Starting phenix.real_space_refine on Mon Feb 19 10:15:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ddd_7867/02_2024/6ddd_7867_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ddd_7867/02_2024/6ddd_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_7867/02_2024/6ddd_7867.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ddd_7867/02_2024/6ddd_7867.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ddd_7867/02_2024/6ddd_7867_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ddd_7867/02_2024/6ddd_7867_trim_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 30.06, per 1000 atoms: 0.38 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: 31.89 Conformation dependent library (CDL) restraints added in 3.5 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: 36.93 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: 112.34 Time building geometry restraints manager: 34.57 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: 48398 35.98 - 71.95: 6189 71.95 - 107.93: 624 107.93 - 143.91: 15 143.91 - 179.88: 34 Dihedral angle restraints: 55260 sinusoidal: 47994 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 55257 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: 2.680 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: 12.520 Check model and map are aligned: 0.900 Set scattering table: 0.560 Process input model: 262.350 Find NCS groups from input model: 1.170 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:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 283.060 ------------------------------------------------------------------------------- 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 : 23.613 179.882 50577 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 % Allowed : 2.65 % Favored : 97.31 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.005 TRP B 213 HIS 0.015 0.003 HIS E 102 PHE 0.044 0.003 PHE L 127 TYR 0.036 0.003 TYR F 58 ARG 0.017 0.002 ARG X 18 *********************** 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 : 3.116 Fit side-chains REVERT: C 91 ASN cc_start: 0.8567 (p0) cc_final: 0.8304 (p0) REVERT: D 69 LYS cc_start: 0.7445 (mmtt) cc_final: 0.7214 (mmmt) REVERT: D 78 ARG cc_start: 0.7848 (ptt180) cc_final: 0.7551 (ptt180) REVERT: E 59 GLU cc_start: 0.5888 (pp20) cc_final: 0.5660 (pp20) REVERT: F 12 ILE cc_start: 0.8380 (pt) cc_final: 0.8054 (tp) REVERT: H 68 LYS cc_start: 0.6803 (pttp) cc_final: 0.6126 (mptt) REVERT: I 61 ARG cc_start: 0.8741 (ppt-90) cc_final: 0.8424 (ptt90) REVERT: I 90 TYR cc_start: 0.6906 (m-10) cc_final: 0.6690 (m-80) REVERT: K 54 LYS cc_start: 0.8812 (mmmm) cc_final: 0.8533 (mmmt) REVERT: L 8 ARG cc_start: 0.8465 (ttm-80) cc_final: 0.8159 (ttm170) REVERT: O 21 LYS cc_start: 0.7738 (pttt) cc_final: 0.7045 (ttmt) REVERT: P 7 GLN cc_start: 0.8889 (mm110) cc_final: 0.8678 (mm-40) REVERT: S 77 THR cc_start: 0.8687 (p) cc_final: 0.8427 (t) REVERT: S 179 GLN cc_start: 0.7139 (tp40) cc_final: 0.6786 (mm-40) REVERT: V 121 LYS cc_start: 0.8124 (ptpt) cc_final: 0.7772 (pttt) REVERT: W 59 LYS cc_start: 0.8241 (mttt) cc_final: 0.7851 (mtmt) REVERT: X 38 GLN cc_start: 0.8429 (tt0) cc_final: 0.8158 (tt0) REVERT: X 73 GLU cc_start: 0.6135 (pt0) cc_final: 0.5849 (pt0) REVERT: Y 26 TYR cc_start: 0.8029 (m-80) cc_final: 0.7770 (m-10) REVERT: Y 48 GLU cc_start: 0.6933 (mm-30) cc_final: 0.6277 (mm-30) REVERT: Z 79 GLN cc_start: 0.7070 (mt0) cc_final: 0.6693 (mt0) REVERT: a 8 ASN cc_start: 0.7242 (t0) cc_final: 0.7020 (t0) outliers start: 1 outliers final: 1 residues processed: 748 average time/residue: 0.8885 time to fit residues: 1067.4808 Evaluate side-chains 543 residues out of total 2153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 542 time to evaluate : 3.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 18 THR 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: 8.9990 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: 2.2986 ------------------------------------------------------------------------------- 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 40 ASN E 57 ASN E 60 HIS E 61 ASN F 34 ASN F 57 ASN 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 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: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 86434 Z= 0.228 Angle : 0.625 11.213 130233 Z= 0.322 Chirality : 0.038 0.273 16792 Planarity : 0.005 0.059 6241 Dihedral : 23.912 179.476 45377 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 3.53 % Allowed : 10.13 % Favored : 86.34 % 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: -3.54 (0.14), residues: 2500 helix: -1.70 (0.19), residues: 603 sheet: -2.50 (0.20), residues: 495 loop : -2.64 (0.14), residues: 1402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 213 HIS 0.009 0.001 HIS B 53 PHE 0.019 0.002 PHE Y 32 TYR 0.018 0.002 TYR F 58 ARG 0.005 0.001 ARG W 71 *********************** 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 637 residues out of total 2153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 561 time to evaluate : 3.085 Fit side-chains revert: symmetry clash REVERT: B 153 GLN cc_start: 0.8096 (mt0) cc_final: 0.7865 (mt0) REVERT: D 69 LYS cc_start: 0.7378 (mmtt) cc_final: 0.7105 (mmmt) REVERT: I 33 ARG cc_start: 0.8938 (mmt180) cc_final: 0.8727 (mmt-90) REVERT: L 162 ARG cc_start: 0.8666 (OUTLIER) cc_final: 0.7357 (ppt-90) REVERT: L 182 ASN cc_start: 0.8418 (m-40) cc_final: 0.8087 (m-40) REVERT: M 52 HIS cc_start: 0.9033 (OUTLIER) cc_final: 0.8651 (p-80) REVERT: P 34 ARG cc_start: 0.8387 (ttp-170) cc_final: 0.8132 (ttp-110) REVERT: S 179 GLN cc_start: 0.7099 (tp40) cc_final: 0.6845 (mm-40) REVERT: X 73 GLU cc_start: 0.6100 (pt0) cc_final: 0.5856 (pt0) REVERT: Y 48 GLU cc_start: 0.6879 (mm-30) cc_final: 0.6072 (mm-30) REVERT: a 55 GLN cc_start: 0.7092 (OUTLIER) cc_final: 0.5895 (tp-100) outliers start: 76 outliers final: 48 residues processed: 590 average time/residue: 0.9015 time to fit residues: 887.7016 Evaluate side-chains 550 residues out of total 2153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 499 time to evaluate : 3.