Starting phenix.real_space_refine on Sat Feb 17 03:43:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xn5_22268/02_2024/6xn5_22268.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xn5_22268/02_2024/6xn5_22268.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xn5_22268/02_2024/6xn5_22268.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xn5_22268/02_2024/6xn5_22268.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xn5_22268/02_2024/6xn5_22268.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xn5_22268/02_2024/6xn5_22268.pdb" } resolution = 2.97 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= 0.013 sd= 1.147 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 31 5.49 5 S 47 5.16 5 C 10948 2.51 5 N 2946 2.21 5 O 3428 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "I GLU 69": "OE1" <-> "OE2" Residue "I ARG 90": "NH1" <-> "NH2" Residue "I GLU 147": "OE1" <-> "OE2" Residue "I GLU 163": "OE1" <-> "OE2" Residue "I GLU 191": "OE1" <-> "OE2" Residue "F GLU 76": "OE1" <-> "OE2" Residue "F GLU 120": "OE1" <-> "OE2" Residue "F GLU 163": "OE1" <-> "OE2" Residue "H GLU 69": "OE1" <-> "OE2" Residue "H GLU 136": "OE1" <-> "OE2" Residue "H GLU 159": "OE1" <-> "OE2" Residue "H GLU 163": "OE1" <-> "OE2" Residue "A PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 47": "OE1" <-> "OE2" Residue "A GLU 93": "OE1" <-> "OE2" Residue "A ARG 121": "NH1" <-> "NH2" Residue "A GLU 173": "OE1" <-> "OE2" Residue "A GLU 183": "OE1" <-> "OE2" Residue "A GLU 240": "OE1" <-> "OE2" Residue "A GLU 293": "OE1" <-> "OE2" Residue "A GLU 351": "OE1" <-> "OE2" Residue "A ARG 365": "NH1" <-> "NH2" Residue "A GLU 404": "OE1" <-> "OE2" Residue "A GLU 414": "OE1" <-> "OE2" Residue "A GLU 480": "OE1" <-> "OE2" Residue "A ARG 694": "NH1" <-> "NH2" Residue "A ARG 740": "NH1" <-> "NH2" Residue "B PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 116": "OE1" <-> "OE2" Residue "B ARG 117": "NH1" <-> "NH2" Residue "B GLU 129": "OE1" <-> "OE2" Residue "B GLU 160": "OE1" <-> "OE2" Residue "B GLU 168": "OE1" <-> "OE2" Residue "B GLU 192": "OE1" <-> "OE2" Residue "B GLU 195": "OE1" <-> "OE2" Residue "B GLU 266": "OE1" <-> "OE2" Residue "B PHE 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 6": "OE1" <-> "OE2" Residue "G ARG 133": "NH1" <-> "NH2" Residue "G GLU 163": "OE1" <-> "OE2" Residue "J ARG 6": "NH1" <-> "NH2" Residue "J ARG 123": "NH1" <-> "NH2" Residue "J ARG 288": "NH1" <-> "NH2" Residue "J ARG 304": "NH1" <-> "NH2" Residue "J ARG 311": "NH1" <-> "NH2" Residue "J GLU 341": "OE1" <-> "OE2" Residue "J ARG 346": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 17400 Number of models: 1 Model: "" Number of chains: 8 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: "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: 1629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1629 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 5, 'TRANS': 202} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "A" Number of atoms: 5939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 735, 5939 Classifications: {'peptide': 735} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 7, 'TRANS': 723} Chain breaks: 3 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: 2278 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 282, 2276 Classifications: {'peptide': 282} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 272} 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: 282, 2276 Classifications: {'peptide': 282} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 272} 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: 2323 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: "J" Number of atoms: 1917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1917 Classifications: {'peptide': 239} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 9, 'TRANS': 227} Chain breaks: 3 Chain: "R" Number of atoms: 674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 674 Classifications: {'RNA': 32} Modifications used: {'5*END': 1, 'rna2p_pur': 10, 'rna2p_pyr': 7, 'rna3p_pur': 6, 'rna3p_pyr': 9} Link IDs: {'rna2p': 17, 'rna3p': 14} Time building chain proxies: 10.21, per 1000 atoms: 0.59 Number of scatterers: 17400 At special positions: 0 Unit cell: (122.436, 126.732, 205.134, 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 47 16.00 P 31 15.00 O 3428 8.00 N 2946 7.00 C 10948 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=2.00 Simple disulfide: pdb=" SG CYS A 405 " - pdb=" SG CYS A 421 " distance=2.07 Simple disulfide: pdb=" SG CYS A 418 " - pdb=" SG CYS A 421 " distance=2.02 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: 6.12 Conformation dependent library (CDL) restraints added in 3.0 seconds 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3908 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 27 sheets defined 37.5% alpha, 16.4% beta 0 base pairs and 7 stacking pairs defined. Time for finding SS restraints: 5.16 Creating SS restraints... Processing helix chain 'I' and resid 45 through 61 Processing helix chain 'I' and resid 74 through 81 Processing helix chain 'I' and resid 103 through 109 removed outlier: 3.700A pdb=" N LEU I 107 " --> pdb=" O ASN I 103 " (cutoff:3.500A) Processing helix chain 'I' and resid 157 through 173 Processing helix chain 'I' and resid 204 through 213 removed outlier: 4.285A pdb=" N LEU I 208 " --> pdb=" O LYS I 204 " (cutoff:3.500A) 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 removed outlier: 3.910A pdb=" N PHE F 110 " --> pdb=" O GLU F 106 " (cutoff:3.500A) Processing helix chain 'F' and resid 154 through 156 No H-bonds generated for 'chain 'F' and resid 154 through 156' Processing helix chain 'F' and resid 157 through 174 Processing helix chain 'F' and resid 205 through 213 Processing helix chain 'H' and resid 45 through 61 Processing helix chain 'H' and resid 74 through 82 Processing helix chain 'H' and resid 103 through 110 removed outlier: 3.614A pdb=" N PHE H 110 " --> pdb=" O GLU H 106 " (cutoff:3.500A) Processing helix chain 'H' and resid 154 through 156 No H-bonds generated for 'chain 'H' and resid 154 through 156' Processing helix chain 'H' and resid 157 through 173 Processing helix chain 'H' and resid 205 through 213 Processing helix chain 'A' and resid 3 through 13 Processing helix chain 'A' and resid 15 through 21 Processing helix chain 'A' and resid 28 through 40 Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 56 through 63 Processing helix chain 'A' and resid 72 through 85 removed outlier: 3.596A pdb=" N THR A 76 " --> pdb=" O LEU A 72 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLY A 85 " --> pdb=" O ASN A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 113 Processing helix chain 'A' and resid 150 through 166 removed outlier: 3.636A pdb=" N GLN A 166 " --> pdb=" O LYS A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 173 No H-bonds