Starting phenix.real_space_refine on Wed May 15 00:28:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qyn_18759/05_2024/8qyn_18759_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qyn_18759/05_2024/8qyn_18759.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qyn_18759/05_2024/8qyn_18759.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qyn_18759/05_2024/8qyn_18759.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qyn_18759/05_2024/8qyn_18759_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qyn_18759/05_2024/8qyn_18759_updated.pdb" } resolution = 2.88 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= 0.018 sd= 0.125 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: 4 Type Number sf(0) Gaussians S 184 5.16 5 C 18477 2.51 5 N 4971 2.21 5 O 5483 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "F PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 52": "OE1" <-> "OE2" Residue "I TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 153": "NH1" <-> "NH2" Residue "O GLU 59": "OE1" <-> "OE2" Residue "O GLU 234": "OE1" <-> "OE2" Residue "Q GLU 30": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 29115 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 1805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1805 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 221} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 1937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1937 Classifications: {'peptide': 247} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 241} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 1826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1826 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 226} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 1840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1840 Unusual residues: {'ACE': 1} Classifications: {'peptide': 241, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'ACE_C-N': 1, 'PTRANS': 8, 'TRANS': 232} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Chain: "E" Number of atoms: 1889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1889 Unusual residues: {'ACE': 1} Classifications: {'peptide': 240, 'undetermined': 1} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 10, 'TRANS': 229} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "F" Number of atoms: 1885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1885 Classifications: {'peptide': 242} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 236} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "G" Number of atoms: 1892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1892 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 8, 'TRANS': 234} Chain: "H" Number of atoms: 1008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1008 Unusual residues: {'ACE': 1} Classifications: {'peptide': 127, 'undetermined': 1} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 7, 'TRANS': 119} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "I" Number of atoms: 2180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2180 Classifications: {'peptide': 273} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 259} Chain breaks: 2 Chain: "J" Number of atoms: 1952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1952 Unusual residues: {'ACE': 1} Classifications: {'peptide': 249, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 15, 'TRANS': 233} Chain breaks: 2 Chain: "K" Number of atoms: 1696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1696 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 11, 'TRANS': 218} Chain breaks: 3 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'UNK:plan-1': 16} Unresolved non-hydrogen planarities: 16 Chain: "L" Number of atoms: 1412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1412 Classifications: {'peptide': 180} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 170} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "M" Number of atoms: 1581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1581 Unusual residues: {'ACE': 1} Classifications: {'peptide': 197, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 8, 'TRANS': 188} Chain: "N" Number of atoms: 1651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1651 Unusual residues: {'ACE': 1} Classifications: {'peptide': 216, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'ACE_C-N': 1, 'PTRANS': 6, 'TRANS': 209} Chain breaks: 3 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "O" Number of atoms: 1509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1509 Classifications: {'peptide': 197} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 190} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "P" Number of atoms: 1537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1537 Classifications: {'peptide': 198} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 190} Chain breaks: 1 Chain: "Q" Number of atoms: 1515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1515 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 194} Chain breaks: 2 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Time building chain proxies: 15.22, per 1000 atoms: 0.52 Number of scatterers: 29115 At special positions: 0 Unit cell: (148.96, 143.853, 148.109, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 184 16.00 O 5483 8.00 N 4971 7.00 C 18477 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.25 Conformation dependent library (CDL) restraints added in 5.3 seconds 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6936 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 104 helices and 30 sheets defined 35.2% alpha, 18.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.31 Creating SS restraints... Processing helix chain 'A' and resid 4 through 6 No H-bonds generated for 'chain 'A' and resid 4 through 6' Processing helix chain 'A' and resid 20 through 31 Processing helix chain 'A' and resid 81 through 101 removed outlier: 3.805A pdb=" N VAL A 85 " --> pdb=" O PRO A 81 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU A 86 " --> pdb=" O ASP A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 122 removed outlier: 3.757A pdb=" N GLU A 120 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N TYR A 121 " --> pdb=" O VAL A 117 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N THR A 122 " --> pdb=" O MET A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 176 Processing helix chain 'A' and resid 184 through 198 removed outlier: 4.107A pdb=" N SER A 198 " --> pdb=" O THR A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 233 removed outlier: 3.542A pdb=" N ILE A 233 " --> pdb=" O TYR A 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 30 removed outlier: 3.927A pdb=" N ILE B 28 " --> pdb=" O ALA B 24 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N GLY B 29 " --> pdb=" O MET B 25 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N HIS B 30 " --> pdb=" O GLU B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 101 removed outlier: 3.624A pdb=" N VAL B 85 " --> pdb=" O SER B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 122 removed outlier: 3.635A pdb=" N