Starting phenix.real_space_refine on Thu Feb 22 14:55:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xte_6774/02_2024/5xte_6774_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xte_6774/02_2024/5xte_6774.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xte_6774/02_2024/5xte_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_6774/02_2024/5xte_6774_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xte_6774/02_2024/5xte_6774_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xte_6774/02_2024/5xte_6774.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xte_6774/02_2024/5xte_6774.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xte_6774/02_2024/5xte_6774_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xte_6774/02_2024/5xte_6774_updated.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians 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. 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: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 18.06, per 1000 atoms: 0.52 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: 15.20 Conformation dependent library (CDL) restraints added in 6.3 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: 6.54 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: 11.79 Time building geometry restraints manager: 15.99 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 - 35.85: 20600 35.85 - 71.70: 522 71.70 - 107.54: 42 107.54 - 143.39: 11 143.39 - 179.24: 11 Dihedral angle restraints: 21186 sinusoidal: 8929 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 21183 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 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: 5.890 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: 0.030 Extract box with map and model: 23.490 Check model and map are aligned: 0.530 Set scattering table: 0.320 Process input model: 99.820 Find NCS groups from input model: 2.220 Set up NCS constraints: 0.350 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:3.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 135.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 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= 0.546 Angle : 1.282 17.128 47868 Z= 0.853 Chirality : 0.051 0.389 5162 Planarity : 0.005 0.086 6010 Dihedral : 14.871 179.241 13292 Min Nonbonded Distance : 1.408 Molprobity Statistics. All-atom Clashscore : 20.93 Ramachandran Plot: Outliers : 1.36 % Allowed : 5.03 % Favored : 93.61 % Rotamer: Outliers : 1.49 % Allowed : 1.55 % Favored : 96.96 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP H 96 HIS 0.015 0.002 HIS K 291 PHE 0.021 0.002 PHE E 74 TYR 0.032 0.002 TYR Y 186 ARG 0.012 0.001 ARG C 204 *********************** 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 : 3.668 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 REVERT: A 25 ARG cc_start: 0.8776 (OUTLIER) cc_final: 0.7495 (tpt170) REVERT: A 43 ARG cc_start: 0.8365 (ttp-110) cc_final: 0.8007 (mtt180) REVERT: A 66 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.7841 (tp30) REVERT: B 1 MET cc_start: 0.6273 (ttt) cc_final: 0.6013 (ttp) REVERT: E 50 LEU cc_start: 0.8430 (tt) cc_final: 0.8044 (tp) REVERT: E 79 ASP cc_start: 0.7845 (m-30) cc_final: 0.7608 (m-30) REVERT: J 72 ASP cc_start: 0.7185 (m-30) cc_final: 0.6942 (m-30) REVERT: J 150 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8355 (mt) REVERT: N 25 ARG cc_start: 0.7479 (ptt180) cc_final: 0.6141 (tpt-90) REVERT: P 98 ASP cc_start: 0.4258 (p0) cc_final: 0.3851 (p0) REVERT: P 145 ASP cc_start: 0.8379 (p0) cc_final: 0.7853 (p0) REVERT: T 40 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.7376 (mp) REVERT: T 41 ILE cc_start: 0.8121 (mp) cc_final: 0.7687 (mm) REVERT: U 115 GLN cc_start: 0.8115 (mt0) cc_final: 0.7709 (mt0) REVERT: U 216 THR cc_start: 0.8926 (m) cc_final: 0.8544 (p) REVERT: V 17 SER cc_start: 0.8261 (p) cc_final: 0.7997 (p) outliers start: 53 outliers final: 29 residues processed: 1008 average time/residue: 0.5426 time to fit residues: 838.8605 Evaluate side-chains 542 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 509 time to evaluate : 3.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ARG Chi-restraints excluded: chain A residue 40 ARG Chi-restraints excluded: chain A residue 48 ARG Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain E residue 28 ASP Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain F residue 29 LYS Chi-restraints excluded: chain F residue 33 MET Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 41 ASP Chi-restraints excluded: chain F residue 60 MET Chi-restraints excluded: chain F residue 71 LEU Chi-restraints excluded: chain J residue 124 MET Chi-restraints excluded: chain J residue 150 LEU Chi-restraints excluded: chain K residue 365 ASN Chi-restraints excluded: chain R residue 78 ARG Chi-restraints excluded: chain R residue 81 CYS Chi-restraints excluded: chain T residue 40 LEU Chi-restraints excluded: chain U residue 292 MET Chi-restraints excluded: chain V residue 147 THR Chi-restraints excluded: chain V residue 149 LEU Chi-restraints excluded: chain V residue 185 LEU Chi-restraints excluded: chain V residue 192 LEU Chi-restraints excluded: chain V residue 299 LEU Chi-restraints excluded: chain W residue 254 ARG Chi-restraints excluded: chain W residue 451 ASP Chi-restraints excluded: chain W residue 453 LEU Chi-restraints excluded: chain Y residue 96 LEU Chi-restraints excluded: chain Y residue 422 ARG Chi-restraints excluded: chain Y residue 423 ARG 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: 0.5980 chunk 124 optimal weight: 0.6980 chunk 196 optimal weight: 0.9990 chunk 240 optimal weight: 2.9990 chunk 374 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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** J 322 GLN ** 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: 50 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 35333 Z= 0.271 Angle : 0.757 15.630 47868 Z= 0.374 Chirality : 0.045 0.243 5162 Planarity : 0.005 0.047 6010 Dihedral : 17.174 178.931 5636 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.36 % Allowed : 3.95 % Favored : 95.69 % Rotamer: Outliers : 2.68 % Allowed : 9.22 % Favored : 88.10 % 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: -0.07 (0.13), residues: 4178 helix: 0.16 (0.11), residues: 2018 sheet: -1.88 (0.25), residues: 378 loop : 0.42 (0.16), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP P 169 HIS 0.018 0.002 HIS V 83 PHE 0.035 0.002 PHE Y 98 TYR 0.028 0.002 TYR Y 186 ARG 0.014 0.001 ARG E 56 *********************** 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 640 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 545 time to evaluate : 3.954 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: A 25 ARG cc_start: 0.8841 (OUTLIER) cc_final: 0.7561 (tpt170) REVERT: A 43 ARG cc_start: 0.8395 (ttp-110) cc_final: 0.8059 (mtt180) REVERT: B 1 MET cc_start: 0.6154 (ttt) cc_final: 0.5946 (ttp) REVERT: E 51 GLU cc_start: 0.8004 (pp20) cc_final: 0.7763 (pp20) REVERT: H 102 LEU cc_start: 0.9030 (mt) cc_final: 0.8799 (mt) REVERT: L 229 MET cc_start: 0.7475 (mtt) cc_final: 0.7270 (mtt) REVERT: N 25 ARG cc_start: 0.7579 (ptt180) cc_final: 0.6208 (tpt-90) REVERT: T 23 THR cc_start: 0.8972 (m) cc_final: 0.8755 (p) REVERT: T 40 LEU cc_start: 0.7448 (pp) cc_final: 0.7118 (mp) REVERT: U 216 THR cc_start: 0.8776 (m) cc_final: 0.8387 (p) REVERT: V 15 ASN cc_start: 0.9027 (t0) cc_final: 0.8798 (t0) outliers start: 95 outliers final: 57 residues processed: 611 average time/residue: 0.4925 time to fit residues: 477.6440 Evaluate side-chains 522 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 464 time to evaluate : 4.