Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 29 09:48:24 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ddd_7867/04_2023/6ddd_7867_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ddd_7867/04_2023/6ddd_7867.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ddd_7867/04_2023/6ddd_7867.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ddd_7867/04_2023/6ddd_7867.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ddd_7867/04_2023/6ddd_7867_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ddd_7867/04_2023/6ddd_7867_trim_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.006 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: 7 Type Number sf(0) Gaussians P 2747 5.49 5 S 54 5.16 5 Cl 2 4.86 5 C 38916 2.51 5 N 14700 2.21 5 O 22698 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 23": "NH1" <-> "NH2" Residue "A ARG 41": "NH1" <-> "NH2" Residue "A ARG 53": "NH1" <-> "NH2" Residue "A ARG 64": "NH1" <-> "NH2" Residue "A ARG 91": "NH1" <-> "NH2" Residue "A ARG 103": "NH1" <-> "NH2" Residue "A ARG 111": "NH1" <-> "NH2" Residue "B ARG 261": "NH1" <-> "NH2" Residue "C ARG 3": "NH1" <-> "NH2" Residue "C ARG 13": "NH1" <-> "NH2" Residue "C ARG 48": "NH1" <-> "NH2" Residue "C ARG 70": "NH1" <-> "NH2" Residue "D ARG 67": "NH1" <-> "NH2" Residue "D ARG 78": "NH1" <-> "NH2" Residue "D ARG 84": "NH1" <-> "NH2" Residue "E ARG 84": "NH1" <-> "NH2" Residue "E ARG 88": "NH1" <-> "NH2" Residue "F ARG 32": "NH1" <-> "NH2" Residue "F ARG 64": "NH1" <-> "NH2" Residue "F ARG 76": "NH1" <-> "NH2" Residue "I ARG 22": "NH1" <-> "NH2" Residue "I ARG 28": "NH1" <-> "NH2" Residue "I ARG 49": "NH1" <-> "NH2" Residue "J ARG 18": "NH1" <-> "NH2" Residue "J ARG 37": "NH1" <-> "NH2" Residue "K ARG 7": "NH1" <-> "NH2" Residue "K ARG 29": "NH1" <-> "NH2" Residue "K ARG 47": "NH1" <-> "NH2" Residue "K ARG 52": "NH1" <-> "NH2" Residue "K ARG 60": "NH1" <-> "NH2" Residue "L ARG 86": "NH1" <-> "NH2" Residue "L ARG 92": "NH1" <-> "NH2" Residue "L ARG 138": "NH1" <-> "NH2" Residue "M ARG 10": "NH1" <-> "NH2" Residue "M ARG 44": "NH1" <-> "NH2" Residue "N ARG 6": "NH1" <-> "NH2" Residue "N ARG 7": "NH1" <-> "NH2" Residue "P ARG 4": "NH1" <-> "NH2" Residue "P ARG 20": "NH1" <-> "NH2" Residue "P ARG 22": "NH1" <-> "NH2" Residue "P ARG 34": "NH1" <-> "NH2" Residue "Q ARG 13": "NH1" <-> "NH2" Residue "Q ARG 42": "NH1" <-> "NH2" Residue "Q ARG 57": "NH1" <-> "NH2" Residue "S ARG 54": "NH1" <-> "NH2" Residue "S ARG 62": "NH1" <-> "NH2" Residue "S ARG 107": "NH1" <-> "NH2" Residue "S ARG 168": "NH1" <-> "NH2" Residue "V ARG 2": "NH1" <-> "NH2" Residue "V ARG 14": "NH1" <-> "NH2" Residue "V ARG 38": "NH1" <-> "NH2" Residue "V ARG 144": "NH1" <-> "NH2" Residue "Y ARG 10": "NH1" <-> "NH2" Residue "Y ARG 45": "NH1" <-> "NH2" Residue "Y ARG 51": "NH1" <-> "NH2" Residue "Y ARG 56": "NH1" <-> "NH2" Residue "Y ARG 115": "NH1" <-> "NH2" Residue "Z ARG 67": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 79118 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 915 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 4, 'TRANS': 108} Chain: "B" Number of atoms: 2094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2094 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 17, 'TRANS': 256} Chain: "C" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 943 Classifications: {'peptide': 116} Link IDs: {'TRANS': 115} Chain: "D" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 785 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 2, 'TRANS': 97} Chain: "E" Number of atoms: 853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 853 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 4, 'TRANS': 106} Chain: "F" Number of atoms: 711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 711 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 2, 'TRANS': 84} Chain: "G" Number of atoms: 730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 730 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 4, 'TRANS': 90} Chain breaks: 1 Chain: "H" Number of atoms: 727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 727 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 592 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 1, 'TRANS': 75} Chain: "J" Number of atoms: 463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 463 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 1, 'TRANS': 57} Chain: "K" Number of atoms: 472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 472 Classifications: {'peptide': 57} Link IDs: {'TRANS': 56} Chain: "L" Number of atoms: 1628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1628 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 8, 'TRANS': 206} Chain: "M" Number of atoms: 432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 432 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 2, 'TRANS': 53} Chain: "N" Number of atoms: 397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 397 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 3, 'TRANS': 46} Chain: "O" Number of atoms: 382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 382 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "P" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 372 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "Q" Number of atoms: 521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 521 Classifications: {'peptide': 64} Link IDs: {'TRANS': 63} Chain: "R" Number of atoms: 296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 296 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 3, 'TRANS': 33} Chain: "S" Number of atoms: 1318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1318 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 7, 'TRANS': 163} Chain breaks: 2 Chain: "V" Number of atoms: 1138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1138 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 6, 'TRANS': 136} Chain: "W" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 