ILE B 117 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N TYR B 121 " --> pdb=" O ILE B 117 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N THR B 122 " --> pdb=" O LYS B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 178 removed outlier: 3.651A pdb=" N GLN B 177 " --> pdb=" O SER B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 200 Processing helix chain 'B' and resid 230 through 247 Processing helix chain 'C' and resid 17 through 28 removed outlier: 3.612A pdb=" N ALA C 25 " --> pdb=" O TYR C 21 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N VAL C 26 " --> pdb=" O ALA C 22 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LYS C 27 " --> pdb=" O GLN C 23 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N LYS C 28 " --> pdb=" O GLU C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 59 Processing helix chain 'C' and resid 77 through 97 removed outlier: 3.559A pdb=" N ARG C 81 " --> pdb=" O THR C 77 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ILE C 82 " --> pdb=" O ALA C 78 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL C 83 " --> pdb=" O ASP C 79 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ARG C 95 " --> pdb=" O CYS C 91 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU C 96 " --> pdb=" O GLN C 92 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR C 97 " --> pdb=" O SER C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 118 removed outlier: 3.978A pdb=" N TYR C 118 " --> pdb=" O LEU C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 175 Processing helix chain 'C' and resid 184 through 197 removed outlier: 3.786A pdb=" N GLU C 197 " --> pdb=" O LYS C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 233 Processing helix chain 'D' and resid 22 through 33 removed outlier: 3.868A pdb=" N ILE D 31 " --> pdb=" O ALA D 27 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LYS D 32 " --> pdb=" O ILE D 28 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N LEU D 33 " --> pdb=" O GLU D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 63 No H-bonds generated for 'chain 'D' and resid 61 through 63' Processing helix chain 'D' and resid 82 through 103 removed outlier: 3.589A pdb=" N LYS D 86 " --> pdb=" O ILE D 82 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N THR D 87 " --> pdb=" O ALA D 83 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU D 88 " --> pdb=" O ASP D 84 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASP D 90 " --> pdb=" O LYS D 86 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LYS D 91 " --> pdb=" O THR D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 120 removed outlier: 3.982A pdb=" N LEU D 119 " --> pdb=" O ALA D 115 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA D 120 " --> pdb=" O VAL D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 182 Processing helix chain 'D' and resid 191 through 205 Processing helix chain 'D' and resid 231 through 238 Processing helix chain 'E' and resid 20 through 31 removed outlier: 3.675A pdb=" N GLU E 27 " --> pdb=" O GLU E 23 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ALA E 28 " --> pdb=" O TYR E 24 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N VAL E 29 " --> pdb=" O ALA E 25 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N LYS E 30 " --> pdb=" O MET E 26 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N GLN E 31 " --> pdb=" O GLU E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 99 Processing helix chain 'E' and resid 105 through 120 removed outlier: 4.154A pdb=" N ILE E 118 " --> pdb=" O SER E 114 " (cutoff:3.500A) Proline residue: E 119 - end of helix Processing helix chain 'E' and resid 166 through 174 Processing helix chain 'E' and resid 176 through 181 removed outlier: 3.661A pdb=" N PHE E 179 " --> pdb=" O MET E 176 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N MET E 180 " --> pdb=" O SER E 177 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLU E 181 " --> pdb=" O GLU E 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 176 through 181' Processing helix chain 'E' and resid 184 through 198 removed outlier: 5.970A pdb=" N LYS E 189 " --> pdb=" O ASN E 185 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU E 197 " --> pdb=" O ARG E 193 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N THR E 198 " --> pdb=" O ALA E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 226 through 233 removed outlier: 3.604A pdb=" N SER E 230 " --> pdb=" O ASP E 227 " (cutoff:3.500A) Proline residue: E 231 - end of helix Processing helix chain 'F' and resid 22 through 33 removed outlier: 3.683A pdb=" N VAL F 31 " --> pdb=" O ALA F 27 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N GLU F 32 " --> pdb=" O MET F 28 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ASN F 33 " --> pdb=" O LYS F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 103 Processing helix chain 'F' and resid 109 through 124 removed outlier: 4.119A pdb=" N TYR F 123 " --> pdb=" O TYR F 119 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N THR F 124 " --> pdb=" O VAL F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 170 through 179 removed outlier: 4.079A pdb=" N LYS F 179 " --> pdb=" O THR F 175 " (cutoff:3.500A) Processing helix chain 'F' and resid 182 through 184 No H-bonds generated for 'chain 'F' and resid 182 through 184' Processing helix chain 'F' and resid 187 through 201 removed outlier: 4.564A pdb=" N LYS F 192 " --> pdb=" O ARG F 188 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLU F 193 " --> pdb=" O ASP F 189 " (cutoff:3.500A) Processing helix chain 'F' and resid 230 through 244 Processing helix chain 'G' and resid 23 through 34 removed outlier: 3.737A pdb=" N ILE G 32 " --> pdb=" O ALA G 28 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ASN G 33 " --> pdb=" O PHE G 29 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N GLN G 34 " --> pdb=" O LYS G 30 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 65 No H-bonds generated for 'chain 'G' and resid 63 through 65' Processing helix chain 'G' and resid 84 through 105 Processing helix chain 'G' and resid 111 through 126 removed outlier: 3.821A pdb=" N VAL G 124 " --> pdb=" O ASP G 120 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N TYR G 125 " --> pdb=" O ILE G 121 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N THR G 126 " --> pdb=" O SER G 122 " (cutoff:3.500A) Processing helix chain 'G' and resid 172 through 185 Processing helix chain 'G' and resid 191 through 206 removed outlier: 3.664A pdb=" N LEU G 202 " --> pdb=" O ALA G 198 " (cutoff:3.500A) Processing helix chain 'G' and resid 232 through 243 Processing helix chain 'H' and resid 38 through 42 Processing helix chain 'H' and resid 49 through 53 Processing helix chain 'H' and resid 55 through 70 Processing helix chain 'H' and resid 73 through 88 removed outlier: 3.747A pdb=" N GLN H 88 " --> pdb=" O LYS H 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 106 Processing helix chain 'H' and resid 114 through 117 No H-bonds generated for 'chain 'H' and resid 114 through 117' Processing helix chain 'H' and resid 121 through 123 No H-bonds generated for 'chain 'H' and