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ARG Chi-restraints excluded: chain A residue 40 ARG Chi-restraints excluded: chain A residue 48 ARG Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 161 GLU Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain E residue 28 ASP Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain F residue 33 MET Chi-restraints excluded: chain F residue 41 ASP Chi-restraints excluded: chain F residue 60 MET Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 124 CYS Chi-restraints excluded: chain J residue 58 ASP Chi-restraints excluded: chain J residue 197 LEU Chi-restraints excluded: chain J residue 334 ILE Chi-restraints excluded: chain K residue 61 ILE Chi-restraints excluded: chain K residue 122 THR Chi-restraints excluded: chain K residue 365 ASN Chi-restraints excluded: chain L residue 365 ILE Chi-restraints excluded: chain N residue 50 VAL Chi-restraints excluded: chain N residue 64 THR Chi-restraints excluded: chain N residue 81 ASP Chi-restraints excluded: chain P residue 159 ILE Chi-restraints excluded: chain Q residue 38 GLN Chi-restraints excluded: chain R residue 78 ARG Chi-restraints excluded: chain S residue 17 ILE Chi-restraints excluded: chain S residue 43 ASP Chi-restraints excluded: chain U residue 89 LEU Chi-restraints excluded: chain U residue 155 GLN Chi-restraints excluded: chain U residue 223 THR Chi-restraints excluded: chain U residue 292 MET Chi-restraints excluded: chain V residue 147 THR Chi-restraints excluded: chain V residue 149 LEU Chi-restraints excluded: chain V residue 185 LEU Chi-restraints excluded: chain V residue 192 LEU Chi-restraints excluded: chain V residue 205 SER Chi-restraints excluded: chain V residue 284 VAL Chi-restraints excluded: chain V residue 298 ILE Chi-restraints excluded: chain V residue 299 LEU Chi-restraints excluded: chain V residue 316 MET Chi-restraints excluded: chain V residue 379 TRP Chi-restraints excluded: chain W residue 92 LYS Chi-restraints excluded: chain W residue 106 VAL Chi-restraints excluded: chain W residue 118 ASN Chi-restraints excluded: chain W residue 194 ASP Chi-restraints excluded: chain W residue 254 ARG Chi-restraints excluded: chain W residue 265 SER Chi-restraints excluded: chain W residue 365 ASN Chi-restraints excluded: chain Y residue 120 LEU Chi-restraints excluded: chain Y residue 150 ILE Chi-restraints excluded: chain Y residue 287 VAL Chi-restraints excluded: chain Y residue 416 SER Chi-restraints excluded: chain Y residue 422 ARG 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: 1.9990 chunk 254 optimal weight: 0.5980 chunk 103 optimal weight: 0.9990 chunk 374 optimal weight: 6.9990 chunk 404 optimal weight: 2.9990 chunk 333 optimal weight: 0.5980 chunk 371 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 300 optimal weight: 0.1980 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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** H 205 HIS H 282 HIS J 267 HIS K 81 HIS ** 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 ** P 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 28 ASN U 115 GLN U 155 GLN ** U 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 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: 0.7939 moved from start: 0.3196 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= 0.271 Angle : 0.691 16.740 47868 Z= 0.339 Chirality : 0.044 0.496 5162 Planarity : 0.004 0.048 6010 Dihedral : 16.176 177.660 5604 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.38 % Favored : 95.36 % Rotamer: Outliers : 2.65 % Allowed : 11.50 % Favored : 85.85 % 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: 0.22 (0.13), residues: 4178 helix: 0.79 (0.11), residues: 2028 sheet: -1.85 (0.24), residues: 404 loop : 0.08 (0.15), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP L 296 HIS 0.015 0.002 HIS V 83 PHE 0.032 0.002 PHE Y 98 TYR 0.032 0.002 TYR S 22 ARG 0.010 0.001 ARG R 56 *********************** 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 602 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 508 time to evaluate : 4.318 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: A 25 ARG cc_start: 0.8906 (OUTLIER) cc_final: 0.7635 (tpt170) REVERT: A 43 ARG cc_start: 0.8392 (ttp-110) cc_final: 0.8048 (mtt180) REVERT: C 242 HIS cc_start: 0.6781 (m-70) cc_final: 0.6462 (m-70) REVERT: E 79 ASP cc_start: 0.8215 (m-30) cc_final: 0.8004 (m-30) REVERT: L 139 ASP cc_start: 0.6786 (t0) cc_final: 0.6378 (t0) REVERT: L 181 ASP cc_start: 0.7506 (p0) cc_final: 0.7284 (p0) REVERT: N 25 ARG cc_start: 0.7686 (ptt180) cc_final: 0.6258 (tpt-90) REVERT: R 35 GLU cc_start: 0.8194 (mt-10) cc_final: 0.7939 (tt0) REVERT: T 23 THR cc_start: 0.9032 (m) cc_final: 0.8747 (p) REVERT: U 244 MET cc_start: 0.8943 (ttp) cc_final: 0.8634 (ttp) REVERT: Y 296 TRP cc_start: 0.7580 (OUTLIER) cc_final: 0.7140 (t-100) outliers start: 94 outliers final: 67 residues processed: 570 average time/residue: 0.4926 time to fit residues: 449.3237 Evaluate side-chains 522 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 453 time to evaluate : 3.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ARG Chi-restraints excluded: chain A residue 40 ARG Chi-restraints excluded: chain A residue 48 ARG Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 71 LYS Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 161 GLU Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain E residue 28 ASP Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 61 SER Chi-restraints excluded: chain E residue 81 CYS Chi-restraints excluded: chain F residue 41 ASP Chi-restraints excluded: chain F residue 60 MET Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 227 LEU Chi-restraints excluded: chain H residue 263 MET Chi-restraints excluded: chain J residue 12 LYS Chi-restraints excluded: chain J residue 17 SER Chi-restraints excluded: chain J residue 197 LEU Chi-restraints excluded: chain J residue 206 ASN Chi-restraints excluded: chain J residue 218 ILE Chi-restraints excluded: chain J residue 334 ILE Chi-restraints excluded: chain K residue 61 ILE Chi-restraints excluded: chain K residue 122 THR Chi-restraints excluded: chain K residue 365 ASN Chi-restraints excluded: chain K residue 451 ASP Chi-restraints excluded: chain L residue 215 ASP Chi-restraints excluded: chain L residue 359 VAL Chi-restraints excluded: chain N residue 50 VAL Chi-restraints excluded: chain N residue 64 THR Chi-restraints excluded: chain N residue 65 GLU Chi-restraints excluded: chain N residue 66 GLU Chi-restraints excluded: chain N residue 81 ASP Chi-restraints excluded: chain P residue 149 LEU Chi-restraints excluded: chain P residue 159 ILE Chi-restraints excluded: chain Q residue 38 GLN Chi-restraints excluded: chain Q residue 47 ILE Chi-restraints excluded: chain R residue 78 ARG Chi-restraints excluded: chain S residue 43 ASP Chi-restraints excluded: chain T residue 32 LEU Chi-restraints excluded: chain U residue 159 ASN Chi-restraints excluded: chain U residue 292 MET Chi-restraints excluded: chain V residue 16 HIS Chi-restraints excluded: chain V residue 46 THR Chi-restraints excluded: chain V residue 149 LEU Chi-restraints excluded: chain V residue 185 LEU Chi-restraints excluded: chain V residue 192 LEU Chi-restraints excluded: chain V residue 205 SER Chi-restraints excluded: chain V residue 284 VAL Chi-restraints excluded: chain V residue 298 ILE Chi-restraints excluded: chain V residue 299 LEU Chi-restraints excluded: chain V residue 316 MET Chi-restraints excluded: chain V residue 336 THR Chi-restraints excluded: chain V residue 379 TRP Chi-restraints excluded: chain W residue 92 LYS Chi-restraints excluded: chain W residue 106 VAL Chi-restraints excluded: chain W residue 194 ASP Chi-restraints excluded: chain W residue 317 THR Chi-restraints excluded: chain W residue 365 ASN Chi-restraints excluded: chain W residue 447 THR Chi-restraints excluded: chain Y residue 120 LEU Chi-restraints excluded: chain Y residue 150 ILE Chi-restraints excluded: chain Y residue 287 VAL Chi-restraints excluded: chain Y residue 296 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 370 optimal weight: 1.9990 chunk 281 optimal weight: 1.9990 chunk 194 