Starting phenix.real_space_refine on Tue Feb 20 03:38:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7crr_30457/02_2024/7crr_30457_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7crr_30457/02_2024/7crr_30457.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7crr_30457/02_2024/7crr_30457.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7crr_30457/02_2024/7crr_30457.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7crr_30457/02_2024/7crr_30457_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7crr_30457/02_2024/7crr_30457_updated.pdb" } resolution = 3.48 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 12070 atoms to isotropic. 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 Zn 3 6.06 5 P 336 5.49 5 S 29 5.16 5 C 8248 2.51 5 N 2788 2.21 5 O 3435 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 74": "OE1" <-> "OE2" Residue "D GLU 102": "OE1" <-> "OE2" Residue "E ARG 129": "NH1" <-> "NH2" Residue "H ARG 26": "NH1" <-> "NH2" Residue "H TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 1097": "NH1" <-> "NH2" Residue "I GLU 1113": "OE1" <-> "OE2" Residue "I ARG 1133": "NH1" <-> "NH2" Residue "I ARG 1142": "NH1" <-> "NH2" Residue "I ARG 1160": "NH1" <-> "NH2" Residue "I GLU 1181": "OE1" <-> "OE2" Residue "I GLU 1182": "OE1" <-> "OE2" Residue "I ARG 1220": "NH1" <-> "NH2" Residue "I GLU 1231": "OE1" <-> "OE2" Residue "I ARG 1242": "NH1" <-> "NH2" Residue "I ARG 1270": "NH1" <-> "NH2" Residue "I GLU 1272": "OE1" <-> "OE2" Residue "I ARG 1287": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 14839 Number of models: 1 Model: "" Number of chains: 11 Chain: "M" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 833 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 98} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1, 'NLE:plan-1': 3} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 837 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 103} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 746 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 803 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1, 'NLE:plan-1': 2} Unresolved non-hydrogen planarities: 7 Chain: "F" Number of atoms: 676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 676 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 84} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Chain: "G" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 850 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "H" Number of atoms: 766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 766 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "A" Number of atoms: 3420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 3420 Classifications: {'DNA': 168} Link IDs: {'rna3p': 167} Chain: "K" Number of atoms: 3468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 3468 Classifications: {'DNA': 168} Link IDs: {'rna3p': 167} Chain: "I" Number of atoms: 1787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1787 Unusual residues: {' ZN': 3} Classifications: {'peptide': 223, 'undetermined': 3} Link IDs: {'PTRANS': 12, 'TRANS': 210, None: 3} Not linked: pdbres="SAM I1501 " pdbres=" ZN I1502 " Not linked: pdbres=" ZN I1502 " pdbres=" ZN I1503 " Not linked: pdbres=" ZN I1503 " pdbres=" ZN I1504 " Chain breaks: 1 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14351 SG CYS I1226 38.218 63.873 58.261 1.00113.15 S ATOM 14727 SG CYS I1275 38.079 65.107 53.684 1.00119.40 S ATOM 13313 SG CYS I1098 59.658 91.848 72.527 1.00 91.57 S ATOM 13327 SG CYS I1100 61.798 91.590 69.925 1.00 96.58 S ATOM 13386 SG CYS I1108 58.780 92.971 68.769 1.00 94.35 S ATOM 13428 SG CYS I1114 57.707 89.812 70.185 1.00 82.06 S ATOM 13386 SG CYS I1108 58.780 92.971 68.769 1.00 94.35 S ATOM 13507 SG CYS I1123 55.139 94.831 69.726 1.00 83.93 S ATOM 13546 SG CYS I1128 58.262 96.686 69.941 1.00 98.17 S ATOM 13587 SG CYS I1134 55.714 95.818 66.274 1.00102.54 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N SAM I1501 " occ=0.93 ... (25 atoms not shown) pdb=" O4' SAM I1501 " occ=0.93 Time building chain proxies: 7.72, per 1000 atoms: 0.52 Number of scatterers: 14839 At special positions: 0 Unit cell: (133.92, 145.8, 171.72, 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) Zn 3 29.99 S 29 16.00 P 336 15.00 O 3435 8.00 N 2788 7.00 C 8248 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: 6.89 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN I1502 " pdb="ZN ZN I1502 " - pdb=" SG CYS I1275 " pdb="ZN ZN I1502 " - pdb=" SG CYS I1226 " pdb=" ZN I1503 " pdb="ZN ZN I1503 " - pdb=" SG CYS I1108 " pdb="ZN ZN I1503 " - pdb=" SG CYS I1114 " pdb="ZN ZN I1503 " - pdb=" SG CYS I1100 " pdb="ZN ZN I1503 " - pdb=" SG CYS I1098 " pdb=" ZN I1504 " pdb="ZN ZN I1504 " - pdb=" SG CYS I1123 " pdb="ZN ZN I1504 " - pdb=" SG CYS I1108 " pdb="ZN ZN I1504 " - pdb=" SG CYS I1134 " pdb="ZN ZN I1504 " - pdb=" SG CYS I1128 " Number of angles added : 12 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1866 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 37 helices and 3 sheets defined 45.5% alpha, 1.6% beta 122 base pairs and 272 stacking pairs defined. Time for finding SS restraints: 7.72 Creating SS restraints... Processing helix chain 'M' and resid 48 through 54 Processing helix chain 'M' and resid 64 through 77 removed outlier: 3.518A pdb=" N LEU M 70 " --> pdb=" O PRO M 66 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN M 76 " --> pdb=" O ARG M 72 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ASP M 77 " --> pdb=" O GLU M 73 " (cutoff:3.500A) Processing helix chain 'M' and resid 88 through 113 removed outlier: 4.088A pdb=" N LEU M 92 " --> pdb=" O VAL M 89 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N