generated for 'chain 'A' and resid 171 through 173' Processing helix chain 'A' and resid 174 through 186 Processing helix chain 'A' and resid 202 through 224 Processing helix chain 'A' and resid 228 through 235 removed outlier: 3.953A pdb=" N GLU A 232 " --> pdb=" O ASP A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 244 Processing helix chain 'A' and resid 256 through 262 Processing helix chain 'A' and resid 268 through 271 removed outlier: 3.531A pdb=" N LYS A 271 " --> pdb=" O LYS A 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 268 through 271' Processing helix chain 'A' and resid 272 through 295 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 353 through 358 Processing helix chain 'A' and resid 363 through 381 removed outlier: 4.178A pdb=" N TYR A 368 " --> pdb=" O TYR A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 394 Processing helix chain 'A' and resid 418 through 430 Processing helix chain 'A' and resid 458 through 463 removed outlier: 3.581A pdb=" N ASP A 462 " --> pdb=" O SER A 459 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LYS A 463 " --> pdb=" O GLN A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 507 removed outlier: 3.720A pdb=" N VAL A 507 " --> pdb=" O MET A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 531 Processing helix chain 'A' and resid 533 through 537 Processing helix chain 'A' and resid 538 through 564 removed outlier: 3.745A pdb=" N LYS A 564 " --> pdb=" O LEU A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 603 removed outlier: 4.298A pdb=" N ILE A 592 " --> pdb=" O LEU A 588 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N VAL A 593 " --> pdb=" O ASP A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 638 removed outlier: 3.518A pdb=" N TYR A 638 " --> pdb=" O ALA A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 681 Processing helix chain 'A' and resid 686 through 704 removed outlier: 3.919A pdb=" N ALA A 690 " --> pdb=" O GLU A 686 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 725 removed outlier: 3.678A pdb=" N ILE A 710 " --> pdb=" O GLN A 706 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N SER A 718 " --> pdb=" O ALA A 714 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N GLU A 722 " --> pdb=" O SER A 718 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N LYS A 723 " --> pdb=" O ARG A 719 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N ILE A 724 " --> pdb=" O MET A 720 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY A 725 " --> pdb=" O GLU A 721 " (cutoff:3.500A) Processing helix chain 'A' and resid 731 through 736 Processing helix chain 'A' and resid 740 through 754 Processing helix chain 'B' and resid 27 through 42 Processing helix chain 'B' and resid 44 through 54 removed outlier: 3.537A pdb=" N ASN B 54 " --> pdb=" O GLN B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 108 Processing helix chain 'B' and resid 163 through 175 removed outlier: 3.770A pdb=" N TYR B 175 " --> pdb=" O GLU B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 205 removed outlier: 3.681A pdb=" N ALA B 205 " --> pdb=" O ASP B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 227 Processing helix chain 'G' and resid 45 through 61 removed outlier: 3.501A 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 174 removed outlier: 3.527A pdb=" N VAL G 158 " --> pdb=" O ASP G 154 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N GLU G 159 " --> pdb=" O ILE G 155 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N LYS G 160 " --> pdb=" O LYS G 156 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N PHE G 174 " --> pdb=" O ASP G 170 " (cutoff:3.500A) Processing helix chain 'G' and resid 205 through 212 Processing helix chain 'J' and resid 127 through 139 removed outlier: 4.124A pdb=" N LEU J 131 " --> pdb=" O PRO J 127 " (cutoff:3.500A) Processing helix chain 'J' and resid 209 through 227 removed outlier: 3.897A pdb=" N ASN J 215 " --> pdb=" O LYS J 211 " (cutoff:3.500A) Processing helix chain 'J' and resid 228 through 235 removed outlier: 3.570A pdb=" N GLY J 232 " --> pdb=" O TRP J 228 " (cutoff:3.500A) Processing helix chain 'J' and resid 288 through 300 Processing sheet with id=AA1, first strand: chain 'I' and resid 188 through 191 removed outlier: 3.750A pdb=" N ILE I 196 " --> pdb=" O VAL I 4 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'I' and resid 188 through 191 removed outlier: 6.271A pdb=" N GLU I 147 " --> pdb=" O ASN I 97 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N ASN I 97 " --> pdb=" O GLU I 147 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N GLY H 184 " --> pdb=" O LEU I 94 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N PHE I 96 " --> pdb=" O GLY H 184 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'I' and resid 43 through 44 Processing sheet with id=AA4, first strand: chain 'I' and resid 115 through 119 Processing sheet with id=AA5, first strand: chain 'F' and resid 188 through 199 removed outlier: 5.286A pdb=" N PHE F 190 " --> pdb=" O VAL F 10 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N VAL F 10 " --> pdb=" O PHE F 190 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N ASN F 192 " --> pdb=" O THR F 8 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N THR F 8 " --> pdb=" O ASN F 192 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N LYS F 2 " --> pdb=" O ALA F 198 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N GLU F 147 " --> pdb=" O ASN F 97 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ASN F 97 " --> pdb=" O GLU F 147 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N GLY B 185 " --> pdb=" O LEU F 94 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N PHE F 96 " --> pdb=" O GLY B 185 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 43 through 44 Processing sheet with id=AA7, first strand: chain 'F' and resid 83 through 84 Processing sheet with id=AA8, first strand: chain 'F' and resid 115 through 120 Processing sheet with id=AA9, first strand: chain 'F' and resid 183 through 184 removed outlier: 4.119A pdb=" N ASN G 97 " --> pdb=" O GLU G 147 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N GLU G 147 " --> pdb=" O ASN G 97 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N THR G 8 " --> pdb=" O ASN G 192 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N ASN G 192 " --> pdb=" O THR G 8 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N VAL G 10 " --> pdb=" O PHE G 190 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N PHE G 190 " --> pdb=" O VAL G 10 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 143 through 151 removed outlier: 4.718A pdb=" N THR H 8 " --> pdb=" O ASN H 192 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N ASN H 192 " --> pdb=" O THR H 8 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N VAL H 10 " --> pdb=" O PHE H 190 