Starting phenix.real_space_refine on Sat Feb 17 00:57:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8foh_29349/02_2024/8foh_29349_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8foh_29349/02_2024/8foh_29349.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8foh_29349/02_2024/8foh_29349.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8foh_29349/02_2024/8foh_29349.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8foh_29349/02_2024/8foh_29349_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8foh_29349/02_2024/8foh_29349_updated.pdb" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Fe 4 7.16 5 P 20 5.49 5 S 93 5.16 5 C 10746 2.51 5 N 2926 2.21 5 O 3207 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "1 PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 TYR 359": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 TYR 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 TYR 472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ARG 490": "NH1" <-> "NH2" Residue "1 TYR 564": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ASP 581": "OD1" <-> "OD2" Residue "1 GLU 616": "OE1" <-> "OE2" Residue "1 ASP 646": "OD1" <-> "OD2" Residue "1 PHE 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 798": "OE1" <-> "OE2" Residue "1 PHE 805": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 810": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 875": "OE1" <-> "OE2" Residue "1 GLU 976": "OE1" <-> "OE2" Residue "1 ASP 1007": "OD1" <-> "OD2" Residue "1 GLU 1105": "OE1" <-> "OE2" Residue "1 TYR 1107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ASP 1108": "OD1" <-> "OD2" Residue "1 TYR 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 1111": "OE1" <-> "OE2" Residue "1 PHE 1294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 TYR 1305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 1396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 1432": "OE1" <-> "OE2" Residue "A GLU 16": "OE1" <-> "OE2" Residue "A TYR 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 46": "OE1" <-> "OE2" Residue "A PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 73": "OE1" <-> "OE2" Residue "A PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 81": "OE1" <-> "OE2" Residue "A TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 92": "OE1" <-> "OE2" Residue "A GLU 107": "OE1" <-> "OE2" Residue "A GLU 150": "OE1" <-> "OE2" Residue "A PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 173": "OD1" <-> "OD2" Residue "A GLU 218": "OE1" <-> "OE2" Residue "A PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 230": "OE1" <-> "OE2" Residue "A GLU 231": "OE1" <-> "OE2" Residue "A GLU 236": "OE1" <-> "OE2" Residue "A ASP 237": "OD1" <-> "OD2" Residue "A ASP 251": "OD1" <-> "OD2" Residue "A TYR 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 272": "OE1" <-> "OE2" Residue "A GLU 299": "OE1" <-> "OE2" Residue "A GLU 302": "OE1" <-> "OE2" Residue "A GLU 316": "OE1" <-> "OE2" Residue "A GLU 344": "OE1" <-> "OE2" Residue "A PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 349": "OE1" <-> "OE2" Residue "B GLU 46": "OE1" <-> "OE2" Residue "B GLU 47": "OE1" <-> "OE2" Residue "B TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 56": "OE1" <-> "OE2" Residue "B GLU 73": "OE1" <-> "OE2" Residue "B GLU 76": "OE1" <-> "OE2" Residue "B GLU 88": "OE1" <-> "OE2" Residue "B GLU 90": "OE1" <-> "OE2" Residue "B GLU 101": "OE1" <-> "OE2" Residue "B GLU 103": "OE1" <-> "OE2" Residue "B GLU 119": "OE1" <-> "OE2" Residue "B GLU 122": "OE1" <-> "OE2" Residue "B TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 143": "OE1" <-> "OE2" Residue "B GLU 146": "OE1" <-> "OE2" Residue "B PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 152": "OE1" <-> "OE2" Residue "B PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 186": "OE1" <-> "OE2" Residue "B GLU 187": "OE1" <-> "OE2" Residue "B GLU 190": "OE1" <-> "OE2" Residue "B TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 211": "OE1" <-> "OE2" Residue "B GLU 212": "OE1" <-> "OE2" Residue "B PHE 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 222": "OE1" <-> "OE2" Residue "B PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 230": "OE1" <-> "OE2" Residue "B GLU 234": "OE1" <-> "OE2" Residue "B PHE 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 262": "OE1" <-> "OE2" Residue "B PHE 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 270": "OE1" <-> "OE2" Residue "B TYR 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 283": "OE1" <-> "OE2" Residue "B TYR 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 394": "OE1" <-> "OE2" Residue "B TYR 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 442": "OE1" <-> "OE2" Residue "B ASP 463": "OD1" <-> "OD2" Residue "B PHE 478": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 508": "NH1" <-> "NH2" Residue "C TYR 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 498": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 530": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 665": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 16996 Number of models: 1 Model: "" Number of chains: 7 Chain: "1" Number of atoms: 7136 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 893, 7128 Classifications: {'peptide': 893} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 41, 'TRANS': 851} Chain breaks: 12 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 3, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 38 Conformer: "B" Number of residues, atoms: 893, 7128 Classifications: {'peptide': 893} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 41, 'TRANS': 851} Chain breaks: 12 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 3, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 38 bond proxies already assigned to first conformer: 7245 Chain: "A" Number of atoms: 2780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2780 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 319} Chain breaks: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 18 Chain: "B" Number of atoms: 