GLN M 93 " --> pdb=" O NLE M 90 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU M 94 " --> pdb=" O ALA M 91 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N SER M 96 " --> pdb=" O GLN M 93 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N GLU M 97 " --> pdb=" O GLU M 94 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N VAL M 101 " --> pdb=" O ALA M 98 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N PHE M 104 " --> pdb=" O VAL M 101 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLU M 105 " --> pdb=" O GLY M 102 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N THR M 107 " --> pdb=" O PHE M 104 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASN M 108 " --> pdb=" O GLU M 105 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU M 109 " --> pdb=" O ASP M 106 " (cutoff:3.500A) Processing helix chain 'M' and resid 122 through 131 removed outlier: 3.958A pdb=" N LEU M 126 " --> pdb=" O LYS M 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 28 Processing helix chain 'B' and resid 31 through 41 removed outlier: 3.658A pdb=" N LEU B 37 " --> pdb=" O ALA B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 76 removed outlier: 4.072A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLY B 56 " --> pdb=" O GLU B 52 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N VAL B 60 " --> pdb=" O GLY B 56 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLU B 63 " --> pdb=" O LYS B 59 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ASN B 64 " --> pdb=" O VAL B 60 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL B 65 " --> pdb=" O PHE B 61 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 93 removed outlier: 3.790A pdb=" N VAL B 87 " --> pdb=" O ALA B 83 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 37 removed outlier: 3.783A pdb=" N ARG C 32 " --> pdb=" O GLY C 28 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY C 37 " --> pdb=" O LEU C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 60 removed outlier: 3.730A pdb=" N ALA C 53 " --> pdb=" O VAL C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 72 removed outlier: 3.530A pdb=" N ALA C 66 " --> pdb=" O ILE C 62 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASN C 68 " --> pdb=" O GLU C 64 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASP C 72 " --> pdb=" O ASN C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 88 Processing helix chain 'C' and resid 93 through 96 No H-bonds generated for 'chain 'C' and resid 93 through 96' Processing helix chain 'D' and resid 35 through 45 removed outlier: 3.743A pdb=" N LYS D 40 " --> pdb=" O ILE D 36 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLN D 44 " --> pdb=" O LYS D 40 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL D 45 " --> pdb=" O VAL D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 80 removed outlier: 4.194A pdb=" N SER D 61 " --> pdb=" O SER D 57 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLU D 68 " --> pdb=" O ASN D 64 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLY D 72 " --> pdb=" O GLU D 68 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLU D 73 " --> pdb=" O ARG D 69 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ARG D 76 " --> pdb=" O GLY D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 96 removed outlier: 3.694A pdb=" N VAL D 95 " --> pdb=" O ILE D 91 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG D 96 " --> pdb=" O GLN D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 119 removed outlier: 4.153A pdb=" N VAL D 108 " --> pdb=" O ALA D 104 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N SER D 109 " --> pdb=" O LYS D 105 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ALA D 114 " --> pdb=" O GLU D 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 54 removed outlier: 3.980A pdb=" N ARG E 52 " --> pdb=" O LEU E 48 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ARG E 53 " --> pdb=" O ARG E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 76 removed outlier: 3.732A pdb=" N LEU E 70 " --> pdb=" O PRO E 66 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLN E 76 " --> pdb=" O ARG E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 113 removed outlier: 3.758A pdb=" N GLY E 102 " --> pdb=" O ALA E 98 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ASP E 106 " --> pdb=" O GLY E 102 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU E 109 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ILE E 112 " --> pdb=" O ASN E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 131 removed outlier: 3.779A pdb=" N LEU E 126 " --> pdb=" O LYS E 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 26 through 28 No H-bonds generated for 'chain 'F' and resid 26 through 28' Processing helix chain 'F' and resid 31 through 41 removed outlier: 3.833A pdb=" N LEU F 37 " --> pdb=" O ALA F 33 " (cutoff:3.500A) Processing helix chain 'F' and resid 50 through 76 removed outlier: 3.804A pdb=" N ARG F 55 " --> pdb=" O TYR F 51 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLY F 56 " --> pdb=" O GLU F 52 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL F 60 " --> pdb=" O GLY F 56 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLU F 63 " --> pdb=" O LYS F 59 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL F 65 " --> pdb=" O PHE F 61 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 93 removed outlier: 3.891A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 17 through 21 removed outlier: 3.525A pdb=" N ALA G 21 " --> pdb=" O ARG G 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 17 through 21' Processing helix chain 'G' and resid 27 through 37 removed outlier: 3.610A pdb=" N