Starting phenix.real_space_refine on Sun Nov 19 02:31:45 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c8y_16495/11_2023/8c8y_16495.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c8y_16495/11_2023/8c8y_16495.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c8y_16495/11_2023/8c8y_16495.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c8y_16495/11_2023/8c8y_16495.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c8y_16495/11_2023/8c8y_16495.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c8y_16495/11_2023/8c8y_16495.pdb" } resolution = 3.03 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= 0.008 sd= 0.148 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2667 5.49 5 S 59 5.16 5 C 38106 2.51 5 N 14416 2.21 5 O 22068 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "O PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 77316 Number of models: 1 Model: "" Number of chains: 25 Chain: "V" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 753 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "A" Number of atoms: 54738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2548, 54738 Classifications: {'RNA': 2548} Modifications used: {'rna2p_pur': 250, 'rna2p_pyr': 137, 'rna3p_pur': 1233, 'rna3p_pyr': 928} Link IDs: {'rna2p': 387, 'rna3p': 2160} Chain breaks: 7 Chain: "C" Number of atoms: 1894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1894 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 13, 'TRANS': 232} Chain breaks: 1 Chain: "D" Number of atoms: 1379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1379 Classifications: {'peptide': 184} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 179} Chain breaks: 1 Chain: "E" Number of atoms: 1481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1481 Classifications: {'peptide': 192} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 186} Chain breaks: 1 Chain: "J" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1129 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "K" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 938 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "L" Number of atoms: 844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 844 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 113} Chain breaks: 1 Chain: "N" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 960 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "P" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 917 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "Q" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "R" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "S" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 857 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "T" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 738 Classifications: {'peptide': 93} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 90} Chain: "U" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 779 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "X" Number of atoms: 609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 609 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain breaks: 1 Chain: "Y" Number of atoms: 499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 499 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "0" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 444 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "2" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 377 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "O" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 892 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "F" Number of atoms: 1410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1410 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "B" Number of atoms: 2549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 2549 Classifications: {'RNA': 119} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 6, 'rna3p_pur': 57, 'rna3p_pyr': 49} Link IDs: {'rna2p': 13, 'rna3p': 105} Chain: "Z" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 449 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "H" Number of atoms: 384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 384 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "W" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 533 Classifications: {'peptide': 71} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 69} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU%COO:plan': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 30.74, per 1000 atoms: 0.40 Number of scatterers: 77316 At special positions: 0 Unit cell: (191.25, 233.75, 218.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 59 16.00 P 2667 15.00 O 22068 8.00 N 14416 7.00 C 38106 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: 35.22 Conformation dependent library (CDL) restraints added in 3.1 seconds 5018 Ramachandran restraints generated. 2509 Oldfield, 0 Emsley, 2509 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4702 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 37 sheets defined 30.8% alpha, 19.2% beta 891 base pairs and 1351 stacking pairs defined. Time for finding SS restraints: 28.43 Creating SS restraints... Processing helix chain 'V' and resid 13 through 23 Processing helix chain 'V' and resid 44 through 52 removed outlier: 3.750A pdb=" N ALA V 52 " --> pdb=" O MET V 48 " (cutoff:3.500A) Processing helix chain 'V' and resid 55 through 59 removed outlier: 3.686A pdb=" N GLU V 59 " --> pdb=" O PHE V 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 31 No H-bonds generated for 'chain 'C' and resid 29 through 31' Processing helix chain 'C' and resid 132 through 134 No H-bonds generated for 'chain 'C' and resid 132 through 134' Processing helix chain 'C' and resid 206 through 214 removed outlier: 4.142A pdb=" N ALA C 210 " --> pdb=" O LYS C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 264 No H-bonds generated for 'chain 'C' and resid 262 through 264' Processing helix chain 'D' and resid 56 through 60 removed outlier: 3.689A pdb=" N VAL D 60 " --> pdb=" O ALA D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 72 Processing helix chain 'D' and resid 97 through 101 removed outlier: 3.513A pdb=" N LEU D 100 " --> pdb=" O SER D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 125 Processing helix chain 'E' and resid 15 through 20 Processing helix chain 'E' and resid 24 through 40 Processing helix chain 'E' and resid 97 through 115 Processing helix chain 'E' and resid 130 through 142 Processing helix chain 'E' and resid 154 through 160 removed outlier: 3.766A pdb=" N ALA E 160 " --> pdb=" O ASN E 156 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 183 Processing helix chain 'E' and resid 190 through 201 removed outlier: 3.591A pdb=" N LYS E 194 " --> pdb=" O ALA E 190 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 38 Processing helix chain 'J' and resid 58 through 62 Processing helix chain 'J' and resid 67 through 72 Processing helix chain 'J' and resid 89 through 96 Processing helix chain 'J' and resid 96 through 109 removed outlier: 4.322A pdb=" N VAL J 100 " --> pdb=" O ARG J 96 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ILE J 101 " --> pdb=" O PRO J 97 " (cutoff:3.500A) Processing helix chain 'J' and resid 112 through 121 removed outlier: 3.770A pdb=" N LYS J 121 " --> pdb=" O ALA J 117 " (cutoff:3.500A) Processing helix chain 'J' and resid 132 through 136 removed outlier: 3.789A pdb=" N GLN J 135 " --> pdb=" O HIS J 132 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLN J 136 " --> pdb=" O ALA J 133 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 132 through 136' Processing helix chain 'K' and resid 109 through 111 No H-bonds generated for 'chain 'K' and resid 109 through 111' Processing helix chain 'K' and resid 112 through 118 Processing helix chain 'L' and resid 69 through 74 removed outlier: 3.811A pdb=" N ILE L 73 " --> pdb=" O ARG L 69 " (cutoff:3.500A) Processing helix chain 'L' and resid 128 through 137 Processing helix chain 'N' and resid 13 through 32 Processing helix chain 'N' and resid 38 through 56 removed outlier: 3.614A pdb=" N ARG N 45 " --> pdb=" O ALA N 41 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ARG N 46 " --> pdb=" O LYS N 42 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N VAL N 47 " --> pdb=" O GLU N 43 " (cutoff:3.500A) Proline residue: N 50 - end of helix Processing helix chain 'N' and resid 59 through 69 Processing helix chain 'N' and resid 72 through 79 removed outlier: 3.743A pdb=" N VAL N 76 " --> pdb=" O ASP N 72 " (cutoff:3.500A) Processing helix chain 'N' and resid 82 through 87 Processing helix chain 'P' and resid 2 through 10 Processing helix chain 'P' and resid 52 through 55 Processing helix chain 'P' and resid 103 through 108 removed outlier: 3.840A pdb=" N ARG P 108 " --> pdb=" O GLY P 104 " (cutoff:3.500A) Processing helix chain 'Q' and resid 5 through 19 removed outlier: 3.858A pdb=" N GLN Q 19 " --> pdb=" O LYS Q 15 " (cutoff:3.500A) Processing helix chain 'Q' and resid 25 through 30 Processing helix chain 'Q' and resid 30 through 72 removed outlier: 4.195A pdb=" N ARG Q 50 " --> pdb=" O TYR Q 46 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N LYS Q 53 " --> pdb=" O ARG Q 49 " (cutoff:3.500A) Processing helix chain 'Q' and resid 74 through 85 Processing helix chain 'Q' and resid 90 through 101 Processing helix chain 'Q' and resid 101 through 117 Processing helix chain 'S' and resid 13 through 22 removed outlier: 3.745A pdb=" N LEU S 19 " --> pdb=" O GLN S 15 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N VAL S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 38 Processing helix chain 'S' and resid 41 through 61 Processing helix chain 'S' and resid 89 through 91 No H-bonds generated for 'chain 'S' and resid 89 through 91' Processing helix chain 'T' and resid 3 through 10 removed outlier: 3.758A pdb=" N VAL T 10 " --> pdb=" O ARG T 6 " (cutoff:3.500A) Processing helix chain 'T' and resid 17 through 27 removed outlier: 3.539A pdb=" N GLU T 25 " --> pdb=" O SER T 21 " (cutoff:3.500A) Processing helix chain 'T' and resid 39 through 51 Processing helix chain 'X' and resid 52 through 62 Processing helix chain 'X' and resid 62 through 73 Processing helix chain 'Y' and resid 9 through 34 removed outlier: 4.187A pdb=" N GLN Y 25 " --> pdb=" O LEU Y 21 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N PHE Y 26 " --> pdb=" O LEU Y 22 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER Y 34 " --> pdb=" O MET Y 30 " (cutoff:3.500A) Processing helix chain 'Y' and resid 40 through 45 removed outlier: 4.114A pdb=" N LYS Y 44 " --> pdb=" O SER Y 40 " (cutoff:3.500A) Processing helix chain 'Y' and resid 46 through 56 removed outlier: 3.942A pdb=" N ALA Y 51 " --> pdb=" O ARG Y 47 " (cutoff:3.500A) Processing helix chain '0' and resid 8 through 17 Processing helix chain '0' and resid 18 through 20 No H-bonds generated for 'chain '0' and resid 18 through 20' Processing helix chain '2' and resid 8 through 17 Processing helix chain '2' and resid 17 through 23 Processing helix chain '2' and resid 24 through 38 Processing helix chain 'O' and resid 3 through 22 removed outlier: 3.924A pdb=" N ARG O 13 " --> pdb=" O ARG O 9 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ALA O 14 " --> pdb=" O ARG O 10 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLN O 19 " --> pdb=" O ARG O 15 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU O 20 " --> pdb=" O ARG O 16 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N LEU O 21 " --> pdb=" O LYS O 17 " (cutoff:3.500A) Processing helix chain 'O' and resid 55 through 60 removed outlier: 3.605A pdb=" N ALA O 59 " --> pdb=" O GLU O 55 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLU O 60 " --> pdb=" O LYS O 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 55 through 60' Processing helix chain 'O' and resid 67 through 86 Processing helix chain 'O' and resid 101 through 113 removed outlier: 3.726A pdb=" N ALA O 113 " --> pdb=" O ALA O 109 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 20 removed outlier: 4.369A pdb=" N VAL F 12 " --> pdb=" O LYS F 8 