3381 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 406, 3358 Classifications: {'peptide': 406} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 13, 'TRANS': 392} Chain breaks: 8 Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 40 Conformer: "B" Number of residues, atoms: 406, 3358 Classifications: {'peptide': 406} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 13, 'TRANS': 392} Chain breaks: 8 Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 40 bond proxies already assigned to first conformer: 3402 Chain: "C" Number of atoms: 3273 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 410, 3255 Classifications: {'peptide': 410} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 5, 'PTRANS': 23, 'TRANS': 381} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 410, 3255 Classifications: {'peptide': 410} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 5, 'PTRANS': 23, 'TRANS': 381} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 3308 Chain: "T" Number of atoms: 241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 241 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Chain: "P" Number of atoms: 177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 177 Classifications: {'RNA': 8} Modifications used: {'rna3p_pur': 6, 'rna3p_pyr': 2} Link IDs: {'rna3p': 7} Chain: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12081 SG CYS B 336 85.739 58.913 110.097 1.00 16.40 S ATOM 12802 SG CYS B 434 84.469 61.343 104.265 1.00 18.69 S ATOM 12670 SG CYS B 417 85.146 54.838 105.091 1.00 17.89 S ATOM 13072 SG CYS B 474 90.063 58.277 105.062 1.00 16.49 S Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N AASP 11414 " occ=0.50 ... (14 atoms not shown) pdb=" OD2BASP 11414 " occ=0.50 residue: pdb=" N AASP C 263 " occ=0.50 ... (14 atoms not shown) pdb=" OD2BASP C 263 " occ=0.50 residue: pdb=" N AHIS C 495 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS C 495 " occ=0.50 Time building chain proxies: 15.49, per 1000 atoms: 0.91 Number of scatterers: 16996 At special positions: 0 Unit cell: (111.78, 119.232, 197.892, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 4 26.01 S 93 16.00 P 20 15.00 O 3207 8.00 N 2926 7.00 C 10746 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.50 Conformation dependent library (CDL) restraints added in 5.9 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 B 601 " pdb="FE3 SF4 B 601 " - pdb=" SG CYS B 417 " pdb="FE1 SF4 B 601 " - pdb=" SG CYS B 336 " pdb="FE4 SF4 B 601 " - pdb=" SG CYS B 474 " pdb="FE2 SF4 B 601 " - pdb=" SG CYS B 434 " Number of angles added : 12 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3948 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 87 helices and 15 sheets defined 44.5% alpha, 11.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.97 Creating SS restraints... Processing helix chain '1' and resid 403 through 418 Proline residue: 1 412 - end of helix Processing helix chain '1' and resid 481 through 488 Processing helix chain '1' and resid 522 through 524 No H-bonds generated for 'chain '1' and resid 522 through 524' Processing helix chain '1' and resid 616 through 630 Processing helix chain '1' and resid 644 through 654 Processing helix chain '1' and resid 660 through 663 Processing helix chain '1' and resid 680 through 691 removed outlier: 3.747A pdb=" N HIS 1 684 " --> pdb=" O SER 1 680 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N PHE 1 685 " --> pdb=" O ASN 1 681 " (cutoff:3.500A) Processing helix chain '1' and resid 702 through 707 removed outlier: 3.678A pdb=" N LEU 1 707 " --> pdb=" O MET 1 703 " (cutoff:3.500A) Processing helix chain '1' and resid 716 through 724 Processing helix chain '1' and resid 738 through 742 removed outlier: 3.580A pdb=" N ASN 1 742 " --> pdb=" O GLN 1 739 " (cutoff:3.500A) Processing helix chain '1' and resid 744 through 767 Processing helix chain '1' and resid 770 through 781 Processing helix chain '1' and resid 785 through 790 Processing helix chain '1' and resid 796 through 807 removed outlier: 3.591A pdb=" N ILE 1 800 " --> pdb=" O ARG 1 796 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N LEU 1 801 " --> pdb=" O ASN 1 797 " (cutoff:3.500A) Processing helix chain '1' and resid 866 through 875 removed outlier: 4.138A pdb=" N TYR 1 869 " --> pdb=" O ASN 1 866 " (cutoff:3.500A) Proline residue: 1 870 - end of helix Processing helix chain '1' and resid 906 through 926 removed outlier: 3.711A pdb=" N THR 1 926 " --> pdb=" O LYS 1 922 " (cutoff:3.500A) Processing helix chain '1' and resid 930 through 949 Processing helix chain '1' and resid 951 through 955 Processing helix chain '1' and resid 964 through 988 Processing helix chain '1' and resid 1009 through 1026 Processing helix chain '1' and resid 1072 through 1074 No H-bonds generated for 'chain '1' and resid 1072 through 1074' Processing helix chain '1' and resid 1080 through 1093 Processing helix chain '1' and resid 1102 through 1118 removed outlier: 3.527A pdb=" N ASP 11112 " --> pdb=" O ASP 11108 " (cutoff:3.500A) Processing helix chain '1' and resid 1211 through 1215 Processing helix chain '1' and resid 1219 through 1225 Processing helix chain '1' and resid 1234 through 1239 Processing helix chain '1' and resid 1323 through 1343 removed outlier: 4.263A pdb=" N GLN 11329 " --> pdb=" O GLN 11325 " (cutoff:3.500A) Processing helix chain '1' and resid 1382 through 1396 removed outlier: 3.818A pdb=" N PHE 11396 " --> pdb=" O PHE 11392 " (cutoff:3.500A) Processing helix chain '1' and resid 1398 through 1402 Processing helix chain '1' and resid 1424 through 1433 Processing helix chain '1' and resid 1435 through 1449 removed outlier: 3.608A pdb=" N VAL 11445 " --> pdb=" O GLY 11441 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N TYR 11448 " --> pdb=" O VAL 11444 " (cutoff:3.500A) Processing helix chain 'A' and resid 12 through 21 Processing helix chain 'A' and resid 25 through 33 Processing helix chain 'A' and resid 40 through 43 No H-bonds generated for 'chain 'A' and resid 40 through 43' Processing helix chain 'A' and resid 65 through 