HIS G 31 " --> pdb=" O VAL G 27 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG G 32 " --> pdb=" O GLY G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 47 through 53 removed outlier: 3.681A pdb=" N ALA G 53 " --> pdb=" O VAL G 49 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 73 removed outlier: 3.719A pdb=" N ILE G 62 " --> pdb=" O LEU G 58 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP G 72 " --> pdb=" O ASN G 68 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ASN G 73 " --> pdb=" O ALA G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 87 removed outlier: 3.504A pdb=" N GLN G 84 " --> pdb=" O PRO G 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 96 No H-bonds generated for 'chain 'G' and resid 93 through 96' Processing helix chain 'H' and resid 38 through 45 removed outlier: 4.311A pdb=" N LYS H 43 " --> pdb=" O TYR H 39 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLN H 44 " --> pdb=" O LYS H 40 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL H 45 " --> pdb=" O VAL H 41 " (cutoff:3.500A) Processing helix chain 'H' and resid 56 through 80 removed outlier: 3.872A pdb=" N GLU H 68 " --> pdb=" O ASN H 64 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG H 69 " --> pdb=" O ASP H 65 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA H 74 " --> pdb=" O ILE H 70 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ARG H 76 " --> pdb=" O GLY H 72 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 98 Processing helix chain 'H' and resid 103 through 120 removed outlier: 4.721A pdb=" N VAL H 108 " --> pdb=" O ALA H 104 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N SER H 109 " --> pdb=" O LYS H 105 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N THR H 116 " --> pdb=" O THR H 112 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N TYR H 118 " --> pdb=" O ALA H 114 " (cutoff:3.500A) Processing helix chain 'I' and resid 1115 through 1119 Processing helix chain 'I' and resid 1181 through 1193 Processing sheet with id= A, first strand: chain 'I' and resid 1177 through 1179 removed outlier: 3.737A pdb=" N ARG I1208 " --> pdb=" O THR I1205 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR I1205 " --> pdb=" O ARG I1208 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N ILE I1210 " --> pdb=" O THR I1203 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N THR I1203 " --> pdb=" O ILE I1210 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'I' and resid 1230 through 1232 Processing sheet with id= C, first strand: chain 'I' and resid 1235 through 1237 239 hydrogen bonds defined for protein. 669 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 316 hydrogen bonds 628 hydrogen bond angles 0 basepair planarities 122 basepair parallelities 272 stacking parallelities Total time for adding SS restraints: 5.50 Time building geometry restraints manager: 7.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2956 1.33 - 1.45: 4947 1.45 - 1.57: 7177 1.57 - 1.69: 670 1.69 - 1.81: 41 Bond restraints: 15791 Sorted by residual: bond pdb=" C8 SAM I1501 " pdb=" N7 SAM I1501 " ideal model delta sigma weight residual 1.298 1.352 -0.054 2.00e-02 2.50e+03 7.32e+00 bond pdb=" C2 SAM I1501 " pdb=" N3 SAM I1501 " ideal model delta sigma weight residual 1.322 1.375 -0.053 2.00e-02 2.50e+03 7.02e+00 bond pdb=" C2 SAM I1501 " pdb=" N1 SAM I1501 " ideal model delta sigma weight residual 1.329 1.378 -0.049 2.00e-02 2.50e+03 6.12e+00 bond pdb=" CA LYS I1077 " pdb=" C LYS I1077 " ideal model delta sigma weight residual 1.522 1.552 -0.031 1.32e-02 5.74e+03 5.35e+00 bond pdb=" CA ALA H 114 " pdb=" C ALA H 114 " ideal model delta sigma weight residual 1.522 1.491 0.031 1.38e-02 5.25e+03 5.20e+00 ... (remaining 15786 not shown) Histogram of bond angle deviations from ideal: 97.80 - 105.04: 1459 105.04 - 112.27: 8720 112.27 - 119.51: 4952 119.51 - 126.74: 6664 126.74 - 133.98: 974 Bond angle restraints: 22769 Sorted by residual: angle pdb=" N LYS D 31 " pdb=" CA LYS D 31 " pdb=" C LYS D 31 " ideal model delta sigma weight residual 110.80 99.62 11.18 2.13e+00 2.20e-01 2.75e+01 angle pdb=" O ASP I1180 " pdb=" C ASP I1180 " pdb=" N GLU I1181 " ideal model delta sigma weight residual 122.68 117.08 5.60 1.17e+00 7.31e-01 2.29e+01 angle pdb=" N VAL G 54 " pdb=" CA VAL G 54 " pdb=" C VAL G 54 " ideal model delta sigma weight residual 113.22 107.57 5.65 1.23e+00 6.61e-01 2.11e+01 angle pdb=" C4' DA A 27 " pdb=" C3' DA A 27 " pdb=" O3' DA A 27 " ideal model delta sigma weight residual 110.00 116.64 -6.64 1.50e+00 4.44e-01 1.96e+01 angle pdb=" O3' DA A 27 " pdb=" C3' DA A 27 " pdb=" C2' DA A 27 " ideal model delta sigma weight residual 111.50 105.03 6.47 1.50e+00 4.44e-01 1.86e+01 ... (remaining 22764 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.28: 6951 34.28 - 68.55: 1659 68.55 - 102.83: 28 102.83 - 137.11: 0 137.11 - 171.39: 1 Dihedral angle restraints: 8639 sinusoidal: 5743 harmonic: 2896 Sorted by residual: dihedral pdb=" CA ASP I1146 " pdb=" C ASP I1146 " pdb=" N ALA I1147 " pdb=" CA ALA I1147 " ideal model delta harmonic sigma weight residual -180.00 -151.64 -28.36 0 5.00e+00 4.00e-02 3.22e+01 dihedral pdb=" CA HIS E 39 " pdb=" C HIS E 39 " pdb=" N ARG E 40 " pdb=" CA ARG E 40 " ideal model delta harmonic sigma weight residual 180.00 156.08 23.92 0 5.00e+00 4.00e-02 2.29e+01 dihedral pdb=" CA LEU I1143 " pdb=" C LEU I1143 " pdb=" N TYR I1144 " pdb=" CA TYR I1144 " ideal model delta harmonic sigma weight residual -180.00 -158.54 -21.46 0 5.00e+00 4.00e-02 1.84e+01 ... (remaining 8636 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 2218 0.060 - 0.120: 332 0.120 - 0.180: 19 0.180 - 0.240: 3 0.240 - 0.299: 1 Chirality restraints: 2573 