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N LYS F 13 " --> pdb=" O ASP F 9 " (cutoff:3.500A) Processing helix chain 'F' and resid 23 through 27 removed outlier: 4.409A pdb=" N VAL F 27 " --> pdb=" O VAL F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 60 removed outlier: 4.184A pdb=" N LEU F 49 " --> pdb=" O ASP F 45 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 106 Processing helix chain 'F' and resid 133 through 137 Processing helix chain 'F' and resid 141 through 145 removed outlier: 3.528A pdb=" N VAL F 145 " --> pdb=" O TYR F 142 " (cutoff:3.500A) Processing helix chain 'F' and resid 161 through 172 removed outlier: 3.889A pdb=" N GLY F 165 " --> pdb=" O SER F 161 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N PHE F 172 " --> pdb=" O LEU F 168 " (cutoff:3.500A) Processing helix chain 'Z' and resid 16 through 27 Processing helix chain 'Z' and resid 40 through 50 removed outlier: 3.649A pdb=" N VAL Z 50 " --> pdb=" O MET Z 46 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 27 Processing helix chain 'H' and resid 42 through 50 Processing sheet with id=AA1, first strand: chain 'V' and resid 7 through 8 removed outlier: 6.942A pdb=" N GLN V 87 " --> pdb=" O LYS V 25 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ILE V 89 " --> pdb=" O PRO V 27 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N LEU V 86 " --> pdb=" O ARG V 79 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N ARG V 79 " --> pdb=" O LEU V 86 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N HIS V 88 " --> pdb=" O VAL V 77 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N VAL V 77 " --> pdb=" O HIS V 88 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ASP V 90 " --> pdb=" O GLN V 75 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 2 through 4 Processing sheet with id=AA3, first strand: chain 'C' and resid 33 through 34 removed outlier: 3.523A pdb=" N GLU C 34 " --> pdb=" O TYR C 61 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TYR C 61 " --> pdb=" O GLU C 34 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 104 removed outlier: 6.920A pdb=" N ILE C 90 " --> pdb=" O LEU C 80 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N LEU C 80 " --> pdb=" O ILE C 90 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N LEU C 92 " --> pdb=" O GLU C 78 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 128 through 130 removed outlier: 6.679A pdb=" N THR C 172 " --> pdb=" O VAL C 164 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N MET C 180 " --> pdb=" O VAL C 267 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 143 through 144 removed outlier: 6.411A pdb=" N VAL C 143 " --> pdb=" O GLN C 152 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 169 through 175 removed outlier: 6.014A pdb=" N VAL D 107 " --> pdb=" O SER D 174 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N THR D 112 " --> pdb=" O ASP D 200 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N ASP D 200 " --> pdb=" O THR D 112 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N LYS D 8 " --> pdb=" O GLU D 28 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N GLU D 28 " --> pdb=" O LYS D 8 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLY D 10 " --> pdb=" O VAL D 26 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N LEU D 186 " --> pdb=" O VAL D 180 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N VAL D 180 " --> pdb=" O LEU D 186 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LEU D 188 " --> pdb=" O VAL D 178 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 78 through 83 removed outlier: 4.201A pdb=" N GLY D 78 " --> pdb=" O THR D 52 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N THR D 52 " --> pdb=" O GLY D 78 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN D 36 " --> pdb=" O GLN D 49 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N THR D 51 " --> pdb=" O VAL D 34 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N VAL D 34 " --> pdb=" O THR D 51 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 115 through 119 removed outlier: 3.548A pdb=" N GLY D 117 " --> pdb=" O MET D 165 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 2 through 3 removed outlier: 3.567A pdb=" N LEU E 3 " --> pdb=" O LEU E 12 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU E 12 " --> pdb=" O LEU E 3 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'E' and resid 118 through 121 Processing sheet with id=AB3, first strand: chain 'J' and resid 122 through 124 removed outlier: 6.775A pdb=" N TRP J 15 " --> pdb=" O GLN J 138 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'J' and resid 73 through 77 Processing sheet with id=AB5, first strand: chain 'K' and resid 7 through 10 removed outlier: 6.052A pdb=" N ARG K 18 " --> pdb=" O LYS K 44 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N LYS K 40 " --> pdb=" O ILE K 22 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N VAL K 24 " --> pdb=" O ILE K 38 " (cutoff:3.500A) removed outlier: 8.228A pdb=" N ILE K 38 " --> pdb=" O VAL K 24 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ALA K 83 " --> pdb=" O VAL K 63 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N CYS K 84 " --> pdb=" O MET K 7 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N ASN K 9 " --> pdb=" O CYS K 84 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N LEU K 86 " --> pdb=" O ASN K 9 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'K' and resid 69 through 70 removed outlier: 3.980A pdb=" N VAL K 76 " --> pdb=" O VAL P 72 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL P 72 " --> pdb=" O VAL K 76 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ALA P 48 " --> pdb=" O THR P 59 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ARG P 61 " --> pdb=" O VAL P 46 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N VAL P 46 " --> pdb=" O ARG P 61 " (cutoff:3.500A) removed outlier: 8.379A pdb=" N ILE P 63 " --> pdb=" O GLY P 44 " (cutoff:3.500A) removed outlier: 8.439A pdb=" N GLY P 44 " --> pdb=" O ILE P 63 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG P 87 " --> pdb=" O THR P 24 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N GLU P 26 " --> pdb=" O VAL P 85 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N VAL P 85 " --> pdb=" O GLU P 26 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N LYS P 28 " --> pdb=" O ILE P 83 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N ILE P 83 " --> pdb=" O LYS P 28 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N TRP P 30 " --> pdb=" O ASP P 81 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ASP P 81 " --> pdb=" O TRP P 30 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 121 through 122 removed outlier: 3.623A pdb=" N VAL L 122 " --> pdb=" O LYS L 141 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'N' and resid 33 through 37 removed outlier: 5.322A pdb=" N MET N 110 " --> pdb=" O CYS N 100 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'R' and resid 11 through 15 removed outlier: 3.824A pdb=" N TYR R 2 " --> pdb=" O ALA R 42 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA R 42 " --> pdb=" O TYR R 2 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL R 4 " --> pdb=" O MET R 40 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N MET R 40 " --> pdb=" O VAL R 4 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'R' and resid 19 through 23 removed outlier: 6.656A pdb=" N TRP R 92 " --> pdb=" O ARG R 68 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ARG R 68 " --> pdb=" O TRP R 92 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N THR R 94 " --> pdb=" O HIS R 66 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N HIS R 66 " --> pdb=" O THR R 94 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N VAL R 96 " --> pdb=" O VAL R 64 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N VAL R 64 " --> pdb=" O VAL R 96 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N ILE R 98 " --> pdb=" O GLU R 62 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N GLU R 62 " --> pdb=" O ILE R 98 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL R 58 " --> pdb=" O SER R 102 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'R' and resid 72 through 78 removed outlier: 4.325A pdb=" N TYR R 83 " --> pdb=" O ARG R 78 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'S' and resid 3 through 10 removed outlier: 5.432A pdb=" N ILE S 4 " --> pdb=" O VAL S 107 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N VAL S 107 " --> pdb=" O ILE S 4 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N LYS S 6 " --> pdb=" O VAL S 105 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N VAL S 105 " --> pdb=" O LYS S 6 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N ARG S 8 " --> pdb=" O ILE S 103 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ILE S 103 " --> pdb=" O ARG S 8 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'S' and resid 82 through 87 Processing sheet with id=AC5, first strand: chain 'T' and resid 11 through 14 removed outlier: 4.116A pdb=" N LYS T 81 " --> pdb=" O VAL T 34 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'U' and resid 21 through 22 removed outlier: 3.928A pdb=" N ILE U 71 " --> pdb=" O ASP U 80 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'U' and resid 24 through 27 removed outlier: 6.733A pdb=" N ILE U 34 " --> pdb=" O LYS U 25 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N VAL U 27 " --> pdb=" O LYS U 32 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LYS U 32 " --> pdb=" O VAL U 27 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'U' and resid 40 through 44 Processing sheet with id=AC9, first strand: chain 'U' and resid 82 through 85 removed outlier: 3.678A pdb=" N ARG U 85 " --> pdb=" O VAL U 92 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N VAL U 92 " --> pdb=" O ARG U 85 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'X' and resid 12 through 15 removed outlier: 3.587A pdb=" N VAL X 12 " --> pdb=" O PHE X 28 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'X' and resid 32 through 39 removed outlier: 3.819A pdb=" N VAL X 39 " --> pdb=" O ARG X 44 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG X 44 " --> pdb=" O VAL X 39 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain '0' and resid 28 through 29 Processing sheet with id=AD4, first strand: chain '0' and resid 47 through 48 Processing sheet with id=AD5, first strand: chain 'O' and resid 47 through 52 removed outlier: 3.857A pdb=" N VAL O 49 " --> pdb=" O VAL O 39 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 65 through 67 removed outlier: 3.668A pdb=" N LEU F 65 " --> pdb=" O LYS F 87 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LYS F 87 " --> pdb=" O LEU F 65 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N GLY F 85 " --> pdb=" O THR F 67 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU F 90 " --> pdb=" O ILE F 33 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N THR F 34 " --> pdb=" O THR F 154 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N THR F 154 " --> pdb=" O THR F 34 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR F 127 " --> pdb=" O ILE F 155 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'Z' and resid 34 through 38 removed outlier: 4.191A pdb=" N LYS Z 5 " --> pdb=" O GLU Z 57 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 4 through 5 Processing sheet with id=AD9, first strand: chain 'W' and resid 26 through 27 Processing sheet with id=AE1, first strand: chain 'W' and resid 32 through 35 removed outlier: 3.821A pdb=" N VAL W 34 " --> pdb=" O LEU W 55 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU W 55 " --> pdb=" O VAL W 34 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 722 hydrogen bonds defined for protein. 