optimal weight: 0.0170 chunk 41 optimal weight: 0.9980 chunk 178 optimal weight: 0.9980 chunk 251 optimal weight: 0.3980 chunk 376 optimal weight: 0.8980 chunk 398 optimal weight: 3.9990 chunk 196 optimal weight: 1.9990 chunk 356 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 overall best weight: 0.6618 ------------------------------------------------------------------------------- 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** ** G 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 137 GLN ** 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 ** P 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 242 HIS ** 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 178 HIS W 232 GLN W 236 GLN W 311 GLN Y 342 GLN ** 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: 0.7935 moved from start: 0.3512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 35333 Z= 0.226 Angle : 0.652 15.996 47868 Z= 0.318 Chirality : 0.042 0.223 5162 Planarity : 0.004 0.052 6010 Dihedral : 15.492 177.695 5590 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.29 % Allowed : 4.12 % Favored : 95.60 % Rotamer: Outliers : 3.16 % Allowed : 12.63 % Favored : 84.21 % 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: 0.37 (0.13), residues: 4178 helix: 1.09 (0.11), residues: 2028 sheet: -1.76 (0.25), residues: 408 loop : -0.11 (0.15), residues: 1742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP V 379 HIS 0.014 0.001 HIS V 83 PHE 0.026 0.001 PHE C 175 TYR 0.016 0.001 TYR V 278 ARG 0.008 0.000 ARG H 228 *********************** 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 587 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 475 time to evaluate : 4.571 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 revert: symmetry clash REVERT: A 25 ARG cc_start: 0.8951 (OUTLIER) cc_final: 0.7615 (tpt170) REVERT: A 43 ARG cc_start: 0.8339 (ttp-110) cc_final: 0.8020 (mtt180) REVERT: E 79 ASP cc_start: 0.8257 (m-30) cc_final: 0.8018 (m-30) REVERT: J 287 LYS cc_start: 0.7636 (mttt) cc_final: 0.7170 (mttp) REVERT: N 25 ARG cc_start: 0.7734 (ptt180) cc_final: 0.6266 (tpt-90) REVERT: R 81 CYS cc_start: 0.8321 (OUTLIER) cc_final: 0.7967 (p) REVERT: U 244 MET cc_start: 0.8942 (ttp) cc_final: 0.8674 (ttp) REVERT: W 214 THR cc_start: 0.8338 (OUTLIER) cc_final: 0.7952 (p) REVERT: Y 42 LEU cc_start: 0.6581 (mt) cc_final: 0.5781 (tt) REVERT: Y 296 TRP cc_start: 0.7614 (OUTLIER) cc_final: 0.6908 (t-100) outliers start: 112 outliers final: 71 residues processed: 552 average time/residue: 0.4768 time to fit residues: 421.2456 Evaluate side-chains 526 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 451 time to evaluate : 3.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ARG Chi-restraints excluded: chain A residue 40 ARG Chi-restraints excluded: chain A residue 48 ARG Chi-restraints excluded: chain A residue 71 LYS Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 161 GLU Chi-restraints excluded: chain E residue 28 ASP Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain F residue 41 ASP Chi-restraints excluded: chain F residue 60 MET Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 124 CYS Chi-restraints excluded: chain J residue 12 LYS Chi-restraints excluded: chain J residue 17 SER Chi-restraints excluded: chain J residue 58 ASP Chi-restraints excluded: chain J residue 197 LEU Chi-restraints excluded: chain J residue 206 ASN Chi-restraints excluded: chain J residue 218 ILE Chi-restraints excluded: chain J residue 334 ILE Chi-restraints excluded: chain K residue 61 ILE Chi-restraints excluded: chain K residue 122 THR Chi-restraints excluded: chain K residue 124 GLU Chi-restraints excluded: chain K residue 272 VAL Chi-restraints excluded: chain K residue 415 GLN Chi-restraints excluded: chain K residue 425 ILE Chi-restraints excluded: chain L residue 215 ASP Chi-restraints excluded: chain L residue 296 TRP Chi-restraints excluded: chain L residue 365 ILE Chi-restraints excluded: chain N residue 15 ILE Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 50 VAL Chi-restraints excluded: chain N residue 71 LYS Chi-restraints excluded: chain N residue 81 ASP Chi-restraints excluded: chain P residue 134 THR Chi-restraints excluded: chain P residue 149 LEU Chi-restraints excluded: chain P residue 211 VAL Chi-restraints excluded: chain Q residue 47 ILE Chi-restraints excluded: chain R residue 78 ARG Chi-restraints excluded: chain R residue 81 CYS Chi-restraints excluded: chain S residue 43 ASP Chi-restraints excluded: chain S residue 86 GLU Chi-restraints excluded: chain T residue 18 VAL Chi-restraints excluded: chain U residue 141 THR Chi-restraints excluded: chain U residue 155 GLN Chi-restraints excluded: chain U residue 159 ASN Chi-restraints excluded: chain U residue 292 MET Chi-restraints excluded: chain V residue 16 HIS Chi-restraints excluded: chain V residue 46 THR Chi-restraints excluded: chain V residue 147 THR Chi-restraints excluded: chain V residue 149 LEU Chi-restraints excluded: chain V residue 192 LEU Chi-restraints excluded: chain V residue 202 GLU Chi-restraints excluded: chain V residue 284 VAL Chi-restraints excluded: chain V residue 291 VAL Chi-restraints excluded: chain V residue 298 ILE Chi-restraints excluded: chain V residue 299 LEU Chi-restraints excluded: chain V residue 316 MET Chi-restraints excluded: chain V residue 336 THR Chi-restraints excluded: chain V residue 379 TRP Chi-restraints excluded: chain W residue 92 LYS Chi-restraints excluded: chain W residue 106 VAL Chi-restraints excluded: chain W residue 194 ASP Chi-restraints excluded: chain W residue 214 THR Chi-restraints excluded: chain W residue 232 GLN Chi-restraints excluded: chain W residue 317 THR Chi-restraints excluded: chain W residue 365 ASN Chi-restraints excluded: chain W residue 416 ILE Chi-restraints excluded: chain W residue 447 THR Chi-restraints excluded: chain Y residue 120 LEU Chi-restraints excluded: chain Y residue 150 ILE Chi-restraints excluded: chain Y residue 287 VAL Chi-restraints excluded: chain Y residue 296 TRP 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: 5.9990 chunk 5 optimal weight: 2.9990 chunk 296 optimal weight: 1.9990 chunk 164 optimal weight: 3.9990 chunk 339 optimal weight: 1.9990 chunk 275 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 203 optimal weight: 0.9990 chunk 357 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- 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 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 284 ASN ** 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 176 ASN W 311 GLN Y 277 HIS ** Y 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.3885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.116 35333 Z= 0.454 Angle : 0.773 21.042 47868 Z= 0.374 Chirality : 0.046 0.236 5162 Planarity : 0.005 0.076 6010 Dihedral : 15.420 177.406 5585 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.03 % Favored : 94.66 % Rotamer: Outliers : 4.03 % Allowed : 13.25 % Favored : 82.72 % 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: 0.13 (0.13), residues: 4178 helix: 0.96 (0.11), residues: 2032 sheet: -1.87 (0.24), residues: 426 loop : -0.31 (0.15), residues: 1720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP V 379 HIS 0.013 0.002 HIS J 196 PHE 0.023 0.002 PHE C 175 TYR 0.022 0.002 TYR K 355 ARG 0.007 0.001 ARG R 56 *********************** 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 592 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 449 time to evaluate : 4.279 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 revert: symmetry clash REVERT: A 25 ARG cc_start: 0.9015 (ptm-80) cc_final: 0.7677 (tpt170) REVERT: A 43 ARG cc_start: 0.8383 (ttp-110) cc_final: 0.7912 (mtt180) REVERT: A 69 ARG cc_start: 0.7652 (ttp-110) cc_final: 0.7158 (ttm110) REVERT: C 101 LYS cc_start: 0.7822 (mmtt) cc_final: 0.7542 (tttp) REVERT: E 51 GLU cc_start: 0.7754 (pp20) cc_final: 0.7530 (pp20) REVERT: E 79 ASP cc_start: 0.8287 (m-30) cc_final: 0.7983 (m-30) REVERT: J 124 MET cc_start: 0.8565 (mmm) cc_final: 0.8215 (mtp) REVERT: J 287 LYS cc_start: 0.7609 (mttt) cc_final: 0.7145 (mttp) REVERT: K 237 PHE cc_start: 0.7175 (t80) cc_final: 0.6888 (t80) REVERT: L 305 GLN cc_start: 0.8292 (mp10) cc_final: 0.7995 (mp10) REVERT: N 25 ARG cc_start: 0.7812 (ptt180) cc_final: 0.6185 (tpt-90) REVERT: R 81 CYS cc_start: 0.8465 (OUTLIER) cc_final: 0.8018 (p) REVERT: T 48 ILE cc_start: 0.7309 (OUTLIER) cc_final: 0.6729 (tp) REVERT: U 244 MET cc_start: 0.9119 (ttp) cc_final: 0.8638 (ttp) REVERT: W 214 THR cc_start: 0.8449 (OUTLIER) cc_final: 0.8221 (p) REVERT: Y 153 ASN cc_start: 0.7565 (OUTLIER) cc_final: 0.7033 (p0) outliers start: 143 outliers final: 96 residues processed: 553 average time/residue: 0.4707 time to fit residues: 420.5998 Evaluate side-chains 527 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 427 time to evaluate : 4.