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N PHE H 190 " --> pdb=" O VAL H 10 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 43 through 44 Processing sheet with id=AB3, first strand: chain 'H' and resid 96 through 97 removed outlier: 6.715A pdb=" N PHE H 96 " --> pdb=" O GLY G 184 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'H' and resid 115 through 120 Processing sheet with id=AB5, first strand: chain 'A' and resid 107 through 108 removed outlier: 4.497A pdb=" N LEU A 107 " --> pdb=" O TYR A 126 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 302 through 305 removed outlier: 6.730A pdb=" N TYR A 311 " --> pdb=" O LEU A 303 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N VAL A 305 " --> pdb=" O HIS A 309 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N HIS A 309 " --> pdb=" O VAL A 305 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR A 344 " --> pdb=" O SER A 255 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 302 through 305 removed outlier: 6.730A pdb=" N TYR A 311 " --> pdb=" O LEU A 303 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N VAL A 305 " --> pdb=" O HIS A 309 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N HIS A 309 " --> pdb=" O VAL A 305 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR A 350 " --> pdb=" O MET A 249 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 445 through 447 removed outlier: 3.700A pdb=" N LYS A 451 " --> pdb=" O MET A 447 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 568 through 572 removed outlier: 6.482A pdb=" N PHE A 579 " --> pdb=" O ILE A 571 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR A 653 " --> pdb=" O ALA A 610 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 97 through 99 Processing sheet with id=AC2, first strand: chain 'B' and resid 123 through 132 Processing sheet with id=AC3, first strand: chain 'B' and resid 264 through 265 Processing sheet with id=AC4, first strand: chain 'B' and resid 234 through 237 removed outlier: 3.505A pdb=" N LEU B 256 " --> pdb=" O ARG B 237 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 272 through 277 removed outlier: 3.592A pdb=" N ASP B 272 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N VAL B 284 " --> pdb=" O VAL B 276 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 43 through 44 Processing sheet with id=AC7, first strand: chain 'G' and resid 115 through 120 Processing sheet with id=AC8, first strand: chain 'J' and resid 158 through 161 removed outlier: 4.073A pdb=" N VAL J 158 " --> pdb=" O SER J 202 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N SER J 202 " --> pdb=" O VAL J 158 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N ASP J 160 " --> pdb=" O THR J 200 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N THR J 200 " --> pdb=" O ASP J 160 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N PHE J 203 " --> pdb=" O LYS J 3 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N THR J 8 " --> pdb=" O LYS J 348 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LYS J 348 " --> pdb=" O THR J 8 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR J 10 " --> pdb=" O ARG J 346 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG J 346 " --> pdb=" O THR J 10 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA J 345 " --> pdb=" O ILE J 268 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ILE J 268 " --> pdb=" O ALA J 345 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'J' and resid 169 through 172 removed outlier: 3.932A pdb=" N LYS J 170 " --> pdb=" O CYS J 190 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N CYS J 190 " --> pdb=" O LYS J 170 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N TYR J 172 " --> pdb=" O ARG J 188 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ARG J 188 " --> pdb=" O TYR J 172 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 690 hydrogen bonds defined for protein. 1983 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 7 stacking parallelities Total time for adding SS restraints: 5.07 Time building geometry restraints manager: 6.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 5533 1.34 - 1.46: 4258 1.46 - 1.59: 7833 1.59 - 1.72: 42 1.72 - 1.84: 87 Bond restraints: 17753 Sorted by residual: bond pdb=" CA GLU A 704 " pdb=" C GLU A 704 " ideal model delta sigma weight residual 1.523 1.575 -0.052 1.80e-02 3.09e+03 8.24e+00 bond pdb=" CB PRO I 70 " pdb=" CG PRO I 70 " ideal model delta sigma weight residual 1.492 1.624 -0.132 5.00e-02 4.00e+02 6.93e+00 bond pdb=" N PRO I 70 " pdb=" CD PRO I 70 " ideal model delta sigma weight residual 1.473 1.504 -0.031 1.40e-02 5.10e+03 4.80e+00 bond pdb=" CG1 ILE G 139 " pdb=" CD1 ILE G 139 " ideal model delta sigma weight residual 1.513 1.429 0.084 3.90e-02 6.57e+02 4.62e+00 bond pdb=" N ASP J 112 " pdb=" CA ASP J 112 " ideal model delta sigma weight residual 1.457 1.483 -0.026 1.29e-02 6.01e+03 3.93e+00 ... (remaining 17748 not shown) Histogram of bond angle deviations from ideal: 96.31 - 104.01: 253 104.01 - 111.72: 7617 111.72 - 119.43: 7023 119.43 - 127.13: 8967 127.13 - 134.84: 180 Bond angle restraints: 24040 Sorted by residual: angle pdb=" CA PRO I 70 " pdb=" N PRO I 70 " pdb=" CD PRO I 70 " ideal model delta sigma weight residual 112.00 98.55 13.45 1.40e+00 5.10e-01 9.24e+01 angle pdb=" N ILE A 341 " pdb=" CA ILE A 341 " pdb=" C ILE A 341 " ideal model delta sigma weight residual 113.71 106.06 7.65 9.50e-01 1.11e+00 6.49e+01 angle pdb=" C LYS A 683 " pdb=" N LEU A 684 " pdb=" CA LEU A 684 " ideal model delta sigma weight residual 121.70 133.14 -11.44 1.80e+00 3.09e-01 4.04e+01 angle pdb=" N VAL J 277 " pdb=" CA VAL J 277 " pdb=" C VAL J 277 " ideal model delta sigma weight residual 112.96 107.06 5.90 1.00e+00 1.00e+00 3.48e+01 angle pdb=" CA CYS A 405 " pdb=" CB CYS A 405 " pdb=" SG CYS A 405 " ideal model delta sigma weight residual 114.40 125.57 -11.17 2.30e+00 1.89e-01 2.36e+01 ... (remaining 24035 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.81: 10404 31.81 - 63.62: 329 63.62 - 95.43: 34 95.43 - 127.24: 0 127.24 - 159.05: 4 Dihedral angle restraints: 10771 sinusoidal: 4698 harmonic: 6073 Sorted by residual: dihedral pdb=" CA ASN G 62 " pdb=" C ASN G 62 " pdb=" N ASN G 63 " pdb=" CA ASN G 63 " ideal model delta harmonic sigma weight residual -180.00 -127.51 -52.49 0 5.00e+00 4.00e-02 1.10e+02 dihedral pdb=" O4' C R 24 " pdb=" C1' C R 24 " pdb=" N1 C R 24 " pdb=" C2 C R 24 " ideal model delta sinusoidal sigma weight residual 200.00 40.95 159.05 1 1.50e+01 4.44e-03 8.25e+01 dihedral pdb=" O4' C R 28 " pdb=" C1' C R 28 " pdb=" N1 C R 28 " pdb=" C2 C R 28 " ideal model delta sinusoidal sigma weight residual 200.00 48.56 151.44 1 1.50e+01 4.44e-03 8.01e+01 ... (remaining 10768 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 2180 0.073 - 0.145: 442 0.145 - 0.218: 67 0.218 - 0.291: 13 0.291 - 0.363: 6 Chirality restraints: 