060 Ramachandran restraints generated. 2530 Oldfield, 0 Emsley, 2530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5060 Ramachandran restraints generated. 2530 Oldfield, 0 Emsley, 2530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 416 time to evaluate : 2.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5379 (ttp) cc_final: 0.5119 (tpp) REVERT: A 181 MET cc_start: 0.3333 (mmp) cc_final: 0.3108 (mmt) REVERT: A 230 GLN cc_start: 0.6032 (pp30) cc_final: 0.5718 (pp30) REVERT: A 253 ASP cc_start: 0.8505 (t0) cc_final: 0.8092 (t0) REVERT: A 464 LEU cc_start: 0.5552 (OUTLIER) cc_final: 0.5084 (tm) REVERT: A 558 ASN cc_start: 0.7240 (m110) cc_final: 0.6711 (m110) REVERT: A 637 ASP cc_start: 0.7408 (m-30) cc_final: 0.6957 (m-30) REVERT: B 232 TYR cc_start: 0.7499 (p90) cc_final: 0.7200 (p90) REVERT: F 15 MET cc_start: 0.8638 (OUTLIER) cc_final: 0.7363 (tmm) REVERT: F 120 GLU cc_start: 0.7135 (OUTLIER) cc_final: 0.6493 (mm-30) REVERT: J 21 GLU cc_start: 0.6646 (tp30) cc_final: 0.6437 (tp30) REVERT: J 39 MET cc_start: 0.7955 (OUTLIER) cc_final: 0.7472 (mtt) REVERT: J 47 LYS cc_start: 0.8402 (mmtt) cc_final: 0.7657 (pptt) REVERT: J 186 LEU cc_start: 0.8537 (tp) cc_final: 0.8207 (tt) REVERT: J 292 ARG cc_start: 0.5715 (mmt180) cc_final: 0.5497 (mmp-170) REVERT: J 315 ASP cc_start: 0.7151 (t0) cc_final: 0.6848 (t0) REVERT: C 44 ASN cc_start: 0.7530 (p0) cc_final: 0.7109 (p0) REVERT: C 118 THR cc_start: 0.8116 (p) cc_final: 0.7854 (p) REVERT: E 70 ARG cc_start: 0.8131 (OUTLIER) cc_final: 0.7618 (ttt-90) outliers start: 100 outliers final: 64 residues processed: 457 average time/residue: 1.0002 time to fit residues: 545.1620 Evaluate side-chains 461 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 392 time to evaluate : 2.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 186 TRP Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 368 TYR Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 520 ASP Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 600 ASP Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 135 ASP Chi-restraints excluded: chain B residue 183 ASN Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain F residue 15 MET Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain F residue 22 ASP Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 41 LEU Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 120 GLU Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain H residue 127 THR Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 197 THR Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 48 SER Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 212 LEU Chi-restraints excluded: chain I residue 13 THR Chi-restraints excluded: chain I residue 17 ILE Chi-restraints excluded: chain I residue 36 ASP Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain I residue 53 MET Chi-restraints excluded: chain I residue 109 THR Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain I residue 127 THR Chi-restraints excluded: chain I residue 175 ASP Chi-restraints excluded: chain I residue 207 THR Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 39 MET Chi-restraints excluded: chain J residue 58 PHE Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 163 THR Chi-restraints excluded: chain J residue 349 LEU Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain E residue 70 ARG Chi-restraints excluded: chain E residue 82 ASN Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 125 THR Chi-restraints excluded: chain E residue 140 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 240 optimal weight: 8.9990 chunk 28 optimal weight: 9.9990 chunk 142 optimal weight: 5.9990 chunk 182 optimal weight: 0.4980 chunk 141 optimal weight: 10.0000 chunk 210 optimal weight: 9.9990 chunk 139 optimal weight: 10.0000 chunk 248 optimal weight: 1.9990 chunk 155 optimal weight: 6.9990 chunk 151 optimal weight: 5.9990 chunk 114 optimal weight: 0.9980 overall best weight: 3.