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 74 MET Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain G residue 27 LEU Chi-restraints excluded: chain G residue 66 SER Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain I residue 71 ILE Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 88 SER Chi-restraints excluded: chain I residue 92 VAL Chi-restraints excluded: chain J residue 46 LYS Chi-restraints excluded: chain K residue 20 SER Chi-restraints excluded: chain K residue 28 LEU Chi-restraints excluded: chain L residue 13 THR Chi-restraints excluded: chain L residue 96 VAL Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 162 ARG Chi-restraints excluded: chain M residue 18 THR Chi-restraints excluded: chain M residue 52 HIS Chi-restraints excluded: chain N residue 48 SER Chi-restraints excluded: chain O residue 37 SER Chi-restraints excluded: chain Q residue 29 THR Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 70 THR Chi-restraints excluded: chain V residue 3 GLN Chi-restraints excluded: chain V residue 35 SER Chi-restraints excluded: chain V residue 71 THR Chi-restraints excluded: chain X residue 99 SER Chi-restraints excluded: chain Y residue 1 MET Chi-restraints excluded: chain Y residue 75 THR Chi-restraints excluded: chain Y residue 132 VAL Chi-restraints excluded: chain Z residue 42 SER Chi-restraints excluded: chain Z residue 89 ILE Chi-restraints excluded: chain a residue 44 ILE Chi-restraints excluded: chain a residue 45 ILE Chi-restraints excluded: chain a residue 53 LEU Chi-restraints excluded: chain a residue 55 GLN Chi-restraints excluded: chain a residue 93 VAL 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: 0.3980 chunk 393 optimal weight: 7.9990 chunk 321 optimal weight: 7.9990 chunk 130 optimal weight: 8.9990 chunk 473 optimal weight: 8.9990 chunk 511 optimal weight: 10.0000 chunk 421 optimal weight: 10.0000 chunk 469 optimal weight: 10.0000 chunk 161 optimal weight: 6.9990 chunk 379 optimal weight: 10.0000 overall best weight: 6.4788 ------------------------------------------------------------------------------- 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 81 ASN F 54 ASN L 33 ASN L 192 ASN L 200 ASN O 45 HIS ** Q 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 67 GLN ** S 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 8 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 a 55 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.103 86434 Z= 0.573 Angle : 0.907 12.521 130233 Z= 0.447 Chirality : 0.051 0.321 16792 Planarity : 0.008 0.094 6241 Dihedral : 24.097 179.342 45377 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.44 % Favored : 89.56 % Rotamer: Outliers : 5.90 % Allowed : 13.47 % Favored : 80.63 % 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: -3.45 (0.14), residues: 2500 helix: -1.73 (0.19), residues: 608 sheet: -2.28 (0.21), residues: 489 loop : -2.60 (0.14), residues: 1403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.004 TRP J 29 HIS 0.019 0.002 HIS M 52 PHE 0.029 0.003 PHE L 91 TYR 0.029 0.003 TYR F 58 ARG 0.008 0.001 ARG W 107 *********************** 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 607 residues out of total 2153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 480 time to evaluate : 3.096 Fit side-chains REVERT: A 18 ASP cc_start: 0.4642 (OUTLIER) cc_final: 0.4356 (p0) REVERT: B 147 LYS cc_start: 0.8371 (mmtp) cc_final: 0.8032 (mtpt) REVERT: D 69 LYS cc_start: 0.7582 (mmtt) cc_final: 0.7281 (mmmt) REVERT: G 57 LEU cc_start: 0.5919 (OUTLIER) cc_final: 0.5638 (tp) REVERT: I 33 ARG cc_start: 0.9054 (mmt180) cc_final: 0.8797 (mmt-90) REVERT: L 44 ASP cc_start: 0.7259 (OUTLIER) cc_final: 0.6823 (p0) REVERT: L 103 GLN cc_start: 0.7632 (OUTLIER) cc_final: 0.7352 (pt0) REVERT: L 162 ARG cc_start: 0.8769 (OUTLIER) cc_final: 0.7358 (ppt-90) REVERT: L 210 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.7699 (mp0) REVERT: N 7 ARG cc_start: 0.8603 (OUTLIER) cc_final: 0.8386 (ptt180) REVERT: Q 52 LYS cc_start: 0.8075 (ptpt) cc_final: 0.7720 (mmtm) REVERT: V 137 GLN cc_start: 0.7881 (OUTLIER) cc_final: 0.6927 (mp-120) REVERT: W 120 GLU cc_start: 0.7414 (OUTLIER) cc_final: 0.7070 (pt0) REVERT: Y 48 GLU cc_start: 0.6993 (mm-30) cc_final: 0.6242 (mm-30) REVERT: Z 44 VAL cc_start: 0.9383 (p) cc_final: 0.9045 (t) REVERT: Z 118 ILE cc_start: 0.9045 (mt) cc_final: 0.8735 (mt) outliers start: 127 outliers final: 91 residues processed: 555 average time/residue: 0.8896 time to fit residues: 836.0818 Evaluate side-chains 565 residues out of total 2153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 465 time to evaluate : 3.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 18 ASP Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 134 ASN Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 257 LYS Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 74 MET Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain F residue 23 ASP Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain G residue 27 LEU Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain G residue 66 SER Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain I residue 71 ILE Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 88 SER Chi-restraints excluded: chain J residue 46 LYS Chi-restraints excluded: chain K residue 20 SER Chi-restraints excluded: chain K residue 28 LEU Chi-restraints excluded: chain K residue 37 LEU Chi-restraints excluded: chain K residue 39 GLU Chi-restraints excluded: chain K residue 43 ILE Chi-restraints excluded: chain L residue 13 THR Chi-restraints excluded: chain L residue 44 ASP Chi-restraints excluded: chain L residue 96 VAL Chi-restraints excluded: chain L residue 103 GLN Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 121 VAL Chi-restraints excluded: chain L residue 122 SER Chi-restraints excluded: chain L residue 137 SER Chi-restraints excluded: chain L residue 162 ARG Chi-restraints excluded: chain L residue 200 ASN Chi-restraints excluded: chain L residue 210 GLU Chi-restraints excluded: chain M residue 18 THR Chi-restraints excluded: chain M residue 23 VAL Chi-restraints excluded: chain M residue 43 ILE Chi-restraints excluded: chain N residue 7 ARG Chi-restraints excluded: chain N residue 18 THR Chi-restraints excluded: chain N residue 48 SER Chi-restraints excluded: chain O residue 10 THR Chi-restraints excluded: chain O residue 33 LYS Chi-restraints excluded: chain O residue 37 SER Chi-restraints excluded: chain O residue 43 THR Chi-restraints excluded: chain P residue 34 ARG Chi-restraints excluded: chain Q residue 29 THR Chi-restraints excluded: chain R residue 7 VAL Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 70 THR Chi-restraints excluded: chain V residue 3 GLN Chi-restraints excluded: chain V residue 35 SER Chi-restraints excluded: chain V residue 66 THR Chi-restraints excluded: chain V residue 71 THR Chi-restraints excluded: chain V residue 87 SER Chi-restraints excluded: chain V residue 105 SER Chi-restraints excluded: chain V residue 137 GLN Chi-restraints excluded: chain W residue 98 ILE Chi-restraints excluded: chain W residue 120 GLU Chi-restraints excluded: chain Y residue 1 MET Chi-restraints excluded: chain Y residue 42 ILE Chi-restraints excluded: chain Y residue 75 THR Chi-restraints excluded: chain Y residue 129 THR Chi-restraints excluded: chain Y residue 132 VAL Chi-restraints excluded: chain Z residue 42 SER Chi-restraints excluded: chain Z residue 71 ILE Chi-restraints excluded: chain Z residue 89 ILE Chi-restraints excluded: chain Z residue 119 ILE Chi-restraints excluded: chain a residue 44 ILE Chi-restraints excluded: chain a residue 45 ILE Chi-restraints excluded: chain a residue 53 LEU Chi-restraints excluded: chain a residue 92 ILE Chi-restraints excluded: chain a residue 93 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 467 optimal weight: 4.9990 chunk 355 optimal weight: 6.9990 chunk 245 optimal weight: 6.9990 chunk 52 optimal weight: 2.9990 chunk 225 optimal weight: 2.9990 chunk 317 optimal weight: 3.9990 chunk 474 optimal weight: 6.9990 chunk 502 optimal weight: 4.9990 chunk 248 optimal weight: 4.9990 chunk 449 optimal weight: 4.9990 chunk 135 optimal weight: 6.