850 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 3, 'TRANS': 108} Chain breaks: 1 Chain: "X" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 938 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 5, 'TRANS': 119} Chain breaks: 2 Chain: "Y" Number of atoms: 1089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1089 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "Z" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 902 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 1, 'TRANS': 112} Chain breaks: 1 Chain: "a" Number of atoms: 583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 583 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain breaks: 2 Chain: "1" Number of atoms: 56747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2646, 56747 Inner-chain residues flagged as termini: ['pdbres=" A 11459 "', 'pdbres=" G 11556 "'] Classifications: {'RNA': 2646} Modifications used: {'5*END': 3, 'rna2p_pur': 267, 'rna2p_pyr': 131, 'rna3p_pur': 1257, 'rna3p_pyr': 991} Link IDs: {'rna2p': 398, 'rna3p': 2247} Chain breaks: 9 Chain: "2" Number of atoms: 2214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 2214 Classifications: {'RNA': 104} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 6, 'rna3p_pur': 46, 'rna3p_pyr': 44} Link IDs: {'rna2p': 14, 'rna3p': 89} Chain: "1" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'G6V': 1} Classifications: {'undetermined': 1} Time building chain proxies: 34.27, per 1000 atoms: 0.43 Number of scatterers: 79118 At special positions: 0 Unit cell: (192.92, 232.14, 186.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Cl 2 17.00 S 54 16.00 P 2747 15.00 F 1 9.00 O 22698 8.00 N 14700 7.00 C 38916 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS N 33 " - pdb=" SG CYS N 43 " distance=2.03 Simple disulfide: pdb=" SG CYS O 12 " - pdb=" SG CYS O 36 " distance=2.04 Simple disulfide: pdb=" SG CYS R 14 " - pdb=" SG CYS R 27 " distance=2.03 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: 33.48 Conformation dependent library (CDL) restraints added in 2.7 seconds 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4674 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 62 helices and 37 sheets defined 20.4% alpha, 16.4% beta 853 base pairs and 1482 stacking pairs defined. Time for finding SS restraints: 31.62 Creating SS restraints... Processing helix chain 'A' and resid 100 through 104 Processing helix chain 'B' and resid 31 through 33 No H-bonds generated for 'chain 'B' and resid 31 through 33' Processing helix chain 'B' and resid 198 through 201 removed outlier: 4.332A pdb=" N GLU B 201 " --> pdb=" O LEU B 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 198 through 201' Processing helix chain 'B' and resid 222 through 224 No H-bonds generated for 'chain 'B' and resid 222 through 224' Processing helix chain 'B' and resid 265 through 267 No H-bonds generated for 'chain 'B' and resid 265 through 267' Processing helix chain 'C' and resid 10 through 19 Processing helix chain 'C' and resid 26 through 30 Processing helix chain 'C' and resid 32 through 72 removed outlier: 4.226A pdb=" N GLN C 37 " --> pdb=" O LYS C 33 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ARG C 51 " --> pdb=" O PHE C 47 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLN C 71 " --> pdb=" O ALA C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 82 Processing helix chain 'C' and resid 92 through 101 Processing helix chain 'C' and resid 103 through 116 removed outlier: 3.936A pdb=" N ALA C 107 " --> pdb=" O GLU C 103 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLN C 108 " --> pdb=" O LYS C 104 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA C 116 " --> pdb=" O LYS C 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 18 through 21 No H-bonds generated for 'chain 'E' and resid 18 through 21' Processing helix chain 'E' and resid 29 through 38 Processing helix chain 'E' and resid 44 through 61 Processing helix chain 'F' and resid 35 through 45 Processing helix chain 'G' and resid 65 through 67 No H-bonds generated for 'chain 'G' and resid 65 through 67' Processing helix chain 'H' and resid 15 through 23 Processing helix chain 'H' and resid 45 through 52 Processing helix chain 'H' and resid 65 through 67 No H-bonds generated for 'chain 'H' and resid 65 through 67' Processing helix chain 'K' and resid 11 through 22 Processing helix chain 'K' and resid 24 through 34 Processing helix chain 'K' and resid 41 through 59 Processing helix chain 'L' and resid 71 through 79 Processing helix chain 'L' and resid 107 through 109 No H-bonds generated for 'chain 'L' and resid 107 through 109' Processing helix chain 'L' and resid 129 through 134 Processing helix chain 'M' and resid 17 through 25 Processing helix chain 'M' and resid 42 through 49 removed outlier: 3.633A pdb=" N ILE M 47 " --> pdb=" O ILE M 43 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS M 49 " --> pdb=" O GLY M 45 " (cutoff:3.500A) Processing helix chain 'N' and resid 12 through 19 removed outlier: 4.839A pdb=" N HIS N 19 " --> pdb=" O LYS N 15 " (cutoff:3.500A) Processing helix chain 'P' and resid 10 through 17 Processing helix chain 'P' and resid 19 through 23 Processing helix chain 'P' and resid 26 through 38 Processing helix chain 'Q' and resid 38 through 45 removed outlier: 3.538A pdb=" N LEU Q 44 " --> pdb=" O GLN Q 40 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ARG Q 45 " --> pdb=" O LYS Q 41 " (cutoff:3.500A) Processing helix chain 'Q' and resid 52 through 57 Processing helix chain 'R' and resid 30 through 32 No H-bonds generated for 'chain 'R' and resid 30 through 32' Processing helix chain 'S' and resid 30 through 43 removed outlier: 4.152A pdb=" N GLU S 35 " --> pdb=" O SER S 31 " (cutoff:3.500A) Processing helix chain 'S' and resid 103 through 118 Processing helix chain 'S' and resid 136 through 145 Processing helix chain 'S' and