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 109 GLN E 18 ASN E 50 GLN E 65 ASN E 69 ASN ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 22571 Z= 0.262 Angle : 0.662 16.623 30725 Z= 0.341 Chirality : 0.044 0.441 3495 Planarity : 0.004 0.042 3683 Dihedral : 14.488 172.097 3844 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.64 % Favored : 93.32 % Rotamer: Outliers : 4.86 % Allowed : 23.39 % Favored : 71.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.36 % 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: -1.31 (0.16), residues: 2530 helix: 0.50 (0.16), residues: 1082 sheet: -1.13 (0.26), residues: 370 loop : -2.22 (0.17), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 334 HIS 0.005 0.001 HIS G 180 PHE 0.019 0.001 PHE A 73 TYR 0.018 0.001 TYR E 89 ARG 0.004 0.000 ARG I 125 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5060 Ramachandran restraints generated. 2530 Oldfield, 0 Emsley, 2530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5060 Ramachandran restraints generated. 2530 Oldfield, 0 Emsley, 2530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 412 time to evaluate : 2.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5508 (ttp) cc_final: 0.5174 (tpp) REVERT: A 181 MET cc_start: 0.2944 (mmp) cc_final: 0.2662 (mmt) REVERT: A 253 ASP cc_start: 0.8511 (t0) cc_final: 0.8093 (t0) REVERT: A 464 LEU cc_start: 0.5609 (OUTLIER) cc_final: 0.5144 (tm) REVERT: A 491 MET cc_start: 0.8250 (tmt) cc_final: 0.7907 (tmt) REVERT: A 558 ASN cc_start: 0.7284 (m110) cc_final: 0.6740 (m110) REVERT: A 632 GLU cc_start: 0.7545 (tm-30) cc_final: 0.7335 (tm-30) REVERT: A 637 ASP cc_start: 0.7509 (m-30) cc_final: 0.7058 (m-30) REVERT: B 232 TYR cc_start: 0.7528 (p90) cc_final: 0.7171 (p90) REVERT: F 15 MET cc_start: 0.8652 (OUTLIER) cc_final: 0.7347 (tmm) REVERT: F 120 GLU cc_start: 0.7121 (OUTLIER) cc_final: 0.6395 (mm-30) REVERT: J 21 GLU cc_start: 0.6702 (tp30) cc_final: 0.6470 (tp30) REVERT: J 39 MET cc_start: 0.7902 (OUTLIER) cc_final: 0.7474 (mtt) REVERT: J 47 LYS cc_start: 0.8460 (mmtt) cc_final: 0.7781 (pptt) REVERT: J 292 ARG cc_start: 0.5759 (mmt180) cc_final: 0.5553 (mmp-170) REVERT: J 315 ASP cc_start: 0.7144 (t0) cc_final: 0.6847 (t0) REVERT: C 44 ASN cc_start: 0.7442 (p0) cc_final: 0.7093 (p0) REVERT: C 118 THR cc_start: 0.8114 (p) cc_final: 0.7875 (p) REVERT: D 134 ARG cc_start: 0.8290 (OUTLIER) cc_final: 0.8066 (mtt-85) REVERT: E 70 ARG cc_start: 0.8219 (OUTLIER) cc_final: 0.7657 (ttt-90) REVERT: E 100 ARG cc_start: 0.8105 (tpm170) cc_final: 0.7816 (tpp-160) REVERT: E 110 ARG cc_start: 0.8227 (mtp180) cc_final: 0.7933 (mtp180) outliers start: 108 outliers final: 65 residues processed: 465 average time/residue: 0.9941 time to fit residues: 548.8288 Evaluate side-chains 469 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 398 time to evaluate : 2.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 186 TRP Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 368 TYR Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 600 ASP Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 135 ASP Chi-restraints excluded: chain B residue 183 ASN Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain F residue 15 MET Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain F residue 22 ASP Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 41 LEU Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 120 GLU Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain H residue 127 THR Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 153 ASP Chi-restraints excluded: chain H residue 197 THR Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 48 SER Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain G residue 147 GLU Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 212 LEU Chi-restraints excluded: chain I residue 13 THR Chi-restraints excluded: chain I residue 17 ILE Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain I residue 53 MET Chi-restraints excluded: chain I residue 109 THR Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain I residue 127 THR Chi-restraints excluded: chain I residue 175 ASP Chi-restraints excluded: chain I residue 207 THR Chi-restraints excluded: chain J residue 39 MET Chi-restraints excluded: chain J residue 58 PHE Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 