Starting phenix.real_space_refine (version: dev) on Mon Dec 19 04:45:26 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xte_6774/12_2022/5xte_6774_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xte_6774/12_2022/5xte_6774.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xte_6774/12_2022/5xte_6774_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xte_6774/12_2022/5xte_6774_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xte_6774/12_2022/5xte_6774_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xte_6774/12_2022/5xte_6774.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xte_6774/12_2022/5xte_6774.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xte_6774/12_2022/5xte_6774_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xte_6774/12_2022/5xte_6774_updated.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ARG 3": "NH1" <-> "NH2" Residue "A ARG 10": "NH1" <-> "NH2" Residue "A ARG 40": "NH1" <-> "NH2" Residue "A ARG 72": "NH1" <-> "NH2" Residue "D ARG 16": "NH1" <-> "NH2" Residue "D ARG 17": "NH1" <-> "NH2" Residue "F GLU 46": "OE1" <-> "OE2" Residue "G ARG 39": "NH1" <-> "NH2" Residue "K ARG 148": "NH1" <-> "NH2" Residue "K ARG 183": "NH1" <-> "NH2" Residue "K ARG 259": "NH1" <-> "NH2" Residue "K ARG 301": "NH1" <-> "NH2" Residue "L ARG 58": "NH1" <-> "NH2" Residue "L ARG 80": "NH1" <-> "NH2" Residue "L PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 422": "NH1" <-> "NH2" Residue "L ARG 423": "NH1" <-> "NH2" Residue "L ARG 479": "NH1" <-> "NH2" Residue "N ARG 3": "NH1" <-> "NH2" Residue "N ARG 10": "NH1" <-> "NH2" Residue "N ARG 72": "NH1" <-> "NH2" Residue "S ARG 49": "NH1" <-> "NH2" Residue "T ARG 39": "NH1" <-> "NH2" Residue "U ARG 99": "NH1" <-> "NH2" Residue "U ARG 133": "NH1" <-> "NH2" Residue "V PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 282": "NH1" <-> "NH2" Residue "W ARG 183": "NH1" <-> "NH2" Residue "W ARG 301": "NH1" <-> "NH2" Residue "Y ARG 80": "NH1" <-> "NH2" Residue "Y ARG 422": "NH1" <-> "NH2" Residue "Y ARG 423": "NH1" <-> "NH2" Residue "Y ARG 479": "NH1" <-> "NH2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 34492 Number of models: 1 Model: "" Number of chains: 35 Chain: "A" Number of atoms: 694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 694 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 5, 'TRANS': 75} Chain: "B" Number of atoms: 413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 413 Classifications: {'peptide': 57} Link IDs: {'CIS': 1, 'PTRANS': 7, 'TRANS': 48} Chain: "C" Number of atoms: 1521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1521 Classifications: {'peptide': 196} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 185} Chain: "D" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 509 Classifications: {'peptide': 62} Modifications used: {'COO': 1} Link IDs: {'TRANS': 61} Chain: "E" Number of atoms: 580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 580 Classifications: {'peptide': 74} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 1, 'TRANS': 72} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 8} Unresolved non-hydrogen planarities: 32 Chain: "F" Number of atoms: 921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 921 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 102} Chain: "G" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 425 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 3, 'TRANS': 47} Chain: "H" Number of atoms: 1924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1924 Classifications: {'peptide': 241} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 219} Chain: "J" Number of atoms: 3009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 3009 Classifications: {'peptide': 378} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 354} Chain: "K" Number of atoms: 3159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3159 Classifications: {'peptide': 419} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 13, 'TRANS': 404} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 3453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3453 Classifications: {'peptide': 446} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 426} Chain: "N" Number of atoms: 687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 687 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 75} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "O" Number of atoms: 409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 409 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 7, 'TRANS': 48} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "P" Number of atoms: 1521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1521 Classifications: {'peptide': 196} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 185} Chain: "Q" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 509 Classifications: {'peptide': 62} Modifications used: {'COO': 1} Link IDs: {'TRANS': 61} Chain: "R" Number of atoms: 580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 580 Classifications: {'peptide': 74} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 1, 'TRANS': 72} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 8} Unresolved non-hydrogen planarities: 32 Chain: "S" Number of atoms: 921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 921 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 102} Chain: "T" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 425 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 3, 'TRANS': 47} Chain: "U" Number of atoms: 1924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1924 Classifications: {'peptide': 241} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 219} Chain: "V" Number of atoms: 3009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 3009 Classifications: {'peptide': 378} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 354} Chain: "W" Number of atoms: 3162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3162 Classifications: {'peptide': 419} Link IDs: {'CIS': 1, 'PTRANS': 13, 'TRANS': 404} Chain: "Y" Number of atoms: 3453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3453 Classifications: {'peptide': 446} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 426} Chain: "A" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 64 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 36 Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 64 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 36 Chain: "H" Number of atoms: 156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 156 Unusual residues: {'CDL': 1, 'HEC': 1, 'PEE': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 38 Chain: "J" Number of atoms: 263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 263 Unusual residues: {'CDL': 2, 'HEM': 2, 'PEE': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 74 Chain: "L" Number of atoms: 165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 165 Unusual residues: {'CDL': 1, 'PEE': 1, 'PLX': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 38 Chain: "N" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 64 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 36 Chain: "P" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'PLX': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'PLX': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 148 Unusual residues: {'CDL': 1, 'HEC': 1, 'PEE': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 46 Chain: "V" Number of atoms: 135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 135 Unusual residues: {'HEM': 2, 'PEE': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "Y" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 113 Unusual residues: {'CDL': 1, 'PEE': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 38 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 18936 SG CYS P 236 76.516 48.096 24.127 1.00 35.05 S Time building chain proxies: 19.53, per 1000 atoms: 0.57 Number of scatterers: 34492 At special positions: 0 Unit cell: (150.537, 142.956, 177.612, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 10 26.01 S 160 16.00 P 27 15.00 O 6349 8.00 N 5724 7.00 C 22222 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS C 222 " - pdb=" SG CYS C 238 " distance=2.03 Simple disulfide: pdb=" SG CYS P 222 " - pdb=" SG CYS P 238 " distance=2.04 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=9, symmetry=0 Number of additional bonds: simple=9, symmetry=0 Coordination: Other bonds: Time building additional restraints: 14.51 Conformation dependent library (CDL) restraints added in 5.0 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES C 301 " pdb=" FE2 FES C 301 " - pdb=" ND1 HIS C 219 " pdb=" FE2 FES C 301 " - pdb=" ND1 HIS C 239 " pdb=" FE1 FES C 301 " - pdb=" SG CYS C 217 " pdb=" FE1 FES C 301 " - pdb=" SG CYS C 236 " pdb=" FES P 301 " pdb=" FE2 FES P 301 " - pdb=" ND1 HIS P 239 " pdb=" FE2 FES P 301 " - pdb=" ND1 HIS P 219 " pdb=" FE1 FES P 301 " - pdb=" SG CYS P 236 " pdb=" FE1 FES P 301 " - pdb=" SG CYS P 217 " Number of angles added : 6 8356 Ramachandran restraints generated. 