resid 178 through 180 No H-bonds generated for 'chain 'S' and resid 178 through 180' Processing helix chain 'S' and resid 184 through 187 No H-bonds generated for 'chain 'S' and resid 184 through 187' Processing helix chain 'S' and resid 196 through 205 removed outlier: 3.646A pdb=" N LYS S 200 " --> pdb=" O GLU S 196 " (cutoff:3.500A) Processing helix chain 'V' and resid 26 through 38 removed outlier: 4.253A pdb=" N GLU V 32 " --> pdb=" O ARG V 28 " (cutoff:3.500A) Processing helix chain 'V' and resid 60 through 62 No H-bonds generated for 'chain 'V' and resid 60 through 62' Processing helix chain 'V' and resid 90 through 96 removed outlier: 3.609A pdb=" N ARG V 95 " --> pdb=" O GLY V 91 " (cutoff:3.500A) Processing helix chain 'V' and resid 98 through 107 removed outlier: 4.048A pdb=" N GLU V 103 " --> pdb=" O GLU V 99 " (cutoff:3.500A) Processing helix chain 'V' and resid 114 through 122 removed outlier: 3.732A pdb=" N LYS V 118 " --> pdb=" O ARG V 114 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS V 122 " --> pdb=" O LYS V 118 " (cutoff:3.500A) Processing helix chain 'V' and resid 134 through 136 No H-bonds generated for 'chain 'V' and resid 134 through 136' Processing helix chain 'W' and resid 104 through 108 Processing helix chain 'W' and resid 112 through 117 removed outlier: 3.959A pdb=" N LEU W 117 " --> pdb=" O LYS W 113 " (cutoff:3.500A) Processing helix chain 'X' and resid 51 through 53 No H-bonds generated for 'chain 'X' and resid 51 through 53' Processing helix chain 'X' and resid 57 through 59 No H-bonds generated for 'chain 'X' and resid 57 through 59' Processing helix chain 'X' and resid 93 through 98 Processing helix chain 'X' and resid 130 through 135 Processing helix chain 'Y' and resid 44 through 57 removed outlier: 4.318A pdb=" N SER Y 49 " --> pdb=" O ARG Y 45 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ILE Y 52 " --> pdb=" O GLU Y 48 " (cutoff:3.500A) Processing helix chain 'Y' and resid 111 through 121 Processing helix chain 'Z' and resid 10 through 27 Processing helix chain 'Z' and resid 34 through 42 removed outlier: 4.038A pdb=" N SER Z 42 " --> pdb=" O LYS Z 38 " (cutoff:3.500A) Processing helix chain 'Z' and resid 47 through 53 Processing helix chain 'Z' and resid 56 through 65 removed outlier: 4.139A pdb=" N THR Z 65 " --> pdb=" O ASN Z 61 " (cutoff:3.500A) Processing helix chain 'Z' and resid 82 through 86 Processing helix chain 'Z' and resid 88 through 92 removed outlier: 4.055A pdb=" N ARG Z 92 " --> pdb=" O GLU Z 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 88 through 92' Processing helix chain 'a' and resid 7 through 16 removed outlier: 3.672A pdb=" N LEU a 12 " --> pdb=" O ASN a 8 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LYS a 13 " --> pdb=" O LYS a 9 " (cutoff:3.500A) Processing helix chain 'a' and resid 104 through 109 Processing sheet with id= A, first strand: chain 'A' and resid 86 through 90 removed outlier: 6.933A pdb=" N THR A 27 " --> pdb=" O LYS A 89 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL A 32 " --> pdb=" O GLN A 43 " (cutoff:3.500A) removed outlier: 9.727A pdb=" N GLU A 46 " --> pdb=" O ILE A 66 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ILE A 66 " --> pdb=" O GLU A 46 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N THR A 62 " --> pdb=" O ILE A 50 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N ARG A 52 " --> pdb=" O THR A 60 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N THR A 60 " --> pdb=" O ARG A 52 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 100 through 105 removed outlier: 4.186A pdb=" N GLU B 100 " --> pdb=" O TYR B 96 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N SER B 80 " --> pdb=" O LEU B 93 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N VAL B 95 " --> pdb=" O VAL B 78 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N VAL B 78 " --> pdb=" O VAL B 95 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 129 through 131 Processing sheet with id= D, first strand: chain 'B' and resid 171 through 175 Processing sheet with id= E, first strand: chain 'D' and resid 11 through 14 removed outlier: 3.973A pdb=" N PHE D 40 " --> pdb=" O ILE D 4 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N GLU D 6 " --> pdb=" O VAL D 38 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N VAL D 38 " --> pdb=" O GLU D 6 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 19 through 22 Processing sheet with id= G, first strand: chain 'D' and resid 32 through 35 removed outlier: 6.425A pdb=" N THR D 61 " --> pdb=" O ILE D 97 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N ILE D 97 " --> pdb=" O THR D 61 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 71 through 77 removed outlier: 4.252A pdb=" N SER D 82 " --> pdb=" O LYS D 77 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 2 through 7 removed outlier: 6.485A pdb=" N SER E 108 " --> pdb=" O VAL E 71 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N VAL E 71 " --> pdb=" O SER E 108 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 82 through 86 Processing sheet with id= K, first strand: chain 'F' and resid 52 through 58 removed outlier: 3.905A pdb=" N ARG F 75 " --> pdb=" O TYR F 58 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ARG F 76 " --> pdb=" O VAL F 29 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'G' and resid 9 through 11 Processing sheet with id= M, first strand: chain 'G' and resid 32 through 34 Processing sheet with id= N, first strand: chain 'G' and resid 40 through 44 Processing sheet with id= O, first strand: chain 'G' and resid 81 through 84 Processing sheet with id= P, first strand: chain 'H' and resid 39 through 44 removed outlier: 10.314A pdb=" N GLN H 85 " --> pdb=" O LYS H 26 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N THR H 87 " --> pdb=" O PRO H 28 " (cutoff:3.500A) removed outlier: 8.719A pdb=" N VAL H 30 " --> pdb=" O THR H 87 