157 GLN Chi-restraints excluded: chain J residue 163 THR Chi-restraints excluded: chain J residue 317 VAL Chi-restraints excluded: chain J residue 349 LEU Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 134 ARG Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain E residue 70 ARG Chi-restraints excluded: chain E residue 82 ASN Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 125 THR Chi-restraints excluded: chain E residue 140 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 153 optimal weight: 7.9990 chunk 99 optimal weight: 6.9990 chunk 148 optimal weight: 0.5980 chunk 74 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 158 optimal weight: 0.9990 chunk 169 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 23 optimal weight: 20.0000 chunk 195 optimal weight: 9.9990 chunk 226 optimal weight: 2.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 134 GLN D 109 GLN E 18 ASN E 50 GLN E 69 ASN ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 22571 Z= 0.204 Angle : 0.638 16.535 30725 Z= 0.328 Chirality : 0.044 0.415 3495 Planarity : 0.003 0.041 3683 Dihedral : 14.408 173.600 3844 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.72 % Favored : 93.24 % Rotamer: Outliers : 4.09 % Allowed : 24.07 % Favored : 71.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.36 % 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: -1.20 (0.16), residues: 2530 helix: 0.59 (0.16), residues: 1088 sheet: -1.04 (0.26), residues: 360 loop : -2.19 (0.17), residues: 1082 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 334 HIS 0.003 0.001 HIS G 180 PHE 0.018 0.001 PHE A 73 TYR 0.017 0.001 TYR E 96 ARG 0.004 0.000 ARG H 183 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5060 Ramachandran restraints generated. 2530 Oldfield, 0 Emsley, 2530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5060 Ramachandran restraints generated. 2530 Oldfield, 0 Emsley, 2530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 412 time to evaluate : 2.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5545 (ttp) cc_final: 0.5057 (tpp) REVERT: A 181 MET cc_start: 0.3054 (mmp) cc_final: 0.2835 (mmt) REVERT: A 230 GLN cc_start: 0.6155 (pp30) cc_final: 0.5915 (pp30) REVERT: A 253 ASP cc_start: 0.8441 (t0) cc_final: 0.8026 (t0) REVERT: A 415 ASP cc_start: 0.7477 (t70) cc_final: 0.7198 (t70) REVERT: A 464 LEU cc_start: 0.5792 (OUTLIER) cc_final: 0.5337 (tm) REVERT: A 491 MET cc_start: 0.8229 (tmt) cc_final: 0.7885 (tmt) REVERT: A 558 ASN cc_start: 0.7213 (m110) cc_final: 0.6655 (m110) REVERT: A 637 ASP cc_start: 0.7375 (m-30) cc_final: 0.6927 (m-30) REVERT: F 15 MET cc_start: 0.8624 (OUTLIER) cc_final: 0.7329 (tmm) REVERT: F 120 GLU cc_start: 0.7014 (OUTLIER) cc_final: 0.6425 (mm-30) REVERT: J 21 GLU cc_start: 0.6697 (tp30) cc_final: 0.6470 (tp30) REVERT: J 30 PHE cc_start: 0.6873 (t80) cc_final: 0.6336 (t80) REVERT: J 39 MET cc_start: 0.7795 (OUTLIER) cc_final: 0.7332 (mtt) REVERT: J 47 LYS cc_start: 0.8401 (mmtt) cc_final: 0.7758 (pptt) REVERT: C 44 ASN cc_start: 0.7397 (p0) cc_final: 0.7038 (p0) REVERT: E 70 ARG cc_start: 0.8208 (OUTLIER) cc_final: 0.7604 (ttt-90) REVERT: E 100 ARG cc_start: 0.8125 (tpm170) cc_final: 0.7829 (tpp-160) outliers start: 91 outliers final: 61 residues processed: 447 average time/residue: 1.0118 time to fit residues: 539.8737 Evaluate side-chains 459 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 393 time to evaluate : 2.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 186 TRP Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 368 TYR Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 520 ASP Chi-restraints excluded: chain A residue 600 ASP Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 754 THR Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 183 ASN Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain F residue 15 MET Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain F residue 22 ASP Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 41 LEU Chi-restraints excluded: chain F residue 120 GLU Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain H residue 127 THR Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 