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 40 ARG Chi-restraints excluded: chain A residue 48 ARG Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 145 ASP Chi-restraints excluded: chain E residue 28 ASP Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 61 SER Chi-restraints excluded: chain E residue 81 CYS Chi-restraints excluded: chain F residue 41 ASP Chi-restraints excluded: chain F residue 60 MET Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 124 CYS Chi-restraints excluded: chain H residue 227 LEU Chi-restraints excluded: chain H residue 263 MET Chi-restraints excluded: chain J residue 17 SER Chi-restraints excluded: chain J residue 27 ILE Chi-restraints excluded: chain J residue 58 ASP Chi-restraints excluded: chain J residue 61 THR Chi-restraints excluded: chain J residue 185 LEU Chi-restraints excluded: chain J residue 197 LEU Chi-restraints excluded: chain J residue 198 LEU Chi-restraints excluded: chain J residue 206 ASN Chi-restraints excluded: chain J residue 218 ILE Chi-restraints excluded: chain J residue 334 ILE Chi-restraints excluded: chain J residue 379 TRP Chi-restraints excluded: chain K residue 61 ILE Chi-restraints excluded: chain K residue 122 THR Chi-restraints excluded: chain K residue 124 GLU Chi-restraints excluded: chain K residue 272 VAL Chi-restraints excluded: chain K residue 386 VAL Chi-restraints excluded: chain K residue 425 ILE Chi-restraints excluded: chain K residue 441 SER Chi-restraints excluded: chain K residue 451 ASP Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 83 THR Chi-restraints excluded: chain L residue 215 ASP Chi-restraints excluded: chain L residue 296 TRP Chi-restraints excluded: chain L residue 359 VAL Chi-restraints excluded: chain L residue 365 ILE Chi-restraints excluded: chain N residue 15 ILE Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 50 VAL Chi-restraints excluded: chain N residue 64 THR Chi-restraints excluded: chain N residue 71 LYS Chi-restraints excluded: chain N residue 81 ASP Chi-restraints excluded: chain O residue 45 LEU Chi-restraints excluded: chain P residue 83 ILE Chi-restraints excluded: chain P residue 134 THR Chi-restraints excluded: chain P residue 149 LEU Chi-restraints excluded: chain P residue 211 VAL Chi-restraints excluded: chain P residue 218 THR Chi-restraints excluded: chain Q residue 47 ILE Chi-restraints excluded: chain R residue 39 GLN Chi-restraints excluded: chain R residue 78 ARG Chi-restraints excluded: chain R residue 81 CYS Chi-restraints excluded: chain S residue 43 ASP Chi-restraints excluded: chain S residue 86 GLU Chi-restraints excluded: chain T residue 18 VAL Chi-restraints excluded: chain T residue 48 ILE Chi-restraints excluded: chain U residue 156 ASP Chi-restraints excluded: chain U residue 159 ASN Chi-restraints excluded: chain U residue 253 LEU Chi-restraints excluded: chain U residue 292 MET Chi-restraints excluded: chain V residue 16 HIS Chi-restraints excluded: chain V residue 46 THR Chi-restraints excluded: chain V residue 147 THR Chi-restraints excluded: chain V residue 149 LEU Chi-restraints excluded: chain V residue 205 SER Chi-restraints excluded: chain V residue 242 LEU Chi-restraints excluded: chain V residue 291 VAL Chi-restraints excluded: chain V residue 298 ILE Chi-restraints excluded: chain V residue 299 LEU Chi-restraints excluded: chain V residue 316 MET Chi-restraints excluded: chain V residue 336 THR Chi-restraints excluded: chain V residue 379 TRP Chi-restraints excluded: chain W residue 92 LYS Chi-restraints excluded: chain W residue 100 THR Chi-restraints excluded: chain W residue 106 VAL Chi-restraints excluded: chain W residue 134 MET Chi-restraints excluded: chain W residue 194 ASP Chi-restraints excluded: chain W residue 214 THR Chi-restraints excluded: chain W residue 265 SER Chi-restraints excluded: chain W residue 317 THR Chi-restraints excluded: chain W residue 365 ASN Chi-restraints excluded: chain W residue 416 ILE Chi-restraints excluded: chain W residue 418 SER Chi-restraints excluded: chain W residue 447 THR Chi-restraints excluded: chain Y residue 120 LEU Chi-restraints excluded: chain Y residue 150 ILE Chi-restraints excluded: chain Y residue 153 ASN Chi-restraints excluded: chain Y residue 190 THR Chi-restraints excluded: chain Y residue 287 VAL Chi-restraints excluded: chain Y residue 296 TRP Chi-restraints excluded: chain Y residue 366 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 133 optimal weight: 0.0770 chunk 358 optimal weight: 4.9990 chunk 78 optimal weight: 0.5980 chunk 233 optimal weight: 0.5980 chunk 98 optimal weight: 0.7980 chunk 398 optimal weight: 0.9990 chunk 330 optimal weight: 0.8980 chunk 184 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 209 optimal weight: 1.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- 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** ** K 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 415 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** ** U 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.3971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 35333 Z= 0.210 Angle : 0.635 16.513 47868 Z= 0.310 Chirality : 0.041 0.217 5162 Planarity : 0.004 0.047 6010 Dihedral : 14.742 178.260 5579 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.31 % Allowed : 3.93 % Favored : 95.76 % Rotamer: Outliers : 3.10 % Allowed : 14.66 % Favored : 82.24 % 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: 1.21 (0.12), residues: 2037 sheet: -1.65 (0.25), residues: 406 loop : -0.37 (0.15), residues: 1735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP V 379 HIS 0.012 0.001 HIS V 83 PHE 0.023 0.001 PHE C 175 TYR 0.019 0.001 TYR Y 420 ARG 0.007 0.000 ARG A 10 *********************** 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 574 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 464 time to evaluate : 3.949 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: A 25 ARG cc_start: 0.8986 (OUTLIER) cc_final: 0.7620 (tpt170) REVERT: A 43 ARG cc_start: 0.8372 (ttp-110) cc_final: 0.7899 (mtt180) REVERT: C 101 LYS cc_start: 0.7807 (mmtt) cc_final: 0.7446 (tttp) REVERT: E 79 ASP cc_start: 0.8349 (m-30) cc_final: 0.8061 (m-30) REVERT: J 124 MET cc_start: 0.8544 (mmm) cc_final: 0.8324 (mtp) REVERT: J 287 LYS cc_start: 0.7613 (mttt) cc_final: 0.7168 (mttp) REVERT: N 25 ARG cc_start: 0.7667 (ptt180) cc_final: 0.6074 (tpt-90) REVERT: N 50 VAL cc_start: 0.9065 (OUTLIER) cc_final: 0.8824 (t) REVERT: R 81 CYS cc_start: 0.8342 (OUTLIER) cc_final: 0.7957 (p) REVERT: U 216 THR cc_start: 0.8722 (m) cc_final: 0.8517 (p) REVERT: U 244 MET cc_start: 0.9006 (ttp) cc_final: 0.8703 (ttp) REVERT: W 214 THR cc_start: 0.8369 (OUTLIER) cc_final: 0.8006 (p) REVERT: W 416 ILE cc_start: 0.8509 (OUTLIER) cc_final: 0.7982 (mt) REVERT: Y 153 ASN cc_start: 0.7525 (OUTLIER) cc_final: 0.6975 (p0) REVERT: Y 296 TRP cc_start: 0.7564 (OUTLIER) cc_final: 0.6667 (t-100) outliers start: 110 outliers final: 75 residues processed: 540 average time/residue: 0.4705 time to fit residues: 408.1298 Evaluate side-chains 515 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 433 time to evaluate : 4.