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ILE H 89 " --> pdb=" O VAL H 30 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N TYR H 32 " --> pdb=" O ILE H 89 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N PHE H 91 " --> pdb=" O TYR H 32 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N GLN H 78 " --> pdb=" O THR H 87 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N ILE H 89 " --> pdb=" O ASP H 76 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ASP H 76 " --> pdb=" O ILE H 89 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'I' and resid 59 through 61 Processing sheet with id= R, first strand: chain 'I' and resid 73 through 80 Processing sheet with id= S, first strand: chain 'J' and resid 13 through 17 Processing sheet with id= T, first strand: chain 'J' and resid 33 through 38 Processing sheet with id= U, first strand: chain 'L' and resid 177 through 180 removed outlier: 4.596A pdb=" N VAL L 121 " --> pdb=" O LEU L 208 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N LEU L 208 " --> pdb=" O VAL L 121 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N VAL L 27 " --> pdb=" O ILE L 10 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N MET L 12 " --> pdb=" O VAL L 25 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N VAL L 25 " --> pdb=" O MET L 12 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N GLN L 14 " --> pdb=" O ILE L 23 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ILE L 23 " --> pdb=" O GLN L 14 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN L 187 " --> pdb=" O LEU L 196 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N LYS L 198 " --> pdb=" O VAL L 185 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N VAL L 185 " --> pdb=" O LYS L 198 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'L' and resid 49 through 51 Processing sheet with id= W, first strand: chain 'M' and resid 5 through 7 Processing sheet with id= X, first strand: chain 'N' and resid 27 through 29 Processing sheet with id= Y, first strand: chain 'O' and resid 3 through 6 Processing sheet with id= Z, first strand: chain 'O' and resid 32 through 36 Processing sheet with id= AA, first strand: chain 'R' and resid 15 through 19 Processing sheet with id= AB, first strand: chain 'S' and resid 191 through 194 removed outlier: 6.679A pdb=" N GLN S 174 " --> pdb=" O VAL S 154 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N THR S 156 " --> pdb=" O GLN S 174 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N THR S 176 " --> pdb=" O THR S 156 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'V' and resid 16 through 20 removed outlier: 6.908A pdb=" N TYR V 54 " --> pdb=" O TYR V 17 " (cutoff:3.500A) removed outlier: 8.202A pdb=" N ILE V 19 " --> pdb=" O TYR V 54 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ILE V 56 " --> pdb=" O ILE V 19 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'V' and resid 74 through 78 Processing sheet with id= AE, first strand: chain 'W' and resid 7 through 9 removed outlier: 4.134A pdb=" N GLU W 18 " --> pdb=" O ASN W 45 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASN W 45 " --> pdb=" O GLU W 18 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N LEU W 20 " --> pdb=" O VAL W 43 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N VAL W 43 " --> pdb=" O LEU W 20 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N LYS W 59 " --> pdb=" O ILE W 87 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ALA W 83 " --> pdb=" O VAL W 63 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'X' and resid 75 through 77 Processing sheet with id= AG, first strand: chain 'Y' and resid 32 through 36 Processing sheet with id= AH, first strand: chain 'Y' and resid 40 through 43 removed outlier: 6.835A pdb=" N TYR Y 74 " --> pdb=" O GLU Y 91 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N TRP Y 93 " --> pdb=" O THR Y 72 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N THR Y 72 " --> pdb=" O TRP Y 93 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'Y' and resid 63 through 66 Processing sheet with id= AJ, first strand: chain 'Z' and resid 29 through 33 removed outlier: 6.416A pdb=" N ILE Z 118 " --> pdb=" O LYS Z 105 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N LYS Z 105 " --> pdb=" O ILE Z 118 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N GLU Z 120 " --> pdb=" O ILE Z 103 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N ILE Z 103 " --> pdb=" O GLU Z 120 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'a' and resid 30 through 34 496 hydrogen bonds defined for protein. 1383 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2129 hydrogen bonds 3406 hydrogen bond angles 0 basepair planarities 853 basepair parallelities 1482 stacking parallelities Total time for adding SS restraints: 115.62 Time building geometry restraints manager: 36.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 7356 1.31 - 1.44: 39475 1.44 - 1.57: 34023 1.57 - 1.71: 5484 1.71 - 1.84: 96 Bond restraints: 86434 Sorted by residual: bond pdb=" C ARG M 20 " pdb=" O ARG M 20 " ideal model delta sigma weight residual 1.237 1.174 0.062 1.17e-02 7.31e+03 2.83e+01 bond pdb=" C1' U 2 68 " pdb=" N1 U 2 68 " ideal model delta sigma weight residual 1.480 1.556 -0.076 1.50e-02 4.44e+03 2.57e+01 bond pdb=" C10 G6V 13001 " pdb=" C20 G6V 13001 " ideal model delta sigma weight residual 1.511 1.598 -0.087 2.00e-02 2.50e+03 1.88e+01 bond pdb=" C30 G6V 13001 " pdb=" N29 G6V 13001 " ideal model delta sigma weight residual 1.336 1.420 -0.084 2.00e-02 2.50e+03 1.76e+01 bond pdb=" C31 G6V 13001 " pdb="CL33 G6V 13001 " ideal model delta sigma weight residual 1.758 1.838 -0.080 2.00e-02 2.50e+03 1.60e+01 ... (remaining 86429 not shown) Histogram of bond angle deviations from ideal: 85.68 - 95.53: 5 95.53 - 105.38: 13426 105.38 - 115.23: 60752 115.23 - 125.08: 45402 125.08 - 134.93: 10648 Bond angle restraints: 130233 Sorted by