153 ASP Chi-restraints excluded: chain H residue 197 THR Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 48 SER Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 212 LEU Chi-restraints excluded: chain I residue 13 THR Chi-restraints excluded: chain I residue 17 ILE Chi-restraints excluded: chain I residue 36 ASP Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain I residue 53 MET Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain I residue 127 THR Chi-restraints excluded: chain I residue 175 ASP Chi-restraints excluded: chain I residue 207 THR Chi-restraints excluded: chain J residue 39 MET Chi-restraints excluded: chain J residue 58 PHE Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 157 GLN Chi-restraints excluded: chain J residue 163 THR Chi-restraints excluded: chain J residue 307 TYR Chi-restraints excluded: chain J residue 349 LEU Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain E residue 70 ARG Chi-restraints excluded: chain E residue 82 ASN Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 125 THR Chi-restraints excluded: chain E residue 140 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 238 optimal weight: 0.9990 chunk 217 optimal weight: 5.9990 chunk 231 optimal weight: 0.9990 chunk 139 optimal weight: 6.9990 chunk 100 optimal weight: 9.9990 chunk 181 optimal weight: 0.0980 chunk 71 optimal weight: 8.9990 chunk 209 optimal weight: 9.9990 chunk 219 optimal weight: 3.9990 chunk 230 optimal weight: 8.9990 chunk 152 optimal weight: 1.9990 overall best weight: 1.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 134 GLN J 173 GLN J 214 GLN D 109 GLN E 50 GLN E 69 ASN ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 22571 Z= 0.192 Angle : 0.646 16.288 30725 Z= 0.330 Chirality : 0.043 0.405 3495 Planarity : 0.003 0.042 3683 Dihedral : 14.365 173.544 3844 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.56 % Favored : 93.40 % Rotamer: Outliers : 3.42 % Allowed : 25.15 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.36 % 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: -1.13 (0.16), residues: 2530 helix: 0.67 (0.16), residues: 1087 sheet: -1.02 (0.26), residues: 358 loop : -2.16 (0.17), residues: 1085 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 334 HIS 0.003 0.001 HIS J 65 PHE 0.020 0.001 PHE E 29 TYR 0.018 0.001 TYR E 96 ARG 0.008 0.000 ARG C 110 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5060 Ramachandran restraints generated. 2530 Oldfield, 0 Emsley, 2530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5060 Ramachandran restraints generated. 2530 Oldfield, 0 Emsley, 2530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 420 time to evaluate : 2.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5403 (ttp) cc_final: 0.5119 (tpp) REVERT: A 86 MET cc_start: 0.4337 (pmm) cc_final: 0.3993 (pmm) REVERT: A 161 MET cc_start: 0.6219 (tmm) cc_final: 0.4496 (ttt) REVERT: A 230 GLN cc_start: 0.6073 (pp30) cc_final: 0.5838 (pp30) REVERT: A 253 ASP cc_start: 0.8456 (t0) cc_final: 0.8031 (t0) REVERT: A 358 MET cc_start: 0.7331 (tpt) cc_final: 0.7048 (tpt) REVERT: A 420 ILE cc_start: 0.7944 (OUTLIER) cc_final: 0.7537 (pp) REVERT: A 464 LEU cc_start: 0.5853 (OUTLIER) cc_final: 0.5389 (tm) REVERT: A 491 MET cc_start: 0.8312 (tmt) cc_final: 0.7794 (tmt) REVERT: A 558 ASN cc_start: 0.7181 (m110) cc_final: 0.6634 (m110) REVERT: A 600 ASP cc_start: 0.7854 (OUTLIER) cc_final: 0.7545 (m-30) REVERT: A 637 ASP cc_start: 0.7384 (m-30) cc_final: 0.6929 (m-30) REVERT: F 120 GLU cc_start: 0.7083 (OUTLIER) cc_final: 0.6496 (mm-30) REVERT: J 21 GLU cc_start: 0.6562 (tp30) cc_final: 0.6341 (tp30) REVERT: J 39 MET cc_start: 0.7549 (OUTLIER) cc_final: 0.7222 (mtt) REVERT: J 47 LYS cc_start: 0.8352 (mmtt) cc_final: 0.7755 (pptt) REVERT: J 204 ASP cc_start: 0.6733 (OUTLIER) cc_final: 0.6518 (p0) REVERT: C 44 ASN cc_start: 0.7390 (p0) cc_final: 0.7025 (p0) REVERT: C 106 ASP cc_start: 0.7158 (t70) cc_final: 0.6830 (t70) REVERT: E 70 ARG cc_start: 0.8186 (OUTLIER) cc_final: 0.7554 (ttt-90) REVERT: E 100 ARG cc_start: 0.8114 (tpm170) cc_final: 0.7819 (tpp-160) REVERT: E 105 LYS cc_start: 0.7647 (ttmm) cc_final: 0.7061 (mtpt) outliers start: 76 outliers final: 51 residues processed: 447 average time/residue: 0.9741 time to fit residues: 517.3614 Evaluate side-chains 455 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 397 time to evaluate : 2.