4178 Oldfield, 0 Emsley, 4178 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7888 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 184 helices and 18 sheets defined 52.1% alpha, 5.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.89 Creating SS restraints... Processing helix chain 'A' and resid 21 through 23 No H-bonds generated for 'chain 'A' and resid 21 through 23' Processing helix chain 'A' and resid 30 through 81 removed outlier: 4.417A pdb=" N ILE A 35 " --> pdb=" O PHE A 31 " (cutoff:3.500A) Proline residue: A 36 - end of helix removed outlier: 4.724A pdb=" N PHE A 47 " --> pdb=" O ARG A 43 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ARG A 48 " --> pdb=" O GLU A 44 " (cutoff:3.500A) Proline residue: A 51 - end of helix removed outlier: 3.812A pdb=" N LYS A 73 " --> pdb=" O ARG A 69 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N ASN A 74 " --> pdb=" O SER A 70 " (cutoff:3.500A) Proline residue: A 75 - end of helix removed outlier: 3.601A pdb=" N TYR A 78 " --> pdb=" O ASN A 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 6 No H-bonds generated for 'chain 'B' and resid 4 through 6' Processing helix chain 'B' and resid 31 through 34 No H-bonds generated for 'chain 'B' and resid 31 through 34' Processing helix chain 'C' and resid 94 through 96 No H-bonds generated for 'chain 'C' and resid 94 through 96' Processing helix chain 'C' and resid 104 through 141 removed outlier: 3.901A pdb=" N GLU C 108 " --> pdb=" O ARG C 104 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N ALA C 109 " --> pdb=" O GLU C 105 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LEU C 116 " --> pdb=" O GLY C 112 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS C 130 " --> pdb=" O ALA C 126 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLN C 135 " --> pdb=" O ASN C 131 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N MET C 140 " --> pdb=" O PHE C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 149 Processing helix chain 'C' and resid 181 through 188 Processing helix chain 'C' and resid 201 through 204 No H-bonds generated for 'chain 'C' and resid 201 through 204' Processing helix chain 'D' and resid 6 through 13 removed outlier: 3.725A pdb=" N SER D 12 " --> pdb=" O SER D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 47 removed outlier: 4.014A pdb=" N ARG D 34 " --> pdb=" O MET D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 60 removed outlier: 5.160A pdb=" N HIS D 58 " --> pdb=" O LYS D 54 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N LYS D 59 " --> pdb=" O HIS D 55 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N TYR D 60 " --> pdb=" O ILE D 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 26 Processing helix chain 'E' and resid 29 through 39 removed outlier: 3.969A pdb=" N GLU E 38 " --> pdb=" O ARG E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 41 through 58 Processing helix chain 'E' and resid 68 through 83 removed outlier: 4.117A pdb=" N ALA E 77 " --> pdb=" O ASP E 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 11 through 24 removed outlier: 3.605A pdb=" N GLY F 16 " --> pdb=" O LYS F 12 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE F 17 " --> pdb=" O TRP F 13 " (cutoff:3.500A) Processing helix chain 'F' and resid 27 through 30 Processing helix chain 'F' and resid 34 through 37 No H-bonds generated for 'chain 'F' and resid 34 through 37' Processing helix chain 'F' and resid 42 through 50 removed outlier: 3.676A pdb=" N ARG F 50 " --> pdb=" O GLU F 46 " (cutoff:3.500A) Processing helix chain 'F' and resid 53 through 72 removed outlier: 3.589A pdb=" N ASP F 58 " --> pdb=" O ASN F 54 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS F 72 " --> pdb=" O ASP F 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 80 No H-bonds generated for 'chain 'F' and resid 78 through 80' Processing helix chain 'F' and resid 92 through 110 Processing helix chain 'G' and resid 3 through 5 No H-bonds generated for 'chain 'G' and resid 3 through 5' Processing helix chain 'G' and resid 8 through 35 removed outlier: 3.993A pdb=" N GLU G 12 " --> pdb=" O PRO G 8 " (cutoff:3.500A) Proline residue: G 19 - end of helix Processing helix chain 'G' and resid 39 through 42 No H-bonds generated for 'chain 'G' and resid 39 through 42' Processing helix chain 'H' and resid 97 through 99 No H-bonds generated for 'chain 'H' and resid 97 through 99' Processing helix chain 'H' and resid 107 through 117 Processing helix chain 'H' and resid 135 through 138 No H-bonds generated for 'chain 'H' and resid 135 through 138' Processing helix chain 'H' and resid 142 through 151 removed outlier: 3.641A pdb=" N ALA H 150 " --> pdb=" O LYS H 146 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLU H 151 " --> pdb=" O GLU H 147 " (cutoff:3.500A) Processing helix chain 'H' and resid 182 through 189 Processing helix chain 'H' and resid 200 through 203 No H-bonds generated for 'chain 'H' and resid 200 through 203' Processing helix chain 'H' and resid 207 through 216 removed outlier: 3.876A pdb=" N PHE H 212 " --> pdb=" O ASP H 209 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N SER H 213 " --> pdb=" O TYR H 210 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR H 216 " --> pdb=" O SER H 213 " (cutoff:3.500A) Processing helix chain 'H' and resid 263 through 278 Processing helix chain 'H' and resid 282 through 315 removed outlier: 3.584A pdb=" N ARG H 287 " --> pdb=" O ASP H 283 " (cutoff:3.500A) Proline residue: H 301 - end of helix removed outlier: 5.091A pdb=" N VAL H 313 " --> pdb=" O HIS H 309 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N LEU H 314 " --> pdb=" O LYS H 310 " (cutoff:3.500A) Processing helix chain 'J' and resid 4 through 7 No H-bonds generated for 'chain 'J' and resid 4 through 7' Processing helix chain 'J' and resid 9 through 17 removed outlier: 4.000A pdb=" N LEU J 13 " --> pdb=" O PRO J 9 " (cutoff:3.500A) Processing helix chain 'J' and resid 29 through 53 removed outlier: 3.846A pdb=" N GLY J 34 " --> pdb=" O TRP J 31 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ILE J 45 " --> pdb=" O ILE J 42 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N THR J 46 " --> pdb=" O LEU J 43 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N THR J 47 " --> pdb=" O GLN J 44 " (cutoff:3.500A) Processing helix chain 'J' and resid 61 through 70 Processing helix chain 'J' and resid 76 through 104 removed outlier: 3.842A pdb=" N SER J 88 " --> pdb=" O ALA J 84 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLY J 101 " --> pdb=" O HIS J 97 " (cutoff:3.500A) Processing helix chain 'J' and resid 106 through 108 No H-bonds generated for 'chain 'J' and resid 106 through 108' Processing helix chain 'J' and resid 110 through 131 Processing helix chain 'J' and resid 137 through 152 removed outlier: 3.722A pdb=" N TRP J 141 " --> pdb=" O GLN J 137 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N LEU J 150 " --> pdb=" O ILE J 146 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N SER J 151 " --> pdb=" O THR J 147 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ALA J 152 " --> pdb=" O ASN J 148 " (cutoff:3.500A) Processing helix chain 'J' and resid 157 through 165 Processing helix chain 'J' and resid 172 through 200 Proline residue: J 186 - end of helix removed outlier: 3.699A pdb=" N ALA J 191 " --> pdb=" O PHE J 187 " (cutoff:3.500A) Processing helix chain 'J' and resid 214 through 216 No H-bonds generated for 'chain 'J' and resid 214 through 216' Processing helix chain 'J' and resid 220 through 244 removed outlier: 4.444A pdb=" N ILE J 226 " --> pdb=" O PRO J 222 " (cutoff:3.500A) Processing helix chain 'J' and resid 272 through 283 removed outlier: 3.971A pdb=" N PHE