residual: angle pdb=" O2' G 11931 " pdb=" C2' G 11931 " pdb=" C1' G 11931 " ideal model delta sigma weight residual 108.40 85.68 22.72 1.50e+00 4.44e-01 2.29e+02 angle pdb=" C4' A 2 20 " pdb=" C3' A 2 20 " pdb=" O3' A 2 20 " ideal model delta sigma weight residual 113.00 126.89 -13.89 1.50e+00 4.44e-01 8.57e+01 angle pdb=" O2' A 2 81 " pdb=" C2' A 2 81 " pdb=" C1' A 2 81 " ideal model delta sigma weight residual 108.40 94.63 13.77 1.50e+00 4.44e-01 8.43e+01 angle pdb=" O2' G 2 80 " pdb=" C2' G 2 80 " pdb=" C1' G 2 80 " ideal model delta sigma weight residual 108.40 95.20 13.20 1.50e+00 4.44e-01 7.75e+01 angle pdb=" O2' G 2 19 " pdb=" C2' G 2 19 " pdb=" C1' G 2 19 " ideal model delta sigma weight residual 108.40 95.24 13.16 1.50e+00 4.44e-01 7.70e+01 ... (remaining 130228 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 43672 35.98 - 71.95: 1834 71.95 - 107.93: 132 107.93 - 143.91: 15 143.91 - 179.88: 33 Dihedral angle restraints: 45686 sinusoidal: 38420 harmonic: 7266 Sorted by residual: dihedral pdb=" O4' U 12361 " pdb=" C1' U 12361 " pdb=" N1 U 12361 " pdb=" C2 U 12361 " ideal model delta sinusoidal sigma weight residual 200.00 20.12 179.88 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' C 11781 " pdb=" C1' C 11781 " pdb=" N1 C 11781 " pdb=" C2 C 11781 " ideal model delta sinusoidal sigma weight residual 200.00 21.71 178.29 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U 12417 " pdb=" C1' U 12417 " pdb=" N1 U 12417 " pdb=" C2 U 12417 " ideal model delta sinusoidal sigma weight residual -160.00 17.68 -177.68 1 1.50e+01 4.44e-03 8.53e+01 ... (remaining 45683 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 15535 0.085 - 0.169: 1126 0.169 - 0.254: 114 0.254 - 0.338: 15 0.338 - 0.422: 2 Chirality restraints: 16792 Sorted by residual: chirality pdb=" C3' A 2 20 " pdb=" C4' A 2 20 " pdb=" O3' A 2 20 " pdb=" C2' A 2 20 " both_signs ideal model delta sigma weight residual False -2.48 -2.05 -0.42 2.00e-01 2.50e+01 4.46e+00 chirality pdb=" C3' U 2 89 " pdb=" C4' U 2 89 " pdb=" O3' U 2 89 " pdb=" C2' U 2 89 " both_signs ideal model delta sigma weight residual False -2.48 -2.11 -0.37 2.00e-01 2.50e+01 3.42e+00 chirality pdb=" C1' A 1 125 " pdb=" O4' A 1 125 " pdb=" C2' A 1 125 " pdb=" N9 A 1 125 " both_signs ideal model delta sigma weight residual False 2.46 2.13 0.33 2.00e-01 2.50e+01 2.73e+00 ... (remaining 16789 not shown) Planarity restraints: 6241 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A 11955 " 0.060 2.00e-02 2.50e+03 3.47e-02 3.32e+01 pdb=" N9 A 11955 " -0.096 2.00e-02 2.50e+03 pdb=" C8 A 11955 " 0.002 2.00e-02 2.50e+03 pdb=" N7 A 11955 " 0.018 2.00e-02 2.50e+03 pdb=" C5 A 11955 " 0.005 2.00e-02 2.50e+03 pdb=" C6 A 11955 " 0.005 2.00e-02 2.50e+03 pdb=" N6 A 11955 " 0.004 2.00e-02 2.50e+03 pdb=" N1 A 11955 " 0.000 2.00e-02 2.50e+03 pdb=" C2 A 11955 " -0.001 2.00e-02 2.50e+03 pdb=" N3 A 11955 " -0.002 2.00e-02 2.50e+03 pdb=" C4 A 11955 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A 2 20 " -0.052 2.00e-02 2.50e+03 3.10e-02 2.65e+01 pdb=" N9 A 2 20 " 0.086 2.00e-02 2.50e+03 pdb=" C8 A 2 20 " -0.007 2.00e-02 2.50e+03 pdb=" N7 A 2 20 " -0.008 2.00e-02 2.50e+03 pdb=" C5 A 2 20 " -0.017 2.00e-02 2.50e+03 pdb=" C6 A 2 20 " -0.004 2.00e-02 2.50e+03 pdb=" N6 A 2 20 " -0.001 2.00e-02 2.50e+03 pdb=" N1 A 2 20 " -0.002 2.00e-02 2.50e+03 pdb=" C2 A 2 20 " 0.003 2.00e-02 2.50e+03 pdb=" N3 A 2 20 " 0.002 2.00e-02 2.50e+03 pdb=" C4 A 2 20 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A 2 82 " 0.045 2.00e-02 2.50e+03 2.49e-02 1.71e+01 pdb=" N9 A 2 82 " -0.068 2.00e-02 2.50e+03 pdb=" C8 A 2 82 " 0.009 2.00e-02 2.50e+03 pdb=" N7 A 2 82 " 0.004 2.00e-02 2.50e+03 pdb=" C5 A 2 82 " 0.003 2.00e-02 2.50e+03 pdb=" C6 A 2 82 " 0.003 2.00e-02 2.50e+03 pdb=" N6 A 2 82 " 0.006 2.00e-02 2.50e+03 pdb=" N1 A 2 82 " 0.003 2.00e-02 2.50e+03 pdb=" C2 A 2 82 " -0.002 2.00e-02 2.50e+03 pdb=" N3 A 2 82 " -0.002 2.00e-02 2.50e+03 pdb=" C4 A 2 82 " -0.002 2.00e-02 2.50e+03 ... (remaining 6238 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 1158 2.58 - 3.16: 60941 3.16 - 3.74: 148444 3.74 - 4.32: 223265 4.32 - 4.90: 298180 Nonbonded interactions: 731988 Sorted by model distance: nonbonded pdb=" OP1 U 11063 " pdb=" O2' U 11079 " model vdw 1.998 2.440 nonbonded pdb=" OH TYR F 58 " pdb=" OP2 U 11377 " model vdw 2.003 2.440 nonbonded pdb=" OP2 A 11070 " pdb=" O2' C 11178 " model vdw 2.016 2.440 nonbonded pdb=" O2' C 11423 " pdb=" O2 U 11512 " model vdw 2.027 2.440 nonbonded pdb=" O2' A 12060 " pdb=" OP2 G 12062 " model vdw 2.032 2.440 ... (remaining 731983 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 2.580 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: 14.950 Check model and map are aligned: 0.900 Set scattering table: 0.560 Process input model: 269.580 Find NCS groups from input model: 1.350 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 292.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 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 : 0.008 0.106 86434 Z= 0.489 Angle : 0.854 22.717 130233 Z= 0.455 Chirality : 0.048 0.422 16792 Planarity : 0.006 0.068 6241 Dihedral : 16.158 179.882 41003 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 16.