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 186 TRP Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 368 TYR Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 580 MET Chi-restraints excluded: chain A residue 600 ASP Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 754 THR Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 183 ASN Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain F residue 22 ASP Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 41 LEU Chi-restraints excluded: chain F residue 120 GLU Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain H residue 127 THR Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 197 THR Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 48 SER Chi-restraints excluded: chain G residue 147 GLU Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain I residue 13 THR Chi-restraints excluded: chain I residue 17 ILE Chi-restraints excluded: chain I residue 36 ASP Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain I residue 127 THR Chi-restraints excluded: chain I residue 175 ASP Chi-restraints excluded: chain I residue 207 THR Chi-restraints excluded: chain J residue 39 MET Chi-restraints excluded: chain J residue 58 PHE Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 163 THR Chi-restraints excluded: chain J residue 204 ASP Chi-restraints excluded: chain J residue 307 TYR Chi-restraints excluded: chain J residue 349 LEU Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain E residue 70 ARG Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 125 THR Chi-restraints excluded: chain E residue 140 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 245 optimal weight: 8.9990 chunk 149 optimal weight: 4.9990 chunk 116 optimal weight: 0.9980 chunk 170 optimal weight: 0.0020 chunk 257 optimal weight: 10.0000 chunk 236 optimal weight: 1.9990 chunk 204 optimal weight: 3.9990 chunk 21 optimal weight: 9.9990 chunk 158 optimal weight: 5.9990 chunk 125 optimal weight: 0.9990 chunk 162 optimal weight: 3.9990 overall best weight: 1.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 131 ASN ** I 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 214 GLN D 109 GLN E 18 ASN E 50 GLN E 69 ASN ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.2962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 22571 Z= 0.197 Angle : 0.651 16.493 30725 Z= 0.333 Chirality : 0.044 0.404 3495 Planarity : 0.003 0.043 3683 Dihedral : 14.364 173.809 3844 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.68 % Favored : 93.28 % Rotamer: Outliers : 2.83 % Allowed : 26.27 % Favored : 70.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.36 % 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: -1.10 (0.16), residues: 2530 helix: 0.68 (0.16), residues: 1087 sheet: -1.00 (0.26), residues: 358 loop : -2.14 (0.17), residues: 1085 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 334 HIS 0.004 0.001 HIS J 65 PHE 0.020 0.001 PHE E 29 TYR 0.022 0.001 TYR E 96 ARG 0.008 0.000 ARG H 137 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5060 Ramachandran restraints generated. 2530 Oldfield, 0 Emsley, 2530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5060 Ramachandran restraints generated. 2530 Oldfield, 0 Emsley, 2530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 403 time to evaluate : 2.