J 276 " --> pdb=" O TRP J 272 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N ALA J 277 " --> pdb=" O TYR J 273 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TYR J 278 " --> pdb=" O PHE J 274 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR J 279 " --> pdb=" O LEU J 275 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ILE J 280 " --> pdb=" O PHE J 276 " (cutoff:3.500A) Processing helix chain 'J' and resid 289 through 307 removed outlier: 3.952A pdb=" N ILE J 298 " --> pdb=" O LEU J 294 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N LEU J 301 " --> pdb=" O SER J 297 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N ALA J 302 " --> pdb=" O ILE J 298 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N MET J 303 " --> pdb=" O LEU J 299 " (cutoff:3.500A) Proline residue: J 305 - end of helix Processing helix chain 'J' and resid 315 through 317 No H-bonds generated for 'chain 'J' and resid 315 through 317' Processing helix chain 'J' and resid 319 through 339 removed outlier: 3.541A pdb=" N LEU J 324 " --> pdb=" O LEU J 320 " (cutoff:3.500A) Processing helix chain 'J' and resid 345 through 363 removed outlier: 3.577A pdb=" N ILE J 350 " --> pdb=" O PRO J 346 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ILE J 362 " --> pdb=" O TYR J 358 " (cutoff:3.500A) Processing helix chain 'J' and resid 365 through 376 Processing helix chain 'K' and resid 69 through 71 No H-bonds generated for 'chain 'K' and resid 69 through 71' Processing helix chain 'K' and resid 79 through 83 Processing helix chain 'K' and resid 85 through 88 removed outlier: 4.102A pdb=" N SER K 88 " --> pdb=" O LEU K 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 85 through 88' Processing helix chain 'K' and resid 96 through 106 Processing helix chain 'K' and resid 127 through 142 removed outlier: 3.879A pdb=" N VAL K 130 " --> pdb=" O ARG K 127 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N ASP K 131 " --> pdb=" O GLY K 128 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N MET K 134 " --> pdb=" O ASP K 131 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N LEU K 138 " --> pdb=" O GLU K 135 " (cutoff:3.500A) Processing helix chain 'K' and resid 148 through 167 Proline residue: K 156 - end of helix removed outlier: 4.205A pdb=" N LYS K 159 " --> pdb=" O GLN K 155 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE K 160 " --> pdb=" O PRO K 156 " (cutoff:3.500A) Processing helix chain 'K' and resid 169 through 181 removed outlier: 4.513A pdb=" N ASN K 176 " --> pdb=" O HIS K 172 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N ALA K 179 " --> pdb=" O GLU K 175 " (cutoff:3.500A) Processing helix chain 'K' and resid 185 through 187 No H-bonds generated for 'chain 'K' and resid 185 through 187' Processing helix chain 'K' and resid 194 through 196 No H-bonds generated for 'chain 'K' and resid 194 through 196' Processing helix chain 'K' and resid 202 through 212 Processing helix chain 'K' and resid 227 through 233 removed outlier: 3.853A pdb=" N GLN K 232 " --> pdb=" O PRO K 228 " (cutoff:3.500A) Processing helix chain 'K' and resid 235 through 238 Processing helix chain 'K' and resid 281 through 292 Processing helix chain 'K' and resid 308 through 314 Processing helix chain 'K' and resid 347 through 362 removed outlier: 3.669A pdb=" N LYS K 352 " --> pdb=" O GLY K 348 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE K 361 " --> pdb=" O GLN K 357 " (cutoff:3.500A) Processing helix chain 'K' and resid 368 through 387 removed outlier: 3.607A pdb=" N GLN K 372 " --> pdb=" O ASN K 368 " (cutoff:3.500A) Processing helix chain 'K' and resid 389 through 403 removed outlier: 3.557A pdb=" N VAL K 402 " --> pdb=" O SER K 398 " (cutoff:3.500A) Processing helix chain 'K' and resid 409 through 417 Processing helix chain 'K' and resid 421 through 433 Processing helix chain 'L' and resid 38 through 44 removed outlier: 3.935A pdb=" N GLN L 43 " --> pdb=" O ALA L 39 " (cutoff:3.500A) Processing helix chain 'L' and resid 84 through 86 No H-bonds generated for 'chain 'L' and resid 84 through 86' Processing helix chain 'L' and resid 89 through 96 Processing helix chain 'L' and resid 106 through 116 Processing helix chain 'L' and resid 137 through 150 Proline residue: L 141 - end of helix removed outlier: 4.021A pdb=" N GLU L 145 " --> pdb=" O LYS L 142 " (cutoff:3.500A) Processing helix chain 'L' and resid 158 through 177 removed outlier: 3.701A pdb=" N ASP L 166 " --> pdb=" O GLU L 162 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLN L 173 " --> pdb=" O LEU L 169 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ASP L 176 " --> pdb=" O MET L 172 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N ALA L 177 " --> pdb=" O GLN L 173 " (cutoff:3.500A) Processing helix chain 'L' and resid 181 through 192 Processing helix chain 'L' and resid 196 through 198 No H-bonds generated for 'chain 'L' and resid 196 through 198' Processing helix chain 'L' and resid 205 through 208 No H-bonds generated for 'chain 'L' and resid 205 through 208' Processing helix chain 'L' and resid 213 through 222 Processing helix chain 'L' and resid 239 through 252 removed outlier: 3.530A pdb=" N HIS L 249 " --> pdb=" O LEU L 245 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N GLY L 252 " --> pdb=" O LYS L 248 " (cutoff:3.500A) Processing helix chain 'L' and resid 258 through 260 No H-bonds generated for 'chain 'L' and resid 258 through 260' Processing helix chain 'L' and resid 299 through 311 removed outlier: 3.554A pdb=" N ILE L 311 " --> pdb=" O ASN L 308 " (cutoff:3.500A) Processing helix chain 'L' and resid 327 through 332 Processing helix chain 'L' and resid 362 through 380 removed outlier: 4.033A pdb=" N ILE L 365 " --> pdb=" O ARG L 362 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N ASP L 366 " --> pdb=" O MET L 363 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N MET L 368 " --> pdb=" O ILE L 365 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL L 371 " --> pdb=" O MET L 368 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLN L 373 " --> pdb=" O PHE L 370 " (cutoff:3.500A) Processing helix chain 'L' and resid 385 through 403 removed outlier: 4.171A pdb=" N LEU L 403 " --> pdb=" O LEU L 399 " (cutoff:3.500A) Processing helix chain 'L' and resid 406 through 419 removed outlier: 3.763A pdb=" N THR L 419 " --> pdb=" O ARG L 415 " (cutoff:3.500A) Processing helix chain 'L' and resid 426 through 434 Processing helix chain 'L' and resid 438 through 448 Processing helix chain 'L' and resid 468 through 475 Processing helix chain 'N' and resid 5 through 7 No H-bonds generated for 'chain 'N' and resid 5 through 7' Processing helix chain 'N' and resid 21 through 23 No H-bonds generated for 'chain 'N' and resid 21 through 23' Processing helix chain 'N' and resid 30 through 81 removed outlier: 5.054A pdb=" N ILE N 35 " --> pdb=" O PHE N 31 " (cutoff:3.500A) Proline residue: N 36 - end of helix removed outlier: 5.046A pdb=" N PHE N 47 " --> pdb=" O ARG N 43 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N ARG N 48 " --> pdb=" O GLU N 44 " (cutoff:3.500A) Proline residue: N 51 - end of helix Proline residue: N 75 - end of helix Processing helix chain 'O' and resid 31 through 33 No H-bonds generated for 'chain 'O' and resid 31 through 33' Processing helix chain 'P' and resid 94 through 96 No H-bonds generated for 'chain 'P' and resid 94 through 96' Processing helix chain 'P' and resid 103 through 140 removed outlier: 4.687A pdb=" N GLU P 108 " --> pdb=" O ARG P 104 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ALA P 109 " --> pdb=" O GLU P 105 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER P 114 " --> pdb=" O ARG P 110 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N MET P 140 " --> pdb=" O PHE P 136 " (cutoff:3.500A) Processing helix chain 'P' and resid 144 through 149 Processing helix chain 'P' and resid 181 through 189 Processing helix chain 'P' and resid 201 through 204 No H-bonds generated for 'chain 'P' and resid 201 through 204' Processing helix chain 'Q' and resid 6 through 12 Processing helix chain 'Q' and resid 18 through 47 removed outlier: 4.510A pdb=" N ARG Q 34 " --> pdb=" O MET Q 30 " (cutoff:3.500A) Processing helix chain 'Q' and resid 53 through 59 removed outlier: 5.457A pdb=" N HIS Q 58 " --> pdb=" O LYS Q 54 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N LYS Q 59 " --> pdb=" O