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 200 ASN M 52 HIS O 4 ASN Q 7 HIS Q 31 HIS S 67 GLN ** S 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 3 GLN V 8 ASN V 137 GLN W 13 ASN ** 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: 0.8149 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 86434 Z= 0.361 Angle : 0.717 12.345 130233 Z= 0.363 Chirality : 0.043 0.309 16792 Planarity : 0.006 0.072 6241 Dihedral : 23.916 178.862 45377 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer: Outliers : 5.81 % Allowed : 15.47 % Favored : 78.73 % 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: -3.10 (0.15), residues: 2500 helix: -1.39 (0.20), residues: 606 sheet: -2.02 (0.21), residues: 497 loop : -2.42 (0.14), residues: 1397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP B 250 HIS 0.007 0.001 HIS E 102 PHE 0.019 0.002 PHE L 91 TYR 0.017 0.002 TYR Z 93 ARG 0.006 0.001 ARG S 84 *********************** 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 605 residues out of total 2153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 480 time to evaluate : 3.081 Fit side-chains REVERT: B 180 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.6859 (tt0) REVERT: G 16 ASP cc_start: 0.6452 (m-30) cc_final: 0.6182 (m-30) REVERT: G 57 LEU cc_start: 0.6035 (OUTLIER) cc_final: 0.5782 (tp) REVERT: L 32 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7491 (mt-10) REVERT: L 44 ASP cc_start: 0.7214 (OUTLIER) cc_final: 0.6807 (p0) REVERT: L 103 GLN cc_start: 0.7446 (OUTLIER) cc_final: 0.7127 (pt0) REVERT: L 162 ARG cc_start: 0.8731 (OUTLIER) cc_final: 0.7359 (ppt-90) REVERT: L 210 GLU cc_start: 0.7969 (OUTLIER) cc_final: 0.7745 (mp0) REVERT: M 52 HIS cc_start: 0.9024 (OUTLIER) cc_final: 0.8654 (p-80) REVERT: S 67 GLN cc_start: 0.7655 (OUTLIER) cc_final: 0.7277 (tt0) REVERT: S 162 ASN cc_start: 0.7134 (t0) cc_final: 0.6850 (t0) REVERT: Y 48 GLU cc_start: 0.6920 (mm-30) cc_final: 0.6236 (mm-30) REVERT: Z 44 VAL cc_start: 0.9365 (p) cc_final: 0.9015 (t) REVERT: Z 118 ILE cc_start: 0.9002 (mt) cc_final: 0.8674 (mt) outliers start: 125 outliers final: 90 residues processed: 551 average time/residue: 0.8002 time to fit residues: 743.6994 Evaluate side-chains 563 residues out of total 2153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 464 time to evaluate : 3.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 257 LYS Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 74 MET Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain F residue 6 ILE Chi-restraints excluded: chain F residue 23 ASP Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain G residue 27 LEU Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain G residue 66 SER Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 40 THR Chi-restraints excluded: chain I residue 71 ILE Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 88 SER Chi-restraints excluded: chain J residue 46 LYS Chi-restraints excluded: chain K residue 20 SER Chi-restraints excluded: chain K residue 28 LEU Chi-restraints excluded: chain K residue 39 GLU Chi-restraints excluded: chain K residue 43 ILE Chi-restraints excluded: chain L residue 13 THR Chi-restraints excluded: chain L residue 32 GLU Chi-restraints excluded: chain L residue 33 ASN Chi-restraints excluded: chain L residue 44 ASP Chi-restraints excluded: chain L residue 96 VAL Chi-restraints excluded: chain L residue 103 GLN Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 121 VAL Chi-restraints excluded: chain L residue 122 SER Chi-restraints excluded: chain L residue 137 SER Chi-restraints excluded: chain L residue 162 ARG Chi-restraints excluded: chain L residue 190 THR Chi-restraints excluded: chain L residue 210 GLU Chi-restraints excluded: chain M residue 18 THR Chi-restraints excluded: chain M residue 23 VAL Chi-restraints excluded: chain M residue 43 ILE Chi-restraints excluded: chain M residue 52 HIS Chi-restraints excluded: chain N residue 18 THR Chi-restraints excluded: chain N residue 48 SER Chi-restraints excluded: chain O residue 4 ASN Chi-restraints excluded: chain O residue 10 THR Chi-restraints excluded: chain O residue 33 LYS Chi-restraints excluded: chain O residue 37 SER Chi-restraints excluded: chain O residue 41 LYS Chi-restraints excluded: chain P residue 25 THR Chi-restraints excluded: chain Q residue 29 THR Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 67 GLN Chi-restraints excluded: chain S residue 70 THR Chi-restraints excluded: chain V residue 3 GLN Chi-restraints excluded: chain V residue 10 SER Chi-restraints excluded: chain V residue 35 SER Chi-restraints excluded: chain V residue 53 ASP Chi-restraints excluded: chain V residue 66 THR Chi-restraints excluded: chain V residue 71 THR Chi-restraints excluded: chain V residue 105 SER Chi-restraints excluded: chain W residue 90 ASP Chi-restraints excluded: chain W residue 113 LYS Chi-restraints excluded: chain Y residue 1 MET Chi-restraints excluded: chain Y residue 75 THR Chi-restraints excluded: chain Y residue 129 THR Chi-restraints excluded: chain Y residue 132 VAL Chi-restraints excluded: chain Z residue 42 SER Chi-restraints excluded: chain Z residue 71 ILE Chi-restraints excluded: chain Z residue 89 ILE Chi-restraints excluded: chain Z residue 119 ILE Chi-restraints excluded: chain a residue 22 LEU Chi-restraints excluded: chain a residue 44 ILE Chi-restraints excluded: chain a residue 45 ILE Chi-restraints excluded: chain a residue 53 LEU Chi-restraints excluded: chain a residue 92 ILE Chi-restraints excluded: chain a residue 93 VAL 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: 0.6980 chunk 374 optimal weight: 6.9990 chunk 207 optimal weight: 8.9990 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: 3.9990 overall best weight: 5.7388 ------------------------------------------------------------------------------- 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 200 ASN M 52 HIS O 4 ASN P 17 HIS Q 7 HIS ** S 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 59 ASN V 137 GLN W 13 ASN X 4 HIS ** Y 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 61 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.098 86434 Z= 0.507 Angle : 0.838 13.893 130233 Z= 0.416 Chirality : 0.048 0.318 16792 Planarity : 0.007 0.083 6241 Dihedral : 24.002 179.941 45377 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.48 % Favored : 89.52 % Rotamer: Outliers : 7.90 % Allowed : 15.70 % Favored : 76.41 % 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: -3.08 (0.15), residues: 2500 