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 HIS Chi-restraints excluded: chain A residue 25 ARG Chi-restraints excluded: chain A residue 40 ARG Chi-restraints excluded: chain A residue 48 ARG Chi-restraints excluded: chain A residue 71 LYS Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 161 GLU Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain E residue 28 ASP Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 81 CYS Chi-restraints excluded: chain F residue 41 ASP Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 124 CYS Chi-restraints excluded: chain H residue 227 LEU Chi-restraints excluded: chain J residue 12 LYS Chi-restraints excluded: chain J residue 27 ILE Chi-restraints excluded: chain J residue 58 ASP Chi-restraints excluded: chain J residue 281 LEU Chi-restraints excluded: chain J residue 334 ILE Chi-restraints excluded: chain J residue 379 TRP Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 61 ILE Chi-restraints excluded: chain K residue 122 THR Chi-restraints excluded: chain K residue 272 VAL Chi-restraints excluded: chain K residue 441 SER Chi-restraints excluded: chain K residue 451 ASP Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 296 TRP Chi-restraints excluded: chain L residue 340 SER Chi-restraints excluded: chain N residue 15 ILE Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 50 VAL Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain N residue 64 THR Chi-restraints excluded: chain N residue 65 GLU Chi-restraints excluded: chain N residue 66 GLU Chi-restraints excluded: chain N residue 71 LYS Chi-restraints excluded: chain N residue 81 ASP Chi-restraints excluded: chain O residue 45 LEU Chi-restraints excluded: chain P residue 134 THR Chi-restraints excluded: chain P residue 211 VAL Chi-restraints excluded: chain R residue 38 GLU Chi-restraints excluded: chain R residue 78 ARG Chi-restraints excluded: chain R residue 81 CYS Chi-restraints excluded: chain S residue 43 ASP Chi-restraints excluded: chain S residue 86 GLU Chi-restraints excluded: chain T residue 18 VAL Chi-restraints excluded: chain T residue 32 LEU Chi-restraints excluded: chain U residue 141 THR Chi-restraints excluded: chain U residue 159 ASN Chi-restraints excluded: chain U residue 253 LEU Chi-restraints excluded: chain U residue 292 MET Chi-restraints excluded: chain V residue 16 HIS Chi-restraints excluded: chain V residue 46 THR Chi-restraints excluded: chain V residue 147 THR Chi-restraints excluded: chain V residue 149 LEU Chi-restraints excluded: chain V residue 185 LEU Chi-restraints excluded: chain V residue 205 SER Chi-restraints excluded: chain V residue 298 ILE Chi-restraints excluded: chain V residue 299 LEU Chi-restraints excluded: chain W residue 92 LYS Chi-restraints excluded: chain W residue 106 VAL Chi-restraints excluded: chain W residue 173 VAL Chi-restraints excluded: chain W residue 194 ASP Chi-restraints excluded: chain W residue 214 THR Chi-restraints excluded: chain W residue 265 SER Chi-restraints excluded: chain W residue 317 THR Chi-restraints excluded: chain W residue 365 ASN Chi-restraints excluded: chain W residue 416 ILE Chi-restraints excluded: chain W residue 418 SER Chi-restraints excluded: chain W residue 447 THR Chi-restraints excluded: chain Y residue 120 LEU Chi-restraints excluded: chain Y residue 150 ILE Chi-restraints excluded: chain Y residue 153 ASN Chi-restraints excluded: chain Y residue 287 VAL Chi-restraints excluded: chain Y residue 296 TRP Chi-restraints excluded: chain Y residue 366 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 384 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 227 optimal weight: 0.0070 chunk 291 optimal weight: 1.9990 chunk 225 optimal weight: 2.9990 chunk 335 optimal weight: 1.9990 chunk 222 optimal weight: 2.9990 chunk 397 optimal weight: 0.9980 chunk 248 optimal weight: 9.9990 chunk 242 optimal weight: 3.9990 chunk 183 optimal weight: 0.9980 overall best weight: 1.2002 ------------------------------------------------------------------------------- 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** ** K 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 184 ASN ** K 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 95 HIS ** L 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.4133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 35333 Z= 0.329 Angle : 0.692 18.714 47868 Z= 0.335 Chirality : 0.043 0.216 5162 Planarity : 0.005 0.052 6010 Dihedral : 14.542 176.092 5576 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.29 % Allowed : 4.79 % Favored : 94.93 % Rotamer: Outliers : 3.24 % Allowed : 15.08 % Favored : 81.67 % 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: 1.19 (0.12), residues: 2037 sheet: -1.64 (0.26), residues: 404 loop : -0.49 (0.15), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP V 379 HIS 0.011 0.002 HIS V 83 PHE 0.024 0.002 PHE Y 358 TYR 0.023 0.002 TYR V 278 ARG 0.008 0.001 ARG S 100 *********************** 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 563 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 448 time to evaluate : 4.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 ARG cc_start: 0.8992 (OUTLIER) cc_final: 0.7644 (tpt170) REVERT: A 43 ARG cc_start: 0.8390 (ttp-110) cc_final: 0.7843 (mtt180) REVERT: C 101 LYS cc_start: 0.7899 (mmtt) cc_final: 0.7600 (tttp) REVERT: E 28 ASP cc_start: 0.8338 (OUTLIER) cc_final: 0.7978 (t0) REVERT: E 79 ASP cc_start: 0.8323 (m-30) cc_final: 0.8007 (m-30) REVERT: J 281 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.7919 (mm) REVERT: J 287 LYS cc_start: 0.7671 (mttt) cc_final: 0.7243 (mttp) REVERT: N 25 ARG cc_start: 0.7750 (ptt180) cc_final: 0.6127 (tpt-90) REVERT: N 50 VAL cc_start: 0.9096 (OUTLIER) cc_final: 0.8872 (t) REVERT: Q 30 MET cc_start: 0.8051 (tpp) cc_final: 0.7769 (ttp) REVERT: R 81 CYS cc_start: 0.8366 (OUTLIER) cc_final: 0.7986 (p) REVERT: U 244 MET cc_start: 0.9087 (ttp) cc_final: 0.8574 (ttp) REVERT: W 214 THR cc_start: 0.8441 (OUTLIER) cc_final: 0.8141 (p) REVERT: Y 153 ASN cc_start: 0.7488 (OUTLIER) cc_final: 0.7010 (p0) REVERT: Y 296 TRP cc_start: 0.7697 (OUTLIER) cc_final: 0.6727 (t-100) outliers start: 115 outliers final: 84 residues processed: 529 average time/residue: 0.4816 time to fit residues: 411.6441 Evaluate side-chains 529 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 437 time to evaluate : 3.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 HIS Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 25 ARG Chi-restraints excluded: chain A residue 40 ARG Chi-restraints excluded: chain A residue 48 ARG Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 145 ASP Chi-restraints excluded: chain C residue 161 GLU Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 38 GLN Chi-restraints excluded: chain E residue 28 ASP Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 81 CYS Chi-restraints excluded: chain F residue 41 ASP Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 124 CYS Chi-restraints excluded: chain H residue 227 LEU Chi-restraints excluded: chain H residue 263 MET Chi-restraints excluded: chain J residue 12 LYS Chi-restraints excluded: chain J residue 27 ILE Chi-restraints excluded: chain J residue 58 ASP Chi-restraints excluded: chain J residue 185 LEU Chi-restraints excluded: chain J residue 206 ASN Chi-restraints excluded: chain J residue 218 ILE Chi-restraints excluded: chain J residue 281 LEU Chi-restraints excluded: chain J residue 334 ILE Chi-restraints excluded: chain J residue 379 TRP Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 61 ILE Chi-restraints excluded: chain K residue 122 THR Chi-restraints excluded: chain K residue 184 ASN Chi-restraints excluded: chain K residue 272 VAL Chi-restraints excluded: chain K residue 425 