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5250 (ttp) cc_final: 0.4974 (tpp) REVERT: A 86 MET cc_start: 0.4358 (pmm) cc_final: 0.4029 (pmm) REVERT: A 230 GLN cc_start: 0.6055 (pp30) cc_final: 0.5819 (pp30) REVERT: A 253 ASP cc_start: 0.8453 (t0) cc_final: 0.7982 (t0) REVERT: A 358 MET cc_start: 0.7337 (tpt) cc_final: 0.7059 (tpt) REVERT: A 464 LEU cc_start: 0.5916 (OUTLIER) cc_final: 0.5452 (tm) REVERT: A 558 ASN cc_start: 0.7175 (m110) cc_final: 0.6625 (m110) REVERT: A 637 ASP cc_start: 0.7380 (m-30) cc_final: 0.6905 (m-30) REVERT: F 120 GLU cc_start: 0.7167 (OUTLIER) cc_final: 0.6573 (mm-30) REVERT: F 154 ASP cc_start: 0.7656 (t0) cc_final: 0.7055 (t70) REVERT: J 21 GLU cc_start: 0.6569 (tp30) cc_final: 0.6357 (tp30) REVERT: J 39 MET cc_start: 0.7521 (OUTLIER) cc_final: 0.7182 (mtt) REVERT: J 47 LYS cc_start: 0.8347 (mmtt) cc_final: 0.7754 (pptt) REVERT: J 204 ASP cc_start: 0.6693 (OUTLIER) cc_final: 0.6471 (p0) REVERT: C 44 ASN cc_start: 0.7470 (p0) cc_final: 0.7120 (p0) REVERT: C 106 ASP cc_start: 0.7183 (t70) cc_final: 0.6843 (t70) REVERT: E 70 ARG cc_start: 0.8250 (OUTLIER) cc_final: 0.7854 (ttt-90) REVERT: E 100 ARG cc_start: 0.8089 (tpm170) cc_final: 0.7787 (tpp-160) outliers start: 63 outliers final: 47 residues processed: 423 average time/residue: 1.0026 time to fit residues: 504.0203 Evaluate side-chains 445 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 393 time to evaluate : 4.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 186 TRP Chi-restraints excluded: chain A residue 250 MET Chi-restraints excluded: chain A residue 368 TYR Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 580 MET Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 183 ASN Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain F residue 22 ASP Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 41 LEU Chi-restraints excluded: chain F residue 120 GLU Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain H residue 127 THR Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 197 THR Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 48 SER Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain I residue 13 THR Chi-restraints excluded: chain I residue 127 THR Chi-restraints excluded: chain I residue 175 ASP Chi-restraints excluded: chain I residue 207 THR Chi-restraints excluded: chain J residue 39 MET Chi-restraints excluded: chain J residue 58 PHE Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 163 THR Chi-restraints excluded: chain J residue 204 ASP Chi-restraints excluded: chain J residue 307 TYR Chi-restraints excluded: chain J residue 349 LEU Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain E residue 70 ARG Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 125 THR Chi-restraints excluded: chain E residue 140 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 218 optimal weight: 9.9990 chunk 62 optimal weight: 5.9990 chunk 188 optimal weight: 1.9990 chunk 30 optimal weight: 10.0000 chunk 56 optimal weight: 9.9990 chunk 205 optimal weight: 6.9990 chunk 85 optimal weight: 9.9990 chunk 210 optimal weight: 8.9990 chunk 25 optimal weight: 2.9990 chunk 37 optimal weight: 10.0000 chunk 179 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 GLN B 134 HIS ** B 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 214 GLN D 109 GLN E 18 ASN E 50 GLN E 69 ASN E 73 ASN ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.148299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.118673 restraints weight = 39699.166| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 2.73 r_work: 0.3381 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3388 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3388 r_free = 0.3388 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3388 r_free = 0.3388 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3388 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 22571 Z= 0.369 Angle : 0.749 17.049 30725 Z= 0.384 Chirality : 0.048 0.473 3495 Planarity : 0.004 0.060 3683 Dihedral : 14.524 169.757 3844 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.43 % Favored : 92.53 % Rotamer: Outliers : 3.06 % Allowed : 26.36 % Favored : 70.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.36 % 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: -1.33 (0.16), residues: 2530 helix: 0.51 (0.16), residues: 1085 sheet: -1.19 (0.26), residues: 367 loop : -2.25 (0.17), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 186 HIS 0.006 0.001 HIS G 180 PHE 0.023 0.002 PHE A 73 TYR 0.023 0.002 TYR E 96 ARG 0.008 0.001 ARG C 110 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8540.52 seconds wall clock time: 152 minutes 50.07 seconds (9170.07 seconds total)