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.64 % Favored : 89.36 % Rotamer Outliers : 0.05 % 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: -4.62 (0.13), residues: 2500 helix: -2.93 (0.16), residues: 596 sheet: -3.09 (0.19), residues: 501 loop : -3.19 (0.13), residues: 1403 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 748 residues out of total 2153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 747 time to evaluate : 3.258 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 748 average time/residue: 0.8935 time to fit residues: 1072.9609 Evaluate side-chains 539 residues out of total 2153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 538 time to evaluate : 3.303 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.5699 time to fit residues: 4.4470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 439 optimal weight: 5.9990 chunk 394 optimal weight: 5.9990 chunk 218 optimal weight: 5.9990 chunk 134 optimal weight: 1.9990 chunk 265 optimal weight: 3.9990 chunk 210 optimal weight: 0.9990 chunk 407 optimal weight: 7.9990 chunk 157 optimal weight: 0.6980 chunk 247 optimal weight: 5.9990 chunk 303 optimal weight: 3.9990 chunk 472 optimal weight: 0.7980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 61 GLN B 128 ASN B 199 GLN B 200 HIS C 37 GLN C 38 GLN E 28 ASN E 57 ASN E 60 HIS E 61 ASN F 34 ASN F 57 ASN G 44 HIS G 76 ASN H 38 ASN H 88 HIS L 128 GLN L 134 HIS L 143 HIS L 146 HIS L 182 ASN L 192 ASN M 52 HIS N 45 ASN O 4 ASN O 25 ASN O 26 ASN ** O 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 7 HIS ** Q 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 67 GLN S 75 GLN S 162 ASN S 169 ASN V 3 GLN V 8 ASN V 68 ASN V 119 GLN V 137 GLN X 17 ASN X 38 GLN Y 13 HIS Y 35 GLN ** Y 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 61 ASN a 39 HIS a 55 GLN Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 86434 Z= 0.184 Angle : 0.597 10.443 130233 Z= 0.308 Chirality : 0.036 0.270 16792 Planarity : 0.005 0.059 6241 Dihedral : 15.796 179.875 35802 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer Outliers : 3.11 % 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: -3.46 (0.15), residues: 2500 helix: -1.62 (0.19), residues: 603 sheet: -2.43 (0.21), residues: 499 loop : -2.61 (0.14), residues: 1398 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 638 residues out of total 2153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 571 time to evaluate : 3.310 Fit side-chains outliers start: 67 outliers final: 43 residues processed: 597 average time/residue: 0.8542 time to fit residues: 839.7987 Evaluate side-chains 550 residues out of total 2153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 507 time to evaluate : 3.325 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 0 residues processed: 43 average time/residue: 0.5933 time to fit residues: 52.3113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 262 optimal weight: 10.0000 chunk 146 optimal weight: 0.0060 chunk 393 optimal weight: 7.9990 chunk 321 optimal weight: 7.9990 chunk 130 optimal weight: 9.9990 chunk 473 optimal weight: 8.9990 chunk 511 optimal weight: 9.9990 chunk 421 optimal weight: 10.0000 chunk 469 optimal weight: 10.0000 chunk 161 optimal weight: 8.9990 chunk 379 optimal weight: 10.0000 overall best weight: 6.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 200 HIS C 37 GLN C 81 ASN E 40 ASN E 97 ASN F 54 ASN K 31 GLN L 33 ASN L 192 ASN L 200 ASN O 45 HIS ** Q 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 59 ASN V 68 ASN V 81 HIS V 137 GLN ** W 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 35 GLN ** Y 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 61 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.010 0.108 86434 Z= 0.595 Angle : 0.926 13.000 130233 Z= 0.455 Chirality : 0.052 0.325 16792 Planarity : 0.008 0.101 6241 Dihedral : 16.397 179.236 35802 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.36 % Favored : 89.64 % Rotamer Outliers : 3.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.41 (0.15), residues: 2500 helix: -1.76 (0.19), residues: 613 sheet: -2.23 (0.21), residues: 498 loop : -2.56 (0.14), residues: 1389 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 574 residues out of total 2153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 489 time to evaluate : 3.291 Fit side-chains outliers start: 85 outliers final: 53 residues processed: 545 average time/residue: 0.8301 time to fit residues: 753.1214 Evaluate side-chains 519 residues out of total 2153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 466 time to evaluate : 3.249 Switching outliers to nearest non-outliers outliers start: 53 outliers final: 0 residues processed: 53 average time/residue: 0.5840 time to fit residues: 62.4216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 467 optimal weight: 3.9990 chunk 355 optimal weight: 6.9990 chunk 245 optimal weight: 6.9990 chunk 52 optimal weight: 0.9990 chunk 225 optimal weight: 3.9990 chunk 317 optimal weight: 3.9990 chunk 474 optimal weight: 6.9990 chunk 502 optimal weight: 4.9990 chunk 248 optimal weight: 3.9990 chunk 449 optimal weight: 4.9990 chunk 135 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 200 HIS L 182 ASN O 4 ASN Q 7 HIS Q 31 HIS ** S 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 137 GLN ** Y 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 61 ASN a 55 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.059 86434 Z= 0.282 Angle : 0.650 11.437 130233 Z= 0.334 Chirality : 0.039 0.299 16792 Planarity : 0.005 0.058 6241 Dihedral : 15.886 178.028 35802 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer Outliers : 2.42 % 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: -2.94 (0.15), residues: 2500 helix: -1.24 (0.20), residues: 605 sheet: -1.90 (0.21), residues: 515 loop : -2.34 (0.15), residues: 1380 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 2153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 497 time to evaluate : 3.371 Fit side-chains outliers start: 52 outliers final: 34 residues processed: 523 average time/residue: 0.8479 time to fit residues: 736.4513 Evaluate side-chains 507 residues out of total 2153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 473 time to evaluate : 3.348 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 0.6490 time to fit residues: 44.6995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 418 optimal weight: 10.0000 chunk 285 optimal weight: 7.9990 chunk 7 optimal weight: 0.0870 chunk 374 optimal weight: 6.9990 chunk 207 optimal weight: 9.9990 chunk 428 optimal weight: 8.9990 chunk 347 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 256 optimal weight: 10.0000 chunk 451 optimal weight: 10.0000 chunk 126 optimal weight: 2.9990 overall best weight: 5.