Sorted by residual: chirality pdb=" C1' SAM I1501 " pdb=" C2' SAM I1501 " pdb=" N9 SAM I1501 " pdb=" O4' SAM I1501 " both_signs ideal model delta sigma weight residual False 2.30 2.60 -0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" CA LYS D 31 " pdb=" N LYS D 31 " pdb=" C LYS D 31 " pdb=" CB LYS D 31 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CA SER G 113 " pdb=" N SER G 113 " pdb=" C SER G 113 " pdb=" CB SER G 113 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.21 2.00e-01 2.50e+01 1.05e+00 ... (remaining 2570 not shown) Planarity restraints: 1730 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE I1076 " -0.013 2.00e-02 2.50e+03 2.48e-02 6.17e+00 pdb=" C ILE I1076 " 0.043 2.00e-02 2.50e+03 pdb=" O ILE I1076 " -0.016 2.00e-02 2.50e+03 pdb=" N LYS I1077 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR I1261 " 0.012 2.00e-02 2.50e+03 2.41e-02 5.81e+00 pdb=" C TYR I1261 " -0.042 2.00e-02 2.50e+03 pdb=" O TYR I1261 " 0.016 2.00e-02 2.50e+03 pdb=" N ASN I1262 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP I1180 " 0.012 2.00e-02 2.50e+03 2.33e-02 5.45e+00 pdb=" C ASP I1180 " -0.040 2.00e-02 2.50e+03 pdb=" O ASP I1180 " 0.015 2.00e-02 2.50e+03 pdb=" N GLU I1181 " 0.013 2.00e-02 2.50e+03 ... (remaining 1727 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 208 2.61 - 3.18: 11878 3.18 - 3.75: 24035 3.75 - 4.33: 33967 4.33 - 4.90: 49006 Nonbonded interactions: 119094 Sorted by model distance: nonbonded pdb=" N2 DG A 26 " pdb=" N3 DT K 163 " model vdw 2.037 3.200 nonbonded pdb=" NZ LYS G 119 " pdb=" OE2 GLU I1111 " model vdw 2.114 2.520 nonbonded pdb=" C2 DA A 27 " pdb=" O2 DC K 162 " model vdw 2.151 3.340 nonbonded pdb=" N1 DA A 27 " pdb=" O2 DC K 162 " model vdw 2.186 3.120 nonbonded pdb=" OP1 DC K 165 " pdb=" NZ LYS I1074 " model vdw 2.188 2.520 ... (remaining 119089 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 'B' and (resid 20 through 22 or (resid 23 and (name N or name CA or name \ C or name O or name CB )) or resid 24 through 101)) selection = (chain 'F' and ((resid 20 and (name N or name CA or name C or name O or name CB \ )) or resid 21 through 101)) } ncs_group { reference = chain 'C' selection = (chain 'G' and (resid 10 through 117 or (resid 118 and (name N or name CA or nam \ e C or name O or name CB )))) } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 27 through 121) } ncs_group { reference = chain 'E' selection = (chain 'M' and resid 37 through 134) } 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=0.93 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: 1.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.160 Construct map_model_manager: 0.010 Extract box with map and model: 3.290 Check model and map are aligned: 0.200 Set scattering table: 0.130 Process input model: 47.780 Find NCS groups from input model: 0.530 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 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 0.054 15791 Z= 0.448 Angle : 0.752 11.177 22769 Z= 0.456 Chirality : 0.042 0.299 2573 Planarity : 0.004 0.050 1730 Dihedral : 27.668 171.385 6773 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.22 % Favored : 89.78 % Rotamer: Outliers : 1.56 % Allowed : 4.80 % Favored : 93.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.14 (0.19), residues: 969 helix: -3.06 (0.16), residues: 522 sheet: -4.28 (0.88), residues: 16 loop : -3.80 (0.21), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP I1157 HIS 0.006 0.001 HIS C 31 PHE 0.011 0.002 PHE H 67 TYR 0.015 0.002 TYR H 118 ARG 0.005 0.001 ARG I1220 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 150 time to evaluate : 1.096 Fit side-chains revert: symmetry clash REVERT: M 79 LYS cc_start: 0.8761 (tttt) cc_final: 0.8464 (tttp) REVERT: B 35 ARG cc_start: 0.8748 (mtp85) cc_final: 0.8417 (mtt-85) REVERT: D 110 GLU cc_start: 0.8887 (tp30) cc_final: 0.8531 (tp30) REVERT: F 25 ASN cc_start: 0.8638 (m-40) cc_final: 0.8363 (m-40) REVERT: G 75 LYS cc_start: 0.8843 (mttm) cc_final: 0.8639 (mttt) REVERT: H 28 LYS cc_start: 0.7062 (ptmm) cc_final: 0.6537 (ttmm) REVERT: H 39 TYR cc_start: 0.7972 (t80) cc_final: 0.7746 (t80) REVERT: H 65 ASP cc_start: 0.8785 (t70) cc_final: 0.8493 (t0) REVERT: H 105 LYS cc_start: 0.9005 (ttpt) cc_final: 0.8718 (ttmt) REVERT: I 1073 TYR cc_start: 0.7178 (p90) cc_final: 0.6888 (p90) REVERT: I 1222 MET cc_start: 0.7350 (mmm) cc_final: 0.6233 (mmm) outliers start: 13 outliers final: 4 residues processed: 159 average time/residue: 0.4315 time to fit residues: 89.4399 Evaluate side-chains 114 residues out of total 841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 110 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 119 LYS Chi-restraints excluded: chain I residue 1200 TYR Chi-restraints excluded: chain I residue 1201 MET Chi-restraints excluded: chain I residue 1262 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 108 optimal weight: 20.0000 chunk 97 optimal weight: 6.9990 chunk 53 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.0670 chunk 51 optimal weight: 0.6980 chunk 100 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 74 optimal weight: 30.0000 chunk 116 optimal weight: 0.7980 overall best weight: 0.6720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 68 GLN C 104 GLN C 112 GLN E 68 GLN G 38 ASN G 104 GLN H 44 GLN H 106 HIS I1137 GLN ** I1172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1229 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15791 Z= 0.165 Angle : 0.559 5.570 22769 Z= 0.328 Chirality : 0.035 0.177 2573 Planarity : 0.004 0.053 1730 Dihedral : 30.322 172.269 4818 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 0.84 % Allowed : 10.91 % Favored : 88.