resid 121 through 123' Processing helix chain 'H' and resid 130 through 138 Processing helix chain 'I' and resid 18 through 23 removed outlier: 3.546A pdb=" N GLU I 22 " --> pdb=" O THR I 18 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N GLU I 23 " --> pdb=" O GLU I 19 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 18 through 23' Processing helix chain 'I' and resid 32 through 45 removed outlier: 3.595A pdb=" N ARG I 45 " --> pdb=" O LEU I 41 " (cutoff:3.500A) Processing helix chain 'I' and resid 62 through 65 No H-bonds generated for 'chain 'I' and resid 62 through 65' Processing helix chain 'I' and resid 77 through 86 Processing helix chain 'I' and resid 146 through 153 Processing helix chain 'I' and resid 172 through 174 No H-bonds generated for 'chain 'I' and resid 172 through 174' Processing helix chain 'I' and resid 181 through 183 No H-bonds generated for 'chain 'I' and resid 181 through 183' Processing helix chain 'I' and resid 215 through 225 Processing helix chain 'I' and resid 244 through 255 removed outlier: 4.033A pdb=" N PHE I 250 " --> pdb=" O THR I 246 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N LYS I 251 " --> pdb=" O VAL I 247 " (cutoff:3.500A) Proline residue: I 252 - end of helix removed outlier: 4.581A pdb=" N SER I 255 " --> pdb=" O LYS I 251 " (cutoff:3.500A) Processing helix chain 'I' and resid 266 through 278 removed outlier: 3.682A pdb=" N THR I 278 " --> pdb=" O LYS I 274 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 39 removed outlier: 4.162A pdb=" N VAL J 27 " --> pdb=" O VAL J 24 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N GLY J 28 " --> pdb=" O GLY J 25 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU J 39 " --> pdb=" O ILE J 36 " (cutoff:3.500A) Processing helix chain 'J' and resid 100 through 113 Processing helix chain 'J' and resid 149 through 158 Processing helix chain 'J' and resid 187 through 197 Processing helix chain 'J' and resid 214 through 228 removed outlier: 4.049A pdb=" N TRP J 227 " --> pdb=" O TYR J 223 " (cutoff:3.500A) Processing helix chain 'K' and resid 19 through 32 removed outlier: 3.634A pdb=" N ALA K 27 " --> pdb=" O ALA K 23 " (cutoff:3.500A) Processing helix chain 'K' and resid 92 through 113 Processing helix chain 'K' and resid 119 through 132 Processing helix chain 'K' and resid 174 through 183 Processing helix chain 'K' and resid 191 through 203 Processing helix chain 'K' and resid 223 through 225 No H-bonds generated for 'chain 'K' and resid 223 through 225' Processing helix chain 'L' and resid 57 through 78 Processing helix chain 'L' and resid 84 through 98 removed outlier: 3.709A pdb=" N GLU L 97 " --> pdb=" O ASN L 93 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N LYS L 98 " --> pdb=" O LEU L 94 " (cutoff:3.500A) Processing helix chain 'L' and resid 143 through 153 removed outlier: 4.325A pdb=" N GLY L 148 " --> pdb=" O GLU L 144 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N MET L 149 " --> pdb=" O GLN L 145 " (cutoff:3.500A) Processing helix chain 'L' and resid 160 through 172 Processing helix chain 'M' and resid 53 through 71 Processing helix chain 'M' and resid 77 through 94 removed outlier: 3.727A pdb=" N ARG M 93 " --> pdb=" O ALA M 89 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N SER M 94 " --> pdb=" O ASP M 90 " (cutoff:3.500A) Processing helix chain 'M' and resid 136 through 146 Processing helix chain 'M' and resid 153 through 168 removed outlier: 3.761A pdb=" N VAL M 157 " --> pdb=" O ARG M 153 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 6 Processing helix chain 'N' and resid 108 through 129 Processing helix chain 'N' and resid 135 through 149 removed outlier: 3.842A pdb=" N GLN N 148 " --> pdb=" O ASN N 144 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N TYR N 149 " --> pdb=" O MET N 145 " (cutoff:3.500A) Processing helix chain 'N' and resid 191 through 200 Processing helix chain 'N' and resid 208 through 222 Processing helix chain 'O' and resid 86 through 107 Processing helix chain 'O' and resid 113 through 127 removed outlier: 4.067A pdb=" N ARG O 127 " --> pdb=" O ILE O 123 " (cutoff:3.500A) Processing helix chain 'O' and resid 168 through 179 removed outlier: 4.448A pdb=" N ALA O 171 " --> pdb=" O SER O 168 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N MET O 172 " --> pdb=" O ALA O 169 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLN O 174 " --> pdb=" O ALA O 171 " (cutoff:3.500A) Proline residue: O 175 - end of helix Processing helix chain 'O' and resid 196 through 213 removed outlier: 3.869A pdb=" N GLU O 212 " --> pdb=" O ILE O 208 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ARG O 213 " --> pdb=" O SER O 209 " (cutoff:3.500A) Processing helix chain 'P' and resid 102 through 122 removed outlier: 3.921A pdb=" N LEU P 122 " --> pdb=" O ASP P 118 " (cutoff:3.500A) Processing helix chain 'P' and resid 130 through 147 removed outlier: 3.728A pdb=" N LYS P 147 " --> pdb=" O SER P 143 " (cutoff:3.500A) Processing helix chain 'P' and resid 188 through 201 Proline residue: P 193 - end of helix Processing helix chain 'P' and resid 207 through 224 Processing helix chain 'Q' and resid 17 through 20 No H-bonds generated for 'chain 'Q' and resid 17 through 20' Processing helix chain 'Q' and resid 26 through 28 No H-bonds generated for 'chain 'Q' and resid 26 through 28' Processing helix chain 'Q' and resid 83 through 104 Processing helix chain 'Q' and resid 110 through 123 removed outlier: 3.839A pdb=" N MET Q 120 " --> pdb=" O LEU Q 116 " (cutoff:3.500A) Processing helix chain 'Q' and resid 170 through 176 Processing helix chain 'Q' and resid 183 through 198 Processing sheet with id= A, first strand: chain 'A' and resid 160 through 163 Processing sheet with id= B, first strand: chain 'A' and resid 155 through 157 removed outlier: 3.675A pdb=" N ILE A 72 " --> pdb=" O THR A 69 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N LEU A 74 " --> pdb=" O PRO A 67 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 161 through 164 Processing sheet with id= D, first strand: chain 'B' and resid 65 through 67 Processing sheet with id= E, first strand: chain 'C' and resid 158 through 161 Processing sheet with id= F, first strand: chain 'C' and resid 62 through 64 removed outlier: 3.815A pdb=" N VAL C 134 " --> pdb=" O CYS C 70 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY C 135 " --> pdb=" O ARG C 143 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N HIS C 154 " --> pdb=" O GLN C 146 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 167 through 170 Processing sheet with id= H, first strand: chain 'D' and resid 161 through 164 removed outlier: 3.729A pdb=" N THR D 161 " --> pdb=" O ASP D 157 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP D 147 " --> pdb=" O GLY D 150 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLY D 144 " --> pdb=" O GLY D 75 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE D 74 " --> pdb=" O ASP D 71 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N CYS D 76 " --> pdb=" O GLU D 69 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N GLU D 69 " --> pdb=" O CYS D 76 