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 54 HIS ** B 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 200 HIS E 97 ASN L 103 GLN L 200 ASN O 4 ASN P 17 HIS Q 7 HIS ** S 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 137 GLN W 13 ASN ** Y 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 61 ASN Z 106 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.093 86434 Z= 0.479 Angle : 0.812 13.208 130233 Z= 0.405 Chirality : 0.047 0.314 16792 Planarity : 0.006 0.083 6241 Dihedral : 16.159 179.640 35802 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.04 % Favored : 89.96 % Rotamer Outliers : 4.09 % 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: -2.96 (0.15), residues: 2500 helix: -1.35 (0.20), residues: 607 sheet: -1.82 (0.22), residues: 504 loop : -2.35 (0.15), residues: 1389 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 2153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 464 time to evaluate : 3.339 Fit side-chains revert: symmetry clash outliers start: 88 outliers final: 62 residues processed: 513 average time/residue: 0.8398 time to fit residues: 714.3036 Evaluate side-chains 512 residues out of total 2153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 450 time to evaluate : 3.347 Switching outliers to nearest non-outliers outliers start: 62 outliers final: 0 residues processed: 62 average time/residue: 0.6172 time to fit residues: 75.6865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 169 optimal weight: 0.9980 chunk 452 optimal weight: 10.0000 chunk 99 optimal weight: 0.8980 chunk 295 optimal weight: 6.9990 chunk 124 optimal weight: 0.8980 chunk 503 optimal weight: 4.9990 chunk 417 optimal weight: 10.0000 chunk 232 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 chunk 166 optimal weight: 0.2980 chunk 264 optimal weight: 6.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 199 GLN B 200 HIS H 85 GLN L 50 GLN L 76 HIS L 182 ASN P 17 HIS Q 60 GLN S 162 ASN ** V 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 131 HIS V 137 GLN W 13 ASN ** Y 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 61 ASN Z 106 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 86434 Z= 0.121 Angle : 0.531 10.629 130233 Z= 0.277 Chirality : 0.033 0.270 16792 Planarity : 0.004 0.045 6241 Dihedral : 15.449 179.759 35802 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer Outliers : 1.67 % 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: -2.29 (0.16), residues: 2500 helix: -0.58 (0.21), residues: 602 sheet: -1.54 (0.23), residues: 494 loop : -1.96 (0.15), residues: 1404 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 2153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 504 time to evaluate : 3.366 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 18 residues processed: 520 average time/residue: 0.8762 time to fit residues: 756.0824 Evaluate side-chains 487 residues out of total 2153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 469 time to evaluate : 3.325 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.6005 time to fit residues: 24.0344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 485 optimal weight: 8.9990 chunk 56 optimal weight: 9.9990 chunk 286 optimal weight: 8.9990 chunk 367 optimal weight: 8.9990 chunk 284 optimal weight: 10.0000 chunk 423 optimal weight: 10.0000 chunk 280 optimal weight: 10.0000 chunk 501 optimal weight: 9.9990 chunk 313 optimal weight: 10.0000 chunk 305 optimal weight: 6.9990 chunk 231 optimal weight: 0.7980 overall best weight: 6.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 200 HIS C 37 GLN ** C 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN L 50 GLN L 192 ASN L 200 ASN P 17 HIS Q 7 HIS ** S 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 3 GLN V 8 ASN V 137 GLN W 13 ASN X 4 HIS X 78 ASN ** Y 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 55 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.010 0.110 86434 Z= 0.602 Angle : 0.917 12.390 130233 Z= 0.449 Chirality : 0.051 0.321 16792 Planarity : 0.007 0.093 6241 Dihedral : 16.153 179.042 35802 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.88 % Favored : 89.12 % Rotamer Outliers : 3.44 % 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: -2.76 (0.15), residues: 2500 helix: -1.20 (0.20), residues: 610 sheet: -1.62 (0.22), residues: 513 loop : -2.25 (0.15), residues: 1377 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 2153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 448 time to evaluate : 3.460 Fit side-chains revert: symmetry clash outliers start: 74 outliers final: 54 residues processed: 490 average time/residue: 0.8502 time to fit residues: 694.6034 Evaluate side-chains 493 residues out of total 2153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 439 time to evaluate : 3.228 Switching outliers to nearest non-outliers outliers start: 54 outliers final: 0 residues processed: 54 average time/residue: 0.6129 time to fit residues: 66.3274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 310 optimal weight: 3.9990 chunk 200 optimal weight: 1.9990 chunk 299 optimal weight: 4.9990 chunk 150 optimal weight: 0.6980 chunk 98 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 318 optimal weight: 8.9990 chunk 341 optimal weight: 0.9990 chunk 247 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 chunk 393 optimal weight: 1.