HIS Q 55 " (cutoff:3.500A) Processing helix chain 'R' and resid 19 through 26 Processing helix chain 'R' and resid 29 through 39 Processing helix chain 'R' and resid 41 through 59 Processing helix chain 'R' and resid 68 through 89 removed outlier: 4.071A pdb=" N ALA R 77 " --> pdb=" O ASP R 73 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N PHE R 87 " --> pdb=" O ALA R 83 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N ASN R 88 " --> pdb=" O HIS R 84 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ASN R 89 " --> pdb=" O LYS R 85 " (cutoff:3.500A) Processing helix chain 'S' and resid 9 through 24 Processing helix chain 'S' and resid 26 through 30 Processing helix chain 'S' and resid 34 through 36 No H-bonds generated for 'chain 'S' and resid 34 through 36' Processing helix chain 'S' and resid 42 through 49 Processing helix chain 'S' and resid 53 through 71 Processing helix chain 'S' and resid 78 through 80 No H-bonds generated for 'chain 'S' and resid 78 through 80' Processing helix chain 'S' and resid 92 through 109 Processing helix chain 'T' and resid 3 through 5 No H-bonds generated for 'chain 'T' and resid 3 through 5' Processing helix chain 'T' and resid 8 through 36 Proline residue: T 19 - end of helix Processing helix chain 'T' and resid 39 through 42 No H-bonds generated for 'chain 'T' and resid 39 through 42' Processing helix chain 'U' and resid 107 through 117 Processing helix chain 'U' and resid 135 through 138 No H-bonds generated for 'chain 'U' and resid 135 through 138' Processing helix chain 'U' and resid 142 through 151 removed outlier: 3.676A pdb=" N ALA U 150 " --> pdb=" O LYS U 146 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU U 151 " --> pdb=" O GLU U 147 " (cutoff:3.500A) Processing helix chain 'U' and resid 182 through 189 Processing helix chain 'U' and resid 200 through 203 No H-bonds generated for 'chain 'U' and resid 200 through 203' Processing helix chain 'U' and resid 207 through 216 removed outlier: 3.842A pdb=" N PHE U 212 " --> pdb=" O ASP U 209 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER U 213 " --> pdb=" O TYR U 210 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR U 216 " --> pdb=" O SER U 213 " (cutoff:3.500A) Processing helix chain 'U' and resid 263 through 278 Processing helix chain 'U' and resid 282 through 315 Proline residue: U 301 - end of helix removed outlier: 4.694A pdb=" N VAL U 313 " --> pdb=" O HIS U 309 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N LEU U 314 " --> pdb=" O LYS U 310 " (cutoff:3.500A) Processing helix chain 'V' and resid 4 through 6 No H-bonds generated for 'chain 'V' and resid 4 through 6' Processing helix chain 'V' and resid 9 through 17 Processing helix chain 'V' and resid 31 through 51 removed outlier: 3.758A pdb=" N LEU V 41 " --> pdb=" O GLY V 38 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N THR V 47 " --> pdb=" O GLN V 44 " (cutoff:3.500A) Processing helix chain 'V' and resid 62 through 70 removed outlier: 3.529A pdb=" N ILE V 66 " --> pdb=" O ALA V 62 " (cutoff:3.500A) Processing helix chain 'V' and resid 76 through 103 removed outlier: 3.635A pdb=" N SER V 88 " --> pdb=" O ALA V 84 " (cutoff:3.500A) Processing helix chain 'V' and resid 106 through 108 No H-bonds generated for 'chain 'V' and resid 106 through 108' Processing helix chain 'V' and resid 110 through 133 Processing helix chain 'V' and resid 137 through 152 removed outlier: 3.768A pdb=" N LEU V 149 " --> pdb=" O VAL V 145 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LEU V 150 " --> pdb=" O ILE V 146 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER V 151 " --> pdb=" O THR V 147 " (cutoff:3.500A) Processing helix chain 'V' and resid 157 through 165 Processing helix chain 'V' and resid 172 through 202 Proline residue: V 186 - end of helix removed outlier: 4.273A pdb=" N GLU V 202 " --> pdb=" O LEU V 198 " (cutoff:3.500A) Processing helix chain 'V' and resid 214 through 216 No H-bonds generated for 'chain 'V' and resid 214 through 216' Processing helix chain 'V' and resid 224 through 244 Processing helix chain 'V' and resid 272 through 283 removed outlier: 4.768A pdb=" N PHE V 276 " --> pdb=" O TYR V 273 " (cutoff:3.500A) Processing helix chain 'V' and resid 287 through 307 removed outlier: 3.757A pdb=" N ILE V 298 " --> pdb=" O LEU V 294 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N LEU V 301 " --> pdb=" O SER V 297 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N ALA V 302 " --> pdb=" O ILE V 298 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N MET V 303 " --> pdb=" O LEU V 299 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE V 304 " --> pdb=" O ILE V 300 " (cutoff:3.500A) Proline residue: V 305 - end of helix Processing helix chain 'V' and resid 315 through 317 No H-bonds generated for 'chain 'V' and resid 315 through 317' Processing helix chain 'V' and resid 319 through 340 removed outlier: 4.234A pdb=" N GLY V 340 " --> pdb=" O THR V 336 " (cutoff:3.500A) Processing helix chain 'V' and resid 345 through 363 removed outlier: 3.594A pdb=" N ILE V 349 " --> pdb=" O TYR V 345 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ILE V 362 " --> pdb=" O TYR V 358 " (cutoff:3.500A) Processing helix chain 'V' and resid 365 through 376 Processing helix chain 'W' and resid 69 through 71 No H-bonds generated for 'chain 'W' and resid 69 through 71' Processing helix chain 'W' and resid 79 through 83 Processing helix chain 'W' and resid 85 through 88 removed outlier: 4.414A pdb=" N SER W 88 " --> pdb=" O LEU W 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 85 through 88' Processing helix chain 'W' and resid 96 through 106 Processing helix chain 'W' and resid 127 through 141 removed outlier: 4.076A pdb=" N VAL W 130 " --> pdb=" O ARG W 127 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N ASP W 131 " --> pdb=" O GLY W 128 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N MET W 134 " --> pdb=" O ASP W 131 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU W 138 " --> pdb=" O GLU W 135 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N THR W 141 " --> pdb=" O LEU W 138 " (cutoff:3.500A) Processing helix chain 'W' and resid 148 through 166 Proline residue: W 156 - end of helix removed outlier: 4.628A pdb=" N LYS W 159 " --> pdb=" O GLN W 155 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ILE W 160 " --> pdb=" O PRO W 156 " (cutoff:3.500A) Processing helix chain 'W' and resid 169 through 181 removed outlier: 3.698A pdb=" N VAL W 173 " --> pdb=" O PRO W 169 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ASN W 176 " --> pdb=" O HIS W 172 " (cutoff:3.500A) Processing helix chain 'W' and resid 185 through 187 No H-bonds generated for 'chain 'W' and resid 185 through 187' Processing helix chain 'W' and resid 194 through 196 No H-bonds generated for 'chain 'W' and resid 194 through 196' Processing helix chain 'W' and resid 202 through 212 removed outlier: 3.598A pdb=" N ASN W 211 " --> pdb=" O TYR W 207 " (cutoff:3.500A) Processing helix chain 'W' and resid 227 through 238 Processing helix chain 'W' and resid 281 through 292 Processing helix chain 'W' and resid 308 through 316 removed outlier: 4.092A pdb=" N LYS W 315 " --> pdb=" O GLN W 311 " (cutoff:3.500A) Processing helix chain 'W' and resid 344 through 362 removed outlier: 3.637A pdb=" N ALA W 347 " --> pdb=" O ALA W 344 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N GLY W 348 " --> pdb=" O THR W 345 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ILE W 351 " --> pdb=" O GLY W 348 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N LYS W 352 " --> pdb=" O ASP W 349 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ALA W 354 " --> pdb=" O ILE W 351 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N TYR W 355 " --> pdb=" O LYS W 352 " (cutoff:3.500A) Processing helix chain 'W' and resid 368 through 387 Processing helix chain 'W' and resid 389 through 402 removed outlier: 4.451A pdb=" N LEU W 401 " --> pdb=" O GLY W 397 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N VAL W 402 " --> pdb=" O SER W 398 " (cutoff:3.500A) Processing helix chain 'W' and resid 409 through 417 Processing helix chain 'W' and resid 421 through 433 Processing helix chain 'Y' and resid 38 through 43 removed outlier: 3.517A pdb=" N LEU Y 42 " --> pdb=" O PHE Y 38 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N GLN Y 43 " --> pdb=" O