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N MET D 78 " --> pdb=" O ILE D 67 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ILE D 67 " --> pdb=" O MET D 78 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 158 through 161 Processing sheet with id= J, first strand: chain 'E' and resid 153 through 156 removed outlier: 4.319A pdb=" N ILE E 144 " --> pdb=" O CYS E 156 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU E 132 " --> pdb=" O THR E 147 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE E 70 " --> pdb=" O ASP E 67 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ILE E 72 " --> pdb=" O HIS E 65 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N HIS E 65 " --> pdb=" O ILE E 72 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N ILE E 74 " --> pdb=" O ILE E 63 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ILE E 63 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 163 through 166 removed outlier: 3.999A pdb=" N GLY F 45 " --> pdb=" O CYS F 42 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLY F 218 " --> pdb=" O ARG F 224 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ARG F 224 " --> pdb=" O GLY F 218 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 67 through 69 Processing sheet with id= M, first strand: chain 'G' and resid 165 through 169 removed outlier: 6.650A pdb=" N THR G 38 " --> pdb=" O GLN G 53 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLN G 53 " --> pdb=" O THR G 38 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'G' and resid 160 through 163 removed outlier: 4.394A pdb=" N VAL G 151 " --> pdb=" O PHE G 163 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE G 141 " --> pdb=" O GLY G 77 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE G 76 " --> pdb=" O THR G 73 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N THR G 73 " --> pdb=" O ILE G 76 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N CYS G 78 " --> pdb=" O LYS G 71 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N LYS G 71 " --> pdb=" O CYS G 78 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N MET G 80 " --> pdb=" O LEU G 69 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LEU G 69 " --> pdb=" O MET G 80 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'I' and resid 48 through 50 removed outlier: 7.039A pdb=" N PHE I 123 " --> pdb=" O VAL I 96 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N CYS I 98 " --> pdb=" O CYS I 121 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N CYS I 121 " --> pdb=" O CYS I 98 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL I 122 " --> pdb=" O GLN I 136 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ILE I 72 " --> pdb=" O PHE I 133 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N GLN I 163 " --> pdb=" O PHE I 71 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N ILE I 73 " --> pdb=" O GLN I 163 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N THR I 165 " --> pdb=" O ILE I 73 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N ILE I 75 " --> pdb=" O THR I 165 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N LEU I 167 " --> pdb=" O ILE I 75 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'J' and resid 2 through 4 removed outlier: 3.524A pdb=" N SER J 42 " --> pdb=" O SER J 79 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N VAL J 77 " --> pdb=" O ILE J 44 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N TYR J 46 " --> pdb=" O ALA J 75 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N ALA J 75 " --> pdb=" O TYR J 46 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N THR J 16 " --> pdb=" O VAL J 86 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N LEU J 88 " --> pdb=" O THR J 16 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU J 18 " --> pdb=" O LEU J 88 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N LEU J 90 " --> pdb=" O LEU J 18 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ARG J 117 " --> pdb=" O LEU J 17 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N MET J 19 " --> pdb=" O ARG J 117 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ILE J 119 " --> pdb=" O MET J 19 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS J 206 " --> pdb=" O SER J 122 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'K' and resid 167 through 170 removed outlier: 3.924A pdb=" N GLY K 54 " --> pdb=" O TYR K 51 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ASN K 215 " --> pdb=" O THR K 61 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'K' and resid 77 through 79 removed outlier: 3.604A pdb=" N LEU K 143 " --> pdb=" O TYR K 154 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'L' and resid 136 through 140 removed outlier: 6.328A pdb=" N ALA L 10 " --> pdb=" O ASP L 25 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASP L 25 " --> pdb=" O ALA L 10 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE L 186 " --> pdb=" O ALA L 24 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'L' and resid 42 through 44 Processing sheet with id= U, first strand: chain 'M' and resid 129 through 132 removed outlier: 3.578A pdb=" N ILE M 183 " --> pdb=" O VAL M 13 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N VAL M 180 " --> pdb=" O LEU M 191 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE M 182 " --> pdb=" O HIS M 189 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'M' and resid 124 through 126 removed outlier: 3.759A pdb=" N MET M 118 " --> pdb=" O LEU M 102 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N LEU M 102 " --> pdb=" O MET M 118 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE M 42 " --> pdb=" O SER M 39 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N SER M 39 " --> pdb=" O ILE M 42 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N LEU M 44 " --> pdb=" O LYS M 37 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N LYS M 37 " --> pdb=" O LEU M 44 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N CYS M 46 " --> pdb=" O MET M 35 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N MET M 35 " --> pdb=" O CYS M 46 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'N' and resid 184 through 188 removed outlier: 3.654A pdb=" N VAL N 187 " --> pdb=" O THR N 62 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY N 70 " --> pdb=" O PHE N 67 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL N 71 " --> pdb=" O VAL N 238 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL N 73 " --> pdb=" O TYR N 236 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLY N 242 " --> pdb=" O ARG N 239 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'N' and resid 100 through 102 removed outlier: 3.564A pdb=" N GLY N 162 " --> pdb=" O GLY N 169 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'O' and resid 163 through 165 Processing sheet with id= Z, first strand: chain 'O' and resid 159 through 161 removed outlier: 3.535A pdb=" N GLN O 159 " --> pdb=" O SER O 151 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N VAL O 149 " --> pdb=" O ASP O 161 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N THR O 78 " --> pdb=" O THR O 75 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N