2708 Sorted by residual: chirality pdb=" CG LEU H 78 " pdb=" CB LEU H 78 " pdb=" CD1 LEU H 78 " pdb=" CD2 LEU H 78 " both_signs ideal model delta sigma weight residual False -2.59 -2.23 -0.36 2.00e-01 2.50e+01 3.30e+00 chirality pdb=" CB VAL B 131 " pdb=" CA VAL B 131 " pdb=" CG1 VAL B 131 " pdb=" CG2 VAL B 131 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.86e+00 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 -2.29 -0.34 2.00e-01 2.50e+01 2.84e+00 ... (remaining 2705 not shown) Planarity restraints: 2983 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 553 " -0.019 2.00e-02 2.50e+03 3.75e-02 1.40e+01 pdb=" C PHE A 553 " 0.065 2.00e-02 2.50e+03 pdb=" O PHE A 553 " -0.024 2.00e-02 2.50e+03 pdb=" N LYS A 554 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU I 69 " 0.066 5.00e-02 4.00e+02 9.19e-02 1.35e+01 pdb=" N PRO I 70 " -0.158 5.00e-02 4.00e+02 pdb=" CA PRO I 70 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO I 70 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 667 " 0.016 2.00e-02 2.50e+03 3.21e-02 1.03e+01 pdb=" C GLU A 667 " -0.055 2.00e-02 2.50e+03 pdb=" O GLU A 667 " 0.021 2.00e-02 2.50e+03 pdb=" N ASN A 668 " 0.019 2.00e-02 2.50e+03 ... (remaining 2980 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2228 2.75 - 3.29: 16154 3.29 - 3.82: 29425 3.82 - 4.36: 34951 4.36 - 4.90: 60835 Nonbonded interactions: 143593 Sorted by model distance: nonbonded pdb=" O MET B 76 " pdb=" OG SER B 231 " model vdw 2.211 2.440 nonbonded pdb=" OG SER A 202 " pdb=" OD2 ASP A 205 " model vdw 2.258 2.440 nonbonded pdb=" NH1 ARG H 54 " pdb=" OP1 U R 19 " model vdw 2.260 2.520 nonbonded pdb=" O ALA J 291 " pdb=" OG SER J 295 " model vdw 2.282 2.440 nonbonded pdb=" O ALA J 134 " pdb=" OG1 THR J 137 " model vdw 2.285 2.440 ... (remaining 143588 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 'F' and (resid 1 through 20 or resid 27 through 214)) selection = (chain 'G' and (resid 1 through 20 or resid 27 through 65 or resid 73 through 21 \ 4)) selection = (chain 'H' and (resid 1 through 65 or resid 73 through 214)) selection = (chain 'I' and (resid 1 through 20 or resid 27 through 65 or resid 73 through 21 \ 4)) } 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: 1.470 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: 4.890 Check model and map are aligned: 0.270 Set scattering table: 0.170 Process input model: 47.690 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 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 0.132 17753 Z= 0.476 Angle : 1.119 15.796 24040 Z= 0.605 Chirality : 0.063 0.363 2708 Planarity : 0.006 0.092 2983 Dihedral : 15.713 159.048 6854 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 0.06 % Allowed : 0.88 % Favored : 99.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -3.03 (0.16), residues: 2065 helix: -1.97 (0.15), residues: 738 sheet: -1.13 (0.26), residues: 357 loop : -2.32 (0.17), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.003 TRP A 334 HIS 0.007 0.001 HIS A 13 PHE 0.038 0.003 PHE J 296 TYR 0.041 0.003 TYR A 229 ARG 0.024 0.001 ARG A 365 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 234 time to evaluate : 1.941 Fit side-chains REVERT: G 59 LYS cc_start: 0.7049 (tptp) cc_final: 0.6824 (tptt) outliers start: 1 outliers final: 4 residues processed: 235 average time/residue: 1.1990 time to fit residues: 319.9938 Evaluate side-chains 153 residues out of total 1827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 149 time to evaluate : 1.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain A residue 535 ASP Chi-restraints excluded: chain G residue 75 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 176 optimal weight: 0.9980 chunk 158 optimal weight: 0.4980 chunk 87 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 106 optimal weight: 6.9990 chunk 84 optimal weight: 6.9990 chunk 163 optimal weight: 0.9980 chunk 63 optimal weight: 8.9990 chunk 99 optimal weight: 0.9980 chunk 121 optimal weight: 0.8980 chunk 189 optimal weight: 9.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 147 ASN A 734 ASN B 132 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.1332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 17753 Z= 0.174 Angle : 0.607 9.070 24040 Z= 0.320 Chirality : 0.042 0.172 2708 Planarity : 0.004 0.061 2983 Dihedral : 12.343 158.956 2746 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 1.55 % Allowed : 9.73 % Favored : 88.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.17), residues: 2065 helix: -0.48 (0.18), residues: 747 sheet: -0.91 (0.26), residues: 359 loop : -2.05 (0.18), residues: 959 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 735 HIS 0.001 0.001 HIS B 163 PHE 0.027 0.001 PHE J 296 TYR 0.016 0.001 TYR J 225 ARG 0.014 0.000 ARG B 18 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 178 time to evaluate : 1.974 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 174 PHE cc_start: 0.7371 (m-10) cc_final: 0.7031 (m-80) REVERT: H 154 ASP cc_start: 0.6394 (m-30) cc_final: 0.6180 (m-30) REVERT: H 209 ASN cc_start: 0.6315 (OUTLIER) cc_final: 0.5972 (m-40) REVERT: J 310 MET cc_start: 0.4358 (OUTLIER) cc_final: 0.3914 (mtm) outliers start: 28 outliers final: 12 residues processed: 194 average time/residue: 1.0655 time to fit residues: 237.0450 Evaluate side-chains 157 residues out of total 1827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 143 time to evaluate : 2.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 136 GLU Chi-restraints excluded: chain I residue 206 ASN Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain H residue 153 ASP Chi-restraints excluded: chain H residue 209 ASN Chi-restraints excluded: chain A residue 405 CYS Chi-restraints excluded: chain A residue 421 CYS Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 669 ASP Chi-restraints excluded: chain G residue 75 ASP Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 171 VAL Chi-restraints excluded: chain J residue 191 LEU Chi-restraints excluded: chain J residue 310 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 105 optimal weight: 5.9990 chunk 58 optimal weight: 10.0000 chunk 157 optimal weight: 5.9990 chunk 129 optimal weight: 0.9980 chunk 52 optimal weight: 10.0000 chunk 190 optimal weight: 20.0000 chunk 205 optimal weight: 50.0000 chunk 169 optimal weight: 4.9990 chunk 188 optimal weight: 0.0370 chunk 64 optimal weight: 0.9990 chunk 152 optimal weight: 0.9980 overall best weight: 1.6062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 483 GLN A 734 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17753 Z= 0.225 Angle : 0.594 8.762 24040 Z= 0.311 Chirality : 0.043 0.173 2708 Planarity : 0.004 0.046 2983 Dihedral : 12.103 160.824 2741 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 2.43 % Allowed : 13.11 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.18), residues: 2065 helix: 0.22 (0.19), residues: 748 sheet: -0.85 (0.26), residues: 363 loop : -1.96 (0.18), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP J 228 HIS 0.002 0.001 HIS A 13 PHE 0.026 0.001 PHE J 296 TYR 0.020 0.001 TYR H 55 ARG 0.008 0.000 ARG B 18 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 156 time to evaluate : 2.