helix: -1.47 (0.20), residues: 609 sheet: -1.89 (0.22), residues: 502 loop : -2.42 (0.15), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP B 250 HIS 0.009 0.002 HIS E 102 PHE 0.025 0.003 PHE L 91 TYR 0.022 0.003 TYR Z 93 ARG 0.010 0.001 ARG B 260 *********************** 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 630 residues out of total 2153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 460 time to evaluate : 3.129 Fit side-chains REVERT: A 112 ILE cc_start: 0.8116 (OUTLIER) cc_final: 0.7698 (mm) REVERT: B 180 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7141 (tt0) REVERT: E 66 THR cc_start: 0.8263 (p) cc_final: 0.7859 (m) REVERT: G 57 LEU cc_start: 0.5926 (OUTLIER) cc_final: 0.5716 (tp) REVERT: L 32 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7523 (mt-10) REVERT: L 44 ASP cc_start: 0.7253 (OUTLIER) cc_final: 0.6838 (p0) REVERT: L 99 TYR cc_start: 0.7050 (OUTLIER) cc_final: 0.6662 (m-10) REVERT: L 162 ARG cc_start: 0.8749 (OUTLIER) cc_final: 0.7451 (ppt-90) REVERT: L 210 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7733 (mp0) REVERT: M 52 HIS cc_start: 0.9085 (OUTLIER) cc_final: 0.8802 (p-80) REVERT: Q 52 LYS cc_start: 0.8043 (ptpt) cc_final: 0.7644 (mmtm) REVERT: S 162 ASN cc_start: 0.7301 (t0) cc_final: 0.7086 (t0) REVERT: Y 48 GLU cc_start: 0.7037 (mm-30) cc_final: 0.6307 (mm-30) REVERT: Z 44 VAL cc_start: 0.9413 (p) cc_final: 0.9076 (t) outliers start: 170 outliers final: 129 residues processed: 569 average time/residue: 0.8378 time to fit residues: 800.5215 Evaluate side-chains 595 residues out of total 2153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 457 time to evaluate : 3.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 134 ASN Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 257 LYS Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 74 MET Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 108 SER Chi-restraints excluded: chain F residue 6 ILE Chi-restraints excluded: chain F residue 23 ASP Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain G residue 8 ASN Chi-restraints excluded: chain G residue 27 LEU Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 66 SER Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 40 THR Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain I residue 71 ILE Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 88 SER Chi-restraints excluded: chain J residue 7 VAL Chi-restraints excluded: chain J residue 46 LYS Chi-restraints excluded: chain J residue 59 VAL Chi-restraints excluded: chain K residue 20 SER Chi-restraints excluded: chain K residue 28 LEU Chi-restraints excluded: chain K residue 37 LEU Chi-restraints excluded: chain K residue 39 GLU Chi-restraints excluded: chain K residue 43 ILE Chi-restraints excluded: chain L residue 13 THR Chi-restraints excluded: chain L residue 32 GLU Chi-restraints excluded: chain L residue 33 ASN Chi-restraints excluded: chain L residue 44 ASP Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain L residue 62 ASP Chi-restraints excluded: chain L residue 96 VAL Chi-restraints excluded: chain L residue 99 TYR Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 121 VAL Chi-restraints excluded: chain L residue 122 SER Chi-restraints excluded: chain L residue 137 SER Chi-restraints excluded: chain L residue 162 ARG Chi-restraints excluded: chain L residue 190 THR Chi-restraints excluded: chain L residue 200 ASN Chi-restraints excluded: chain L residue 210 GLU Chi-restraints excluded: chain M residue 18 THR Chi-restraints excluded: chain M residue 23 VAL Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 43 ILE Chi-restraints excluded: chain M residue 52 HIS Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 18 THR Chi-restraints excluded: chain N residue 48 SER Chi-restraints excluded: chain O residue 4 ASN Chi-restraints excluded: chain O residue 6 THR Chi-restraints excluded: chain O residue 10 THR Chi-restraints excluded: chain O residue 16 ASN Chi-restraints excluded: chain O residue 33 LYS Chi-restraints excluded: chain O residue 37 SER Chi-restraints excluded: chain O residue 41 LYS Chi-restraints excluded: chain O residue 43 THR Chi-restraints excluded: chain P residue 25 THR Chi-restraints excluded: chain Q residue 29 THR Chi-restraints excluded: chain Q residue 60 GLN Chi-restraints excluded: chain R residue 7 VAL Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 70 THR Chi-restraints excluded: chain S residue 96 SER Chi-restraints excluded: chain V residue 3 GLN Chi-restraints excluded: chain V residue 10 SER Chi-restraints excluded: chain V residue 35 SER Chi-restraints excluded: chain V residue 53 ASP Chi-restraints excluded: chain V residue 66 THR Chi-restraints excluded: chain V residue 71 THR Chi-restraints excluded: chain V residue 87 SER Chi-restraints excluded: chain V residue 105 SER Chi-restraints excluded: chain W residue 77 ILE Chi-restraints excluded: chain W residue 90 ASP Chi-restraints excluded: chain W residue 113 LYS Chi-restraints excluded: chain W residue 115 VAL Chi-restraints excluded: chain X residue 107 SER Chi-restraints excluded: chain Y residue 1 MET Chi-restraints excluded: chain Y residue 5 LYS Chi-restraints excluded: chain Y residue 42 ILE Chi-restraints excluded: chain Y residue 43 THR Chi-restraints excluded: chain Y residue 75 THR Chi-restraints excluded: chain Y residue 129 THR Chi-restraints excluded: chain Z residue 42 SER Chi-restraints excluded: chain Z residue 71 ILE Chi-restraints excluded: chain Z residue 89 ILE Chi-restraints excluded: chain Z residue 119 ILE Chi-restraints excluded: chain a residue 22 LEU Chi-restraints excluded: chain a residue 44 ILE Chi-restraints excluded: chain a residue 45 ILE Chi-restraints excluded: chain a residue 53 LEU Chi-restraints excluded: chain a residue 92 ILE Chi-restraints excluded: chain a residue 93 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 169 optimal weight: 0.6980 chunk 452 optimal weight: 10.0000 chunk 99 optimal weight: 0.7980 chunk 295 optimal weight: 6.9990 chunk 124 optimal weight: 0.7980 chunk 503 optimal weight: 4.9990 chunk 417 optimal weight: 8.9990 chunk 232 optimal weight: 6.9990 chunk 41 optimal weight: 0.7980 chunk 166 optimal weight: 0.8980 chunk 264 optimal weight: 6.