75 Processing helix chain 'A' and resid 90 through 92 No H-bonds generated for 'chain 'A' and resid 90 through 92' Processing helix chain 'A' and resid 115 through 120 removed outlier: 5.101A pdb=" N ALA A 119 " --> pdb=" O ASP A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 150 removed outlier: 3.645A pdb=" N LYS A 135 " --> pdb=" O SER A 131 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N PHE A 136 " --> pdb=" O LYS A 132 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ILE A 137 " --> pdb=" O CYS A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 177 No H-bonds generated for 'chain 'A' and resid 174 through 177' Processing helix chain 'A' and resid 181 through 191 Processing helix chain 'A' and resid 211 through 228 Proline residue: A 222 - end of helix removed outlier: 4.366A pdb=" N VAL A 225 " --> pdb=" O LYS A 221 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N SER A 226 " --> pdb=" O PRO A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 244 Processing helix chain 'A' and resid 246 through 248 No H-bonds generated for 'chain 'A' and resid 246 through 248' Processing helix chain 'A' and resid 252 through 264 Processing helix chain 'A' and resid 270 through 284 removed outlier: 4.061A pdb=" N ASP A 278 " --> pdb=" O TRP A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 309 Processing helix chain 'A' and resid 316 through 319 No H-bonds generated for 'chain 'A' and resid 316 through 319' Processing helix chain 'A' and resid 348 through 350 No H-bonds generated for 'chain 'A' and resid 348 through 350' Processing helix chain 'A' and resid 354 through 357 No H-bonds generated for 'chain 'A' and resid 354 through 357' Processing helix chain 'B' and resid 47 through 54 Processing helix chain 'B' and resid 74 through 94 Processing helix chain 'B' and resid 99 through 113 Proline residue: B 108 - end of helix Processing helix chain 'B' and resid 121 through 138 Processing helix chain 'B' and resid 142 through 162 Processing helix chain 'B' and resid 165 through 173 Processing helix chain 'B' and resid 185 through 190 Processing helix chain 'B' and resid 192 through 207 removed outlier: 4.664A pdb=" N ALA B 201 " --> pdb=" O GLN B 197 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N SER B 202 " --> pdb=" O THR B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 221 removed outlier: 3.575A pdb=" N GLN B 221 " --> pdb=" O GLN B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 237 removed outlier: 4.081A pdb=" N ILE B 233 " --> pdb=" O GLU B 230 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N GLU B 234 " --> pdb=" O ASN B 231 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLY B 237 " --> pdb=" O GLU B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 283 Proline residue: B 279 - end of helix removed outlier: 4.620A pdb=" N GLU B 283 " --> pdb=" O PRO B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 297 Processing helix chain 'B' and resid 323 through 325 No H-bonds generated for 'chain 'B' and resid 323 through 325' Processing helix chain 'B' and resid 327 through 332 removed outlier: 4.857A pdb=" N ASN B 332 " --> pdb=" O GLU B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 347 Processing helix chain 'B' and resid 352 through 365 Processing helix chain 'B' and resid 369 through 379 Processing helix chain 'B' and resid 396 through 403 removed outlier: 3.628A pdb=" N TYR B 403 " --> pdb=" O PHE B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 435 through 438 No H-bonds generated for 'chain 'B' and resid 435 through 438' Processing helix chain 'B' and resid 441 through 448 Processing helix chain 'B' and resid 457 through 466 Processing helix chain 'B' and resid 470 through 481 Processing helix chain 'B' and resid 500 through 511 removed outlier: 3.869A pdb=" N GLN B 511 " --> pdb=" O SER B 507 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 276 removed outlier: 3.684A pdb=" N ILE C 265 " --> pdb=" O LEU C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 282 No H-bonds generated for 'chain 'C' and resid 280 through 282' Processing helix chain 'C' and resid 322 through 325 No H-bonds generated for 'chain 'C' and resid 322 through 325' Processing helix chain 'C' and resid 378 through 388 Processing helix chain 'C' and resid 411 through 422 Processing helix chain 'C' and resid 441 through 445 Processing helix chain 'C' and resid 461 through 468 Processing helix chain 'C' and resid 470 through 475 removed outlier: 3.955A pdb=" N THR C 475 " --> pdb=" O PRO C 471 " (cutoff:3.500A) Processing helix chain 'C' and resid 538 through 541 No H-bonds generated for 'chain 'C' and resid 538 through 541' Processing helix chain 'C' and resid 549 through 553 Processing helix chain 'C' and resid 556 through 567 Processing helix chain 'C' and resid 614 through 620 removed outlier: 4.996A pdb=" N GLY C 618 " --> pdb=" O SER C 615 " (cutoff:3.500A) Processing helix chain 'C' and resid 623 through 625 No H-bonds generated for 'chain 'C' and resid 623 through 625' Processing helix chain 'C' and resid 694 through 697 No H-bonds generated for 'chain 'C' and resid 694 through 697' Processing sheet with id= A, first strand: chain '1' and resid 495 through 499 removed outlier: 3.663A pdb=" N CYS 1 495 " --> pdb=" O TRP 1 356 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N PHE 1 369 " --> pdb=" O LEU 1 357 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N TYR 1 359 " --> pdb=" O ILE 1 367 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ILE 1 367 " --> pdb=" O TYR 1 359 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N GLU 1 361 " --> pdb=" O THR 1 365 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N THR 1 365 " --> pdb=" O GLU 1 361 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU 1 366 " --> pdb=" O ILE 1 386 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N VAL 1 515 " --> pdb=" O MET 1 383 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N GLN 1 385 " --> pdb=" O VAL 1 515 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N VAL 1 517 " --> pdb=" O GLN 