THR O 75 " --> pdb=" O THR O 78 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ILE O 80 " --> pdb=" O LYS O 73 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N LYS O 73 " --> pdb=" O ILE O 80 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N CYS O 82 " --> pdb=" O CYS O 71 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N CYS O 71 " --> pdb=" O CYS O 82 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'P' and resid 181 through 184 Processing sheet with id= AB, first strand: chain 'P' and resid 176 through 178 removed outlier: 3.525A pdb=" N THR P 94 " --> pdb=" O ASN P 91 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN P 91 " --> pdb=" O THR P 94 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N LEU P 96 " --> pdb=" O ARG P 89 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N ARG P 89 " --> pdb=" O LEU P 96 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'Q' and resid 159 through 163 removed outlier: 5.111A pdb=" N THR Q 36 " --> pdb=" O ASP Q 51 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'Q' and resid 75 through 81 removed outlier: 3.678A pdb=" N ASP Q 138 " --> pdb=" O GLY Q 142 " (cutoff:3.500A) 1286 hydrogen bonds defined for protein. 3693 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: 10.62 Time building geometry restraints manager: 12.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6914 1.33 - 1.45: 5744 1.45 - 1.57: 16693 1.57 - 1.69: 0 1.69 - 1.81: 292 Bond restraints: 29643 Sorted by residual: bond pdb=" N ILE M 151 " pdb=" CA ILE M 151 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.25e-02 6.40e+03 9.79e+00 bond pdb=" N THR M 150 " pdb=" CA THR M 150 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.16e-02 7.43e+03 6.78e+00 bond pdb=" N SER M 152 " pdb=" CA SER M 152 " ideal model delta sigma weight residual 1.455 1.486 -0.032 1.25e-02 6.40e+03 6.37e+00 bond pdb=" N GLU M 154 " pdb=" CA GLU M 154 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.18e-02 7.18e+03 6.11e+00 bond pdb=" N ARG M 153 " pdb=" CA ARG M 153 " ideal model delta sigma weight residual 1.459 1.489 -0.029 1.23e-02 6.61e+03 5.72e+00 ... (remaining 29638 not shown) Histogram of bond angle deviations from ideal: 98.70 - 105.76: 555 105.76 - 112.83: 15764 112.83 - 119.90: 9892 119.90 - 126.96: 13571 126.96 - 134.03: 262 Bond angle restraints: 40044 Sorted by residual: angle pdb=" N GLY M 133 " pdb=" CA GLY M 133 " pdb=" C GLY M 133 " ideal model delta sigma weight residual 111.21 115.28 -4.07 1.04e+00 9.25e-01 1.53e+01 angle pdb=" CA TYR M 12 " pdb=" C TYR M 12 " pdb=" O TYR M 12 " ideal model delta sigma weight residual 121.10 117.10 4.00 1.10e+00 8.26e-01 1.32e+01 angle pdb=" CA ASP M 11 " pdb=" C ASP M 11 " pdb=" O ASP M 11 " ideal model delta sigma weight residual 121.20 117.53 3.67 1.04e+00 9.25e-01 1.25e+01 angle pdb=" N GLU L 165 " pdb=" CA GLU L 165 " pdb=" CB GLU L 165 " ideal model delta sigma weight residual 110.12 114.70 -4.58 1.47e+00 4.63e-01 9.70e+00 angle pdb=" C SER F 63 " pdb=" N ASN F 64 " pdb=" CA ASN F 64 " ideal model delta sigma weight residual 121.54 127.00 -5.46 1.91e+00 2.74e-01 8.17e+00 ... (remaining 40039 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 16213 17.70 - 35.39: 1404 35.39 - 53.08: 231 53.08 - 70.78: 48 70.78 - 88.47: 14 Dihedral angle restraints: 17910 sinusoidal: 7099 harmonic: 10811 Sorted by residual: dihedral pdb=" CA PHE O 130 " pdb=" C PHE O 130 " pdb=" N PRO O 131 " pdb=" CA PRO O 131 " ideal model delta harmonic sigma weight residual 180.00 -160.62 -19.38 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CA ASP K 60 " pdb=" CB ASP K 60 " pdb=" CG ASP K 60 " pdb=" OD1 ASP K 60 " ideal model delta sinusoidal sigma weight residual -30.00 -87.77 57.77 1 2.00e+01 2.50e-03 1.12e+01 dihedral pdb=" CA PRO O 131 " pdb=" C PRO O 131 " pdb=" N TYR O 132 " pdb=" CA TYR O 132 " ideal model delta harmonic sigma weight residual 180.00 163.47 16.53 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 17907 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 3057 0.036 - 0.072: 997 0.072 - 0.108: 347 0.108 - 0.144: 110 0.144 - 0.180: 4 Chirality restraints: 4515 Sorted by residual: chirality pdb=" CA VAL M 13 " pdb=" N VAL M 13 " pdb=" C VAL M 13 " pdb=" CB VAL M 13 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 8.09e-01 chirality pdb=" CA ASN F 64 " pdb=" N ASN F 64 " pdb=" C ASN F 64 " pdb=" CB ASN F 64 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.80e-01 chirality pdb=" CA PHE O 207 " pdb=" N PHE O 207 " pdb=" C PHE O 207 " pdb=" CB PHE O 207 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.72e-01 ... (remaining 4512 not shown) Planarity restraints: 5137 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP F 216 " -0.023 2.00e-02 2.50e+03 2.19e-02 1.20e+01 pdb=" CG TRP F 216 " 0.059 2.00e-02 2.50e+03 pdb=" CD1 TRP F 216 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP F 216 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP F 216 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP F 216 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP F 216 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 216 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 216 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP F 216 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU E 186 " 0.016 2.00e-02 2.50e+03 3.15e-02 9.91e+00 pdb=" C GLU E 186 " -0.054 2.00e-02 2.50e+03 pdb=" O GLU E 186 " 0.020 2.00e-02 2.50e+03 pdb=" N LEU E 187 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP D 157 " 0.039 5.00e-02 4.00e+02 5.81e-02 5.41e+00 pdb=" N PRO D 158 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO D 158 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO D 158 " 0.032 5.00e-02 4.00e+02 ... (remaining 5134 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 6770 2.79 - 3.32: 24848 3.32 - 3.85: 44188 3.85 - 4.37: 50832 4.37 - 4.90: 94927 Nonbonded interactions: 221565 Sorted by model distance: nonbonded pdb=" OH TYR I 175 " pdb=" OE1 GLU I 207 " model vdw 2.265 2.440 nonbonded pdb=" O GLY B 165 " pdb=" OG SER B 168 " model vdw 2.273 2.440 nonbonded pdb=" OD1 ASP C 39 " pdb=" NH1 ARG C 213 " model vdw 2.278 2.520 nonbonded pdb=" OG SER C 130 " pdb=" O THR C 147 " model vdw 2.282 2.440 nonbonded pdb=" NH1 ARG E 164 " pdb=" OD2 ASP I 243 " model vdw 2.288 2.520 ... (remaining 221560 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.100 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: 7.390 Check model and map are aligned: 0.230 Set scattering table: 0.280 Process input model: 76.870 Find NCS groups from input model: 1.650 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 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 : 0.004 0.039 29643 Z= 0.239 Angle : 0.497 6.172 40044 Z= 0.272 Chirality : 0.042 0.180 4515 Planarity : 0.004 0.058 5137 Dihedral : 13.482 88.475 10974 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.14), residues: 3663 helix: 2.72 (0.15), residues: 1296 sheet: 0.39 (0.18), residues: 847 loop : -0.98 (0.15), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.001 TRP F 216 HIS 0.005 0.001 HIS M 132 PHE 0.025 0.001 PHE