ALA Y 39 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 38 through 43' Processing helix chain 'Y' and resid 79 through 81 No H-bonds generated for 'chain 'Y' and resid 79 through 81' Processing helix chain 'Y' and resid 84 through 86 No H-bonds generated for 'chain 'Y' and resid 84 through 86' Processing helix chain 'Y' and resid 89 through 96 Processing helix chain 'Y' and resid 106 through 115 Processing helix chain 'Y' and resid 137 through 152 Proline residue: Y 141 - end of helix removed outlier: 4.195A pdb=" N GLU Y 145 " --> pdb=" O LYS Y 142 " (cutoff:3.500A) Processing helix chain 'Y' and resid 158 through 176 removed outlier: 3.978A pdb=" N ASP Y 166 " --> pdb=" O GLU Y 162 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLN Y 173 " --> pdb=" O LEU Y 169 " (cutoff:3.500A) Processing helix chain 'Y' and resid 180 through 192 Processing helix chain 'Y' and resid 196 through 198 No H-bonds generated for 'chain 'Y' and resid 196 through 198' Processing helix chain 'Y' and resid 207 through 210 Processing helix chain 'Y' and resid 213 through 223 Processing helix chain 'Y' and resid 239 through 248 removed outlier: 3.925A pdb=" N LYS Y 248 " --> pdb=" O ASP Y 244 " (cutoff:3.500A) Processing helix chain 'Y' and resid 250 through 252 No H-bonds generated for 'chain 'Y' and resid 250 through 252' Processing helix chain 'Y' and resid 258 through 260 No H-bonds generated for 'chain 'Y' and resid 258 through 260' Processing helix chain 'Y' and resid 299 through 311 Processing helix chain 'Y' and resid 327 through 332 Processing helix chain 'Y' and resid 365 through 380 removed outlier: 3.512A pdb=" N LEU Y 372 " --> pdb=" O MET Y 368 " (cutoff:3.500A) Processing helix chain 'Y' and resid 385 through 403 removed outlier: 4.160A pdb=" N LEU Y 403 " --> pdb=" O LEU Y 399 " (cutoff:3.500A) Processing helix chain 'Y' and resid 406 through 420 removed outlier: 3.936A pdb=" N LEU Y 418 " --> pdb=" O GLY Y 414 " (cutoff:3.500A) Processing helix chain 'Y' and resid 426 through 435 removed outlier: 3.859A pdb=" N GLU Y 435 " --> pdb=" O SER Y 431 " (cutoff:3.500A) Processing helix chain 'Y' and resid 438 through 448 Processing helix chain 'Y' and resid 468 through 475 Processing sheet with id= A, first strand: chain 'C' and resid 164 through 169 Processing sheet with id= B, first strand: chain 'C' and resid 263 through 265 removed outlier: 3.783A pdb=" N GLU C 264 " --> pdb=" O ILE C 272 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE C 272 " --> pdb=" O GLU C 264 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'J' and resid 22 through 24 Processing sheet with id= D, first strand: chain 'K' and resid 48 through 51 removed outlier: 3.545A pdb=" N VAL K 48 " --> pdb=" O MET K 218 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'K' and resid 257 through 259 removed outlier: 7.441A pdb=" N MET K 438 " --> pdb=" O ILE K 258 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA K 439 " --> pdb=" O ALA K 270 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'K' and resid 273 through 275 Processing sheet with id= G, first strand: chain 'L' and resid 68 through 73 Processing sheet with id= H, first strand: chain 'L' and resid 455 through 459 removed outlier: 4.090A pdb=" N TYR L 459 " --> pdb=" O HIS L 286 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'P' and resid 165 through 169 removed outlier: 4.141A pdb=" N MET P 165 " --> pdb=" O VAL P 176 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N VAL P 176 " --> pdb=" O MET P 165 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'P' and resid 234 through 236 Processing sheet with id= K, first strand: chain 'P' and resid 263 through 265 Processing sheet with id= L, first strand: chain 'V' and resid 22 through 24 Processing sheet with id= M, first strand: chain 'W' and resid 48 through 50 Processing sheet with id= N, first strand: chain 'W' and resid 436 through 441 Processing sheet with id= O, first strand: chain 'W' and resid 273 through 275 Processing sheet with id= P, first strand: chain 'Y' and resid 58 through 63 Processing sheet with id= Q, first strand: chain 'Y' and resid 121 through 123 Processing sheet with id= R, first strand: chain 'Y' and resid 274 through 276 removed outlier: 6.457A pdb=" N VAL Y 456 " --> pdb=" O ILE Y 275 " (cutoff:3.500A) 1479 hydrogen bonds defined for protein. 3990 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.58 Time building geometry restraints manager: 15.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.40: 14256 1.40 - 1.60: 20774 1.60 - 1.80: 149 1.80 - 2.00: 122 2.00 - 2.20: 32 Bond restraints: 35333 Sorted by residual: bond pdb=" CB7 CDL H 403 " pdb=" OB8 CDL H 403 " ideal model delta sigma weight residual 1.334 1.455 -0.121 1.10e-02 8.26e+03 1.20e+02 bond pdb=" CB7 CDL G 101 " pdb=" OB8 CDL G 101 " ideal model delta sigma weight residual 1.334 1.455 -0.121 1.10e-02 8.26e+03 1.20e+02 bond pdb=" CA7 CDL J 405 " pdb=" OA8 CDL J 405 " ideal model delta sigma weight residual 1.334 1.454 -0.120 1.10e-02 8.26e+03 1.20e+02 bond pdb=" CB7 CDL U 403 " pdb=" OB8 CDL U 403 " ideal model delta sigma weight residual 1.334 1.453 -0.119 1.10e-02 8.26e+03 1.17e+02 bond pdb=" CB7 CDL Y 501 " pdb=" OB8 CDL Y 501 " ideal model delta sigma weight residual 1.334 1.452 -0.118 1.10e-02 8.26e+03 1.16e+02 ... (remaining 35328 not shown) Histogram of bond angle deviations from ideal: 86.00 - 104.62: 788 104.62 - 123.24: 45096 123.24 - 141.86: 1972 141.86 - 160.48: 0 160.48 - 179.11: 12 Bond angle restraints: 47868 Sorted by residual: angle pdb=" S1 FES P 301 " pdb=" FE2 FES P 301 " pdb=" S2 FES P 301 " ideal model delta sigma weight residual 104.33 90.52 13.81 1.14e+00 7.69e-01 1.47e+02 angle pdb=" S1 FES C 301 " pdb=" FE2 FES C 301 " pdb=" S2 FES C 301 " ideal model delta sigma weight residual 104.33 90.76 13.57 1.14e+00 7.69e-01 1.42e+02 angle pdb=" FE1 FES C 301 " pdb=" S2 FES C 301 " pdb=" FE2 FES C 301 " ideal model delta sigma weight residual 75.66 89.19 -13.53 1.14e+00 7.69e-01 1.41e+02 angle pdb=" FE1 FES P 301 " pdb=" S2 FES P 301 " pdb=" FE2 FES P 301 " ideal model delta sigma weight residual 75.66 88.94 -13.28 1.14e+00 7.69e-01 1.36e+02 angle pdb=" S1 FES P 301 " pdb=" FE1 FES P 301 " pdb=" S2 FES P 301 " ideal model delta sigma weight residual 104.33 90.53 13.80 1.20e+00 6.94e-01 1.32e+02 ... (remaining 47863 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.95: 20402 33.95 - 67.90: 487 67.90 - 101.86: 32 101.86 - 135.81: 4 135.81 - 169.76: 3 Dihedral angle restraints: 20928 sinusoidal: 8671 harmonic: 12257 Sorted by residual: dihedral pdb=" CA GLU V 271 " pdb=" C GLU V 271 " pdb=" N TRP V 272 " pdb=" CA TRP V 272 " ideal model delta harmonic sigma weight residual 180.00 -152.30 -27.70 0 5.00e+00 4.00e-02 3.07e+01 dihedral pdb=" N ASP K 451 " pdb=" C ASP K 451 " pdb=" CA ASP K 451 " pdb=" CB ASP K 451 " ideal model delta harmonic sigma weight residual 122.80 135.43 -12.63 0 2.50e+00 1.60e-01 2.55e+01 dihedral pdb=" CA THR B 37 " pdb=" C THR B 37 " pdb=" N PRO B 38 " pdb=" CA PRO B 38 " ideal model delta harmonic sigma weight residual 180.00 156.42 23.58 0 5.00e+00 4.00e-02 2.22e+01 ... (remaining 20925 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 4553 0.078 - 0.156: 558 0.156 - 0.234: 34 0.234 - 0.311: 12 0.311 - 0.389: 5 Chirality restraints: 5162 Sorted by residual: chirality pdb=" CA ASP K 451 " pdb=" N ASP K 451 " pdb=" C ASP K 451 " pdb=" CB ASP K 451 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.79e+00 chirality pdb=" CA TRP V 141 " pdb=" N TRP V 141 " pdb=" C TRP V 141 " pdb=" CB TRP V 141 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.82e+00 chirality pdb=" CA ILE Y 424 " pdb=" N ILE Y 424 " pdb=" C ILE Y 424 " pdb=" CB ILE Y 424 " both_signs ideal model delta sigma weight residual False 2.43 2.11 0.33 2.00e-01 2.50e+01 2.68e+00 ... (remaining 5159 not shown) Planarity restraints: 6010 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1C HEC H 402 " -0.017 2.00e-02 2.50e+03 4.52e-02 4.61e+01 pdb=" C2C HEC H 402 " 0.124 2.00e-02 2.50e+03 pdb=" C3C HEC H 402 " -0.011 2.00e-02 2.50e+03 pdb=" C4C HEC H 402 " -0.005 2.00e-02 2.50e+03 pdb=" CAC HEC H 402 " -0.028 2.00e-02 2.50e+03 pdb=" CHC HEC H 402 " -0.024 2.00e-02 2.50e+03 pdb=" CHD HEC H 402 " 0.002 2.00e-02 2.50e+03 pdb=" CMC HEC H 402 " -0.036 2.00e-02 2.50e+03 pdb=" NC HEC H 402 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN V 341 " 0.057 5.00e-02 4.00e+02 8.61e-02 1.19e+01 pdb=" N PRO V 342 " -0.149 5.00e-02 4.00e+02 pdb=" CA PRO V 342 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO V 342 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP R 73 " 0.016 2.00e-02 2.50e+03 3.13e-02 9.81e+00 pdb=" C ASP R 73 " -0.054 2.00e-02 2.50e+03 pdb=" O ASP R 73 " 0.021 2.00e-02 2.50e+03 pdb=" N PHE R 74 " 0.018 2.00e-02 2.50e+03 ... (remaining 6007 not shown) Histogram of nonbonded interaction distances: 1.41 - 2.11: 20 2.11 - 2.80: 10046 2.80 - 3.50: 48892 3.50 - 4.20: 82103 4.20 - 4.90: 144398 Nonbonded interactions: 285459 Sorted by model distance: nonbonded pdb=" OE2 GLU Y 411 " pdb=" NH1 ARG Y 415 " model vdw 1.408 2.520 nonbonded pdb=" OH TYR F 22 " pdb=" OE2 GLU F 87 " model vdw 1.490 2.440 nonbonded pdb=" NE1 TRP Y 296 " pdb=" OG1 THR Y 419 " model vdw 1.641 2.520 nonbonded pdb=" CD1 LEU T 40 " pdb=" CD1 ILE T 41 " model vdw 1.658 3.880 nonbonded pdb=" NE1 TRP Y 296 " pdb=" CG2 THR Y 419 " model vdw 1.726 3.540 ... (remaining 285454 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 77 or (resid 78 and (name N or name CA or name C \ or name O or name CB )) or resid 79 through 82 or resid 101)) selection = chain 'N' } ncs_group { reference = (chain 'B' and (resid 1 through 30 or (resid 31 through 32 and (name N or name C \ A or name C or name O or name CB )) or resid 33 through 57)) selection = chain 'O' } ncs_group { reference = chain 'C' selection = chain 'P' } ncs_group { reference = chain 'D' selection = (chain 'Q' and resid 2 through 63) } ncs_group { reference = chain 'E' selection = chain 'R' } ncs_group { reference = chain 'F' selection = chain 'S' } ncs_group { reference = (chain 'G' and resid 2 through 52) selection = (chain 'T' and resid 2 through 52) } ncs_group { reference = (chain 'H' and (resid 85 through 325 or (resid 401 and (name N or name C1 or nam \ e C10 or name C11 or name C12 or name C13 or name C14 or name C15 or name C16 or \ name C17 or name C18 or name C19 or name C2 or name C3 or name C30 or name C31 \ or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name \ C38 or name C39 or name C4 or name C40 or name C41 or name C42 or name C43 or na \ me C44 or name C45 or name C5 or name O1P or name O2 or name O2P or name O3 or n \ ame O3P or name O4 or name O4P or name O5 or name P )) or resid 402 through 403) \ ) selection = chain 'U' } ncs_group { reference = (chain 'J' and (resid 2 through 379 or resid 401 through 403)) selection = chain 'V' } ncs_group { reference = chain 'K' selection = (chain 'W' and (resid 35 through 452 or (resid 453 and (name N or name CA or nam \ e C or name O or name CB )))) } ncs_group { reference = (chain 'L' and resid 35 through 480) selection = (chain 'Y' and resid 35 through 480) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Fe 10 7.16 5 P 27 5.49 5 S 160 5.16 5 C 22222 2.51 5 N 5724 2.21 5 O 6349 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.750 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: 0.040 Extract box with map and model: 24.260 Check model and map are aligned: 0.520 Convert atoms to be neutral: 0.290 Process input model: 92.540 Find NCS groups from input model: 2.210 Set up NCS constraints: 0.350 Set refine NCS operators: 0.000 Set scattering table: 0.020 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:3.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 128.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 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 0.196 35333 Z= 0.544 Angle : 1.281 17.128 47868 Z= 0.853 Chirality : 0.051 0.389 5162 Planarity : 0.005 0.086 6010 Dihedral : 13.123 169.759 13034 Min Nonbonded Distance : 1.408 Molprobity Statistics. All-atom Clashscore : 21.15 Ramachandran Plot: Outliers : 1.36 % Allowed : 5.03 % Favored : 93.61 % Rotamer Outliers : 1.49 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 1.90 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.13), residues: 4178 helix: -1.56 (0.09), residues: 2001 sheet: -1.92 (0.27), residues: 318 loop : 1.18 (0.16), residues: 1859 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8356 Ramachandran restraints generated. 4178 Oldfield, 0 Emsley, 4178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8356 Ramachandran restraints generated. 4178 Oldfield, 0 Emsley, 4178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1026 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 973 time to evaluate : 3.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 53 outliers final: 29 residues processed: 1008 average time/residue: 0.5177 time to fit residues: 805.4010 Evaluate side-chains 531 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 502 time to evaluate : 4.218 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 29 outliers final: 1 residues processed: 29 average time/residue: 0.4714 time to fit residues: 27.4056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 347 optimal weight: 3.9990 chunk 312 optimal weight: 0.8980 chunk 173 optimal weight: 1.9990 chunk 106 optimal weight: 0.6980 chunk 210 optimal weight: 0.7980 chunk 166 optimal weight: 1.9990 chunk 322 optimal weight: 0.6980 chunk 124 optimal weight: 0.6980 chunk 196 optimal weight: 0.9990 chunk 240 optimal weight: 2.9990 chunk 374 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 HIS ** A 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 HIS E 39 GLN F 23 ASN F 70 ASN F 73 HIS F 74 GLN ** G 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 107 HIS H 134 HIS ** H 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 206 ASN ** J 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 139 ASN ** K 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 178 HIS K 184 ASN K 212 HIS K 311 GLN K 319 GLN ** K 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 87 ASN ** L 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 188 HIS L 207 ASN L 239 HIS L 301 ASN ** L 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 373 GLN N 13 HIS ** P 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 135 GLN P 178 HIS P 242 HIS Q 38 GLN ** R 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 80 HIS R 84 HIS S 70 ASN U 155 GLN ** U 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 282 HIS U 284 HIS V 137 GLN V 255 ASN W 81 HIS W 139 ASN W 155 GLN W 212 HIS ** W 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 298 HIS W 311 GLN W 421 ASN Y 87 ASN Y 95 HIS Y 301 ASN Y 339 GLN Y 342 GLN Y 373 GLN Y 469 ASN Total number of N/Q/H flips: 49 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.080 35333 Z= 0.268 Angle : 0.749 15.343 47868 Z= 0.372 Chirality : 0.044 0.203 5162 Planarity : 0.005 0.046 6010 Dihedral : 13.675 166.887 5295 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.36 % Allowed : 3.85 % Favored : 95.79 % Rotamer Outliers : 1.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.90 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.13), residues: 4178 helix: 0.12 (0.10), residues: 2022 sheet: -1.95 (0.24), residues: 398 loop : 0.44 (0.16), residues: 1758 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8356 Ramachandran restraints generated. 4178 Oldfield, 0 Emsley, 4178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8356 Ramachandran restraints generated. 4178 Oldfield, 0 Emsley, 4178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 606 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 538 time to evaluate : 3.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 68 outliers final: 37 residues processed: 586 average time/residue: 0.4756 time to fit residues: 450.6726 Evaluate side-chains 495 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 458 time to evaluate : 3.906 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 0 residues processed: 37 average time/residue: 0.3452 time to fit residues: 28.2644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 207 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 311 optimal weight: 0.5980 chunk 254 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 374 optimal weight: 6.9990 chunk 404 optimal weight: 2.9990 chunk 333 optimal weight: 0.5980 chunk 371 optimal weight: 0.5980 chunk 127 optimal weight: 2.9990 chunk 300 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 74 GLN ** G 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 205 HIS H 282 HIS J 267 HIS J 312 GLN ** J 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 184 ASN K 399 GLN ** L 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 24 GLN ** R 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 28 ASN U 115 GLN ** V 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 284 ASN W 426 ASN Y 119 HIS ** Y 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.083 35333 Z= 0.293 Angle : 0.704 16.783 47868 Z= 0.344 Chirality : 0.043 0.375 5162 Planarity : 0.004 0.046 6010 Dihedral : 12.854 164.043 5295 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.50 % Favored : 95.24 % Rotamer Outliers : 1.