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 ** C 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 97 ASN H 85 GLN L 50 GLN L 76 HIS M 52 HIS O 4 ASN P 17 HIS S 67 GLN ** S 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 131 HIS W 13 ASN ** Y 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 61 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 86434 Z= 0.121 Angle : 0.543 10.098 130233 Z= 0.283 Chirality : 0.033 0.276 16792 Planarity : 0.004 0.046 6241 Dihedral : 23.676 179.693 45377 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 3.53 % Allowed : 19.97 % Favored : 76.50 % 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: -2.33 (0.16), residues: 2500 helix: -0.66 (0.21), residues: 598 sheet: -1.49 (0.23), residues: 488 loop : -2.01 (0.15), residues: 1414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP J 48 HIS 0.009 0.001 HIS M 52 PHE 0.013 0.001 PHE S 139 TYR 0.018 0.001 TYR V 141 ARG 0.004 0.000 ARG Y 56 *********************** 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 585 residues out of total 2153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 509 time to evaluate : 3.126 Fit side-chains REVERT: A 93 LYS cc_start: 0.7525 (tttp) cc_final: 0.7317 (tptt) REVERT: B 187 THR cc_start: 0.7996 (OUTLIER) cc_final: 0.7748 (m) REVERT: E 66 THR cc_start: 0.8310 (p) cc_final: 0.7871 (m) REVERT: G 57 LEU cc_start: 0.5908 (OUTLIER) cc_final: 0.5669 (tp) REVERT: I 84 LYS cc_start: 0.8148 (mmtp) cc_final: 0.7935 (mttm) REVERT: J 37 ARG cc_start: 0.7361 (ttm110) cc_final: 0.7012 (ttm170) REVERT: O 32 MET cc_start: 0.8028 (OUTLIER) cc_final: 0.7729 (mpp) REVERT: S 67 GLN cc_start: 0.7424 (OUTLIER) cc_final: 0.7188 (tt0) REVERT: W 87 ILE cc_start: 0.8585 (mm) cc_final: 0.8181 (pt) REVERT: Y 17 THR cc_start: 0.7853 (OUTLIER) cc_final: 0.7604 (p) outliers start: 76 outliers final: 45 residues processed: 545 average time/residue: 0.8271 time to fit residues: 749.4866 Evaluate side-chains 527 residues out of total 2153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 477 time to evaluate : 3.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 257 LYS Chi-restraints excluded: chain C residue 74 MET Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain G residue 27 LEU Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain G residue 66 SER Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain I residue 40 THR Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 88 SER Chi-restraints excluded: chain J residue 46 LYS Chi-restraints excluded: chain K residue 20 SER Chi-restraints excluded: chain K residue 28 LEU Chi-restraints excluded: chain K residue 37 LEU Chi-restraints excluded: chain L residue 5 ILE Chi-restraints excluded: chain L residue 13 THR Chi-restraints excluded: chain L residue 33 ASN Chi-restraints excluded: chain L residue 96 VAL Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 122 SER Chi-restraints excluded: chain L residue 190 THR Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain N residue 48 SER Chi-restraints excluded: chain O residue 4 ASN Chi-restraints excluded: chain O residue 32 MET Chi-restraints excluded: chain O residue 33 LYS Chi-restraints excluded: chain O residue 37 SER Chi-restraints excluded: chain O residue 43 THR Chi-restraints excluded: chain P residue 25 THR Chi-restraints excluded: chain Q residue 29 THR Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain S residue 67 GLN Chi-restraints excluded: chain S residue 70 THR Chi-restraints excluded: chain V residue 53 ASP Chi-restraints excluded: chain V residue 63 ILE Chi-restraints excluded: chain V residue 102 ILE Chi-restraints excluded: chain W residue 120 GLU Chi-restraints excluded: chain Y residue 5 LYS Chi-restraints excluded: chain Y residue 17 THR Chi-restraints excluded: chain Y residue 42 ILE Chi-restraints excluded: chain Y residue 43 THR Chi-restraints excluded: chain Z residue 89 ILE Chi-restraints excluded: chain a residue 44 ILE Chi-restraints excluded: chain a residue 53 LEU 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: 1.9990 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: 10.0000 chunk 313 optimal weight: 10.0000 chunk 305 optimal weight: 6.9990 chunk 231 optimal weight: 7.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- 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 81 ASN E 97 ASN L 37 GLN L 50 GLN L 66 ASN L 192 ASN L 200 ASN N 32 ASN O 4 ASN P 17 HIS Q 7 HIS ** S 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 68 ASN V 137 GLN W 13 ASN X 78 ASN ** Y 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 55 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.113 86434 Z= 0.604 Angle : 0.923 12.368 130233 Z= 0.452 Chirality : 0.052 0.323 16792 Planarity : 0.007 0.093 6241 Dihedral : 23.958 179.214 45376 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.56 % Favored : 89.44 % Rotamer: Outliers : 6.32 % Allowed : 18.21 % Favored : 75.48 % 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: -2.82 (0.15), residues: 2500 helix: -1.30 (0.20), residues: 613 sheet: -1.63 (0.22), residues: 506 loop : -2.28 (0.15), residues: 1381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.004 TRP J 29 HIS 0.011 0.002 HIS E 102 PHE 0.028 0.003 PHE L 91 TYR 0.025 0.003 TYR Z 93 ARG 0.009 0.001 ARG L 162 *********************** 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 600 residues out of total 2153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 464 time to evaluate : 3.267 Fit side-chains REVERT: A 112 ILE cc_start: 0.8143 (OUTLIER) cc_final: 0.7730 (mm) REVERT: E 66 THR cc_start: 0.8338 (p) cc_final: 0.7924 (m) REVERT: G 57 LEU cc_start: 0.5984 (OUTLIER) cc_final: 0.5718 (tp) REVERT: L 44 ASP cc_start: 0.7246 (OUTLIER) cc_final: 0.6880 (p0) REVERT: L 162 ARG cc_start: 0.8789 (OUTLIER) cc_final: 0.7418 (ppt-90) REVERT: O 32 MET cc_start: 0.8193 (OUTLIER) cc_final: 0.7973 (mpp) REVERT: P 15 LYS cc_start: 0.8806 (mmtp) cc_final: 0.8408 (mmtt) REVERT: Q 52 LYS cc_start: 0.8083 (ptpt) cc_final: 0.7662 (mmtm) REVERT: W 87 ILE cc_start: 0.8635 (mm) cc_final: 0.8270 (pt) outliers start: 136 outliers final: 110 residues processed: 548 average time/residue: 0.8278 time to fit residues: 754.3397 Evaluate side-chains 578 residues out of total 2153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 463 time to evaluate : 3.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 257 LYS Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 74 MET Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 108 SER Chi-restraints excluded: chain F residue 6 ILE Chi-restraints excluded: chain F residue 23 ASP Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain G residue 8 ASN Chi-restraints excluded: chain G residue 27 LEU Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 66 SER Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain I residue 40 THR Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain I residue 71 ILE Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 88 SER Chi-restraints excluded: chain J residue 7 VAL Chi-restraints excluded: chain J residue 46 LYS Chi-restraints excluded: chain J residue 59 VAL Chi-restraints excluded: chain J residue 60 THR Chi-restraints excluded: chain K residue 20 SER Chi-restraints excluded: chain K residue 28 LEU Chi-restraints excluded: chain K residue 37 LEU Chi-restraints excluded: chain L residue 5 ILE Chi-restraints excluded: chain L residue 13 THR Chi-restraints excluded: chain L residue 21 GLU Chi-restraints excluded: chain L residue 33 ASN Chi-restraints excluded: chain L residue 44 ASP Chi-restraints excluded: chain L residue 62 ASP Chi-restraints excluded: chain L residue 96 VAL Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 122 SER Chi-restraints excluded: chain L residue 137 SER Chi-restraints excluded: chain L residue 162 ARG Chi-restraints excluded: chain L residue 190 THR Chi-restraints excluded: chain L residue 200 ASN Chi-restraints excluded: chain M residue 23 VAL Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 43 ILE Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 7 ARG Chi-restraints excluded: chain N residue 29 GLU Chi-restraints excluded: chain N residue 48 SER Chi-restraints excluded: chain O residue 4 ASN Chi-restraints excluded: chain O residue 16 ASN Chi-restraints excluded: chain O residue 32 MET Chi-restraints excluded: chain O residue 33 LYS Chi-restraints excluded: chain O residue 37 SER Chi-restraints excluded: chain O residue 41 LYS Chi-restraints excluded: chain O residue 43 THR Chi-restraints excluded: chain P residue 25 THR Chi-restraints excluded: chain P residue 34 ARG Chi-restraints excluded: chain Q residue 29 THR Chi-restraints excluded: chain Q residue 60 GLN Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain S residue 70 THR Chi-restraints excluded: chain S residue 96 SER Chi-restraints excluded: chain V residue 53 ASP Chi-restraints excluded: chain V residue 66 THR Chi-restraints excluded: chain V residue 71 THR Chi-restraints excluded: chain V residue 87 SER Chi-restraints excluded: chain V residue 105 SER Chi-restraints excluded: chain W residue 77 ILE Chi-restraints excluded: chain W residue 90 ASP Chi-restraints excluded: chain W residue 98 ILE Chi-restraints excluded: chain W residue 120 GLU Chi-restraints excluded: chain X residue 107 SER Chi-restraints excluded: chain Y residue 5 LYS Chi-restraints excluded: chain Y residue 42 ILE Chi-restraints excluded: chain Y residue 43 THR Chi-restraints excluded: chain Y residue 75 THR Chi-restraints excluded: chain Y residue 125 LEU Chi-restraints excluded: chain Y residue 129 THR Chi-restraints excluded: chain Z residue 42 SER Chi-restraints excluded: chain Z residue 45 GLU Chi-restraints excluded: chain Z residue 89 ILE Chi-restraints excluded: chain a residue 44 ILE Chi-restraints excluded: chain a residue 45 ILE Chi-restraints excluded: chain a residue 53 LEU Chi-restraints excluded: chain a residue 55 GLN Chi-restraints excluded: chain a residue 92 ILE Chi-restraints excluded: chain a residue 93 VAL 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: 0.7980 chunk 299 optimal weight: 4.9990 chunk 150 optimal weight: 0.8980 chunk 98 optimal weight: 0.8980 chunk 97 optimal weight: 2.9990 chunk 318 optimal weight: 8.9990 chunk 341 optimal weight: 0.9990 chunk 247 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 393 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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** B 194 GLN B 200 HIS C 37 GLN ** C 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN O 4 ASN S 67 GLN S 162 ASN ** S 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 3 GLN V 68 ASN 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 Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.2298 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= 0.144 Angle : 0.574 11.481 130233 Z= 0.300 Chirality : 0.035 0.287 16792 Planarity : 0.004 0.052 6241 Dihedral : 23.724 179.369 45376 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 4.13 % Allowed : 20.30 % Favored : 75.57 % 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: -2.31 (0.16), residues: 2500 helix: -0.73 (0.21), residues: 599 sheet: -1.45 (0.22), residues: 498 loop : -1.96 (0.15), residues: 1403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 250 HIS 0.004 0.001 HIS C 29 PHE 0.014 0.001 PHE S 139 TYR 0.023 0.001 TYR Y 74 ARG 0.005 0.000 ARG E 92 *********************** 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 573 residues out of total 2153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 484 time to evaluate : 3.111 Fit side-chains revert: symmetry clash REVERT: A 93 LYS cc_start: 0.7683 (tttp) cc_final: 0.7468 (tptt) REVERT: B 180 GLU cc_start: 0.7512 (OUTLIER) cc_final: 0.6799 (tt0) REVERT: D 85 LYS cc_start: 0.8857 (ttmm) cc_final: 0.8636 (ttpp) REVERT: E 66 THR cc_start: 0.8284 (p) cc_final: 0.7875 (m) REVERT: G 57 LEU cc_start: 0.5986 (OUTLIER) cc_final: 0.5726 (tp) REVERT: I 84 LYS cc_start: 0.8185 (mmtp) cc_final: 0.7974 (mttm) REVERT: J 37 ARG cc_start: 0.7358 (ttm110) cc_final: 0.6957 (ttm170) REVERT: O 32 MET cc_start: 0.8056 (OUTLIER) cc_final: 0.7831 (mpp) REVERT: P 15 LYS cc_start: 0.8758 (mmtp) cc_final: 0.8391 (mmtt) REVERT: S 158 ASN cc_start: 0.5559 (OUTLIER) cc_final: 0.5338 (t0) REVERT: W 87 ILE cc_start: 0.8653 (mm) cc_final: 0.8238 (pt) outliers start: 89 outliers final: 74 residues processed: 531 average time/residue: 0.8272 time to fit residues: 730.7128 Evaluate side-chains 549 residues out of total 2153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 471 time to evaluate : 3.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 70 ASN Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 257 LYS Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 74 MET Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain G residue 27 LEU Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 66 SER Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain I residue 40 THR Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 88 SER Chi-restraints excluded: chain J residue 46 LYS Chi-restraints excluded: chain J residue 59 VAL Chi-restraints excluded: chain K residue 20 SER Chi-restraints excluded: chain K residue 28 LEU Chi-restraints excluded: chain K residue 30 PHE Chi-restraints excluded: chain K residue 37 LEU Chi-restraints excluded: chain L residue 5 ILE Chi-restraints excluded: chain L residue 21 GLU Chi-restraints excluded: chain L residue 33 ASN Chi-restraints excluded: chain L residue 96 VAL Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 122 SER Chi-restraints excluded: chain L residue 190 THR Chi-restraints excluded: chain L residue 200 ASN Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain M residue 43 ILE Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 7 ARG Chi-restraints excluded: chain N residue 29 GLU Chi-restraints excluded: chain O residue 4 ASN Chi-restraints excluded: chain O residue 32 MET Chi-restraints excluded: chain O residue 33 LYS Chi-restraints excluded: chain O residue 37 SER Chi-restraints excluded: chain O residue 43 THR Chi-restraints excluded: chain P residue 25 THR Chi-restraints excluded: chain Q residue 29 THR Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain S residue 67 GLN Chi-restraints excluded: chain S residue 70 THR Chi-restraints excluded: chain S residue 158 ASN Chi-restraints excluded: chain S residue 185 ASP Chi-restraints excluded: chain V residue 3 GLN Chi-restraints excluded: chain V residue 53 ASP Chi-restraints excluded: chain V residue 63 ILE Chi-restraints excluded: chain V residue 87 SER Chi-restraints excluded: chain W residue 75 SER Chi-restraints excluded: chain W residue 77 ILE Chi-restraints excluded: chain W residue 98 ILE Chi-restraints excluded: chain W residue 120 GLU Chi-restraints excluded: chain X residue 107 SER Chi-restraints excluded: chain Y residue 5 LYS Chi-restraints excluded: chain Y residue 42 ILE Chi-restraints excluded: chain Y residue 43 THR Chi-restraints excluded: chain Z residue 45 GLU Chi-restraints excluded: chain Z residue 89 ILE Chi-restraints excluded: chain a residue 44 ILE Chi-restraints excluded: chain a residue 45 ILE Chi-restraints excluded: chain a residue 53 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 455 optimal weight: 10.9990 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: 7.9990 chunk 366 optimal weight: 7.9990 chunk 143 optimal weight: 6.9990 chunk 422 optimal weight: 10.0000 chunk 441 optimal weight: 10.0000 chunk 465 optimal weight: 6.