L 69 TYR 0.028 0.001 TYR B 121 ARG 0.003 0.000 ARG F 41 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 3140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 347 time to evaluate : 3.938 Fit side-chains REVERT: B 140 ASP cc_start: 0.8082 (t0) cc_final: 0.7794 (t0) REVERT: C 200 GLN cc_start: 0.7767 (pp30) cc_final: 0.7547 (pp30) REVERT: F 207 ASP cc_start: 0.8213 (m-30) cc_final: 0.7911 (m-30) REVERT: F 222 ASN cc_start: 0.8846 (t0) cc_final: 0.8169 (t0) REVERT: G 236 ASP cc_start: 0.8313 (t70) cc_final: 0.8068 (p0) REVERT: J 32 MET cc_start: 0.8534 (mmm) cc_final: 0.8298 (mmt) REVERT: L 116 THR cc_start: 0.8705 (t) cc_final: 0.8463 (p) REVERT: L 173 ASN cc_start: 0.8423 (m110) cc_final: 0.8004 (m110) REVERT: M 1 MET cc_start: 0.7629 (ptm) cc_final: 0.7163 (ptm) REVERT: M 158 GLU cc_start: 0.8570 (tp30) cc_final: 0.7980 (tp30) REVERT: M 162 LYS cc_start: 0.8122 (mtpt) cc_final: 0.7674 (mtpp) REVERT: N 165 LYS cc_start: 0.9048 (mtmm) cc_final: 0.8787 (mtpt) REVERT: N 221 GLN cc_start: 0.7876 (mm110) cc_final: 0.7485 (mp10) outliers start: 0 outliers final: 2 residues processed: 347 average time/residue: 1.8039 time to fit residues: 712.1653 Evaluate side-chains 273 residues out of total 3140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 271 time to evaluate : 3.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 216 TRP Chi-restraints excluded: chain J residue 55 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 311 optimal weight: 0.0270 chunk 279 optimal weight: 0.9990 chunk 155 optimal weight: 1.9990 chunk 95 optimal weight: 6.9990 chunk 188 optimal weight: 9.9990 chunk 149 optimal weight: 4.9990 chunk 289 optimal weight: 5.9990 chunk 111 optimal weight: 9.9990 chunk 175 optimal weight: 1.9990 chunk 215 optimal weight: 2.9990 chunk 335 optimal weight: 10.0000 overall best weight: 1.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 224 ASN ** H 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 148 GLN J 229 GLN P 83 ASN P 230 ASN Q 188 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.0822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 29643 Z= 0.160 Angle : 0.473 6.873 40044 Z= 0.251 Chirality : 0.041 0.169 4515 Planarity : 0.004 0.051 5137 Dihedral : 3.839 42.735 4093 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.87 % Allowed : 8.21 % Favored : 90.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.14), residues: 3663 helix: 2.73 (0.15), residues: 1288 sheet: 0.59 (0.18), residues: 827 loop : -0.96 (0.15), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 156 HIS 0.003 0.001 HIS I 125 PHE 0.018 0.001 PHE L 69 TYR 0.016 0.001 TYR B 121 ARG 0.005 0.000 ARG O 222 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 3140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 276 time to evaluate : 3.518 Fit side-chains REVERT: B 140 ASP cc_start: 0.7862 (t0) cc_final: 0.7573 (t0) REVERT: C 23 GLN cc_start: 0.7863 (tm-30) cc_final: 0.7525 (tm-30) REVERT: D 211 ASN cc_start: 0.9135 (p0) cc_final: 0.8868 (p0) REVERT: F 207 ASP cc_start: 0.8186 (m-30) cc_final: 0.7879 (m-30) REVERT: F 222 ASN cc_start: 0.8844 (t0) cc_final: 0.8116 (t0) REVERT: G 236 ASP cc_start: 0.8296 (t70) cc_final: 0.8069 (p0) REVERT: I 243 ASP cc_start: 0.8319 (OUTLIER) cc_final: 0.7860 (t0) REVERT: L 14 MET cc_start: 0.8301 (ptp) cc_final: 0.8039 (ptp) REVERT: L 116 THR cc_start: 0.8728 (t) cc_final: 0.8471 (p) REVERT: L 173 ASN cc_start: 0.8584 (m110) cc_final: 0.8085 (m110) REVERT: N 9 ARG cc_start: 0.8311 (tpp80) cc_final: 0.8033 (ptp-110) REVERT: N 56 MET cc_start: 0.7960 (OUTLIER) cc_final: 0.7618 (mtm) REVERT: N 221 GLN cc_start: 0.7891 (mm110) cc_final: 0.7518 (mp10) REVERT: P 212 ASP cc_start: 0.8710 (m-30) cc_final: 0.8495 (m-30) outliers start: 27 outliers final: 8 residues processed: 285 average time/residue: 1.6540 time to fit residues: 542.1425 Evaluate side-chains 275 residues out of total 3140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 265 time to evaluate : 3.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain I residue 243 ASP Chi-restraints excluded: chain J residue 187 THR Chi-restraints excluded: chain M residue 39 SER Chi-restraints excluded: chain M residue 148 THR Chi-restraints excluded: chain N residue 56 MET Chi-restraints excluded: chain N residue 130 LYS Chi-restraints excluded: chain N residue 187 VAL Chi-restraints excluded: chain P residue 230 ASN Chi-restraints excluded: chain Q residue 66 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 186 optimal weight: 9.9990 chunk 103 optimal weight: 8.9990 chunk 278 optimal weight: 7.9990 chunk 228 optimal weight: 8.9990 chunk 92 optimal weight: 10.0000 chunk 335 optimal weight: 9.9990 chunk 362 optimal weight: 3.9990 chunk 298 optimal weight: 6.9990 chunk 332 optimal weight: 0.0970 chunk 114 optimal weight: 10.0000 chunk 269 optimal weight: 7.9990 overall best weight: 5.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 224 ASN ** H 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 108 ASN J 148 GLN J 229 GLN P 83 ASN P 202 GLN P 230 ASN P 233 GLN Q 41 GLN Q 188 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.1094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 29643 Z= 0.413 Angle : 0.584 7.972 40044 Z= 0.307 Chirality : 0.045 0.186 4515 Planarity : 0.005 0.055 5137 Dihedral : 4.271 31.621 4088 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.51 % Allowed : 10.39 % Favored : 88.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.14), residues: 3663 helix: 2.41 (0.15), residues: 1293 sheet: 0.57 (0.18), residues: 817 loop : -1.15 (0.14), residues: 1553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 101 HIS 0.008 0.001 HIS I 125 PHE 0.033 0.002 PHE L 69 TYR 0.040 0.002 TYR B 121 ARG 0.006 0.000 ARG F 41 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 3140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 265 time to evaluate : 3.798 Fit side-chains REVERT: A 60 ARG cc_start: 0.8465 (OUTLIER) cc_final: 0.7919 (mtp85) REVERT: B 140 ASP cc_start: 0.8184 (t0) cc_final: 0.7852 (t0) REVERT: C 23 GLN cc_start: 0.7889 (tm-30) cc_final: 0.7456 (tm-30) REVERT: E 217 LYS cc_start: 0.8553 (OUTLIER) cc_final: 0.8271 (tptm) REVERT: F 222 ASN cc_start: 0.8869 (t0) cc_final: 0.8102 (t0) REVERT: I 33 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7888 (tm-30) REVERT: I 243 ASP cc_start: 0.8373 (OUTLIER) cc_final: 0.7849 (t0) REVERT: L 116 THR cc_start: 0.8738 (t) cc_final: 0.8514 (p) REVERT: L 165 GLU cc_start: 0.8620 (pm20) cc_final: 0.8351 (pm20) REVERT: L 173 ASN cc_start: 0.8670 (m110) cc_final: 0.8172 (m110) REVERT: M 49 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7394 (tt0) REVERT: N 56 MET cc_start: 0.7970 (OUTLIER) cc_final: 0.7636 (mtm) REVERT: N 221 GLN cc_start: 0.7870 (mm110) cc_final: 0.7627 (mm110) REVERT: P 212 ASP cc_start: 0.8730 (m-30) cc_final: 0.8496 (m-30) REVERT: Q 30 GLU cc_start: 0.7392 (pm20) cc_final: 0.6735 (pm20) REVERT: Q 129 MET cc_start: 0.7976 (OUTLIER) cc_final: 0.6745 (mmt) outliers start: 47 outliers final: 16 residues processed: 289 average time/residue: 1.6835 time to fit residues: 559.0712 Evaluate side-chains 283 residues out of total 3140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 260 time to evaluate : 3.