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 62 ASN cc_start: 0.5921 (OUTLIER) cc_final: 0.5064 (p0) REVERT: F 31 SER cc_start: 0.7934 (m) cc_final: 0.7594 (p) REVERT: G 53 MET cc_start: 0.8336 (OUTLIER) cc_final: 0.8133 (mtp) REVERT: J 310 MET cc_start: 0.4450 (OUTLIER) cc_final: 0.3916 (mtm) outliers start: 44 outliers final: 18 residues processed: 188 average time/residue: 1.0843 time to fit residues: 233.4016 Evaluate side-chains 168 residues out of total 1827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 147 time to evaluate : 1.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 62 ASN Chi-restraints excluded: chain I residue 206 ASN Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain H residue 131 ASN Chi-restraints excluded: chain H residue 153 ASP Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 405 CYS Chi-restraints excluded: chain A residue 421 CYS Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 535 ASP Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 624 MET Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain G residue 53 MET Chi-restraints excluded: chain G residue 75 ASP Chi-restraints excluded: chain G residue 114 SER Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 171 VAL Chi-restraints excluded: chain J residue 191 LEU Chi-restraints excluded: chain J residue 310 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 187 optimal weight: 8.9990 chunk 142 optimal weight: 8.9990 chunk 98 optimal weight: 10.0000 chunk 21 optimal weight: 5.9990 chunk 90 optimal weight: 7.9990 chunk 127 optimal weight: 9.9990 chunk 190 optimal weight: 9.9990 chunk 202 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 180 optimal weight: 5.9990 chunk 54 optimal weight: 7.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 530 ASN A 734 ASN G 151 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.078 17753 Z= 0.594 Angle : 0.798 10.084 24040 Z= 0.414 Chirality : 0.050 0.247 2708 Planarity : 0.005 0.079 2983 Dihedral : 12.486 164.567 2741 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 4.31 % Allowed : 14.44 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.77 (0.17), residues: 2065 helix: -0.16 (0.19), residues: 751 sheet: -1.02 (0.25), residues: 370 loop : -2.07 (0.18), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 186 HIS 0.008 0.001 HIS A 13 PHE 0.028 0.003 PHE J 296 TYR 0.025 0.002 TYR H 55 ARG 0.009 0.001 ARG I 90 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 147 time to evaluate : 1.980 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 62 ASN cc_start: 0.6000 (OUTLIER) cc_final: 0.5363 (p0) REVERT: I 174 PHE cc_start: 0.7603 (m-10) cc_final: 0.7314 (m-80) REVERT: F 171 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8638 (mp) REVERT: H 74 GLN cc_start: 0.7710 (OUTLIER) cc_final: 0.6534 (mp10) REVERT: A 503 MET cc_start: 0.8396 (ttp) cc_final: 0.8039 (ttt) REVERT: B 132 GLN cc_start: 0.8740 (OUTLIER) cc_final: 0.7669 (tt0) REVERT: B 235 GLU cc_start: 0.7382 (OUTLIER) cc_final: 0.6993 (tt0) REVERT: J 206 GLU cc_start: 0.2331 (OUTLIER) cc_final: 0.1008 (tt0) REVERT: J 227 LYS cc_start: 0.4914 (mmtp) cc_final: 0.3480 (tptm) REVERT: J 310 MET cc_start: 0.4712 (OUTLIER) cc_final: 0.4208 (mtm) outliers start: 78 outliers final: 29 residues processed: 207 average time/residue: 1.0572 time to fit residues: 250.8845 Evaluate side-chains 164 residues out of total 1827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 128 time to evaluate : 1.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 4 VAL Chi-restraints excluded: chain I residue 62 ASN Chi-restraints excluded: chain I residue 138 VAL Chi-restraints excluded: chain I residue 206 ASN Chi-restraints excluded: chain F residue 4 VAL Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 48 SER Chi-restraints excluded: chain F residue 62 ASN Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 207 THR Chi-restraints excluded: chain H residue 74 GLN Chi-restraints excluded: chain H residue 131 ASN Chi-restraints excluded: chain A residue 44 ARG Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 405 CYS Chi-restraints excluded: chain A residue 421 CYS Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 535 ASP Chi-restraints excluded: chain A residue 614 MET Chi-restraints excluded: chain A residue 624 MET Chi-restraints excluded: chain B residue 132 GLN Chi-restraints excluded: chain B residue 143 ASN Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 235 GLU Chi-restraints excluded: chain G residue 75 ASP Chi-restraints excluded: chain G residue 114 SER Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 171 VAL Chi-restraints excluded: chain J residue 191 LEU Chi-restraints excluded: chain J residue 198 THR Chi-restraints excluded: chain J residue 206 GLU Chi-restraints excluded: chain J residue 310 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 168 optimal weight: 5.9990 chunk 114 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 150 optimal weight: 0.6980 chunk 83 optimal weight: 0.9990 chunk 172 optimal weight: 1.9990 chunk 139 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 103 optimal weight: 5.9990 chunk 181 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 734 ASN B 54 ASN B 152 ASN G 124 ASN G 151 ASN ** J 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17753 Z= 0.173 Angle : 0.576 8.387 24040 Z= 0.300 Chirality : 0.042 0.206 2708 Planarity : 0.003 0.047 2983 Dihedral : 12.122 158.538 2741 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 3.37 % Allowed : 16.43 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.28 (0.18), residues: 2065 helix: 0.38 (0.19), residues: 752 sheet: -0.85 (0.26), residues: 360 loop : -1.87 (0.19), residues: 953 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP J 228 HIS 0.003 0.000 HIS H 16 PHE 0.026 0.001 PHE J 296 TYR 0.019 0.001 TYR H 55 ARG 0.009 0.000 ARG I 90 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 164 time to evaluate : 2.162 Fit side-chains revert: symmetry clash REVERT: I 62 ASN cc_start: 0.5957 (OUTLIER) cc_final: 0.5114 (p0) REVERT: I 174 PHE cc_start: 0.7646 (m-10) cc_final: 0.7377 (m-80) REVERT: F 31 SER cc_start: 0.7870 (m) cc_final: 0.7544 (p) REVERT: H 78 LEU cc_start: 0.8585 (mt) cc_final: 0.8085 (mt) REVERT: A 356 ASP cc_start: 0.7612 (t0) cc_final: 0.7333 (t0) REVERT: A 486 MET cc_start: 0.8244 (ptp) cc_final: 0.8041 (ptp) REVERT: A 503 MET cc_start: 0.8310 (ttp) cc_final: 0.7994 (ttt) REVERT: J 157 GLN cc_start: 0.7125 (OUTLIER) cc_final: 0.6850 (mt0) REVERT: J 196 GLU cc_start: 0.6281 (mm-30) cc_final: 0.5971 (mp0) REVERT: J 206 GLU cc_start: 0.2063 (OUTLIER) cc_final: 0.1392 (tm-30) REVERT: J 310 MET cc_start: 0.4183 (OUTLIER) cc_final: 0.3877 (mtm) outliers start: 61 outliers final: 31 residues processed: 208 average time/residue: 0.9638 time to fit residues: 233.1881 Evaluate side-chains 177 residues out of total 1827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 142 time to evaluate : 2.