1 385 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain '1' and resid 425 through 431 removed outlier: 7.262A pdb=" N ASP 1 444 " --> pdb=" O PRO 1 397 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N HIS 1 473 " --> pdb=" O LEU 1 396 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain '1' and resid 695 through 698 removed outlier: 6.139A pdb=" N LEU 1 546 " --> pdb=" O ILE 1 556 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N ILE 1 556 " --> pdb=" O LEU 1 546 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ASN 1 548 " --> pdb=" O GLN 1 554 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N GLN 1 554 " --> pdb=" O ASN 1 548 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N VAL 1 557 " --> pdb=" O ARG 1 587 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASP 1 581 " --> pdb=" O ALA 1 563 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ARG 1 609 " --> pdb=" O THR 1 584 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N VAL 1 586 " --> pdb=" O ARG 1 609 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ARG 1 611 " --> pdb=" O VAL 1 586 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain '1' and resid 854 through 856 removed outlier: 6.536A pdb=" N LEU 11052 " --> pdb=" O LYS 11039 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N LEU 11041 " --> pdb=" O ALA 11050 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ALA 11050 " --> pdb=" O LEU 11041 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain '1' and resid 1033 through 1038 removed outlier: 4.086A pdb=" N ASP 11033 " --> pdb=" O ASP 1 864 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N VAL 1 862 " --> pdb=" O ASP 11035 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N VAL 11037 " --> pdb=" O VAL 1 860 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N VAL 1 860 " --> pdb=" O VAL 11037 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR 1 994 " --> pdb=" O MET 11001 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ASP 11003 " --> pdb=" O VAL 1 992 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N VAL 1 992 " --> pdb=" O ASP 11003 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain '1' and resid 1284 through 1286 Processing sheet with id= G, first strand: chain '1' and resid 1305 through 1308 Processing sheet with id= H, first strand: chain '1' and resid 1346 through 1348 Processing sheet with id= I, first strand: chain 'A' and resid 47 through 50 Processing sheet with id= J, first strand: chain 'A' and resid 108 through 112 Processing sheet with id= K, first strand: chain 'B' and resid 225 through 228 removed outlier: 3.602A pdb=" N PHE B 242 " --> pdb=" O TYR B 249 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 347 through 352 Processing sheet with id= M, first strand: chain 'C' and resid 340 through 342 Processing sheet with id= N, first strand: chain 'C' and resid 515 through 518 removed outlier: 6.310A pdb=" N THR C 482 " --> pdb=" O LYS C 516 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N MET C 518 " --> pdb=" O THR C 482 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N LEU C 484 " --> pdb=" O MET C 518 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 522 through 526 removed outlier: 6.571A pdb=" N ILE C 630 " --> pdb=" O GLY C 532 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N VAL C 648 " --> pdb=" O MET C 631 " (cutoff:3.500A) 679 hydrogen bonds defined for protein. 1934 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.80 Time building geometry restraints manager: 8.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.42: 7193 1.42 - 1.65: 10067 1.65 - 1.89: 129 1.89 - 2.13: 0 2.13 - 2.37: 12 Bond restraints: 17401 Sorted by residual: bond pdb=" C1' C P 4 " pdb=" N1 C P 4 " ideal model delta sigma weight residual 1.480 1.579 -0.099 1.50e-02 4.44e+03 4.32e+01 bond pdb=" C1' C P 8 " pdb=" N1 C P 8 " ideal model delta sigma weight residual 1.480 1.577 -0.097 1.50e-02 4.44e+03 4.17e+01 bond pdb=" CA VAL C 623 " pdb=" CB VAL C 623 " ideal model delta sigma weight residual 1.536 1.597 -0.061 1.16e-02 7.43e+03 2.75e+01 bond pdb=" C PRO 11408 " pdb=" O PRO 11408 " ideal model delta sigma weight residual 1.233 1.179 0.054 1.10e-02 8.26e+03 2.44e+01 bond pdb=" CA ASN C 693 " pdb=" C ASN C 693 " ideal model delta sigma weight residual 1.527 1.463 0.064 1.32e-02 5.74e+03 2.35e+01 ... (remaining 17396 not shown) Histogram of bond angle deviations from ideal: 70.28 - 83.28: 12 83.28 - 96.29: 10 96.29 - 109.29: 2301 109.29 - 122.29: 18101 122.29 - 135.30: 3202 Bond angle restraints: 23626 Sorted by residual: angle pdb=" O3' G P 6 " pdb=" P G P 7 " pdb=" O5' G P 7 " ideal model delta sigma weight residual 104.00 91.04 12.96 1.50e+00 4.44e-01 7.46e+01 angle pdb=" O3' C P 4 " pdb=" P G P 5 " pdb=" O5' G P 5 " ideal model delta sigma weight residual 104.00 91.06 12.94 1.50e+00 4.44e-01 7.45e+01 angle pdb=" O3' DC T 17 " pdb=" P DC T 18 " pdb=" O5' DC T 18 " ideal model delta sigma weight residual 104.00 91.07 12.93 1.50e+00 4.44e-01 7.44e+01 angle pdb=" O3' G P 7 " pdb=" P C P 8 " pdb=" O5' C P 8 " ideal model delta sigma weight residual 104.00 91.10 12.90 1.50e+00 4.44e-01 7.40e+01 angle pdb=" O3' G P 5 " pdb=" P G P 6 " pdb=" O5' G P 6 " ideal model delta sigma weight residual 104.00 91.12 12.88 1.50e+00 4.44e-01 7.37e+01 ... (remaining 23621 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 9753 17.58 - 35.17: 640 35.17 - 52.75: 124 52.75 - 70.33: 39 70.33 - 87.91: 17 Dihedral angle restraints: 10573 sinusoidal: 4505 harmonic: 6068 Sorted by residual: dihedral pdb=" C ASP C 303 " pdb=" N ASP C 303 " pdb=" CA ASP C 303 " pdb=" CB ASP C 303 " ideal model delta harmonic sigma weight residual -122.60 -137.15 14.55 0 2.50e+00 1.60e-01 3.39e+01 dihedral pdb=" N ASP C 303 " pdb=" C ASP C 303 " pdb=" CA ASP C 303 " pdb=" CB ASP C 303 " ideal model delta harmonic sigma weight residual 122.80 135.25 -12.45 0 2.50e+00 1.60e-01 2.48e+01 dihedral pdb=" CA ARG C 579 " pdb=" C ARG C 579 " pdb=" N THR C 580 " pdb=" CA THR C 580 " ideal model delta harmonic sigma weight residual -180.00 -155.82 -24.18 0 5.00e+00 4.00e-02 2.34e+01 ... (remaining 10570 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.140: 2375 0.140 - 0.280: 223 0.280 - 0.419: 17 0.419 - 0.559: 9 0.559 - 0.699: 2 Chirality restraints: 2626 Sorted by residual: chirality pdb="FE1 SF4 B 601 " pdb=" S2 SF4 B 601 " pdb=" S3 SF4 B 601 " pdb=" S4 SF4 B 601 " both_signs ideal model delta sigma weight residual False -10.55 -11.25 0.70 2.00e-01 2.50e+01 1.22e+01 chirality pdb=" P DG T 10 " pdb=" OP1 DG T 10 " pdb=" OP2 DG T 10 " pdb=" O5' DG T 10 " both_signs ideal model delta sigma weight residual True 2.35 -2.98 -0.64 2.00e-01 2.50e+01 1.02e+01 chirality pdb=" CA ASP C 303 " pdb=" N ASP C 303 " pdb=" C ASP C 303 " pdb=" CB ASP C 303 " both_signs ideal model delta sigma weight residual False 2.51 1.96 0.56 2.00e-01 2.50e+01 7.71e+00 ... (remaining 2623 not shown) Planarity restraints: 2972 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 55 " 0.188 2.00e-02 2.50e+03 1.34e-01 3.60e+02 pdb=" CG TYR B 55 " 0.002 2.00e-02 2.50e+03 pdb=" CD1 TYR B 55 " -0.048 2.00e-02 2.50e+03 pdb=" CD2 TYR B 55 " -0.106 2.00e-02 2.50e+03 pdb=" CE1 TYR B 55 " -0.148 2.00e-02 2.50e+03 pdb=" CE2 TYR B 55 " -0.090 2.00e-02 2.50e+03 pdb=" CZ TYR B 55 " -0.048 2.00e-02 2.50e+03 pdb=" OH TYR B 55 " 0.250 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 209 " -0.140 2.00e-02 2.50e+03 7.32e-02 1.07e+02 pdb=" CG TYR A 209 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 TYR A 209 " 0.052 2.00e-02 2.50e+03 pdb=" CD2 TYR A 209 " 0.083 2.00e-02 2.50e+03 pdb=" CE1 TYR A 209 " 0.039 2.00e-02 2.50e+03 pdb=" CE2 TYR A 209 " 0.023 2.00e-02 2.50e+03 pdb=" CZ TYR A 209 " -0.018 2.00e-02 2.50e+03 pdb=" OH TYR A 209 " -0.093 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 51 " -0.123 2.00e-02 2.50e+03 6.98e-02 9.75e+01 pdb=" CG TYR B 51 " 0.016 2.00e-02 2.50e+03 pdb=" CD1 TYR B 51 " 0.067 2.00e-02 2.50e+03 pdb=" CD2 TYR B 51 " 0.068 2.00e-02 2.50e+03 pdb=" CE1 TYR B 51 " 0.042 2.00e-02 2.50e+03 pdb=" CE2 TYR B 51 " 0.043 2.00e-02 2.50e+03 pdb=" CZ TYR B 51 " -0.011 2.00e-02 2.50e+03 pdb=" OH TYR B 51 " -0.104 2.00e-02 2.50e+03 ... (remaining 2969 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.14: 4 2.14 - 2.83: 4653 2.83 - 3.52: 23679 3.52 - 4.21: 41221 4.21 - 4.90: 69753 Nonbonded interactions: 139310 Sorted by model distance: nonbonded pdb=" N1 DG T 16 " pdb=" N1 G P 6 " model vdw 1.447 3.200 nonbonded pdb=" N2 DG T 16 " pdb=" N2 G P 6 " model vdw 1.565 3.200 nonbonded pdb=" O6 DG T 16 " pdb=" O6 G P 6 " model vdw 1.856 3.040 nonbonded pdb=" N2 DG T 16 " pdb=" C2 G P 6 " model vdw 2.033 3.340 nonbonded pdb=" C2 DG T 16 " pdb=" N2 G P 6 " model vdw 2.151 3.340 ... (remaining 139305 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.990 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: 4.470 Check model and map are aligned: 0.280 Set scattering table: 0.170 Process input model: 61.230 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6953 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 : 0.013 0.132 17401 Z= 0.838 Angle : 1.462 13.159 23626 Z= 0.952 Chirality : 0.088 0.699 2626 Planarity : 0.011 0.218 2972 Dihedral : 13.110 87.912 6625 Min Nonbonded Distance : 1.447 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.61 % Favored : 97.29 % Rotamer: Outliers : 0.49 % Allowed : 3.57 % Favored : 95.94 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.17), residues: 2006 helix: -0.26 (0.15), residues: 949 sheet: -0.37 (0.34), residues: 207 loop : -0.03 (0.20), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.010 TRP B 78 HIS 0.031 0.005 HIS B 348 PHE 0.065 0.007 PHE B 138 TYR 0.250 0.011 TYR B 55 ARG 0.017 0.002 ARG A 45 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 101 time to evaluate : 2.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 652 MET cc_start: 0.8848 (mtt) cc_final: 0.8591 (mtt) REVERT: 1 919 GLU cc_start: 0.9685 (mt-10) cc_final: 0.9442 (mt-10) REVERT: 1 950 MET cc_start: 0.9379 (mmm) cc_final: 0.9077 (mmm) REVERT: 1 1438 MET cc_start: 0.8997 (mmp) cc_final: 0.8757 (mmm) REVERT: A 108 LEU cc_start: 0.9003 (tp) cc_final: 0.8787 (mt) REVERT: A 141 MET cc_start: 0.8933 (mtm) cc_final: 0.8726 (mtm) REVERT: B 128 TYR cc_start: 0.8937 (OUTLIER) cc_final: 0.8690 (t80) outliers start: 9 outliers final: 0 residues processed: 110 average time/residue: 0.3927 time to fit residues: 61.2746 Evaluate side-chains 64 residues out of total 1870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 63 time to evaluate : 2.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 10.0000 chunk 154 optimal weight: 20.0000 chunk 85 optimal weight: 4.9990 chunk 52 optimal weight: 20.0000 chunk 104 optimal weight: 8.9990 chunk 82 optimal weight: 5.9990 chunk 159 optimal weight: 10.0000 chunk 61 optimal weight: 30.0000 chunk 97 optimal weight: 7.9990 chunk 119 optimal weight: 8.9990 chunk 185 optimal weight: 5.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 684 HIS 1 739 GLN ** 1 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 11313 GLN ** 11369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 323 HIS B 347 ASN C 336 GLN C 372 ASN C 450 ASN C 495 HIS A Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7090 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 17401 Z= 0.286 Angle : 0.604 9.032 23626 Z= 0.313 Chirality : 0.041 0.144 2626 Planarity : 0.004 0.039 2972 Dihedral : 8.135 73.237 2483 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.18), residues: 2006 helix: 1.63 (0.16), residues: 942 sheet: 0.24 (0.33), residues: 229 loop : 0.58 (0.21), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 78 HIS 0.011 0.002 HIS 1 407 PHE 0.023 0.002 PHE B 75 TYR 0.018 0.002 TYR B 128 ARG 0.008 0.001 ARG B 135 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 2.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 719 MET cc_start: 0.9109 (mtp) cc_final: 0.8736 (mmm) REVERT: A 228 MET cc_start: 0.8644 (mmm) cc_final: 0.8393 (mmm) REVERT: C 378 SER cc_start: 0.8836 (p) cc_final: 0.8430 (p) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.3434 time to fit residues: 38.4718 Evaluate side-chains 61 residues out of total 1870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 2.