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ARG Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain E residue 217 LYS Chi-restraints excluded: chain F residue 101 SER Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain I residue 33 GLU Chi-restraints excluded: chain I residue 243 ASP Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain K residue 189 MET Chi-restraints excluded: chain L residue 133 THR Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 39 SER Chi-restraints excluded: chain M residue 49 GLU Chi-restraints excluded: chain M residue 148 THR Chi-restraints excluded: chain N residue 56 MET Chi-restraints excluded: chain N residue 73 VAL Chi-restraints excluded: chain N residue 180 ILE Chi-restraints excluded: chain N residue 187 VAL Chi-restraints excluded: chain N residue 219 ILE Chi-restraints excluded: chain P residue 101 ASP Chi-restraints excluded: chain Q residue 66 ASP Chi-restraints excluded: chain Q residue 129 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 331 optimal weight: 5.9990 chunk 252 optimal weight: 30.0000 chunk 174 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 160 optimal weight: 8.9990 chunk 225 optimal weight: 0.7980 chunk 336 optimal weight: 5.9990 chunk 356 optimal weight: 0.9990 chunk 176 optimal weight: 5.9990 chunk 319 optimal weight: 0.8980 chunk 96 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 12 HIS G 224 ASN ** H 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 108 ASN J 229 GLN P 83 ASN P 230 ASN Q 41 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.1083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 29643 Z= 0.159 Angle : 0.460 7.121 40044 Z= 0.244 Chirality : 0.041 0.172 4515 Planarity : 0.004 0.057 5137 Dihedral : 3.928 29.628 4088 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.25 % Allowed : 11.74 % Favored : 87.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.14), residues: 3663 helix: 2.58 (0.15), residues: 1293 sheet: 0.71 (0.18), residues: 814 loop : -1.03 (0.15), residues: 1556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 149 HIS 0.003 0.001 HIS I 125 PHE 0.016 0.001 PHE L 69 TYR 0.019 0.001 TYR L 147 ARG 0.005 0.000 ARG N 9 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 3140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 269 time to evaluate : 3.666 Fit side-chains revert: symmetry clash REVERT: A 166 ASN cc_start: 0.8733 (t0) cc_final: 0.8408 (t0) REVERT: B 140 ASP cc_start: 0.7932 (t0) cc_final: 0.7643 (t0) REVERT: C 23 GLN cc_start: 0.7905 (tm-30) cc_final: 0.7531 (tm-30) REVERT: D 1 MET cc_start: 0.8815 (mtt) cc_final: 0.8570 (mtt) REVERT: E 217 LYS cc_start: 0.8485 (ttpt) cc_final: 0.8209 (tptm) REVERT: F 207 ASP cc_start: 0.8306 (m-30) cc_final: 0.7886 (m-30) REVERT: F 222 ASN cc_start: 0.8804 (t0) cc_final: 0.8012 (t0) REVERT: I 33 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7888 (tm-30) REVERT: I 243 ASP cc_start: 0.8315 (OUTLIER) cc_final: 0.7831 (t0) REVERT: L 116 THR cc_start: 0.8717 (t) cc_final: 0.8487 (p) REVERT: L 173 ASN cc_start: 0.8701 (m110) cc_final: 0.8256 (m110) REVERT: N 56 MET cc_start: 0.7945 (OUTLIER) cc_final: 0.7632 (mtm) REVERT: N 221 GLN cc_start: 0.7859 (mm110) cc_final: 0.7573 (mm110) REVERT: P 212 ASP cc_start: 0.8753 (m-30) cc_final: 0.8500 (m-30) outliers start: 39 outliers final: 19 residues processed: 288 average time/residue: 1.6538 time to fit residues: 549.1538 Evaluate side-chains 290 residues out of total 3140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 268 time to evaluate : 3.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 78 MET Chi-restraints excluded: chain D residue 107 MET Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain I residue 33 GLU Chi-restraints excluded: chain I residue 243 ASP Chi-restraints excluded: chain J residue 187 THR Chi-restraints excluded: chain L residue 88 MET Chi-restraints excluded: chain L residue 165 GLU Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 28 MET Chi-restraints excluded: chain M residue 39 SER Chi-restraints excluded: chain M residue 148 THR Chi-restraints excluded: chain N residue 56 MET Chi-restraints excluded: chain N residue 130 LYS Chi-restraints excluded: chain N residue 187 VAL Chi-restraints excluded: chain P residue 101 ASP Chi-restraints excluded: chain Q residue 150 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 297 optimal weight: 3.9990 chunk 202 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 chunk 265 optimal weight: 4.9990 chunk 147 optimal weight: 10.0000 chunk 304 optimal weight: 10.0000 chunk 246 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 182 optimal weight: 0.5980 chunk 320 optimal weight: 8.9990 chunk 90 optimal weight: 9.9990 overall best weight: 5.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 224 ASN ** H 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 229 GLN P 83 ASN P 230 ASN Q 41 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.1234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 29643 Z= 0.400 Angle : 0.568 7.872 40044 Z= 0.299 Chirality : 0.045 0.172 4515 Planarity : 0.004 0.059 5137 Dihedral : 4.262 32.148 4088 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.76 % Allowed : 12.80 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.14), residues: 3663 helix: 2.40 (0.15), residues: 1291 sheet: 0.58 (0.18), residues: 823 loop : -1.18 (0.15), residues: 1549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 101 HIS 0.007 0.001 HIS I 125 PHE 0.032 0.002 PHE L 69 TYR 0.029 0.002 TYR B 121 ARG 0.007 0.000 ARG K 186 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 3140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 268 time to evaluate : 3.409 Fit side-chains REVERT: B 140 ASP cc_start: 0.8213 (t0) cc_final: 0.7877 (t0) REVERT: C 23 GLN cc_start: 0.7913 (tm-30) cc_final: 0.7439 (tm-30) REVERT: D 211 ASN cc_start: 0.9093 (p0) cc_final: 0.8886 (p0) REVERT: E 217 LYS cc_start: 0.8539 (ttpt) cc_final: 0.8321 (tptt) REVERT: F 222 ASN cc_start: 0.8879 (t0) cc_final: 0.8084 (t0) REVERT: I 33 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7890 (tm-30) REVERT: I 243 ASP cc_start: 0.8349 (OUTLIER) cc_final: 0.7847 (t0) REVERT: L 116 THR cc_start: 0.8746 (t) cc_final: 0.8527 (p) REVERT: L 173 ASN cc_start: 0.8706 (m110) cc_final: 0.8232 (m110) REVERT: M 49 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7410 (tt0) REVERT: N 56 MET cc_start: 0.7958 (OUTLIER) cc_final: 0.7637 (mtm) REVERT: N 221 GLN cc_start: 0.7848 (mm110) cc_final: 0.7576 (mm110) REVERT: O 234 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7876 (pm20) REVERT: P 212 ASP cc_start: 0.8715 (m-30) cc_final: 0.8475 (m-30) REVERT: Q 30 GLU cc_start: 0.7416 (pm20) cc_final: 0.6638 (pm20) REVERT: Q 129 MET cc_start: 0.7918 (OUTLIER) cc_final: 0.6700 (mmt) REVERT: Q 133 ILE cc_start: 0.8286 (OUTLIER) cc_final: 0.7886 (mt) outliers start: 55 outliers final: 25 residues processed: 302 average time/residue: 1.6696 time to fit residues: 581.1057 Evaluate side-chains 294 residues out of total 3140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 262 time to evaluate : 3.