ILE Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 215 ASP Chi-restraints excluded: chain L residue 296 TRP Chi-restraints excluded: chain N residue 15 ILE Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 50 VAL Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain N residue 64 THR Chi-restraints excluded: chain N residue 65 GLU Chi-restraints excluded: chain N residue 66 GLU Chi-restraints excluded: chain N residue 71 LYS Chi-restraints excluded: chain N residue 81 ASP Chi-restraints excluded: chain O residue 45 LEU Chi-restraints excluded: chain P residue 134 THR Chi-restraints excluded: chain P residue 211 VAL Chi-restraints excluded: chain R residue 78 ARG Chi-restraints excluded: chain R residue 81 CYS Chi-restraints excluded: chain S residue 43 ASP Chi-restraints excluded: chain S residue 86 GLU Chi-restraints excluded: chain T residue 18 VAL Chi-restraints excluded: chain U residue 141 THR Chi-restraints excluded: chain U residue 156 ASP Chi-restraints excluded: chain U residue 159 ASN Chi-restraints excluded: chain U residue 253 LEU Chi-restraints excluded: chain U residue 292 MET Chi-restraints excluded: chain V residue 16 HIS Chi-restraints excluded: chain V residue 46 THR Chi-restraints excluded: chain V residue 74 ASN Chi-restraints excluded: chain V residue 147 THR Chi-restraints excluded: chain V residue 205 SER Chi-restraints excluded: chain V residue 298 ILE Chi-restraints excluded: chain V residue 299 LEU Chi-restraints excluded: chain V residue 336 THR Chi-restraints excluded: chain W residue 92 LYS Chi-restraints excluded: chain W residue 100 THR Chi-restraints excluded: chain W residue 106 VAL Chi-restraints excluded: chain W residue 134 MET Chi-restraints excluded: chain W residue 194 ASP Chi-restraints excluded: chain W residue 214 THR Chi-restraints excluded: chain W residue 246 LEU Chi-restraints excluded: chain W residue 265 SER Chi-restraints excluded: chain W residue 317 THR Chi-restraints excluded: chain W residue 329 SER Chi-restraints excluded: chain W residue 365 ASN Chi-restraints excluded: chain W residue 416 ILE Chi-restraints excluded: chain W residue 418 SER Chi-restraints excluded: chain W residue 447 THR Chi-restraints excluded: chain Y residue 120 LEU Chi-restraints excluded: chain Y residue 150 ILE Chi-restraints excluded: chain Y residue 153 ASN Chi-restraints excluded: chain Y residue 190 THR Chi-restraints excluded: chain Y residue 287 VAL Chi-restraints excluded: chain Y residue 296 TRP Chi-restraints excluded: chain Y residue 366 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 245 optimal weight: 2.9990 chunk 158 optimal weight: 0.1980 chunk 237 optimal weight: 6.9990 chunk 119 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 76 optimal weight: 0.7980 chunk 252 optimal weight: 0.8980 chunk 270 optimal weight: 2.9990 chunk 196 optimal weight: 0.9990 chunk 37 optimal weight: 0.2980 chunk 312 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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** J 162 GLN ** K 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 291 HIS ** K 415 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** ** U 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7979 moved from start: 0.4207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 35333 Z= 0.210 Angle : 0.640 16.039 47868 Z= 0.312 Chirality : 0.041 0.207 5162 Planarity : 0.004 0.047 6010 Dihedral : 14.100 175.777 5574 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.33 % Favored : 95.40 % Rotamer: Outliers : 3.02 % Allowed : 15.39 % Favored : 81.59 % 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: 0.39 (0.13), residues: 4178 helix: 1.33 (0.12), residues: 2029 sheet: -1.49 (0.26), residues: 404 loop : -0.51 (0.15), residues: 1745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP V 379 HIS 0.012 0.001 HIS V 83 PHE 0.022 0.001 PHE Y 358 TYR 0.019 0.001 TYR Y 420 ARG 0.014 0.000 ARG E 56 *********************** 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 564 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 457 time to evaluate : 4.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 ARG cc_start: 0.8991 (OUTLIER) cc_final: 0.7606 (tpt170) REVERT: A 43 ARG cc_start: 0.8354 (ttp-110) cc_final: 0.7811 (mtt180) REVERT: C 101 LYS cc_start: 0.7932 (mmtt) cc_final: 0.7460 (tttp) REVERT: E 28 ASP cc_start: 0.8269 (OUTLIER) cc_final: 0.7931 (t0) REVERT: E 79 ASP cc_start: 0.8363 (m-30) cc_final: 0.8071 (m-30) REVERT: J 287 LYS cc_start: 0.7681 (mttt) cc_final: 0.7240 (mttp) REVERT: N 25 ARG cc_start: 0.7765 (ptt180) cc_final: 0.6193 (tpt-90) REVERT: N 50 VAL cc_start: 0.9047 (OUTLIER) cc_final: 0.8820 (t) REVERT: Q 30 MET cc_start: 0.7986 (tpp) cc_final: 0.7748 (ttp) REVERT: R 81 CYS cc_start: 0.8289 (OUTLIER) cc_final: 0.7973 (p) REVERT: U 244 MET cc_start: 0.8914 (ttp) cc_final: 0.8614 (ttp) REVERT: W 214 THR cc_start: 0.8408 (OUTLIER) cc_final: 0.8060 (p) REVERT: Y 153 ASN cc_start: 0.7486 (OUTLIER) cc_final: 0.7004 (p0) REVERT: Y 296 TRP cc_start: 0.7601 (OUTLIER) cc_final: 0.6584 (t-100) outliers start: 107 outliers final: 79 residues processed: 533 average time/residue: 0.4691 time to fit residues: 403.9245 Evaluate side-chains 527 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 441 time to evaluate : 3.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 HIS Chi-restraints excluded: chain A residue 25 ARG Chi-restraints excluded: chain A residue 48 ARG Chi-restraints excluded: chain A residue 71 LYS Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 145 ASP Chi-restraints excluded: chain C residue 161 GLU Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 38 GLN Chi-restraints excluded: chain E residue 28 ASP Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 81 CYS Chi-restraints excluded: chain F residue 41 ASP Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 124 CYS Chi-restraints excluded: chain H residue 227 LEU Chi-restraints excluded: chain H residue 319 LEU Chi-restraints excluded: chain J residue 12 LYS Chi-restraints excluded: chain J residue 27 ILE Chi-restraints excluded: chain J residue 58 ASP Chi-restraints excluded: chain J residue 206 ASN Chi-restraints excluded: chain J residue 334 ILE Chi-restraints excluded: chain J residue 379 TRP Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 61 ILE Chi-restraints excluded: chain K residue 122 THR Chi-restraints excluded: chain K residue 184 ASN Chi-restraints excluded: chain K residue 229 VAL Chi-restraints excluded: chain K residue 267 VAL Chi-restraints excluded: chain K residue 272 VAL Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 296 TRP Chi-restraints excluded: chain N residue 15 ILE Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 50 VAL Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain N residue 64 THR Chi-restraints excluded: chain N residue 65 GLU Chi-restraints excluded: chain N residue 66 GLU Chi-restraints excluded: chain N residue 71 LYS Chi-restraints excluded: chain O residue 45 LEU Chi-restraints excluded: chain P residue 134 THR Chi-restraints excluded: chain P residue 211 VAL Chi-restraints excluded: chain R residue 78 ARG Chi-restraints excluded: chain R residue 81 CYS Chi-restraints excluded: chain S residue 17 ILE Chi-restraints excluded: chain S residue 86 GLU Chi-restraints excluded: chain T residue 18 VAL Chi-restraints excluded: chain U residue 141 THR Chi-restraints excluded: chain U residue 159 ASN Chi-restraints excluded: chain U residue 253 LEU Chi-restraints excluded: chain U residue 292 MET Chi-restraints excluded: chain U residue 313 VAL Chi-restraints excluded: chain V residue 16 HIS Chi-restraints excluded: chain V residue 46 THR Chi-restraints excluded: chain V residue 74 ASN Chi-restraints excluded: chain V residue 147 THR Chi-restraints excluded: chain V residue 205 SER Chi-restraints excluded: chain V residue 298 ILE Chi-restraints excluded: chain V residue 299 LEU Chi-restraints