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 70 ASN C 37 GLN C 81 ASN L 192 ASN L 200 ASN O 4 ASN Q 7 HIS ** S 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 68 ASN V 137 GLN W 13 ASN W 110 ASN ** Y 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.113 86434 Z= 0.641 Angle : 0.947 13.297 130233 Z= 0.462 Chirality : 0.053 0.327 16792 Planarity : 0.007 0.091 6241 Dihedral : 23.986 178.896 45376 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.16 % Favored : 88.84 % Rotamer: Outliers : 5.85 % Allowed : 19.18 % Favored : 74.97 % 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: -2.80 (0.15), residues: 2500 helix: -1.31 (0.20), residues: 613 sheet: -1.60 (0.22), residues: 501 loop : -2.25 (0.15), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.004 TRP J 29 HIS 0.011 0.002 HIS E 102 PHE 0.028 0.003 PHE L 91 TYR 0.027 0.003 TYR V 141 ARG 0.012 0.001 ARG L 162 *********************** 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 587 residues out of total 2153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 461 time to evaluate : 3.163 Fit side-chains REVERT: A 112 ILE cc_start: 0.8144 (OUTLIER) cc_final: 0.7708 (mm) REVERT: B 180 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7273 (tt0) REVERT: E 66 THR cc_start: 0.8313 (p) cc_final: 0.7905 (m) REVERT: G 57 LEU cc_start: 0.6143 (OUTLIER) cc_final: 0.5868 (tp) REVERT: L 44 ASP cc_start: 0.7225 (OUTLIER) cc_final: 0.6862 (p0) REVERT: L 162 ARG cc_start: 0.8782 (OUTLIER) cc_final: 0.7485 (ppt-90) REVERT: L 198 LYS cc_start: 0.8356 (OUTLIER) cc_final: 0.8105 (mtpp) REVERT: O 32 MET cc_start: 0.8217 (OUTLIER) cc_final: 0.7975 (mpp) REVERT: P 15 LYS cc_start: 0.8844 (mmtp) cc_final: 0.8443 (mmtt) REVERT: Q 52 LYS cc_start: 0.8069 (ptpt) cc_final: 0.7641 (mmtm) REVERT: S 67 GLN cc_start: 0.7746 (OUTLIER) cc_final: 0.7118 (tt0) REVERT: W 87 ILE cc_start: 0.8683 (mm) cc_final: 0.8312 (pt) REVERT: Z 28 GLU cc_start: 0.7778 (mm-30) cc_final: 0.7166 (tp30) outliers start: 126 outliers final: 106 residues processed: 538 average time/residue: 0.8526 time to fit residues: 768.0869 Evaluate side-chains 569 residues out of total 2153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 455 time to evaluate : 3.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 70 ASN Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 257 LYS Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 74 MET Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain F residue 23 ASP Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain G residue 27 LEU Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 66 SER Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain I residue 40 THR Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain I residue 71 ILE Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 88 SER Chi-restraints excluded: chain J residue 7 VAL Chi-restraints excluded: chain J residue 46 LYS Chi-restraints excluded: chain J residue 59 VAL Chi-restraints excluded: chain J residue 60 THR Chi-restraints excluded: chain K residue 19 LYS Chi-restraints excluded: chain K residue 20 SER Chi-restraints excluded: chain K residue 28 LEU Chi-restraints excluded: chain K residue 37 LEU Chi-restraints excluded: chain L residue 5 ILE Chi-restraints excluded: chain L residue 21 GLU Chi-restraints excluded: chain L residue 33 ASN Chi-restraints excluded: chain L residue 44 ASP Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 62 ASP Chi-restraints excluded: chain L residue 96 VAL Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 122 SER Chi-restraints excluded: chain L residue 137 SER Chi-restraints excluded: chain L residue 162 ARG Chi-restraints excluded: chain L residue 190 THR Chi-restraints excluded: chain L residue 198 LYS Chi-restraints excluded: chain L residue 200 ASN Chi-restraints excluded: chain M residue 18 THR Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain M residue 40 ASN Chi-restraints excluded: chain M residue 43 ILE Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 7 ARG Chi-restraints excluded: chain N residue 29 GLU Chi-restraints excluded: chain O residue 4 ASN Chi-restraints excluded: chain O residue 16 ASN Chi-restraints excluded: chain O residue 32 MET Chi-restraints excluded: chain O residue 33 LYS Chi-restraints excluded: chain O residue 37 SER Chi-restraints excluded: chain O residue 43 THR Chi-restraints excluded: chain P residue 25 THR Chi-restraints excluded: chain Q residue 29 THR Chi-restraints excluded: chain Q residue 60 GLN Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain S residue 67 GLN Chi-restraints excluded: chain S residue 70 THR Chi-restraints excluded: chain S residue 96 SER Chi-restraints excluded: chain S residue 185 ASP Chi-restraints excluded: chain V residue 35 SER Chi-restraints excluded: chain V residue 53 ASP Chi-restraints excluded: chain V residue 66 THR Chi-restraints excluded: chain V residue 71 THR Chi-restraints excluded: chain V residue 87 SER Chi-restraints excluded: chain V residue 105 SER Chi-restraints excluded: chain W residue 75 SER Chi-restraints excluded: chain W residue 77 ILE Chi-restraints excluded: chain W residue 98 ILE Chi-restraints excluded: chain W residue 115 VAL Chi-restraints excluded: chain W residue 120 GLU Chi-restraints excluded: chain X residue 107 SER Chi-restraints excluded: chain Y residue 5 LYS Chi-restraints excluded: chain Y residue 42 ILE Chi-restraints excluded: chain Y residue 43 THR Chi-restraints excluded: chain Y residue 125 LEU Chi-restraints excluded: chain Z residue 45 GLU Chi-restraints excluded: chain Z residue 89 ILE Chi-restraints excluded: chain Z residue 118 ILE Chi-restraints excluded: chain a residue 44 ILE Chi-restraints excluded: chain a residue 45 ILE Chi-restraints excluded: chain a residue 53 LEU Chi-restraints excluded: chain a residue 92 ILE Chi-restraints excluded: chain a residue 93 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 306 optimal weight: 0.9980 chunk 493 optimal weight: 0.6980 chunk 301 optimal weight: 2.9990 chunk 234 optimal weight: 2.9990 chunk 343 optimal weight: 0.9990 chunk 518 optimal weight: 8.9990 chunk 476 optimal weight: 5.9990 chunk 412 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 318 optimal weight: 7.9990 chunk 252 optimal weight: 5.