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 194 GLN B 199 GLN B 200 HIS C 37 GLN ** C 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 20 GLN L 37 GLN L 50 GLN L 182 ASN ** S 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 3 GLN V 137 GLN W 13 ASN ** Y 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 61 ASN a 55 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.039 86434 Z= 0.150 Angle : 0.557 11.678 130233 Z= 0.291 Chirality : 0.035 0.283 16792 Planarity : 0.004 0.043 6241 Dihedral : 15.506 179.314 35802 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer Outliers : 1.07 % 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: -2.22 (0.16), residues: 2500 helix: -0.64 (0.21), residues: 601 sheet: -1.37 (0.23), residues: 506 loop : -1.91 (0.15), residues: 1393 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 2153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 482 time to evaluate : 3.355 Fit side-chains outliers start: 23 outliers final: 12 residues processed: 489 average time/residue: 0.8568 time to fit residues: 690.8845 Evaluate side-chains 464 residues out of total 2153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 452 time to evaluate : 3.336 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.5615 time to fit residues: 16.4883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 455 optimal weight: 10.0000 chunk 480 optimal weight: 7.9990 chunk 438 optimal weight: 6.9990 chunk 467 optimal weight: 7.9990 chunk 281 optimal weight: 10.0000 chunk 203 optimal weight: 6.9990 chunk 366 optimal weight: 7.9990 chunk 143 optimal weight: 0.8980 chunk 422 optimal weight: 10.0000 chunk 441 optimal weight: 10.0000 chunk 465 optimal weight: 6.9990 overall best weight: 5.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 70 ASN ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 GLN ** C 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 97 ASN L 37 GLN L 50 GLN L 192 ASN L 200 ASN N 32 ASN ** S 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 137 GLN W 13 ASN ** Y 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 55 GLN a 102 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.100 86434 Z= 0.522 Angle : 0.840 12.307 130233 Z= 0.416 Chirality : 0.048 0.315 16792 Planarity : 0.007 0.086 6241 Dihedral : 16.002 179.214 35802 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.48 % Favored : 89.52 % Rotamer Outliers : 1.86 % 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: -2.59 (0.16), residues: 2500 helix: -1.08 (0.20), residues: 611 sheet: -1.51 (0.22), residues: 510 loop : -2.13 (0.15), residues: 1379 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 2153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 457 time to evaluate : 3.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 31 residues processed: 474 average time/residue: 0.8568 time to fit residues: 672.2813 Evaluate side-chains 485 residues out of total 2153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 454 time to evaluate : 3.363 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.6658 time to fit residues: 40.7039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 306 optimal weight: 2.9990 chunk 493 optimal weight: 2.9990 chunk 301 optimal weight: 5.9990 chunk 234 optimal weight: 0.9990 chunk 343 optimal weight: 4.9990 chunk 518 optimal weight: 10.0000 chunk 476 optimal weight: 6.9990 chunk 412 optimal weight: 4.9990 chunk 42 optimal weight: 0.6980 chunk 318 optimal weight: 10.0000 chunk 252 optimal weight: 8.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 53 HIS B 200 HIS C 37 GLN ** C 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 33 ASN L 37 GLN L 182 ASN L 192 ASN V 137 GLN W 13 ASN ** Y 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 61 ASN ** Z 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 86434 Z= 0.246 Angle : 0.613 13.426 130233 Z= 0.316 Chirality : 0.038 0.299 16792 Planarity : 0.005 0.052 6241 Dihedral : 15.613 178.340 35802 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer Outliers : 0.56 % 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: -2.29 (0.16), residues: 2500 helix: -0.77 (0.21), residues: 603 sheet: -1.36 (0.23), residues: 494 loop : -1.96 (0.15), residues: 1403 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 2153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 467 time to evaluate : 3.357 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 9 residues processed: 470 average time/residue: 0.8719 time to fit residues: 678.9428 Evaluate side-chains 466 residues out of total 2153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 457 time to evaluate : 3.385 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.5836 time to fit residues: 13.6328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 327 optimal weight: 6.9990 chunk 439 optimal weight: 7.9990 chunk 126 optimal weight: 0.1980 chunk 380 optimal weight: 8.9990 chunk 60 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 413 optimal weight: 7.9990 chunk 172 optimal weight: 9.9990 chunk 424 optimal weight: 10.0000 chunk 52 optimal weight: 9.9990 chunk 76 optimal weight: 7.9990 overall best weight: 4.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 37 GLN ** C 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 97 ASN K 36 GLN L 50 GLN L 192 ASN L 200 ASN V 137 GLN W 13 ASN W 110 ASN ** Y 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 61 ASN a 55 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.139050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.123373 restraints weight = 110193.259| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 0.70 r_work: 0.3103 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.078 86434 Z= 0.380 Angle : 0.715 15.159 130233 Z= 0.361 Chirality : 0.042 0.303 16792 Planarity : 0.006 0.072 6241 Dihedral : 15.772 179.581 35802 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.56 % Favored : 90.44 % Rotamer Outliers : 0.79 % 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: -2.39 (0.16), residues: 2500 helix: -0.88 (0.20), residues: 607 sheet: -1.40 (0.23), residues: 494 loop : -2.01 (0.15), residues: 1399 =============================================================================== Job complete usr+sys time: 13394.80 seconds wall clock time: 241 minutes 4.38 seconds (14464.38 seconds total)