excluded: chain W residue 92 LYS Chi-restraints excluded: chain W residue 106 VAL Chi-restraints excluded: chain W residue 134 MET Chi-restraints excluded: chain W residue 194 ASP Chi-restraints excluded: chain W residue 214 THR Chi-restraints excluded: chain W residue 246 LEU Chi-restraints excluded: chain W residue 265 SER Chi-restraints excluded: chain W residue 317 THR Chi-restraints excluded: chain W residue 329 SER Chi-restraints excluded: chain W residue 365 ASN Chi-restraints excluded: chain W residue 416 ILE Chi-restraints excluded: chain W residue 418 SER Chi-restraints excluded: chain W residue 447 THR Chi-restraints excluded: chain Y residue 120 LEU Chi-restraints excluded: chain Y residue 150 ILE Chi-restraints excluded: chain Y residue 153 ASN Chi-restraints excluded: chain Y residue 287 VAL Chi-restraints excluded: chain Y residue 296 TRP Chi-restraints excluded: chain Y residue 366 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 361 optimal weight: 2.9990 chunk 380 optimal weight: 0.0870 chunk 347 optimal weight: 4.9990 chunk 370 optimal weight: 0.9990 chunk 222 optimal weight: 2.9990 chunk 161 optimal weight: 0.9990 chunk 290 optimal weight: 1.9990 chunk 113 optimal weight: 0.5980 chunk 334 optimal weight: 0.3980 chunk 349 optimal weight: 2.9990 chunk 368 optimal weight: 5.9990 overall best weight: 0.6162 ------------------------------------------------------------------------------- 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 162 GLN ** K 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 184 ASN ** K 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 415 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** ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.4290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 35333 Z= 0.216 Angle : 0.641 15.888 47868 Z= 0.310 Chirality : 0.041 0.201 5162 Planarity : 0.004 0.046 6010 Dihedral : 13.669 174.699 5570 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.60 % Favored : 95.17 % Rotamer: Outliers : 2.88 % Allowed : 15.56 % Favored : 81.56 % 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: 0.43 (0.13), residues: 4178 helix: 1.36 (0.12), residues: 2035 sheet: -1.39 (0.26), residues: 404 loop : -0.52 (0.15), residues: 1739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP V 379 HIS 0.011 0.001 HIS V 83 PHE 0.039 0.001 PHE K 237 TYR 0.025 0.001 TYR V 278 ARG 0.013 0.000 ARG E 56 *********************** 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 572 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 470 time to evaluate : 4.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 ARG cc_start: 0.8977 (OUTLIER) cc_final: 0.7606 (tpt170) REVERT: A 43 ARG cc_start: 0.8347 (ttp-110) cc_final: 0.7858 (mtt180) REVERT: A 48 ARG cc_start: 0.8489 (OUTLIER) cc_final: 0.7304 (mpt180) REVERT: B 1 MET cc_start: 0.4398 (ttp) cc_final: 0.4046 (ttt) REVERT: C 101 LYS cc_start: 0.7900 (mmtt) cc_final: 0.7515 (tttp) REVERT: E 28 ASP cc_start: 0.8247 (OUTLIER) cc_final: 0.7931 (t0) REVERT: E 51 GLU cc_start: 0.7710 (pp20) cc_final: 0.7450 (pp20) REVERT: E 79 ASP cc_start: 0.8329 (m-30) cc_final: 0.7986 (m-30) REVERT: J 287 LYS cc_start: 0.7683 (mttt) cc_final: 0.7234 (mttp) REVERT: K 441 SER cc_start: 0.8453 (t) cc_final: 0.8102 (m) REVERT: N 25 ARG cc_start: 0.7730 (ptt180) cc_final: 0.6176 (tpt-90) REVERT: N 50 VAL cc_start: 0.9037 (OUTLIER) cc_final: 0.8823 (t) REVERT: Q 30 MET cc_start: 0.7986 (tpp) cc_final: 0.7763 (ttp) REVERT: R 81 CYS cc_start: 0.8274 (OUTLIER) cc_final: 0.7984 (p) REVERT: U 244 MET cc_start: 0.8981 (ttp) cc_final: 0.8566 (ttp) REVERT: W 214 THR cc_start: 0.8392 (OUTLIER) cc_final: 0.8032 (p) REVERT: Y 153 ASN cc_start: 0.7478 (OUTLIER) cc_final: 0.6989 (p0) REVERT: Y 296 TRP cc_start: 0.7551 (OUTLIER) cc_final: 0.6455 (t-100) outliers start: 102 outliers final: 80 residues processed: 538 average time/residue: 0.5030 time to fit residues: 437.9127 Evaluate side-chains 534 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 446 time to evaluate : 3.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 PHE Chi-restraints excluded: chain A residue 13 HIS Chi-restraints excluded: chain A residue 25 ARG Chi-restraints excluded: chain A residue 48 ARG Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 145 ASP Chi-restraints excluded: chain C residue 161 GLU Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 38 GLN Chi-restraints excluded: chain E residue 28 ASP Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 41 ASP Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 124 CYS Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain H residue 263 MET Chi-restraints excluded: chain H residue 319 LEU Chi-restraints excluded: chain J residue 27 ILE Chi-restraints excluded: chain J residue 58 ASP Chi-restraints excluded: chain J residue 206 ASN Chi-restraints excluded: chain J residue 334 ILE Chi-restraints excluded: chain J residue 379 TRP Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 61 ILE Chi-restraints excluded: chain K residue 122 THR Chi-restraints excluded: chain K residue 229 VAL Chi-restraints excluded: chain K residue 267 VAL Chi-restraints excluded: chain K residue 272 VAL Chi-restraints excluded: chain K residue 386 VAL Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 296 TRP Chi-restraints excluded: chain L residue 350 GLU Chi-restraints excluded: chain L residue 368 MET Chi-restraints excluded: chain N residue 15 ILE Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 50 VAL Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain N residue 64 THR Chi-restraints excluded: chain N residue 65 GLU Chi-restraints excluded: chain N residue 66 GLU Chi-restraints excluded: chain N residue 71 LYS Chi-restraints excluded: chain O residue 45 LEU Chi-restraints excluded: chain P residue 134 THR Chi-restraints excluded: chain P residue 211 VAL Chi-restraints excluded: chain Q residue 47 ILE Chi-restraints excluded: chain R residue 78 ARG Chi-restraints excluded: chain R residue 81 CYS Chi-restraints excluded: chain S residue 17 ILE Chi-restraints excluded: chain S residue 86 GLU Chi-restraints excluded: chain T residue 18 VAL Chi-restraints excluded: chain U residue 141 THR Chi-restraints excluded: chain U residue 159 ASN Chi-restraints excluded: chain U residue 253 LEU Chi-restraints excluded: chain U residue 292 MET Chi-restraints excluded: chain U residue 313 VAL Chi-restraints excluded: chain V residue 16 HIS Chi-restraints excluded: chain V residue 46 THR Chi-restraints excluded: chain V residue 74 ASN Chi-restraints excluded: chain V residue 147 THR Chi-restraints excluded: chain V residue 205 SER Chi-restraints excluded: chain V residue 299 LEU Chi-restraints excluded: chain W residue 92 LYS Chi-restraints excluded: chain W residue 100 THR Chi-restraints excluded: chain W residue 106 VAL Chi-restraints excluded: chain W residue 134 MET Chi-restraints excluded: chain W residue 194 ASP Chi-restraints excluded: chain W residue 214 THR Chi-restraints excluded: chain W residue 265 SER Chi-restraints excluded: chain W residue 317 THR Chi-restraints excluded: chain W residue 329 SER Chi-restraints excluded: chain W residue 365 ASN Chi-restraints excluded: chain W residue 416 ILE Chi-restraints excluded: chain W residue 418 SER Chi-restraints excluded: chain W residue 447 THR Chi-restraints excluded: chain Y residue 120 LEU Chi-restraints excluded: chain Y residue 150 ILE Chi-restraints excluded: chain Y residue 153 ASN Chi-restraints excluded: chain Y residue 287 VAL Chi-restraints excluded: chain Y residue 296 TRP Chi-restraints excluded: chain Y residue 366 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 242 optimal weight: 3.9990 chunk 391 optimal weight: 2.9990 chunk 238 optimal weight: 0.0670 chunk 185 optimal weight: 3.9990 chunk 272 optimal weight: 3.9990 chunk 410 optimal weight: 0.8980 chunk 377 optimal weight: 3.9990 chunk 326 