2052 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2261 hydrogen bonds 3590 hydrogen bond angles 0 basepair planarities 891 basepair parallelities 1351 stacking parallelities Total time for adding SS restraints: 107.62 Time building geometry restraints manager: 37.86 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: 11612 1.33 - 1.45: 35403 1.45 - 1.57: 31988 1.57 - 1.69: 5326 1.69 - 1.81: 110 Bond restraints: 84439 Sorted by residual: bond pdb=" CG PRO F 83 " pdb=" CD PRO F 83 " ideal model delta sigma weight residual 1.503 1.370 0.133 3.40e-02 8.65e+02 1.53e+01 bond pdb=" CB PRO F 83 " pdb=" CG PRO F 83 " ideal model delta sigma weight residual 1.492 1.619 -0.127 5.00e-02 4.00e+02 6.44e+00 bond pdb=" N MET V 1 " pdb=" CA MET V 1 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.12e+00 bond pdb=" N MET D 1 " pdb=" CA MET D 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.06e+00 bond pdb=" N MET H 1 " pdb=" CA MET H 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.03e+00 ... (remaining 84434 not shown) Histogram of bond angle deviations from ideal: 90.64 - 99.34: 3 99.34 - 108.04: 24473 108.04 - 116.74: 52648 116.74 - 125.44: 39902 125.44 - 134.14: 10217 Bond angle restraints: 127243 Sorted by residual: angle pdb=" N PRO F 83 " pdb=" CD PRO F 83 " pdb=" CG PRO F 83 " ideal model delta sigma weight residual 103.20 90.64 12.56 1.50e+00 4.44e-01 7.01e+01 angle pdb=" CA PRO F 83 " pdb=" N PRO F 83 " pdb=" CD PRO F 83 " ideal model delta sigma weight residual 112.00 102.83 9.17 1.40e+00 5.10e-01 4.29e+01 angle pdb=" CA PRO F 83 " pdb=" CB PRO F 83 " pdb=" CG PRO F 83 " ideal model delta sigma weight residual 104.50 96.77 7.73 1.90e+00 2.77e-01 1.65e+01 angle pdb=" C ILE T 2 " pdb=" N ARG T 3 " pdb=" CA ARG T 3 " ideal model delta sigma weight residual 121.70 128.27 -6.57 1.80e+00 3.09e-01 1.33e+01 angle pdb=" C LEU T 87 " pdb=" N LYS T 88 " pdb=" CA LYS T 88 " ideal model delta sigma weight residual 123.91 128.73 -4.82 1.66e+00 3.63e-01 8.43e+00 ... (remaining 127238 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.46: 43121 35.46 - 70.93: 1260 70.93 - 106.39: 134 106.39 - 141.85: 17 141.85 - 177.32: 11 Dihedral angle restraints: 44543 sinusoidal: 37258 harmonic: 7285 Sorted by residual: dihedral pdb=" O4' U A2884 " pdb=" C1' U A2884 " pdb=" N1 U A2884 " pdb=" C2 U A2884 " ideal model delta sinusoidal sigma weight residual 200.00 34.51 165.49 1 1.50e+01 4.44e-03 8.40e+01 dihedral pdb=" O4' U A1584 " pdb=" C1' U A1584 " pdb=" N1 U A1584 " pdb=" C2 U A1584 " ideal model delta sinusoidal sigma weight residual 200.00 41.26 158.74 1 1.50e+01 4.44e-03 8.24e+01 dihedral pdb=" O4' U A1340 " pdb=" C1' U A1340 " pdb=" N1 U A1340 " pdb=" C2 U A1340 " ideal model delta sinusoidal sigma weight residual -128.00 49.32 -177.32 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 44540 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 14190 0.036 - 0.072: 1766 0.072 - 0.108: 314 0.108 - 0.144: 124 0.144 - 0.180: 4 Chirality restraints: 16398 Sorted by residual: chirality pdb=" C1' U A1736 " pdb=" O4' U A1736 " pdb=" C2' U A1736 " pdb=" N1 U A1736 " both_signs ideal model delta sigma weight residual False 2.47 2.29 0.18 2.00e-01 2.50e+01 8.11e-01 chirality pdb=" C1' A A 983 " pdb=" O4' A A 983 " pdb=" C2' A A 983 " pdb=" N9 A A 983 " both_signs ideal model delta sigma weight residual False 2.46 2.29 0.16 2.00e-01 2.50e+01 6.80e-01 chirality pdb=" C3' A A1378 " pdb=" C4' A A1378 " pdb=" O3' A A1378 " pdb=" C2' A A1378 " both_signs ideal model delta sigma weight residual False -2.74 -2.58 -0.16 2.00e-01 2.50e+01 6.60e-01 ... (remaining 16395 not shown) Planarity restraints: 6163 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A A1927 " 0.033 2.00e-02 2.50e+03 1.62e-02 7.22e+00 pdb=" N9 A A1927 " -0.040 2.00e-02 2.50e+03 pdb=" C8 A A1927 " -0.001 2.00e-02 2.50e+03 pdb=" N7 A A1927 " 0.004 2.00e-02 2.50e+03 pdb=" C5 A A1927 " 0.005 2.00e-02 2.50e+03 pdb=" C6 A A1927 " 0.005 2.00e-02 2.50e+03 pdb=" N6 A A1927 " 0.003 2.00e-02 2.50e+03 pdb=" N1 A A1927 " 0.004 2.00e-02 2.50e+03 pdb=" C2 A A1927 " -0.001 2.00e-02 2.50e+03 pdb=" N3 A A1927 " -0.006 2.00e-02 2.50e+03 pdb=" C4 A A1927 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C A2385 " 0.008 2.00e-02 2.50e+03 1.69e-02 6.40e+00 pdb=" N1 C A2385 " -0.001 2.00e-02 2.50e+03 pdb=" C2 C A2385 " -0.043 2.00e-02 2.50e+03 pdb=" O2 C A2385 " 0.021 2.00e-02 2.50e+03 pdb=" N3 C A2385 " 0.006 2.00e-02 2.50e+03 pdb=" C4 C A2385 " -0.008 2.00e-02 2.50e+03 pdb=" N4 C A2385 " 0.011 2.00e-02 2.50e+03 pdb=" C5 C A2385 " 0.002 2.00e-02 2.50e+03 pdb=" C6 C A2385 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A A 983 " -0.030 2.00e-02 2.50e+03 1.37e-02 5.13e+00 pdb=" N9 A A 983 " 0.032 2.00e-02 2.50e+03 pdb=" C8 A A 983 " 0.002 2.00e-02 2.50e+03 pdb=" N7 A A 983 " -0.002 2.00e-02 2.50e+03 pdb=" C5 A A 983 " -0.001 2.00e-02 2.50e+03 pdb=" C6 A A 983 " -0.005 2.00e-02 2.50e+03 pdb=" N6 A A 983 " -0.005 2.00e-02 2.50e+03 pdb=" N1 A A 983 " -0.005 2.00e-02 2.50e+03 pdb=" C2 A A 983 " 0.004 2.00e-02 2.50e+03 pdb=" N3 A A 983 " 0.005 2.00e-02 2.50e+03 pdb=" C4 A A 983 " 0.005 2.00e-02 2.50e+03 ... (remaining 6160 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.42: 333 2.42 - 3.04: 43223 3.04 - 3.66: 140475 3.66 - 4.28: 217222 4.28 - 4.90: 299552 Nonbonded interactions: 700805 Sorted by model distance: nonbonded pdb=" O2' C A2338 " pdb=" OP1 C A2339 " model vdw 1.796 2.440 nonbonded pdb=" O2' A A1927 " pdb=" O5' A A1928 " model vdw 1.852 2.440 nonbonded pdb=" O2' G A2330 " pdb=" O4' G A2331 " model vdw 1.882 2.440 nonbonded pdb=" O2' G B 51 " pdb=" O4' A B 52 " model vdw 1.893 2.440 nonbonded pdb=" O2' G A2115 " pdb=" OP1 G A2116 " model vdw 1.893 2.440 ... (remaining 700800 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.550 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: 0.060 Extract box with map and model: 9.190 Check model and map are aligned: 0.840 Set scattering table: 0.590 Process input model: 258.270 Find NCS groups from input model: 1.250 Set up NCS constraints: 0.170 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: 0.020 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 274.