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 62 ASN Chi-restraints excluded: chain I residue 138 VAL Chi-restraints excluded: chain I residue 206 ASN Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 48 SER Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain H residue 131 ASN Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 405 CYS Chi-restraints excluded: chain A residue 421 CYS Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 535 ASP Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain A residue 669 ASP Chi-restraints excluded: chain B residue 9 GLU Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 143 ASN Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain G residue 75 ASP Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 182 THR Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 157 GLN Chi-restraints excluded: chain J residue 163 THR Chi-restraints excluded: chain J residue 171 VAL Chi-restraints excluded: chain J residue 191 LEU Chi-restraints excluded: chain J residue 203 PHE Chi-restraints excluded: chain J residue 206 GLU Chi-restraints excluded: chain J residue 310 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 67 optimal weight: 10.0000 chunk 181 optimal weight: 0.0570 chunk 39 optimal weight: 5.9990 chunk 118 optimal weight: 3.9990 chunk 49 optimal weight: 0.0970 chunk 202 optimal weight: 0.5980 chunk 167 optimal weight: 7.9990 chunk 93 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 106 optimal weight: 0.0270 overall best weight: 0.9556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 734 ASN ** J 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17753 Z= 0.168 Angle : 0.561 9.152 24040 Z= 0.289 Chirality : 0.042 0.188 2708 Planarity : 0.003 0.040 2983 Dihedral : 11.903 159.658 2741 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 3.43 % Allowed : 18.03 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.05 (0.18), residues: 2065 helix: 0.66 (0.20), residues: 756 sheet: -0.73 (0.26), residues: 356 loop : -1.82 (0.19), residues: 953 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP J 228 HIS 0.003 0.000 HIS H 16 PHE 0.030 0.001 PHE A 728 TYR 0.021 0.001 TYR H 55 ARG 0.015 0.000 ARG I 125 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 154 time to evaluate : 1.881 Fit side-chains revert: symmetry clash REVERT: I 62 ASN cc_start: 0.5751 (OUTLIER) cc_final: 0.5079 (p0) REVERT: I 174 PHE cc_start: 0.7632 (m-10) cc_final: 0.7366 (m-80) REVERT: F 31 SER cc_start: 0.7827 (m) cc_final: 0.7519 (p) REVERT: H 78 LEU cc_start: 0.8557 (mt) cc_final: 0.8056 (mt) REVERT: A 356 ASP cc_start: 0.7532 (t0) cc_final: 0.7228 (t0) REVERT: G 53 MET cc_start: 0.8368 (OUTLIER) cc_final: 0.8152 (mtp) REVERT: J 157 GLN cc_start: 0.7060 (OUTLIER) cc_final: 0.6711 (mt0) REVERT: J 196 GLU cc_start: 0.6213 (mm-30) cc_final: 0.5952 (mp0) REVERT: J 206 GLU cc_start: 0.2172 (OUTLIER) cc_final: 0.1635 (tm-30) REVERT: J 310 MET cc_start: 0.4050 (OUTLIER) cc_final: 0.3588 (mtm) outliers start: 62 outliers final: 33 residues processed: 199 average time/residue: 0.9478 time to fit residues: 220.6333 Evaluate side-chains 172 residues out of total 1827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 134 time to evaluate : 1.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 4 VAL Chi-restraints excluded: chain I residue 62 ASN Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 138 VAL Chi-restraints excluded: chain I residue 206 ASN Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 48 SER Chi-restraints excluded: chain F residue 62 ASN Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain H residue 131 ASN Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 405 CYS Chi-restraints excluded: chain A residue 421 CYS Chi-restraints excluded: chain A residue 535 ASP Chi-restraints excluded: chain A residue 669 ASP Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 143 ASN Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain G residue 53 MET Chi-restraints excluded: chain G residue 75 ASP Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 114 SER Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 182 THR Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 157 GLN Chi-restraints excluded: chain J residue 163 THR Chi-restraints excluded: chain J residue 171 VAL Chi-restraints excluded: chain J residue 191 LEU Chi-restraints excluded: chain J residue 206 GLU Chi-restraints excluded: chain J residue 310 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 194 optimal weight: 9.9990 chunk 22 optimal weight: 1.9990 chunk 115 optimal weight: 5.9990 chunk 147 optimal weight: 3.9990 chunk 114 optimal weight: 0.9980 chunk 170 optimal weight: 2.9990 chunk 112 optimal weight: 9.9990 chunk 201 optimal weight: 3.9990 chunk 126 optimal weight: 5.9990 chunk 122 optimal weight: 0.9990 chunk 93 optimal weight: 3.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 180 HIS ** A 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 734 ASN ** J 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17753 Z= 0.276 Angle : 0.618 9.191 24040 Z= 0.317 Chirality : 0.044 0.191 2708 Planarity : 0.004 0.047 2983 Dihedral : 11.989 162.719 2741 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 3.93 % Allowed : 17.98 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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 (0.18), residues: 2065 helix: 0.60 (0.20), residues: 755 sheet: -0.87 (0.26), residues: 367 loop : -1.78 (0.19), residues: 943 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 186 HIS 0.004 0.001 HIS A 13 PHE 0.029 0.002 PHE J 296 TYR 0.026 0.001 TYR H 176 ARG 0.012 0.000 ARG I 125 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 147 time to evaluate : 2.186 Fit side-chains revert: symmetry clash REVERT: I 62 ASN cc_start: 0.5811 (OUTLIER) cc_final: 0.4930 (p0) REVERT: I 174 PHE cc_start: 0.7625 (m-10) cc_final: 0.7339 (m-80) REVERT: F 31 SER cc_start: 0.7901 (m) cc_final: 0.7612 (p) REVERT: H 78 LEU cc_start: 0.8612 (mt) cc_final: 0.8217 (mt) REVERT: A 181 MET cc_start: 0.8525 (tmm) cc_final: 0.8315 (ttt) REVERT: A 356 ASP cc_start: 0.7573 (t0) cc_final: 0.7294 (t0) REVERT: G 53 MET cc_start: 0.8452 (OUTLIER) cc_final: 0.8229 (mtp) REVERT: J 167 GLU cc_start: 0.5854 (OUTLIER) cc_final: 0.5603 (pm20) REVERT: J 196 GLU cc_start: 0.6409 (mm-30) cc_final: 0.6133 (mp0) REVERT: J 206 GLU cc_start: 0.2038 (OUTLIER) cc_final: 0.1584 (tm-30) REVERT: J 310 MET cc_start: 0.4210 (OUTLIER) cc_final: 0.3760 (mtm) outliers start: 71 outliers final: 44 residues processed: 200 average time/residue: 0.9479 time to fit residues: 221.7235 Evaluate side-chains 183 residues out of total 1827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 134 time to evaluate : 1.