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.51 (0.23), residues: 969 helix: -1.58 (0.21), residues: 523 sheet: -3.94 (0.87), residues: 16 loop : -3.23 (0.24), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP I1157 HIS 0.003 0.001 HIS C 31 PHE 0.008 0.001 PHE I1170 TYR 0.014 0.001 TYR I1218 ARG 0.006 0.000 ARG D 30 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 129 time to evaluate : 1.125 Fit side-chains REVERT: M 79 LYS cc_start: 0.8773 (tttt) cc_final: 0.8420 (tttm) REVERT: M 94 GLU cc_start: 0.8073 (mt-10) cc_final: 0.7837 (tt0) REVERT: B 35 ARG cc_start: 0.8555 (mtp85) cc_final: 0.8195 (mtt-85) REVERT: D 110 GLU cc_start: 0.9009 (tp30) cc_final: 0.8640 (tp30) REVERT: E 123 ASP cc_start: 0.8957 (m-30) cc_final: 0.8619 (m-30) REVERT: G 75 LYS cc_start: 0.8878 (mttm) cc_final: 0.8657 (mttt) REVERT: H 65 ASP cc_start: 0.8749 (t70) cc_final: 0.8393 (t0) REVERT: H 105 LYS cc_start: 0.8867 (ttpt) cc_final: 0.8627 (ttmm) REVERT: I 1222 MET cc_start: 0.7305 (mmm) cc_final: 0.6394 (mmm) outliers start: 7 outliers final: 4 residues processed: 136 average time/residue: 0.3372 time to fit residues: 62.8955 Evaluate side-chains 117 residues out of total 841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 113 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain G residue 119 LYS Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain I residue 1077 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 64 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 96 optimal weight: 8.9990 chunk 79 optimal weight: 8.9990 chunk 32 optimal weight: 3.9990 chunk 116 optimal weight: 8.9990 chunk 125 optimal weight: 9.9990 chunk 103 optimal weight: 8.9990 chunk 115 optimal weight: 0.0670 chunk 39 optimal weight: 6.9990 chunk 93 optimal weight: 10.0000 overall best weight: 4.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 18 HIS ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 84 GLN ** I1136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.1476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 15791 Z= 0.378 Angle : 0.621 6.233 22769 Z= 0.357 Chirality : 0.038 0.145 2573 Planarity : 0.004 0.056 1730 Dihedral : 30.698 174.474 4811 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.46 % Favored : 91.54 % Rotamer: Outliers : 2.64 % Allowed : 12.71 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.13 (0.24), residues: 969 helix: -1.24 (0.22), residues: 520 sheet: -3.34 (0.94), residues: 18 loop : -3.11 (0.24), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP I1235 HIS 0.005 0.001 HIS C 31 PHE 0.017 0.002 PHE I1170 TYR 0.016 0.002 TYR H 118 ARG 0.008 0.001 ARG D 30 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 118 time to evaluate : 1.079 Fit side-chains REVERT: M 79 LYS cc_start: 0.8790 (tttt) cc_final: 0.8520 (tttm) REVERT: B 35 ARG cc_start: 0.8661 (mtp85) cc_final: 0.8288 (mtt-85) REVERT: D 110 GLU cc_start: 0.8986 (tp30) cc_final: 0.8637 (tp30) REVERT: F 18 HIS cc_start: 0.6517 (OUTLIER) cc_final: 0.6150 (t-90) REVERT: G 75 LYS cc_start: 0.8875 (mttm) cc_final: 0.8671 (mttt) REVERT: H 65 ASP cc_start: 0.8804 (t70) cc_final: 0.8469 (t0) REVERT: I 1222 MET cc_start: 0.7371 (mmm) cc_final: 0.6502 (mmm) outliers start: 22 outliers final: 20 residues processed: 135 average time/residue: 0.3354 time to fit residues: 61.9378 Evaluate side-chains 132 residues out of total 841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 111 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 65 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain F residue 18 HIS Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 119 LYS Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain I residue 1077 LYS Chi-restraints excluded: chain I residue 1098 CYS Chi-restraints excluded: chain I residue 1165 ILE Chi-restraints excluded: chain I residue 1203 THR Chi-restraints excluded: chain I residue 1204 VAL Chi-restraints excluded: chain I residue 1232 THR Chi-restraints excluded: chain I residue 1236 THR Chi-restraints excluded: chain I residue 1262 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 115 optimal weight: 9.9990 chunk 87 optimal weight: 10.0000 chunk 60 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 55 optimal weight: 0.0050 chunk 78 optimal weight: 10.0000 chunk 116 optimal weight: 1.9990 chunk 123 optimal weight: 6.9990 chunk 61 optimal weight: 0.7980 chunk 110 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 overall best weight: 1.5600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1217 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15791 Z= 0.183 Angle : 0.531 5.751 22769 Z= 0.313 Chirality : 0.034 0.129 2573 Planarity : 0.004 0.057 1730 Dihedral : 30.429 175.001 4811 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 1.32 % Allowed : 15.35 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.55 (0.25), residues: 969 helix: -0.78 (0.23), residues: 521 sheet: -3.40 (0.87), residues: 16 loop : -2.81 (0.25), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I1157 HIS 0.013 0.001 HIS F 18 PHE 0.013 0.001 PHE I1259 TYR 0.013 0.001 TYR I1073 ARG 0.010 0.000 ARG D 30 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 116 time to evaluate : 1.212 Fit side-chains REVERT: M 79 LYS cc_start: 0.8788 (tttt) cc_final: 0.8426 (tttm) REVERT: B 35 ARG cc_start: 0.8613 (mtp85) cc_final: 0.8276 (mtt-85) REVERT: D 110 GLU cc_start: 0.8985 (tp30) cc_final: 0.8651 (tp30) REVERT: E 123 ASP cc_start: 0.8985 (m-30) cc_final: 0.8615 (m-30) REVERT: G 75 LYS cc_start: 0.8883 (mttm) cc_final: 0.8668 (mttt) REVERT: H 65 ASP cc_start: 0.8760 (t70) cc_final: 0.8432 (t0) REVERT: I 1193 GLU cc_start: 0.5406 (OUTLIER) cc_final: 0.4704 (mm-30) REVERT: I 1222 MET cc_start: 