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 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 : 0.002 0.133 84439 Z= 0.102 Angle : 0.397 12.556 127243 Z= 0.213 Chirality : 0.027 0.180 16398 Planarity : 0.003 0.071 6163 Dihedral : 13.659 177.318 39841 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.22 % Favored : 93.70 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % 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: 0.29 (0.17), residues: 2509 helix: 1.79 (0.21), residues: 706 sheet: 0.15 (0.22), residues: 551 loop : -0.71 (0.17), residues: 1252 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5018 Ramachandran restraints generated. 2509 Oldfield, 0 Emsley, 2509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5018 Ramachandran restraints generated. 2509 Oldfield, 0 Emsley, 2509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 412 time to evaluate : 3.184 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 412 average time/residue: 0.8172 time to fit residues: 573.7342 Evaluate side-chains 310 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 310 time to evaluate : 3.079 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 513 random chunks: chunk 433 optimal weight: 10.0000 chunk 388 optimal weight: 6.9990 chunk 215 optimal weight: 40.0000 chunk 132 optimal weight: 10.0000 chunk 262 optimal weight: 10.0000 chunk 207 optimal weight: 50.0000 chunk 402 optimal weight: 6.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 10.0000 chunk 299 optimal weight: 10.0000 chunk 465 optimal weight: 40.0000 overall best weight: 8.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 ASN D 49 GLN K 3 GLN ** K 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 74 GLN Q 70 GLN R 18 GLN R 86 GLN S 40 ASN ** U 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 4 GLN O 38 GLN Z 19 HIS ** H 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.079 84439 Z= 0.479 Angle : 0.724 10.750 127243 Z= 0.362 Chirality : 0.042 0.320 16398 Planarity : 0.006 0.096 6163 Dihedral : 14.393 178.535 34817 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.37 % Favored : 92.51 % Rotamer: Outliers : 2.64 % Allowed : 9.16 % Favored : 88.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.66 (0.16), residues: 2509 helix: 0.51 (0.19), residues: 708 sheet: -0.28 (0.22), residues: 516 loop : -1.00 (0.16), residues: 1285 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5018 Ramachandran restraints generated. 2509 Oldfield, 0 Emsley, 2509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5018 Ramachandran restraints generated. 2509 Oldfield, 0 Emsley, 2509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 310 time to evaluate : 3.198 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 55 outliers final: 38 residues processed: 342 average time/residue: 0.7477 time to fit residues: 440.3819 Evaluate side-chains 322 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 284 time to evaluate : 3.077 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 0 residues processed: 38 average time/residue: 0.6074 time to fit residues: 48.5555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 513 random chunks: chunk 258 optimal weight: 8.9990 chunk 144 optimal weight: 10.0000 chunk 387 optimal weight: 0.7980 chunk 317 optimal weight: 0.8980 chunk 128 optimal weight: 6.9990 chunk 466 optimal weight: 5.9990 chunk 504 optimal weight: 8.9990 chunk 415 optimal weight: 5.9990 chunk 462 optimal weight: 8.9990 chunk 159 optimal weight: 5.9990 chunk 374 optimal weight: 0.2980 overall best weight: 2.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 GLN K 3 GLN ** K 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 70 HIS ** U 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 28 ASN ** H 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 72 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 84439 Z= 0.180 Angle : 0.505 10.400 127243 Z= 0.260 Chirality : 0.031 0.248 16398 Planarity : 0.004 0.041 6163 Dihedral : 14.096 179.007 34817 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.38 % Favored : 93.54 % Rotamer: Outliers : 1.58 % Allowed : 11.98 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.51 (0.16), residues: 2509 helix: 0.65 (0.20), residues: 713 sheet: -0.26 (0.22), residues: 514 loop : -0.91 (0.17), residues: 1282 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5018 Ramachandran restraints generated. 2509 Oldfield, 0 Emsley, 2509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5018 Ramachandran restraints generated. 2509 Oldfield, 0 Emsley, 2509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 311 time to evaluate : 3.156 Fit side-chains revert: symmetry clash outliers start: 33 outliers final: 17 residues processed: 339 average time/residue: 0.7447 time to fit residues: 435.3002 Evaluate side-chains 311 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 294 time to evaluate : 3.118 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.5760 time to fit residues: 21.7310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 513 random chunks: chunk 461 optimal weight: 30.0000 chunk 350 optimal weight: 6.9990 chunk 242 optimal weight: 10.0000 chunk 51 optimal weight: 10.0000 chunk 222 optimal weight: 30.0000 chunk 313 optimal weight: 7.9990 chunk 468 optimal weight: 30.0000 chunk 495 optimal weight: 40.0000 chunk 244 optimal weight: 10.0000 chunk 443 optimal weight: 8.9990 chunk 133 optimal weight: 10.0000 overall best weight: 8.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 128 ASN ** K 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 72 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.3028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.065 84439 Z= 0.503 Angle : 0.754 11.650 127243 Z= 0.377 Chirality : 0.044 0.328 16398 Planarity : 0.006 0.068 6163 Dihedral : 14.740 177.704 34817 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.97 % Favored : 91.95 % Rotamer: Outliers : 2.64 % Allowed : 14.62 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -1.21 (0.16), residues: 2509 helix: 0.05 (0.19), residues: 711 sheet: -0.64 (0.22), residues: 532 loop : -1.33 (0.16), residues: 1266 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5018 Ramachandran restraints generated. 2509 Oldfield, 0 Emsley, 2509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5018 Ramachandran restraints generated. 