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 3 LEU Chi-restraints excluded: chain I residue 4 VAL Chi-restraints excluded: chain I residue 62 ASN Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 138 VAL Chi-restraints excluded: chain I residue 139 ILE Chi-restraints excluded: chain I residue 206 ASN Chi-restraints excluded: chain I residue 207 THR Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 48 SER Chi-restraints excluded: chain F residue 62 ASN Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain H residue 5 ILE Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain H residue 131 ASN Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 86 MET Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 405 CYS Chi-restraints excluded: chain A residue 421 CYS Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 535 ASP Chi-restraints excluded: chain A residue 576 ASP Chi-restraints excluded: chain A residue 614 MET Chi-restraints excluded: chain A residue 669 ASP Chi-restraints excluded: chain B residue 9 GLU Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 143 ASN Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain G residue 53 MET Chi-restraints excluded: chain G residue 75 ASP Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 114 SER Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 120 GLU Chi-restraints excluded: chain G residue 182 THR Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 163 THR Chi-restraints excluded: chain J residue 167 GLU Chi-restraints excluded: chain J residue 171 VAL Chi-restraints excluded: chain J residue 191 LEU Chi-restraints excluded: chain J residue 198 THR Chi-restraints excluded: chain J residue 206 GLU Chi-restraints excluded: chain J residue 310 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 124 optimal weight: 10.0000 chunk 80 optimal weight: 4.9990 chunk 120 optimal weight: 0.9990 chunk 60 optimal weight: 0.0470 chunk 39 optimal weight: 1.9990 chunk 128 optimal weight: 9.9990 chunk 137 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 158 optimal weight: 0.7980 chunk 183 optimal weight: 10.0000 overall best weight: 1.1684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 734 ASN ** J 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17753 Z= 0.186 Angle : 0.584 10.304 24040 Z= 0.300 Chirality : 0.042 0.180 2708 Planarity : 0.003 0.047 2983 Dihedral : 11.882 160.924 2741 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 2.99 % Allowed : 19.36 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.18), residues: 2065 helix: 0.73 (0.20), residues: 756 sheet: -0.79 (0.26), residues: 361 loop : -1.75 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP J 228 HIS 0.002 0.001 HIS H 16 PHE 0.031 0.001 PHE A 728 TYR 0.023 0.001 TYR H 176 ARG 0.008 0.000 ARG I 125 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 138 time to evaluate : 1.972 Fit side-chains revert: symmetry clash REVERT: I 62 ASN cc_start: 0.5940 (OUTLIER) cc_final: 0.5098 (p0) REVERT: I 174 PHE cc_start: 0.7747 (m-10) cc_final: 0.7488 (m-80) REVERT: F 31 SER cc_start: 0.7829 (m) cc_final: 0.7522 (p) REVERT: H 78 LEU cc_start: 0.8601 (mt) cc_final: 0.8095 (mt) REVERT: A 356 ASP cc_start: 0.7496 (t0) cc_final: 0.7180 (t0) REVERT: G 53 MET cc_start: 0.8391 (OUTLIER) cc_final: 0.8172 (mtp) REVERT: J 196 GLU cc_start: 0.6485 (mm-30) cc_final: 0.6214 (mp0) REVERT: J 206 GLU cc_start: 0.2026 (OUTLIER) cc_final: 0.1577 (tm-30) REVERT: J 310 MET cc_start: 0.4207 (OUTLIER) cc_final: 0.3950 (mtm) outliers start: 54 outliers final: 39 residues processed: 178 average time/residue: 0.8640 time to fit residues: 181.6667 Evaluate side-chains 175 residues out of total 1827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 132 time to evaluate : 1.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 4 VAL Chi-restraints excluded: chain I residue 62 ASN Chi-restraints excluded: chain I residue 138 VAL Chi-restraints excluded: chain I residue 206 ASN Chi-restraints excluded: chain I residue 207 THR Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 48 SER Chi-restraints excluded: chain F residue 62 ASN Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain H residue 5 ILE Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 131 ASN Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 405 CYS Chi-restraints excluded: chain A residue 421 CYS Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 535 ASP Chi-restraints excluded: chain A residue 614 MET Chi-restraints excluded: chain B residue 9 GLU Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 143 ASN Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain G residue 53 MET Chi-restraints excluded: chain G residue 75 ASP Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 114 SER Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 120 GLU Chi-restraints excluded: chain G residue 182 THR Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 163 THR Chi-restraints excluded: chain J residue 171 VAL Chi-restraints excluded: chain J residue 191 LEU Chi-restraints excluded: chain J residue 206 GLU Chi-restraints excluded: chain J residue 310 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 192 optimal weight: 0.0050 chunk 176 optimal weight: 6.9990 chunk 187 optimal weight: 9.9990 chunk 112 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 chunk 147 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 chunk 169 optimal weight: 0.7980 chunk 177 optimal weight: 2.9990 chunk 123 optimal weight: 9.9990 chunk 198 optimal weight: 10.0000 overall best weight: 1.1196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 734 ASN ** J 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17753 Z= 0.181 Angle : 0.571 9.849 24040 Z= 0.293 Chirality : 0.042 0.187 2708 Planarity : 0.003 0.039 2983 Dihedral : 11.775 160.376 2741 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 3.15 % Allowed : 19.80 % Favored : 77.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.18), residues: 2065 helix: 0.80 (0.20), residues: 757 sheet: -0.77 (0.26), residues: 361 loop : -1.72 (0.19), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP J 228 HIS 0.003 0.001 HIS A 13 PHE 0.026 0.001 PHE J 296 TYR 0.023 0.001 TYR H 176 ARG 0.007 0.000 ARG I 125 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 137 time to evaluate : 2.107 Fit side-chains revert: symmetry clash REVERT: I 62 ASN cc_start: 0.5895 (OUTLIER) cc_final: 0.5040 (p0) REVERT: F 31 SER cc_start: 0.7823 (m) cc_final: 0.7521 (p) REVERT: H 78 LEU cc_start: 0.8604 (mt) cc_final: 0.8103 (mt) REVERT: A 356 ASP cc_start: 0.7436 (t0) cc_final: 0.7140 (t0) REVERT: A 612 ILE cc_start: 0.8608 (OUTLIER) cc_final: 0.8349 (mm) REVERT: G 53 MET cc_start: 0.8382 (OUTLIER) cc_final: 0.8168 (mtp) REVERT: J 196 GLU cc_start: 0.6422 (mm-30) cc_final: 0.6159 (mp0) REVERT: J 206 GLU cc_start: 0.2065 (OUTLIER) cc_final: 0.1661 (tm-30) REVERT: J 270 ILE cc_start: 0.6284 (OUTLIER) cc_final: 0.5926 (pt) outliers start: 57 outliers final: 36 residues processed: 180 average time/residue: 0.8760 time to fit residues: 186.6679 Evaluate side-chains 172 residues out of total 1827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 131 time to evaluate : 1.