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 102 optimal weight: 10.0000 chunk 57 optimal weight: 50.0000 chunk 154 optimal weight: 20.0000 chunk 126 optimal weight: 7.9990 chunk 51 optimal weight: 9.9990 chunk 185 optimal weight: 7.9990 chunk 200 optimal weight: 20.0000 chunk 165 optimal weight: 2.9990 chunk 184 optimal weight: 6.9990 chunk 63 optimal weight: 7.9990 chunk 148 optimal weight: 20.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 353 GLN ** 1 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 679 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7154 moved from start: 0.2764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 17401 Z= 0.268 Angle : 0.554 10.176 23626 Z= 0.285 Chirality : 0.040 0.142 2626 Planarity : 0.004 0.048 2972 Dihedral : 8.057 73.139 2483 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.19), residues: 2006 helix: 1.92 (0.17), residues: 945 sheet: 0.50 (0.33), residues: 222 loop : 0.76 (0.22), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP 1 356 HIS 0.011 0.001 HIS 1 407 PHE 0.018 0.002 PHE B 75 TYR 0.016 0.002 TYR B 128 ARG 0.012 0.001 ARG 1 587 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 2.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 354 MET cc_start: 0.8523 (tpp) cc_final: 0.8231 (tpp) REVERT: 1 719 MET cc_start: 0.9061 (mtp) cc_final: 0.8710 (mmm) REVERT: 1 863 MET cc_start: 0.6989 (mmp) cc_final: 0.6586 (mmm) REVERT: 1 1376 MET cc_start: 0.7332 (mmp) cc_final: 0.6454 (mmm) REVERT: A 42 MET cc_start: 0.9372 (mmm) cc_final: 0.9095 (mmm) REVERT: A 141 MET cc_start: 0.9068 (mtm) cc_final: 0.8770 (mtm) REVERT: A 228 MET cc_start: 0.8638 (mmm) cc_final: 0.8436 (mmm) REVERT: A 319 LYS cc_start: 0.6565 (mttm) cc_final: 0.6078 (mttm) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.3416 time to fit residues: 35.0068 Evaluate side-chains 56 residues out of total 1870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 1.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 183 optimal weight: 9.9990 chunk 139 optimal weight: 10.0000 chunk 96 optimal weight: 30.0000 chunk 20 optimal weight: 30.0000 chunk 88 optimal weight: 20.0000 chunk 124 optimal weight: 7.9990 chunk 186 optimal weight: 5.9990 chunk 197 optimal weight: 2.9990 chunk 97 optimal weight: 8.9990 chunk 176 optimal weight: 20.0000 chunk 53 optimal weight: 20.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 407 HIS ** 1 638 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 712 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 moved from start: 0.3288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 17401 Z= 0.282 Angle : 0.556 7.832 23626 Z= 0.283 Chirality : 0.040 0.146 2626 Planarity : 0.004 0.052 2972 Dihedral : 8.050 73.287 2483 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.19), residues: 2006 helix: 2.00 (0.17), residues: 936 sheet: 0.55 (0.34), residues: 198 loop : 0.78 (0.22), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP 1 671 HIS 0.005 0.001 HIS C 606 PHE 0.018 0.002 PHE B 75 TYR 0.016 0.001 TYR B 503 ARG 0.011 0.001 ARG A 207 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 1870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 2.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 430 MET cc_start: 0.6931 (mmm) cc_final: 0.6391 (mmm) REVERT: 1 719 MET cc_start: 0.9045 (mtp) cc_final: 0.8730 (mmm) REVERT: 1 863 MET cc_start: 0.7140 (mmp) cc_final: 0.6683 (mmm) REVERT: 1 924 MET cc_start: 0.8483 (tpp) cc_final: 0.8146 (tpp) REVERT: A 42 MET cc_start: 0.9344 (mmm) cc_final: 0.9061 (mmm) REVERT: A 319 LYS cc_start: 0.6647 (mttm) cc_final: 0.6308 (mttm) outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.3356 time to fit residues: 34.0431 Evaluate side-chains 56 residues out of total 1870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 2.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 164 optimal weight: 9.9990 chunk 111 optimal weight: 3.9990 chunk 2 optimal weight: 0.0370 chunk 146 optimal weight: 0.9990 chunk 81 optimal weight: 20.0000 chunk 168 optimal weight: 7.9990 chunk 136 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 100 optimal weight: 5.9990 chunk 176 optimal weight: 9.9990 chunk 49 optimal weight: 20.0000 overall best weight: 3.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 638 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 11313 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.3332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17401 Z= 0.167 Angle : 0.474 7.174 23626 Z= 0.241 Chirality : 0.038 0.140 2626 Planarity : 0.003 0.052 2972 Dihedral : 7.920 73.338 2483 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.11 (0.19), residues: 2006 helix: 2.19 (0.17), residues: 945 sheet: 0.49 (0.33), residues: 228 loop : 0.89 (0.23), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP 1 671 HIS 0.003 0.001 HIS B 131 PHE 0.015 0.001 PHE B 75 TYR 0.014 0.001 TYR B 503 ARG 0.005 0.000 ARG A 267 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 1870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 1.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 719 MET cc_start: 0.9046 (mtp) cc_final: 0.8364 (mmm) REVERT: 1 863 MET cc_start: 0.6998 (mmp) cc_final: 0.6601 (mmm) REVERT: 1 919 GLU cc_start: 0.9633 (mt-10) cc_final: 0.9383 (mt-10) outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.3248 time to fit residues: 33.3085 Evaluate side-chains 55 residues out of total 1870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 2.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 66 optimal weight: 30.0000 chunk 177 optimal weight: 20.0000 chunk 38 optimal weight: 8.9990 chunk 115 optimal weight: 9.9990 chunk 48 optimal weight: 9.9990 chunk 197 optimal weight: 0.9980 chunk 163 optimal weight: 9.9990 chunk 91 optimal weight: 0.0980 chunk 16 optimal weight: 7.9990 chunk 65 optimal weight: 5.9990 chunk 103 optimal weight: 20.0000 overall best weight: 4.