2509 Oldfield, 0 Emsley, 2509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 312 time to evaluate : 3.231 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 55 outliers final: 35 residues processed: 342 average time/residue: 0.7512 time to fit residues: 442.7257 Evaluate side-chains 334 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 299 time to evaluate : 3.114 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 0.6191 time to fit residues: 43.3328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 513 random chunks: chunk 412 optimal weight: 3.9990 chunk 281 optimal weight: 0.9990 chunk 7 optimal weight: 20.0000 chunk 369 optimal weight: 1.9990 chunk 204 optimal weight: 50.0000 chunk 423 optimal weight: 5.9990 chunk 342 optimal weight: 4.9990 chunk 0 optimal weight: 50.0000 chunk 253 optimal weight: 20.0000 chunk 445 optimal weight: 0.9990 chunk 125 optimal weight: 0.7980 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 13 ASN ** R 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 84439 Z= 0.139 Angle : 0.512 10.074 127243 Z= 0.265 Chirality : 0.031 0.228 16398 Planarity : 0.004 0.042 6163 Dihedral : 14.314 176.776 34817 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.46 % Favored : 93.46 % Rotamer: Outliers : 0.91 % Allowed : 15.96 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -0.83 (0.16), residues: 2509 helix: 0.41 (0.19), residues: 722 sheet: -0.49 (0.22), residues: 498 loop : -1.11 (0.16), residues: 1289 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5018 Ramachandran restraints generated. 2509 Oldfield, 0 Emsley, 2509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5018 Ramachandran restraints generated. 2509 Oldfield, 0 Emsley, 2509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 324 time to evaluate : 3.120 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 7 residues processed: 337 average time/residue: 0.7587 time to fit residues: 440.3779 Evaluate side-chains 310 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 303 time to evaluate : 3.199 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.5932 time to fit residues: 11.1675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 513 random chunks: chunk 166 optimal weight: 10.0000 chunk 446 optimal weight: 4.9990 chunk 98 optimal weight: 10.0000 chunk 291 optimal weight: 7.9990 chunk 122 optimal weight: 10.0000 chunk 496 optimal weight: 10.0000 chunk 412 optimal weight: 0.0670 chunk 229 optimal weight: 30.0000 chunk 41 optimal weight: 10.0000 chunk 164 optimal weight: 10.0000 chunk 260 optimal weight: 10.0000 overall best weight: 6.6130 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 136 GLN N 18 GLN ** U 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.3039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 84439 Z= 0.376 Angle : 0.637 10.830 127243 Z= 0.322 Chirality : 0.038 0.299 16398 Planarity : 0.005 0.049 6163 Dihedral : 14.504 176.998 34817 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.97 % Favored : 91.95 % Rotamer: Outliers : 1.92 % Allowed : 16.63 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -1.06 (0.16), residues: 2509 helix: 0.24 (0.19), residues: 713 sheet: -0.65 (0.22), residues: 521 loop : -1.25 (0.16), residues: 1275 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5018 Ramachandran restraints generated. 2509 Oldfield, 0 Emsley, 2509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5018 Ramachandran restraints generated. 2509 Oldfield, 0 Emsley, 2509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 305 time to evaluate : 3.080 Fit side-chains revert: symmetry clash outliers start: 40 outliers final: 28 residues processed: 329 average time/residue: 0.7455 time to fit residues: 421.1184 Evaluate side-chains 318 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 290 time to evaluate : 4.046 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.6171 time to fit residues: 35.4464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 513 random chunks: chunk 478 optimal weight: 9.9990 chunk 55 optimal weight: 6.9990 chunk 282 optimal weight: 8.9990 chunk 362 optimal weight: 2.9990 chunk 280 optimal weight: 7.9990 chunk 417 optimal weight: 8.9990 chunk 277 optimal weight: 5.9990 chunk 494 optimal weight: 20.0000 chunk 309 optimal weight: 7.9990 chunk 301 optimal weight: 9.9990 chunk 228 optimal weight: 40.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 ASN ** J 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.3316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 84439 Z= 0.362 Angle : 0.632 10.814 127243 Z= 0.321 Chirality : 0.038 0.297 16398 Planarity : 0.005 0.048 6163 Dihedral : 14.656 176.536 34817 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.93 % Favored : 91.99 % Rotamer: Outliers : 1.29 % Allowed : 17.26 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.16), residues: 2509 helix: 0.06 (0.19), residues: 712 sheet: -0.73 (0.22), residues: 518 loop : -1.40 (0.16), residues: 1279 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5018 Ramachandran restraints generated. 2509 Oldfield, 0 Emsley, 2509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5018 Ramachandran restraints generated. 2509 Oldfield, 0 Emsley, 2509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 303 time to evaluate : 3.155 Fit side-chains revert: symmetry clash outliers start: 27 outliers final: 17 residues processed: 320 average time/residue: 0.7433 time to fit residues: 411.9880 Evaluate side-chains 312 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 295 time to evaluate : 3.107 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.5861 time to fit residues: 21.9371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 513 random chunks: chunk 305 optimal weight: 10.0000 chunk 197 optimal weight: 40.0000 chunk 295 optimal weight: 6.9990 chunk 148 optimal weight: 20.0000 chunk 97 optimal weight: 30.0000 chunk 95 optimal weight: 40.0000 chunk 314 optimal weight: 1.9990 chunk 336 optimal weight: 2.9990 chunk 244 optimal weight: 8.9990 chunk 46 optimal weight: 10.0000 chunk 388 optimal weight: 1.