0.7311 (mmm) cc_final: 0.6433 (mmm) outliers start: 11 outliers final: 8 residues processed: 125 average time/residue: 0.3715 time to fit residues: 64.5352 Evaluate side-chains 120 residues out of total 841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 111 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 119 LYS Chi-restraints excluded: chain H residue 39 TYR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain I residue 1077 LYS Chi-restraints excluded: chain I residue 1193 GLU Chi-restraints excluded: chain I residue 1204 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 103 optimal weight: 8.9990 chunk 70 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 92 optimal weight: 20.0000 chunk 51 optimal weight: 2.9990 chunk 105 optimal weight: 30.0000 chunk 85 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 63 optimal weight: 3.9990 chunk 111 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15791 Z= 0.219 Angle : 0.533 5.921 22769 Z= 0.313 Chirality : 0.034 0.134 2573 Planarity : 0.004 0.053 1730 Dihedral : 30.440 176.767 4811 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 2.40 % Allowed : 15.23 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.26 (0.26), residues: 969 helix: -0.58 (0.23), residues: 522 sheet: -3.11 (0.89), residues: 16 loop : -2.63 (0.26), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I1157 HIS 0.004 0.001 HIS F 18 PHE 0.014 0.001 PHE I1221 TYR 0.014 0.001 TYR I1218 ARG 0.009 0.000 ARG I1190 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 109 time to evaluate : 1.272 Fit side-chains REVERT: M 79 LYS cc_start: 0.8767 (tttt) cc_final: 0.8401 (tttm) REVERT: B 35 ARG cc_start: 0.8626 (mtp85) cc_final: 0.8282 (mtt-85) REVERT: D 110 GLU cc_start: 0.8983 (tp30) cc_final: 0.8666 (tp30) REVERT: E 123 ASP cc_start: 0.8981 (m-30) cc_final: 0.8607 (m-30) REVERT: G 75 LYS cc_start: 0.8878 (mttm) cc_final: 0.8661 (mttt) REVERT: H 65 ASP cc_start: 0.8792 (t70) cc_final: 0.8446 (t0) REVERT: I 1193 GLU cc_start: 0.5399 (OUTLIER) cc_final: 0.4610 (mm-30) REVERT: I 1222 MET cc_start: 0.7330 (mmm) cc_final: 0.6448 (mmm) outliers start: 20 outliers final: 16 residues processed: 127 average time/residue: 0.3503 time to fit residues: 61.0452 Evaluate side-chains 124 residues out of total 841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 107 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain H residue 39 TYR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain I residue 1077 LYS Chi-restraints excluded: chain I residue 1098 CYS Chi-restraints excluded: chain I residue 1165 ILE Chi-restraints excluded: chain I residue 1175 VAL Chi-restraints excluded: chain I residue 1193 GLU Chi-restraints excluded: chain I residue 1204 VAL Chi-restraints excluded: chain I residue 1262 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 41 optimal weight: 1.9990 chunk 111 optimal weight: 10.0000 chunk 24 optimal weight: 0.8980 chunk 72 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 chunk 123 optimal weight: 6.9990 chunk 102 optimal weight: 10.0000 chunk 57 optimal weight: 4.9990 chunk 10 optimal weight: 9.9990 chunk 40 optimal weight: 0.9990 chunk 65 optimal weight: 0.0470 overall best weight: 1.7884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 HIS ** I1172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15791 Z= 0.195 Angle : 0.524 5.885 22769 Z= 0.308 Chirality : 0.033 0.133 2573 Planarity : 0.004 0.053 1730 Dihedral : 30.385 177.030 4807 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 2.16 % Allowed : 16.31 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.26), residues: 969 helix: -0.35 (0.23), residues: 519 sheet: -2.98 (0.90), residues: 16 loop : -2.51 (0.26), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP I1157 HIS 0.003 0.001 HIS C 31 PHE 0.011 0.001 PHE I1283 TYR 0.015 0.001 TYR I1174 ARG 0.008 0.000 ARG D 30 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 108 time to evaluate : 1.230 Fit side-chains REVERT: M 79 LYS cc_start: 0.8766 (tttt) cc_final: 0.8408 (tttm) REVERT: B 35 ARG cc_start: 0.8622 (mtp85) cc_final: 0.8301 (mtt-85) REVERT: D 110 GLU cc_start: 0.8978 (tp30) cc_final: 0.8644 (tp30) REVERT: E 123 ASP cc_start: 0.8985 (m-30) cc_final: 0.8626 (m-30) REVERT: G 75 LYS cc_start: 0.8893 (mttm) cc_final: 0.8681 (mttt) REVERT: H 65 ASP cc_start: 0.8770 (t70) cc_final: 0.8435 (t0) REVERT: H 96 ARG cc_start: 0.8519 (mtm-85) cc_final: 0.7972 (mtm-85) REVERT: I 1193 GLU cc_start: 0.5299 (OUTLIER) cc_final: 0.4528 (mm-30) REVERT: I 1222 MET cc_start: 0.7361 (mmm) cc_final: 0.6382 (mmm) outliers start: 18 outliers final: 15 residues processed: 123 average time/residue: 0.3643 time to fit residues: 61.1802 Evaluate side-chains 121 residues out of total 841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 105 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 39 TYR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain I residue 1077 LYS Chi-restraints excluded: chain I residue 1098 CYS Chi-restraints excluded: chain I residue 1165 ILE Chi-restraints excluded: chain I residue 1188 ILE Chi-restraints excluded: chain I residue 1193 GLU Chi-restraints excluded: chain I residue 1204 VAL Chi-restraints excluded: chain I residue 1232 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 119 optimal weight: 9.9990 chunk 13 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 90 optimal weight: 40.0000 chunk 104 optimal weight: 10.0000 chunk 69 optimal weight: 0.8980 chunk 123 optimal weight: 10.0000 chunk 77 optimal weight: 10.0000 chunk 75 optimal weight: 20.0000 chunk 56 optimal weight: 3.9990 chunk 76 optimal weight: 20.0000 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 15791 Z= 0.389 