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.90 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.13), residues: 4178 helix: 0.72 (0.11), residues: 2031 sheet: -1.87 (0.24), residues: 404 loop : 0.10 (0.16), residues: 1743 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8356 Ramachandran restraints generated. 4178 Oldfield, 0 Emsley, 4178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8356 Ramachandran restraints generated. 4178 Oldfield, 0 Emsley, 4178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 497 time to evaluate : 4.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 57 outliers final: 32 residues processed: 532 average time/residue: 0.4681 time to fit residues: 404.5566 Evaluate side-chains 480 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 448 time to evaluate : 3.766 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 0 residues processed: 32 average time/residue: 0.3505 time to fit residues: 25.3325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 370 optimal weight: 0.9980 chunk 281 optimal weight: 0.0470 chunk 194 optimal weight: 0.6980 chunk 41 optimal weight: 0.9980 chunk 178 optimal weight: 2.9990 chunk 251 optimal weight: 0.0370 chunk 376 optimal weight: 1.9990 chunk 398 optimal weight: 3.9990 chunk 196 optimal weight: 1.9990 chunk 356 optimal weight: 3.9990 chunk 107 optimal weight: 0.5980 overall best weight: 0.4756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 81 HIS ** K 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 284 ASN K 415 GLN ** L 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 301 ASN ** L 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 24 GLN ** R 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 206 ASN V 313 GLN ** W 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 311 GLN Y 342 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.3487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.057 35333 Z= 0.198 Angle : 0.646 15.167 47868 Z= 0.314 Chirality : 0.041 0.295 5162 Planarity : 0.004 0.052 6010 Dihedral : 12.136 162.312 5295 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.29 % Allowed : 4.00 % Favored : 95.72 % Rotamer Outliers : 1.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.90 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.13), residues: 4178 helix: 1.07 (0.11), residues: 2029 sheet: -1.75 (0.25), residues: 404 loop : -0.12 (0.15), residues: 1745 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8356 Ramachandran restraints generated. 4178 Oldfield, 0 Emsley, 4178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8356 Ramachandran restraints generated. 4178 Oldfield, 0 Emsley, 4178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 491 time to evaluate : 3.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 49 outliers final: 19 residues processed: 523 average time/residue: 0.4774 time to fit residues: 404.9166 Evaluate side-chains 460 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 441 time to evaluate : 3.908 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.3448 time to fit residues: 16.9732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 331 optimal weight: 1.9990 chunk 226 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 296 optimal weight: 2.9990 chunk 164 optimal weight: 3.9990 chunk 339 optimal weight: 0.9990 chunk 275 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 203 optimal weight: 0.9990 chunk 357 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 74 GLN ** G 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 137 GLN ** J 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 115 GLN ** U 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 139 ASN W 176 ASN W 178 HIS ** W 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 311 GLN ** Y 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.3808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.099 35333 Z= 0.367 Angle : 0.725 19.541 47868 Z= 0.347 Chirality : 0.045 0.272 5162 Planarity : 0.005 0.045 6010 Dihedral : 11.943 157.366 5295 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.34 % Allowed : 4.83 % Favored : 94.83 % Rotamer Outliers : 2.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.90 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.13), residues: 4178 helix: 1.05 (0.12), residues: 2037 sheet: -1.75 (0.25), residues: 408 loop : -0.26 (0.15), residues: 1733 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8356 Ramachandran restraints generated. 4178 Oldfield, 0 Emsley, 4178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8356 Ramachandran restraints generated. 4178 Oldfield, 0 Emsley, 4178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 449 time to evaluate : 4.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 74 outliers final: 40 residues processed: 496 average time/residue: 0.4728 time to fit residues: 382.4233 Evaluate side-chains 465 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 425 time to evaluate : 3.972 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 0 residues processed: 40 average time/residue: 0.3327 time to fit residues: 29.8468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 133 optimal weight: 0.7980 chunk 358 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 233 optimal weight: 0.9990 chunk 98 optimal weight: 0.9990 chunk 398 optimal weight: 0.9990 chunk 330 optimal weight: 2.9990 chunk 184 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 131 optimal weight: 0.8980 chunk 209 optimal weight: 0.7980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 74 GLN ** G 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 115 GLN ** U 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.3979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.079 35333 Z= 0.261 Angle : 0.674 17.145 47868 Z= 0.322 Chirality : 0.042 0.328 5162 Planarity : 0.004 0.046 6010 Dihedral : 11.616 155.722 5295 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.34 % Allowed : 4.14 % Favored : 95.52 % Rotamer Outliers : 1.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.90 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.13), residues: 4178 helix: 1.20 (0.12), residues: 2035 sheet: -1.66 (0.25), residues: 402 loop : -0.37 (0.15), residues: 1741 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8356 Ramachandran restraints generated. 4178 Oldfield, 0 Emsley, 4178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8356 Ramachandran restraints generated. 4178 Oldfield, 0 Emsley, 4178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 456 time to evaluate : 3.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 49 outliers final: 24 residues processed: 490 average time/residue: 0.4829 time to fit residues: 383.9064 Evaluate side-chains 461 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 437 time to evaluate : 3.958 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.3601 time to fit residues: 20.8187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 384 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 227 optimal weight: 0.0980 chunk 291 optimal weight: 1.9990 chunk 225 optimal weight: 1.9990 chunk 335 optimal weight: 1.9990 chunk 222 optimal weight: 0.9980 chunk 397 optimal weight: 0.5980 chunk 248 optimal weight: 10.0000 chunk 242 optimal weight: 3.9990 chunk 183 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 74 GLN ** G 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 95 HIS ** L 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 199 GLN ** L 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 373 GLN U 115 GLN ** U 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 277 HIS ** Y 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.4125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.091 35333 Z= 0.318 Angle : 0.696 18.555 47868 Z= 0.334 Chirality : 0.043 0.358 5162 Planarity : 0.004 0.049 6010 Dihedral : 11.463 153.224 5295 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.29 % Allowed : 4.72 % Favored : 95.00 % Rotamer Outliers : 1.