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 638 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 754 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 11313 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7185 moved from start: 0.3529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17401 Z= 0.208 Angle : 0.494 7.620 23626 Z= 0.250 Chirality : 0.039 0.137 2626 Planarity : 0.003 0.051 2972 Dihedral : 7.901 73.294 2483 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.10 (0.19), residues: 2006 helix: 2.18 (0.17), residues: 949 sheet: 0.41 (0.33), residues: 231 loop : 0.91 (0.23), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP 1 671 HIS 0.004 0.001 HIS B 131 PHE 0.016 0.001 PHE B 75 TYR 0.014 0.001 TYR B 503 ARG 0.004 0.000 ARG B 53 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 1870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 1.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 354 MET cc_start: 0.8269 (tpp) cc_final: 0.7589 (tpp) REVERT: 1 719 MET cc_start: 0.9045 (mtp) cc_final: 0.8348 (mmm) REVERT: 1 863 MET cc_start: 0.7170 (mmp) cc_final: 0.6706 (mmm) REVERT: A 319 LYS cc_start: 0.6480 (mttm) cc_final: 0.5839 (mttp) REVERT: B 480 MET cc_start: 0.6931 (ttp) cc_final: 0.6543 (mtp) outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 0.3360 time to fit residues: 33.6993 Evaluate side-chains 55 residues out of total 1870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 1.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 190 optimal weight: 10.0000 chunk 22 optimal weight: 8.9990 chunk 112 optimal weight: 1.9990 chunk 144 optimal weight: 0.0570 chunk 111 optimal weight: 5.9990 chunk 166 optimal weight: 40.0000 chunk 110 optimal weight: 6.9990 chunk 196 optimal weight: 20.0000 chunk 123 optimal weight: 7.9990 chunk 119 optimal weight: 30.0000 chunk 90 optimal weight: 9.9990 overall best weight: 4.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 638 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 754 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 11369 ASN ** B 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7187 moved from start: 0.3662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17401 Z= 0.194 Angle : 0.488 11.168 23626 Z= 0.248 Chirality : 0.038 0.138 2626 Planarity : 0.003 0.051 2972 Dihedral : 7.879 73.333 2483 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.05 % Allowed : 0.11 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.11 (0.19), residues: 2006 helix: 2.18 (0.17), residues: 948 sheet: 0.41 (0.33), residues: 231 loop : 0.94 (0.23), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP 1 671 HIS 0.004 0.001 HIS B 131 PHE 0.015 0.001 PHE B 75 TYR 0.013 0.001 TYR B 503 ARG 0.004 0.000 ARG 11435 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 1870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 62 time to evaluate : 2.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 354 MET cc_start: 0.8319 (tpp) cc_final: 0.7667 (tpp) REVERT: 1 719 MET cc_start: 0.9013 (mtp) cc_final: 0.8297 (mmm) REVERT: 1 863 MET cc_start: 0.7112 (mmp) cc_final: 0.6663 (mmm) REVERT: 1 1376 MET cc_start: 0.7738 (mmp) cc_final: 0.7534 (mmp) REVERT: A 42 MET cc_start: 0.9156 (mmm) cc_final: 0.8793 (mmm) REVERT: A 307 MET cc_start: 0.9293 (tpp) cc_final: 0.9080 (tpp) REVERT: B 480 MET cc_start: 0.6856 (ttp) cc_final: 0.6523 (ttp) outliers start: 1 outliers final: 0 residues processed: 63 average time/residue: 0.3334 time to fit residues: 33.6703 Evaluate side-chains 54 residues out of total 1870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 1.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 121 optimal weight: 8.9990 chunk 78 optimal weight: 0.6980 chunk 117 optimal weight: 7.9990 chunk 59 optimal weight: 8.9990 chunk 38 optimal weight: 20.0000 chunk 125 optimal weight: 20.0000 chunk 133 optimal weight: 8.9990 chunk 97 optimal weight: 0.0770 chunk 18 optimal weight: 9.9990 chunk 154 optimal weight: 20.0000 chunk 178 optimal weight: 6.9990 overall best weight: 4.9544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 638 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 754 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 11369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 moved from start: 0.3776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 17401 Z= 0.206 Angle : 0.488 6.645 23626 Z= 0.249 Chirality : 0.039 0.141 2626 Planarity : 0.003 0.051 2972 Dihedral : 7.880 73.332 2483 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.12 (0.19), residues: 2006 helix: 2.19 (0.17), residues: 948 sheet: 0.42 (0.33), residues: 230 loop : 0.93 (0.23), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP 1 671 HIS 0.004 0.001 HIS B 131 PHE 0.015 0.001 PHE B 75 TYR 0.013 0.001 TYR B 503 ARG 0.004 0.000 ARG A 207 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 1870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 1.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 354 MET cc_start: 0.8341 (tpp) cc_final: 0.7714 (tpp) REVERT: 1 719 MET cc_start: 0.9006 (mtp) cc_final: 0.8275 (mmm) REVERT: A 42 MET cc_start: 0.9125 (mmm) cc_final: 0.8916 (mmm) REVERT: A 319 LYS cc_start: 0.6533 (mttm) cc_final: 0.5878 (mttp) REVERT: B 480 MET cc_start: 0.6884 (ttp) cc_final: 0.6603 (ttp) outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.3400 time to fit residues: 32.6655 Evaluate side-chains 53 residues out of total 1870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 2.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 188 optimal weight: 20.0000 chunk 171 optimal weight: 20.0000 chunk 183 optimal weight: 10.0000 chunk 110 optimal weight: 3.9990 chunk 79 optimal weight: 0.0040 chunk 143 optimal weight: 10.0000 chunk 56 optimal weight: 30.0000 chunk 165 optimal weight: 0.6980 chunk 173 optimal weight: 40.0000 chunk 182 optimal weight: 5.9990 chunk 120 optimal weight: 30.0000 overall best weight: 4.1400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 638 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 754 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 11310 ASN ** 11369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7187 moved from start: 0.3874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 17401 Z= 0.181 Angle : 0.490 8.919 23626 Z= 0.249 Chirality : 0.039 0.169 2626 Planarity : 0.003 0.051 2972 Dihedral : 7.844 73.371 2483 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.00 % Allowed : 0.05 % Favored : 99.