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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** B 200 HIS ** C 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 67 GLN ** S 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 3 GLN V 68 ASN V 137 GLN W 13 ASN ** Y 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 55 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 86434 Z= 0.161 Angle : 0.568 13.311 130233 Z= 0.295 Chirality : 0.035 0.288 16792 Planarity : 0.004 0.050 6241 Dihedral : 23.662 179.716 45376 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 4.09 % Allowed : 20.53 % Favored : 75.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.26 (0.16), residues: 2500 helix: -0.68 (0.21), residues: 601 sheet: -1.46 (0.22), residues: 513 loop : -1.91 (0.15), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP J 48 HIS 0.004 0.001 HIS C 29 PHE 0.012 0.001 PHE S 139 TYR 0.021 0.001 TYR Y 74 ARG 0.009 0.000 ARG B 69 ********************** 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 567 residues out of total 2153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 479 time to evaluate : 3.150 Fit side-chains revert: symmetry clash REVERT: A 93 LYS cc_start: 0.7625 (tttp) cc_final: 0.7393 (tptt) REVERT: A 112 ILE cc_start: 0.8107 (OUTLIER) cc_final: 0.7725 (mm) REVERT: B 180 GLU cc_start: 0.7424 (OUTLIER) cc_final: 0.6692 (tt0) REVERT: B 225 MET cc_start: 0.8233 (mtt) cc_final: 0.7983 (mtt) REVERT: D 85 LYS cc_start: 0.8852 (ttmm) cc_final: 0.8629 (ttpp) REVERT: E 66 THR cc_start: 0.8330 (p) cc_final: 0.7877 (m) REVERT: E 90 GLN cc_start: 0.8401 (mm-40) cc_final: 0.8166 (mm-40) REVERT: G 57 LEU cc_start: 0.6051 (OUTLIER) cc_final: 0.5791 (tp) REVERT: I 84 LYS cc_start: 0.8154 (mmtp) cc_final: 0.7947 (mttm) REVERT: J 37 ARG cc_start: 0.7304 (ttm110) cc_final: 0.6901 (ttm170) REVERT: L 162 ARG cc_start: 0.8639 (OUTLIER) cc_final: 0.7544 (ppt-90) REVERT: M 44 ARG cc_start: 0.7583 (mmt-90) cc_final: 0.7218 (mmt-90) REVERT: O 32 MET cc_start: 0.8006 (OUTLIER) cc_final: 0.7766 (mpp) REVERT: P 15 LYS cc_start: 0.8737 (mmtp) cc_final: 0.8373 (mmtt) REVERT: W 87 ILE cc_start: 0.8641 (mm) cc_final: 0.8237 (pt) outliers start: 88 outliers final: 67 residues processed: 527 average time/residue: 0.8385 time to fit residues: 739.1770 Evaluate side-chains 541 residues out of total 2153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 469 time to evaluate : 3.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 70 ASN Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 74 MET Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain G residue 8 ASN Chi-restraints excluded: chain G residue 27 LEU Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 66 SER Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain I residue 40 THR Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 88 SER Chi-restraints excluded: chain J residue 46 LYS Chi-restraints excluded: chain J residue 59 VAL Chi-restraints excluded: chain K residue 20 SER Chi-restraints excluded: chain K residue 28 LEU Chi-restraints excluded: chain K residue 30 PHE Chi-restraints excluded: chain K residue 37 LEU Chi-restraints excluded: chain L residue 5 ILE Chi-restraints excluded: chain L residue 96 VAL Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 122 SER Chi-restraints excluded: chain L residue 137 SER Chi-restraints excluded: chain L residue 162 ARG Chi-restraints excluded: chain L residue 190 THR Chi-restraints excluded: chain M residue 23 VAL Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain M residue 43 ILE Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 29 GLU Chi-restraints excluded: chain O residue 16 ASN Chi-restraints excluded: chain O residue 32 MET Chi-restraints excluded: chain O residue 33 LYS Chi-restraints excluded: chain O residue 37 SER Chi-restraints excluded: chain O residue 43 THR Chi-restraints excluded: chain P residue 25 THR Chi-restraints excluded: chain Q residue 29 THR Chi-restraints excluded: chain S residue 70 THR Chi-restraints excluded: chain S residue 185 ASP Chi-restraints excluded: chain V residue 53 ASP Chi-restraints excluded: chain V residue 71 THR Chi-restraints excluded: chain V residue 87 SER Chi-restraints excluded: chain W residue 75 SER Chi-restraints excluded: chain W residue 77 ILE Chi-restraints excluded: chain W residue 98 ILE Chi-restraints excluded: chain W residue 120 GLU Chi-restraints excluded: chain X residue 107 SER Chi-restraints excluded: chain Y residue 42 ILE Chi-restraints excluded: chain Y residue 43 THR Chi-restraints excluded: chain Z residue 45 GLU Chi-restraints excluded: chain Z residue 89 ILE Chi-restraints excluded: chain a residue 44 ILE Chi-restraints excluded: chain a residue 45 ILE Chi-restraints excluded: chain a residue 53 LEU Chi-restraints excluded: chain a residue 55 GLN 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: 0.9980 chunk 380 optimal weight: 8.9990 chunk 60 optimal weight: 1.9990 chunk 114 optimal weight: 8.9990 chunk 413 optimal weight: 7.9990 chunk 172 optimal weight: 9.9990 chunk 424 optimal weight: 10.0000 chunk 52 optimal weight: 8.9990 chunk 76 optimal weight: 0.7980 overall best weight: 3.7586 ------------------------------------------------------------------------------- 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** C 37 GLN ** C 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 20 GLN L 192 ASN L 200 ASN ** S 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 68 ASN 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 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.144121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.128106 restraints weight = 110197.305| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 0.69 r_work: 0.3165 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.130 86434 Z= 0.313 Angle : 0.645 59.164 130233 Z= 0.344 Chirality : 0.039 1.004 16792 Planarity : 0.005 0.151 6241 Dihedral : 23.656 179.858 45376 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 3.76 % Allowed : 20.99 % Favored : 75.24 % Cbeta Deviations : 0.04 % 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: -2.24 (0.16), residues: 2500 helix: -0.67 (0.21), residues: 601 sheet: -1.46 (0.22), residues: 513 loop : -1.88 (0.15), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP Y 65 HIS 0.008 0.001 HIS a 102 PHE 0.013 0.002 PHE C 25 TYR 0.020 0.002 TYR Y 74 ARG 0.004 0.001 ARG J 17 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13606.70 seconds wall clock time: 243 minutes 9.23 seconds (14589.23 seconds total)