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.90 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.13), residues: 4178 helix: 1.17 (0.12), residues: 2041 sheet: -1.60 (0.26), residues: 406 loop : -0.48 (0.15), residues: 1731 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8356 Ramachandran restraints generated. 4178 Oldfield, 0 Emsley, 4178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8356 Ramachandran restraints generated. 4178 Oldfield, 0 Emsley, 4178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 434 time to evaluate : 3.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 22 residues processed: 467 average time/residue: 0.4771 time to fit residues: 362.9601 Evaluate side-chains 444 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 422 time to evaluate : 4.140 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.3632 time to fit residues: 19.8260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 245 optimal weight: 3.9990 chunk 158 optimal weight: 0.4980 chunk 237 optimal weight: 7.9990 chunk 119 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 chunk 76 optimal weight: 0.7980 chunk 252 optimal weight: 1.9990 chunk 270 optimal weight: 3.9990 chunk 196 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 312 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 74 GLN ** G 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 291 HIS L 301 ASN ** L 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 205 HIS ** W 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 343 GLN ** Y 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.4234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.087 35333 Z= 0.284 Angle : 0.681 17.529 47868 Z= 0.327 Chirality : 0.043 0.327 5162 Planarity : 0.004 0.049 6010 Dihedral : 11.282 151.987 5295 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.43 % Favored : 95.31 % Rotamer Outliers : 0.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.90 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.13), residues: 4178 helix: 1.22 (0.12), residues: 2037 sheet: -1.53 (0.26), residues: 402 loop : -0.57 (0.15), residues: 1739 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8356 Ramachandran restraints generated. 4178 Oldfield, 0 Emsley, 4178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8356 Ramachandran restraints generated. 4178 Oldfield, 0 Emsley, 4178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 443 time to evaluate : 4.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 10 residues processed: 457 average time/residue: 0.4714 time to fit residues: 351.7396 Evaluate side-chains 430 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 420 time to evaluate : 4.398 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.3323 time to fit residues: 11.3160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 361 optimal weight: 3.9990 chunk 380 optimal weight: 0.9980 chunk 347 optimal weight: 6.9990 chunk 370 optimal weight: 0.9990 chunk 222 optimal weight: 0.9980 chunk 161 optimal weight: 0.9980 chunk 290 optimal weight: 3.9990 chunk 113 optimal weight: 0.5980 chunk 334 optimal weight: 0.9990 chunk 349 optimal weight: 3.9990 chunk 368 optimal weight: 0.0770 overall best weight: 0.7338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 74 GLN ** G 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 199 GLN ** L 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 74 GLN ** U 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.4306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.072 35333 Z= 0.236 Angle : 0.664 16.570 47868 Z= 0.317 Chirality : 0.042 0.317 5162 Planarity : 0.004 0.057 6010 Dihedral : 11.030 150.817 5295 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.52 % Favored : 95.24 % Rotamer Outliers : 0.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.90 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.13), residues: 4178 helix: 1.28 (0.12), residues: 2044 sheet: -1.42 (0.26), residues: 398 loop : -0.56 (0.15), residues: 1736 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8356 Ramachandran restraints generated. 4178 Oldfield, 0 Emsley, 4178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8356 Ramachandran restraints generated. 4178 Oldfield, 0 Emsley, 4178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 446 time to evaluate : 4.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 10 residues processed: 460 average time/residue: 0.4917 time to fit residues: 367.7812 Evaluate side-chains 442 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 432 time to evaluate : 3.938 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.4189 time to fit residues: 12.3429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 242 optimal weight: 4.9990 chunk 391 optimal weight: 0.9980 chunk 238 optimal weight: 5.9990 chunk 185 optimal weight: 0.6980 chunk 272 optimal weight: 0.9980 chunk 410 optimal weight: 0.7980 chunk 377 optimal weight: 5.9990 chunk 326 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 252 optimal weight: 2.9990 chunk 200 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 74 GLN ** G 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 74 GLN ** U 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.4381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.077 35333 Z= 0.258 Angle : 0.683 17.405 47868 Z= 0.326 Chirality : 0.042 0.316 5162 Planarity : 0.004 0.066 6010 Dihedral : 10.893 149.812 5295 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.52 % Favored : 95.24 % Rotamer Outliers : 0.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.90 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.13), residues: 4178 helix: 1.26 (0.12), residues: 2048 sheet: -1.46 (0.26), residues: 406 loop : -0.58 (0.15), residues: 1724 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8356 Ramachandran restraints generated. 4178 Oldfield, 0 Emsley, 4178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8356 Ramachandran restraints generated. 4178 Oldfield, 0 Emsley, 4178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 444 time to evaluate : 4.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 5 residues processed: 452 average time/residue: 0.4878 time to fit residues: 356.4071 Evaluate side-chains 429 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 424 time to evaluate : 3.616 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.3278 time to fit residues: 7.8470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 259 optimal weight: 0.9990 chunk 348 optimal weight: 4.9990 chunk 100 optimal weight: 0.7980 chunk 301 optimal weight: 0.9980 chunk 48 optimal weight: 0.6980 chunk 90 optimal weight: 0.1980 chunk 327 optimal weight: 0.0370 chunk 137 optimal weight: 1.9990 chunk 336 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 chunk 60 optimal weight: 0.1980 overall best weight: 0.3858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 74 GLN ** G 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 291 HIS ** L 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 74 GLN U 155 GLN V 15 ASN ** W 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 199 GLN ** Y 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.119698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.096601 restraints weight = 66240.400| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.08 r_work: 0.3160 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.4451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 35333 Z= 0.185 Angle : 0.652 15.055 47868 Z= 0.312 Chirality : 0.041 0.283 5162 Planarity : 0.004 0.065 6010 Dihedral : 10.541 147.813 5295 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.26 % Favored : 95.52 % Rotamer Outliers : 0.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.90 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.13), residues: 4178 helix: 1.36 (0.12), residues: 2043 sheet: -1.33 (0.26), residues: 402 loop : -0.56 (0.15), residues: 1733 =============================================================================== Job complete usr+sys time: 8158.41 seconds wall clock time: 147 minutes 50.87 seconds (8870.87 seconds total)