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.15 (0.19), residues: 2006 helix: 2.18 (0.17), residues: 950 sheet: 0.41 (0.34), residues: 216 loop : 1.00 (0.23), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP 1 671 HIS 0.004 0.001 HIS B 131 PHE 0.015 0.001 PHE B 75 TYR 0.013 0.001 TYR B 503 ARG 0.004 0.000 ARG A 207 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 1870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 2.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 354 MET cc_start: 0.8318 (tpp) cc_final: 0.7655 (tpp) REVERT: 1 619 MET cc_start: 0.8566 (tpp) cc_final: 0.8190 (tpp) REVERT: 1 719 MET cc_start: 0.9004 (mtp) cc_final: 0.8256 (mmm) REVERT: 1 1376 MET cc_start: 0.7815 (mmp) cc_final: 0.7475 (mmp) REVERT: A 15 MET cc_start: 0.5732 (mmp) cc_final: 0.5479 (mmp) REVERT: A 42 MET cc_start: 0.9222 (mmm) cc_final: 0.8808 (mmm) REVERT: A 184 ARG cc_start: 0.8319 (mtt-85) cc_final: 0.7874 (mtt-85) REVERT: A 319 LYS cc_start: 0.6536 (mttm) cc_final: 0.5846 (mttp) REVERT: B 480 MET cc_start: 0.6862 (ttp) cc_final: 0.6575 (ttp) outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.3091 time to fit residues: 29.8984 Evaluate side-chains 52 residues out of total 1870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 2.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 193 optimal weight: 20.0000 chunk 118 optimal weight: 1.9990 chunk 91 optimal weight: 0.0040 chunk 134 optimal weight: 8.9990 chunk 203 optimal weight: 10.0000 chunk 187 optimal weight: 0.0000 chunk 161 optimal weight: 8.9990 chunk 16 optimal weight: 3.9990 chunk 125 optimal weight: 20.0000 chunk 99 optimal weight: 8.9990 chunk 128 optimal weight: 0.0170 overall best weight: 1.2038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 638 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 11313 GLN ** 11369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7142 moved from start: 0.3848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 17401 Z= 0.123 Angle : 0.462 7.177 23626 Z= 0.235 Chirality : 0.038 0.164 2626 Planarity : 0.003 0.052 2972 Dihedral : 7.712 73.416 2483 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.28 (0.19), residues: 2006 helix: 2.32 (0.17), residues: 944 sheet: 0.47 (0.34), residues: 216 loop : 1.03 (0.23), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 274 HIS 0.005 0.001 HIS B 131 PHE 0.014 0.001 PHE B 75 TYR 0.013 0.001 TYR B 503 ARG 0.004 0.000 ARG 1 651 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 1870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 2.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 354 MET cc_start: 0.8306 (tpp) cc_final: 0.7656 (tpp) REVERT: 1 619 MET cc_start: 0.8563 (tpp) cc_final: 0.8167 (tpp) REVERT: 1 719 MET cc_start: 0.8986 (mtp) cc_final: 0.8198 (mmm) REVERT: 1 919 GLU cc_start: 0.9577 (mt-10) cc_final: 0.9339 (mt-10) REVERT: 1 1376 MET cc_start: 0.7687 (mmp) cc_final: 0.6496 (mmm) REVERT: A 15 MET cc_start: 0.5725 (mmp) cc_final: 0.5481 (mmp) REVERT: A 42 MET cc_start: 0.9246 (mmm) cc_final: 0.8839 (mmm) REVERT: A 319 LYS cc_start: 0.6349 (mttm) cc_final: 0.5649 (mttp) REVERT: B 480 MET cc_start: 0.6725 (ttp) cc_final: 0.6462 (ttp) outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.3208 time to fit residues: 31.6444 Evaluate side-chains 54 residues out of total 1870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 1.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 20.0000 chunk 49 optimal weight: 20.0000 chunk 149 optimal weight: 20.0000 chunk 23 optimal weight: 20.0000 chunk 44 optimal weight: 40.0000 chunk 162 optimal weight: 20.0000 chunk 67 optimal weight: 8.9990 chunk 166 optimal weight: 1.9990 chunk 20 optimal weight: 0.0570 chunk 29 optimal weight: 0.1980 chunk 142 optimal weight: 30.0000 overall best weight: 6.2506 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 638 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 754 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 11313 GLN ** 11369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 168 HIS ** B 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2613 r_free = 0.2613 target = 0.036202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2309 r_free = 0.2309 target = 0.029857 restraints weight = 520538.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2315 r_free = 0.2315 target = 0.030242 restraints weight = 357265.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2317 r_free = 0.2317 target = 0.030321 restraints weight = 278382.353| |-----------------------------------------------------------------------------| r_work (final): 0.2312 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2312 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2312 r_free = 0.2312 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2312 r_free = 0.2312 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2312 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.4035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 17401 Z= 0.247 Angle : 0.523 6.814 23626 Z= 0.267 Chirality : 0.039 0.137 2626 Planarity : 0.003 0.053 2972 Dihedral : 7.849 73.342 2483 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.00 % Allowed : 0.05 % Favored : 99.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.14 (0.19), residues: 2006 helix: 2.23 (0.17), residues: 946 sheet: 0.42 (0.33), residues: 232 loop : 0.92 (0.23), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP 1 671 HIS 0.004 0.001 HIS B 349 PHE 0.015 0.001 PHE B 75 TYR 0.013 0.001 TYR B 503 ARG 0.003 0.000 ARG A 207 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2793.11 seconds wall clock time: 52 minutes 54.81 seconds (3174.81 seconds total)