Angle : 0.603 6.475 22769 Z= 0.346 Chirality : 0.038 0.141 2573 Planarity : 0.004 0.054 1730 Dihedral : 30.655 177.123 4807 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 3.24 % Allowed : 16.19 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.23 (0.25), residues: 969 helix: -0.57 (0.23), residues: 517 sheet: -3.05 (0.92), residues: 16 loop : -2.58 (0.27), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP I1235 HIS 0.005 0.001 HIS C 31 PHE 0.011 0.002 PHE I1283 TYR 0.017 0.002 TYR I1174 ARG 0.008 0.001 ARG E 129 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 111 time to evaluate : 1.224 Fit side-chains REVERT: M 79 LYS cc_start: 0.8791 (tttt) cc_final: 0.8386 (tttm) REVERT: B 35 ARG cc_start: 0.8681 (mtp85) cc_final: 0.8335 (mtt-85) REVERT: D 110 GLU cc_start: 0.9009 (tp30) cc_final: 0.8716 (tp30) REVERT: G 75 LYS cc_start: 0.8908 (mttm) cc_final: 0.8694 (mttt) REVERT: H 65 ASP cc_start: 0.8833 (t70) cc_final: 0.8532 (t0) REVERT: I 1193 GLU cc_start: 0.5256 (OUTLIER) cc_final: 0.4762 (mm-30) REVERT: I 1222 MET cc_start: 0.7403 (mmm) cc_final: 0.6507 (mmm) outliers start: 27 outliers final: 24 residues processed: 133 average time/residue: 0.3223 time to fit residues: 59.1738 Evaluate side-chains 133 residues out of total 841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 108 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 65 LEU Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 39 TYR Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain I residue 1077 LYS Chi-restraints excluded: chain I residue 1098 CYS Chi-restraints excluded: chain I residue 1165 ILE Chi-restraints excluded: chain I residue 1175 VAL Chi-restraints excluded: chain I residue 1193 GLU Chi-restraints excluded: chain I residue 1203 THR Chi-restraints excluded: chain I residue 1204 VAL Chi-restraints excluded: chain I residue 1232 THR Chi-restraints excluded: chain I residue 1262 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 49 optimal weight: 4.9990 chunk 73 optimal weight: 4.9990 chunk 37 optimal weight: 0.3980 chunk 24 optimal weight: 0.0770 chunk 23 optimal weight: 4.9990 chunk 78 optimal weight: 10.0000 chunk 84 optimal weight: 7.9990 chunk 60 optimal weight: 5.9990 chunk 11 optimal weight: 0.4980 chunk 96 optimal weight: 8.9990 chunk 112 optimal weight: 9.9990 overall best weight: 2.1942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15791 Z= 0.223 Angle : 0.539 6.543 22769 Z= 0.315 Chirality : 0.034 0.130 2573 Planarity : 0.004 0.051 1730 Dihedral : 30.456 177.227 4807 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 2.64 % Allowed : 17.39 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.26), residues: 969 helix: -0.28 (0.23), residues: 518 sheet: -2.86 (0.95), residues: 16 loop : -2.42 (0.27), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP I1157 HIS 0.003 0.001 HIS C 31 PHE 0.012 0.001 PHE I1221 TYR 0.014 0.001 TYR I1174 ARG 0.006 0.000 ARG E 129 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 109 time to evaluate : 1.138 Fit side-chains REVERT: M 79 LYS cc_start: 0.8786 (tttt) cc_final: 0.8404 (tttm) REVERT: B 35 ARG cc_start: 0.8614 (mtp85) cc_final: 0.8277 (mtt-85) REVERT: D 110 GLU cc_start: 0.9002 (tp30) cc_final: 0.8705 (tp30) REVERT: E 123 ASP cc_start: 0.8976 (m-30) cc_final: 0.8605 (m-30) REVERT: G 75 LYS cc_start: 0.8901 (mttm) cc_final: 0.8690 (mttt) REVERT: H 65 ASP cc_start: 0.8801 (t70) cc_final: 0.8483 (t0) REVERT: I 1094 GLU cc_start: 0.6908 (OUTLIER) cc_final: 0.6176 (tm-30) REVERT: I 1193 GLU cc_start: 0.5303 (OUTLIER) cc_final: 0.4804 (mm-30) REVERT: I 1222 MET cc_start: 0.7401 (mmm) cc_final: 0.6500 (mmm) outliers start: 22 outliers final: 20 residues processed: 127 average time/residue: 0.3387 time to fit residues: 58.8695 Evaluate side-chains 130 residues out of total 841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 108 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 65 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 28 LYS Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 39 TYR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain I residue 1077 LYS Chi-restraints excluded: chain I residue 1094 GLU Chi-restraints excluded: chain I residue 1098 CYS Chi-restraints excluded: chain I residue 1165 ILE Chi-restraints excluded: chain I residue 1175 VAL Chi-restraints excluded: chain I residue 1193 GLU Chi-restraints excluded: chain I residue 1204 VAL Chi-restraints excluded: chain I residue 1232 THR Chi-restraints excluded: chain I residue 1262 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 118 optimal weight: 7.9990 chunk 107 optimal weight: 9.9990 chunk 114 optimal weight: 20.0000 chunk 69 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 chunk 90 optimal weight: 40.0000 chunk 35 optimal weight: 0.8980 chunk 103 optimal weight: 10.0000 chunk 108 optimal weight: 3.9990 chunk 75 optimal weight: 20.0000 chunk 121 optimal weight: 0.9980 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15791 Z= 0.215 Angle : 0.534 7.427 22769 Z= 0.313 Chirality : 0.034 0.132 2573 Planarity : 0.004 0.051 1730 Dihedral : 30.433 177.478 4807 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 2.64 % Allowed : 17.27 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.26), residues: 969 helix: -0.16 (0.23), residues: 518 sheet: -2.69 (0.96), residues: 16 loop : -2.37 (0.27), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP I1157 HIS 0.004 0.001 HIS C 31 PHE 0.018 0.001 PHE I1283 TYR 0.017 0.001 TYR I1174 ARG 0.008 0.000 ARG H 30 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 110 time to evaluate : 1.184 Fit side-chains REVERT: M 79 LYS cc_start: 0.8777 (tttt) cc_final: 0.8403 (tttm) REVERT: B 35 ARG cc_start: 0.8608 (mtp85) cc_final: 0.8256 (mtt-85) REVERT: D 110 GLU cc_start: 0.9003 (tp30) cc_final: 0.8713 (tp30) REVERT: E 123 ASP cc_start: 0.8975 (m-30) cc_final: 0.8597 (m-30) REVERT: G 75 LYS cc_start: 0.8900 (mttm) cc_final: 0.8685 (mttt) REVERT: H 65 ASP cc_start: 0.8801 (t70) cc_final: 0.8482 (t0) REVERT: I 1094 GLU cc_start: 0.6868 (OUTLIER) cc_final: 0.6149 (tm-30) REVERT: I 1193 GLU cc_start: 0.5307 (OUTLIER) cc_final: 0.4816 (mm-30) REVERT: I 1222 MET cc_start: 0.7429 (mmm) cc_final: 0.6626 (mmm) outliers start: 22 outliers final: 18 residues processed: 128 average time/residue: 0.3545 time to fit residues: 62.0309 Evaluate side-chains 129 residues out of total 841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 109 time to evaluate : 1.