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 70 HIS ** H 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.3302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 84439 Z= 0.276 Angle : 0.579 11.552 127243 Z= 0.297 Chirality : 0.035 0.274 16398 Planarity : 0.004 0.046 6163 Dihedral : 14.566 176.260 34817 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.77 % Favored : 92.15 % Rotamer: Outliers : 1.15 % Allowed : 17.79 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -1.19 (0.16), residues: 2509 helix: 0.18 (0.19), residues: 717 sheet: -0.71 (0.23), residues: 510 loop : -1.37 (0.16), residues: 1282 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5018 Ramachandran restraints generated. 2509 Oldfield, 0 Emsley, 2509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5018 Ramachandran restraints generated. 2509 Oldfield, 0 Emsley, 2509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 304 time to evaluate : 3.230 Fit side-chains revert: symmetry clash outliers start: 24 outliers final: 15 residues processed: 319 average time/residue: 0.7832 time to fit residues: 430.3700 Evaluate side-chains 314 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 299 time to evaluate : 3.123 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.5768 time to fit residues: 19.7878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 513 random chunks: chunk 449 optimal weight: 8.9990 chunk 473 optimal weight: 6.9990 chunk 432 optimal weight: 3.9990 chunk 460 optimal weight: 10.0000 chunk 277 optimal weight: 3.9990 chunk 200 optimal weight: 50.0000 chunk 361 optimal weight: 0.7980 chunk 141 optimal weight: 10.0000 chunk 416 optimal weight: 0.9980 chunk 435 optimal weight: 10.0000 chunk 459 optimal weight: 20.0000 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 43 ASN ** H 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.3283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 84439 Z= 0.212 Angle : 0.552 15.070 127243 Z= 0.285 Chirality : 0.033 0.266 16398 Planarity : 0.004 0.046 6163 Dihedral : 14.541 176.294 34817 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.49 % Favored : 92.43 % Rotamer: Outliers : 0.58 % Allowed : 18.36 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.16), residues: 2509 helix: 0.25 (0.20), residues: 717 sheet: -0.69 (0.23), residues: 508 loop : -1.34 (0.16), residues: 1284 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5018 Ramachandran restraints generated. 2509 Oldfield, 0 Emsley, 2509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5018 Ramachandran restraints generated. 2509 Oldfield, 0 Emsley, 2509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 303 time to evaluate : 3.155 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 7 residues processed: 311 average time/residue: 0.7577 time to fit residues: 404.1606 Evaluate side-chains 304 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 297 time to evaluate : 3.096 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.5944 time to fit residues: 10.9489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 513 random chunks: chunk 302 optimal weight: 0.9980 chunk 487 optimal weight: 50.0000 chunk 297 optimal weight: 6.9990 chunk 231 optimal weight: 30.0000 chunk 338 optimal weight: 2.9990 chunk 511 optimal weight: 5.9990 chunk 470 optimal weight: 0.7980 chunk 406 optimal weight: 0.9990 chunk 42 optimal weight: 10.0000 chunk 314 optimal weight: 10.0000 chunk 249 optimal weight: 40.0000 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.3222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 84439 Z= 0.164 Angle : 0.527 12.655 127243 Z= 0.273 Chirality : 0.032 0.252 16398 Planarity : 0.004 0.044 6163 Dihedral : 14.476 176.282 34817 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.33 % Favored : 92.59 % Rotamer: Outliers : 0.48 % Allowed : 18.46 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -1.00 (0.16), residues: 2509 helix: 0.39 (0.20), residues: 714 sheet: -0.61 (0.23), residues: 497 loop : -1.27 (0.16), residues: 1298 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5018 Ramachandran restraints generated. 2509 Oldfield, 0 Emsley, 2509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5018 Ramachandran restraints generated. 2509 Oldfield, 0 Emsley, 2509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 302 time to evaluate : 3.074 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 6 residues processed: 309 average time/residue: 0.7613 time to fit residues: 407.4860 Evaluate side-chains 300 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 294 time to evaluate : 3.132 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.5769 time to fit residues: 9.8466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 513 random chunks: chunk 323 optimal weight: 10.0000 chunk 433 optimal weight: 3.9990 chunk 124 optimal weight: 10.0000 chunk 375 optimal weight: 4.9990 chunk 60 optimal weight: 10.0000 chunk 113 optimal weight: 10.0000 chunk 407 optimal weight: 6.9990 chunk 170 optimal weight: 10.0000 chunk 418 optimal weight: 3.9990 chunk 51 optimal weight: 10.0000 chunk 75 optimal weight: 10.0000 overall best weight: 5.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 136 GLN ** K 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.113221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.078609 restraints weight = 188171.744| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 1.36 r_work: 0.3006 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.3424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 84439 Z= 0.346 Angle : 0.619 11.928 127243 Z= 0.315 Chirality : 0.037 0.294 16398 Planarity : 0.005 0.049 6163 Dihedral : 14.613 176.731 34817 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.01 % Favored : 91.91 % Rotamer: Outliers : 0.43 % Allowed : 18.46 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -1.18 (0.16), residues: 2509 helix: 0.18 (0.20), residues: 712 sheet: -0.71 (0.23), residues: 506 loop : -1.35 (0.16), residues: 1291 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11764.80 seconds wall clock time: 211 minutes 30.56 seconds (12690.56 seconds total)