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 4 VAL Chi-restraints excluded: chain I residue 62 ASN Chi-restraints excluded: chain I residue 138 VAL Chi-restraints excluded: chain I residue 206 ASN Chi-restraints excluded: chain I residue 207 THR Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 48 SER Chi-restraints excluded: chain F residue 62 ASN Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain H residue 5 ILE Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 131 ASN Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 405 CYS Chi-restraints excluded: chain A residue 421 CYS Chi-restraints excluded: chain A residue 535 ASP Chi-restraints excluded: chain A residue 576 ASP Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 614 MET Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain G residue 53 MET Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 114 SER Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 120 GLU Chi-restraints excluded: chain G residue 182 THR Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 163 THR Chi-restraints excluded: chain J residue 171 VAL Chi-restraints excluded: chain J residue 191 LEU Chi-restraints excluded: chain J residue 206 GLU Chi-restraints excluded: chain J residue 270 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 121 optimal weight: 4.9990 chunk 94 optimal weight: 4.9990 chunk 137 optimal weight: 4.9990 chunk 208 optimal weight: 9.9990 chunk 191 optimal weight: 8.9990 chunk 165 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 128 optimal weight: 9.9990 chunk 101 optimal weight: 0.5980 chunk 131 optimal weight: 8.9990 chunk 176 optimal weight: 5.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 734 ASN ** J 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 17753 Z= 0.385 Angle : 0.684 10.031 24040 Z= 0.351 Chirality : 0.046 0.200 2708 Planarity : 0.004 0.043 2983 Dihedral : 12.048 165.016 2739 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 2.71 % Allowed : 20.58 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.15 (0.18), residues: 2065 helix: 0.51 (0.19), residues: 753 sheet: -0.93 (0.25), residues: 371 loop : -1.75 (0.19), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 186 HIS 0.006 0.001 HIS A 13 PHE 0.029 0.002 PHE J 296 TYR 0.031 0.002 TYR H 176 ARG 0.009 0.001 ARG I 125 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 133 time to evaluate : 2.030 Fit side-chains revert: symmetry clash REVERT: I 62 ASN cc_start: 0.5828 (OUTLIER) cc_final: 0.4981 (p0) REVERT: I 174 PHE cc_start: 0.7715 (m-80) cc_final: 0.7461 (m-80) REVERT: F 31 SER cc_start: 0.7936 (m) cc_final: 0.7631 (p) REVERT: A 181 MET cc_start: 0.8561 (tmm) cc_final: 0.8340 (ttt) REVERT: A 356 ASP cc_start: 0.7573 (t0) cc_final: 0.7292 (t0) REVERT: A 493 ASP cc_start: 0.7294 (p0) cc_final: 0.7061 (p0) REVERT: J 196 GLU cc_start: 0.6629 (mm-30) cc_final: 0.6176 (mp0) REVERT: J 206 GLU cc_start: 0.2089 (OUTLIER) cc_final: 0.1700 (tm-30) REVERT: J 270 ILE cc_start: 0.6284 (OUTLIER) cc_final: 0.5927 (pt) outliers start: 49 outliers final: 37 residues processed: 169 average time/residue: 0.9106 time to fit residues: 181.3435 Evaluate side-chains 166 residues out of total 1827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 126 time to evaluate : 1.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 3 LEU Chi-restraints excluded: chain I residue 4 VAL Chi-restraints excluded: chain I residue 62 ASN Chi-restraints excluded: chain I residue 138 VAL Chi-restraints excluded: chain I residue 206 ASN Chi-restraints excluded: chain I residue 207 THR Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 48 SER Chi-restraints excluded: chain F residue 62 ASN Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain H residue 5 ILE Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 131 ASN Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 86 MET Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 405 CYS Chi-restraints excluded: chain A residue 421 CYS Chi-restraints excluded: chain A residue 535 ASP Chi-restraints excluded: chain A residue 576 ASP Chi-restraints excluded: chain A residue 614 MET Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 143 ASN Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 114 SER Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 120 GLU Chi-restraints excluded: chain G residue 182 THR Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 171 VAL Chi-restraints excluded: chain J residue 191 LEU Chi-restraints excluded: chain J residue 206 GLU Chi-restraints excluded: chain J residue 270 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 50 optimal weight: 3.9990 chunk 152 optimal weight: 0.9990 chunk 24 optimal weight: 0.0870 chunk 46 optimal weight: 3.9990 chunk 166 optimal weight: 0.5980 chunk 69 optimal weight: 9.9990 chunk 170 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 145 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 overall best weight: 0.6762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 734 ASN ** J 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.140752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.106006 restraints weight = 44720.085| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 2.99 r_work: 0.3271 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3269 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3269 r_free = 0.3269 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3269 r_free = 0.3269 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3269 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 17753 Z= 0.155 Angle : 0.569 10.089 24040 Z= 0.292 Chirality : 0.042 0.203 2708 Planarity : 0.003 0.039 2983 Dihedral : 11.816 159.036 2739 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 2.16 % Allowed : 21.13 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.18), residues: 2065 helix: 0.80 (0.20), residues: 757 sheet: -0.80 (0.25), residues: 367 loop : -1.68 (0.19), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP J 228 HIS 0.002 0.001 HIS A 13 PHE 0.027 0.001 PHE J 296 TYR 0.021 0.001 TYR H 150 ARG 0.006 0.000 ARG I 125 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5018.40 seconds wall clock time: 91 minutes 36.54 seconds (5496.54 seconds total)