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 65 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain D residue 28 LYS Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 39 TYR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain I residue 1077 LYS Chi-restraints excluded: chain I residue 1094 GLU Chi-restraints excluded: chain I residue 1098 CYS Chi-restraints excluded: chain I residue 1165 ILE Chi-restraints excluded: chain I residue 1175 VAL Chi-restraints excluded: chain I residue 1188 ILE Chi-restraints excluded: chain I residue 1193 GLU Chi-restraints excluded: chain I residue 1204 VAL Chi-restraints excluded: chain I residue 1232 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 74 optimal weight: 30.0000 chunk 57 optimal weight: 0.0970 chunk 84 optimal weight: 8.9990 chunk 127 optimal weight: 30.0000 chunk 117 optimal weight: 0.7980 chunk 101 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 chunk 78 optimal weight: 10.0000 chunk 62 optimal weight: 0.9980 chunk 80 optimal weight: 10.0000 chunk 108 optimal weight: 6.9990 overall best weight: 2.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15791 Z= 0.251 Angle : 0.547 7.442 22769 Z= 0.318 Chirality : 0.034 0.138 2573 Planarity : 0.004 0.051 1730 Dihedral : 30.427 177.833 4807 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 2.64 % Allowed : 17.27 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.26), residues: 969 helix: -0.14 (0.23), residues: 518 sheet: -2.73 (0.96), residues: 16 loop : -2.36 (0.27), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP I1157 HIS 0.004 0.001 HIS C 31 PHE 0.022 0.002 PHE I1221 TYR 0.016 0.001 TYR I1174 ARG 0.013 0.000 ARG D 30 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 108 time to evaluate : 1.152 Fit side-chains REVERT: M 79 LYS cc_start: 0.8777 (tttt) cc_final: 0.8400 (tttm) REVERT: B 35 ARG cc_start: 0.8616 (mtp85) cc_final: 0.8278 (mtt-85) REVERT: D 110 GLU cc_start: 0.9004 (tp30) cc_final: 0.8719 (tp30) REVERT: E 123 ASP cc_start: 0.8977 (m-30) cc_final: 0.8596 (m-30) REVERT: G 75 LYS cc_start: 0.8884 (mttm) cc_final: 0.8667 (mttt) REVERT: H 65 ASP cc_start: 0.8809 (t70) cc_final: 0.8486 (t0) REVERT: I 1094 GLU cc_start: 0.6898 (OUTLIER) cc_final: 0.6181 (tm-30) REVERT: I 1193 GLU cc_start: 0.5324 (OUTLIER) cc_final: 0.4834 (mm-30) REVERT: I 1222 MET cc_start: 0.7445 (mmm) cc_final: 0.6651 (mmm) outliers start: 22 outliers final: 20 residues processed: 126 average time/residue: 0.3386 time to fit residues: 58.5435 Evaluate side-chains 130 residues out of total 841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 108 time to evaluate : 1.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 65 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 39 TYR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain I residue 1077 LYS Chi-restraints excluded: chain I residue 1094 GLU Chi-restraints excluded: chain I residue 1098 CYS Chi-restraints excluded: chain I residue 1165 ILE Chi-restraints excluded: chain I residue 1175 VAL Chi-restraints excluded: chain I residue 1193 GLU Chi-restraints excluded: chain I residue 1204 VAL Chi-restraints excluded: chain I residue 1232 THR Chi-restraints excluded: chain I residue 1262 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 31 optimal weight: 2.9990 chunk 93 optimal weight: 10.0000 chunk 14 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 101 optimal weight: 10.0000 chunk 42 optimal weight: 4.9990 chunk 104 optimal weight: 10.0000 chunk 12 optimal weight: 5.9990 chunk 18 optimal weight: 10.0000 chunk 89 optimal weight: 20.0000 chunk 5 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.149061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.094486 restraints weight = 27710.224| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 1.97 r_work: 0.2882 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2878 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2878 r_free = 0.2878 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.93 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2878 r_free = 0.2878 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.91 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2878 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 15791 Z= 0.338 Angle : 0.586 7.734 22769 Z= 0.336 Chirality : 0.037 0.137 2573 Planarity : 0.004 0.053 1730 Dihedral : 30.525 178.043 4807 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 3.12 % Allowed : 16.79 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.26), residues: 969 helix: -0.29 (0.23), residues: 518 sheet: -2.88 (0.95), residues: 16 loop : -2.43 (0.28), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP I1235 HIS 0.004 0.001 HIS C 31 PHE 0.017 0.002 PHE I1283 TYR 0.016 0.002 TYR I1174 ARG 0.008 0.001 ARG E 129 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2594.83 seconds wall clock time: 47 minutes 51.05 seconds (2871.05 seconds total)