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 252 optimal weight: 0.9980 chunk 200 optimal weight: 2.9990 overall best weight: 0.9520 ------------------------------------------------------------------------------- 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 ** H 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 415 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 ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.4374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 35333 Z= 0.276 Angle : 0.674 17.780 47868 Z= 0.325 Chirality : 0.042 0.203 5162 Planarity : 0.004 0.047 6010 Dihedral : 13.547 174.165 5570 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.67 % Favored : 95.09 % Rotamer: Outliers : 2.76 % Allowed : 15.70 % Favored : 81.53 % 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: 0.35 (0.13), residues: 4178 helix: 1.32 (0.12), residues: 2039 sheet: -1.44 (0.26), residues: 408 loop : -0.58 (0.15), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP V 379 HIS 0.011 0.001 HIS V 83 PHE 0.031 0.002 PHE K 237 TYR 0.022 0.001 TYR V 278 ARG 0.013 0.001 ARG E 56 ********************** 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 540 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 442 time to evaluate : 4.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 ARG cc_start: 0.8978 (OUTLIER) cc_final: 0.7625 (tpt170) REVERT: A 43 ARG cc_start: 0.8366 (ttp-110) cc_final: 0.7829 (mtt180) REVERT: A 48 ARG cc_start: 0.8514 (OUTLIER) cc_final: 0.7401 (mpt180) REVERT: B 1 MET cc_start: 0.4397 (ttp) cc_final: 0.3995 (ttt) REVERT: C 101 LYS cc_start: 0.8002 (mmtt) cc_final: 0.7590 (tttp) REVERT: E 28 ASP cc_start: 0.8162 (OUTLIER) cc_final: 0.7884 (t0) REVERT: E 79 ASP cc_start: 0.8289 (m-30) cc_final: 0.7959 (m-30) REVERT: J 287 LYS cc_start: 0.7695 (mttt) cc_final: 0.7261 (mttp) REVERT: N 25 ARG cc_start: 0.7732 (ptt180) cc_final: 0.6113 (tpt-90) REVERT: N 50 VAL cc_start: 0.9050 (OUTLIER) cc_final: 0.8845 (t) REVERT: Q 30 MET cc_start: 0.8027 (tpp) cc_final: 0.7804 (ttp) REVERT: R 81 CYS cc_start: 0.8290 (OUTLIER) cc_final: 0.7997 (p) REVERT: S 100 ARG cc_start: 0.8417 (ttp80) cc_final: 0.7964 (ttp80) REVERT: W 214 THR cc_start: 0.8393 (OUTLIER) cc_final: 0.8048 (p) REVERT: Y 153 ASN cc_start: 0.7488 (OUTLIER) cc_final: 0.7000 (p0) REVERT: Y 296 TRP cc_start: 0.7592 (OUTLIER) cc_final: 0.6468 (t-100) REVERT: Y 369 MET cc_start: 0.8168 (mmm) cc_final: 0.7828 (mmt) outliers start: 98 outliers final: 80 residues processed: 506 average time/residue: 0.4555 time to fit residues: 372.5537 Evaluate side-chains 523 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 435 time to evaluate : 5.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 PHE Chi-restraints excluded: chain A residue 13 HIS Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 25 ARG Chi-restraints excluded: chain A residue 48 ARG Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 145 ASP Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 38 GLN Chi-restraints excluded: chain E residue 28 ASP Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 41 ASP Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 124 CYS Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain H residue 263 MET Chi-restraints excluded: chain J residue 27 ILE Chi-restraints excluded: chain J residue 206 ASN Chi-restraints excluded: chain J residue 334 ILE Chi-restraints excluded: chain J residue 379 TRP Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 61 ILE Chi-restraints excluded: chain K residue 122 THR Chi-restraints excluded: chain K residue 229 VAL Chi-restraints excluded: chain K residue 244 LEU Chi-restraints excluded: chain K residue 267 VAL Chi-restraints excluded: chain K residue 272 VAL Chi-restraints excluded: chain K residue 386 VAL Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 296 TRP Chi-restraints excluded: chain L residue 350 GLU Chi-restraints excluded: chain L residue 368 MET Chi-restraints excluded: chain N residue 15 ILE Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 50 VAL Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain N residue 64 THR Chi-restraints excluded: chain N residue 65 GLU Chi-restraints excluded: chain N residue 66 GLU Chi-restraints excluded: chain N residue 71 LYS Chi-restraints excluded: chain O residue 45 LEU Chi-restraints excluded: chain P residue 134 THR Chi-restraints excluded: chain P residue 211 VAL Chi-restraints excluded: chain R residue 78 ARG Chi-restraints excluded: chain R residue 81 CYS Chi-restraints excluded: chain S residue 86 GLU Chi-restraints excluded: chain T residue 18 VAL Chi-restraints excluded: chain U residue 141 THR Chi-restraints excluded: chain U residue 155 GLN Chi-restraints excluded: chain U residue 156 ASP Chi-restraints excluded: chain U residue 253 LEU Chi-restraints excluded: chain U residue 292 MET Chi-restraints excluded: chain U residue 313 VAL Chi-restraints excluded: chain V residue 16 HIS Chi-restraints excluded: chain V residue 46 THR Chi-restraints excluded: chain V residue 74 ASN Chi-restraints excluded: chain V residue 147 THR Chi-restraints excluded: chain V residue 205 SER Chi-restraints excluded: chain V residue 298 ILE Chi-restraints excluded: chain V residue 299 LEU Chi-restraints excluded: chain W residue 92 LYS Chi-restraints excluded: chain W residue 100 THR Chi-restraints excluded: chain W residue 106 VAL Chi-restraints excluded: chain W residue 134 MET Chi-restraints excluded: chain W residue 194 ASP Chi-restraints excluded: chain W residue 214 THR Chi-restraints excluded: chain W residue 265 SER Chi-restraints excluded: chain W residue 317 THR Chi-restraints excluded: chain W residue 329 SER Chi-restraints excluded: chain W residue 365 ASN Chi-restraints excluded: chain W residue 416 ILE Chi-restraints excluded: chain W residue 418 SER Chi-restraints excluded: chain W residue 447 THR Chi-restraints excluded: chain Y residue 120 LEU Chi-restraints excluded: chain Y residue 150 ILE Chi-restraints excluded: chain Y residue 153 ASN Chi-restraints excluded: chain Y residue 190 THR Chi-restraints excluded: chain Y residue 287 VAL Chi-restraints excluded: chain Y residue 296 TRP Chi-restraints excluded: chain Y residue 366 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 259 optimal weight: 0.8980 chunk 348 optimal weight: 4.9990 chunk 100 optimal weight: 0.5980 chunk 301 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 chunk 90 optimal weight: 0.2980 chunk 327 optimal weight: 0.0980 chunk 137 optimal weight: 0.6980 chunk 336 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 ** H 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 162 GLN ** K 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 415 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 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 313 GLN W 176 ASN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.118881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.095193 restraints weight = 66607.906| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 2.10 r_work: 0.3137 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.4422 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= 0.196 Angle : 0.647 15.752 47868 Z= 0.313 Chirality : 0.041 0.199 5162 Planarity : 0.004 0.048 6010 Dihedral : 13.226 173.503 5570 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.48 % Favored : 95.31 % Rotamer: Outliers : 2.23 % Allowed : 16.52 % Favored : 81.25 % 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: 0.41 (0.13), residues: 4178 helix: 1.37 (0.12), residues: 2038 sheet: -1.30 (0.26), residues: 404 loop : -0.58 (0.15), residues: 1736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP L 296 HIS 0.012 0.001 HIS V 83 PHE 0.033 0.001 PHE K 237 TYR 0.021 0.001 TYR V 278 ARG 0.011 0.000 ARG E 56 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8734.65 seconds wall clock time: 159 minutes 26.37 seconds (9566.37 seconds total)