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain D residue 78 MET Chi-restraints excluded: chain G residue 112 ASP Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain I residue 33 GLU Chi-restraints excluded: chain I residue 243 ASP Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 187 THR Chi-restraints excluded: chain L residue 88 MET Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 28 MET Chi-restraints excluded: chain M residue 39 SER Chi-restraints excluded: chain M residue 49 GLU Chi-restraints excluded: chain M residue 132 HIS Chi-restraints excluded: chain M residue 148 THR Chi-restraints excluded: chain M residue 192 ASP Chi-restraints excluded: chain N residue 7 LEU Chi-restraints excluded: chain N residue 56 MET Chi-restraints excluded: chain N residue 73 VAL Chi-restraints excluded: chain N residue 130 LYS Chi-restraints excluded: chain N residue 187 VAL Chi-restraints excluded: chain N residue 219 ILE Chi-restraints excluded: chain O residue 234 GLU Chi-restraints excluded: chain P residue 201 LYS Chi-restraints excluded: chain Q residue 66 ASP Chi-restraints excluded: chain Q residue 129 MET Chi-restraints excluded: chain Q residue 133 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 120 optimal weight: 0.8980 chunk 321 optimal weight: 5.9990 chunk 70 optimal weight: 6.9990 chunk 209 optimal weight: 10.0000 chunk 88 optimal weight: 8.9990 chunk 357 optimal weight: 9.9990 chunk 296 optimal weight: 10.0000 chunk 165 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 118 optimal weight: 6.9990 chunk 187 optimal weight: 8.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 224 ASN ** H 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 229 GLN P 83 ASN P 230 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.1286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 29643 Z= 0.366 Angle : 0.548 7.250 40044 Z= 0.290 Chirality : 0.044 0.161 4515 Planarity : 0.004 0.061 5137 Dihedral : 4.276 32.948 4088 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.76 % Allowed : 13.69 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.14), residues: 3663 helix: 2.36 (0.15), residues: 1283 sheet: 0.51 (0.18), residues: 832 loop : -1.21 (0.14), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 13 HIS 0.006 0.001 HIS I 125 PHE 0.028 0.001 PHE L 69 TYR 0.022 0.001 TYR L 147 ARG 0.008 0.000 ARG K 186 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 3140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 272 time to evaluate : 3.413 Fit side-chains REVERT: A 166 ASN cc_start: 0.8771 (t0) cc_final: 0.8412 (t0) REVERT: B 140 ASP cc_start: 0.8194 (t0) cc_final: 0.7863 (t0) REVERT: C 23 GLN cc_start: 0.7906 (tm-30) cc_final: 0.7396 (tm-30) REVERT: E 217 LYS cc_start: 0.8546 (ttpt) cc_final: 0.8315 (tptt) REVERT: F 222 ASN cc_start: 0.8880 (t0) cc_final: 0.8065 (t0) REVERT: I 33 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7878 (tm-30) REVERT: J 201 MET cc_start: 0.8831 (ttt) cc_final: 0.8457 (ttt) REVERT: L 116 THR cc_start: 0.8736 (t) cc_final: 0.8512 (p) REVERT: L 173 ASN cc_start: 0.8763 (m110) cc_final: 0.8371 (m110) REVERT: M 49 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7421 (tt0) REVERT: N 56 MET cc_start: 0.7963 (OUTLIER) cc_final: 0.7657 (mtm) REVERT: N 221 GLN cc_start: 0.7848 (mm110) cc_final: 0.7588 (mm110) REVERT: O 234 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7874 (pm20) REVERT: P 212 ASP cc_start: 0.8734 (m-30) cc_final: 0.8475 (m-30) REVERT: Q 30 GLU cc_start: 0.7416 (pm20) cc_final: 0.6658 (pm20) REVERT: Q 129 MET cc_start: 0.7933 (OUTLIER) cc_final: 0.6582 (mmt) outliers start: 55 outliers final: 37 residues processed: 303 average time/residue: 1.6403 time to fit residues: 574.3158 Evaluate side-chains 306 residues out of total 3140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 264 time to evaluate : 3.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 154 HIS Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain D residue 78 MET Chi-restraints excluded: chain E residue 183 ASN Chi-restraints excluded: chain F residue 101 SER Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 112 ASP Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain I residue 33 GLU Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 187 THR Chi-restraints excluded: chain K residue 236 ASN Chi-restraints excluded: chain L residue 26 ARG Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 88 MET Chi-restraints excluded: chain L residue 131 MET Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 28 MET Chi-restraints excluded: chain M residue 39 SER Chi-restraints excluded: chain M residue 49 GLU Chi-restraints excluded: chain M residue 132 HIS Chi-restraints excluded: chain M residue 148 THR Chi-restraints excluded: chain M residue 150 THR Chi-restraints excluded: chain M residue 168 GLN Chi-restraints excluded: chain M residue 192 ASP Chi-restraints excluded: chain N residue 7 LEU Chi-restraints excluded: chain N residue 56 MET Chi-restraints excluded: chain N residue 73 VAL Chi-restraints excluded: chain N residue 130 LYS Chi-restraints excluded: chain N residue 180 ILE Chi-restraints excluded: chain N residue 187 VAL Chi-restraints excluded: chain O residue 233 GLU Chi-restraints excluded: chain O residue 234 GLU Chi-restraints excluded: chain P residue 201 LYS Chi-restraints excluded: chain Q residue 66 ASP Chi-restraints excluded: chain Q residue 129 MET Chi-restraints excluded: chain Q residue 222 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 344 optimal weight: 9.9990 chunk 40 optimal weight: 1.9990 chunk 203 optimal weight: 5.9990 chunk 260 optimal weight: 0.8980 chunk 202 optimal weight: 0.0870 chunk 300 optimal weight: 7.9990 chunk 199 optimal weight: 3.9990 chunk 355 optimal weight: 8.9990 chunk 222 optimal weight: 9.9990 chunk 216 optimal weight: 10.0000 chunk 164 optimal weight: 0.5980 overall best weight: 1.5162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 224 ASN ** H 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 229 GLN P 83 ASN P 230 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.1269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 29643 Z= 0.152 Angle : 0.466 7.020 40044 Z= 0.248 Chirality : 0.041 0.154 4515 Planarity : 0.004 0.061 5137 Dihedral : 3.957 30.165 4088 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.48 % Allowed : 14.62 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.14), residues: 3663 helix: 2.58 (0.15), residues: 1281 sheet: 0.68 (0.18), residues: 817 loop : -1.08 (0.14), residues: 1565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 149 HIS 0.003 0.001 HIS F 121 PHE 0.023 0.001 PHE O 163 TYR 0.022 0.001 TYR P 189 ARG 0.009 0.000 ARG K 186 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 3140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 276 time to evaluate : 3.734 Fit side-chains REVERT: A 166 ASN cc_start: 0.8691 (t0) cc_final: 0.8345 (t0) REVERT: B 140 ASP cc_start: 0.8011 (t0) cc_final: 0.7718 (t0) REVERT: C 23 GLN cc_start: 0.7900 (tm-30) cc_final: 0.7472 (tm-30) REVERT: E 217 LYS cc_start: 0.8507 (ttpt) cc_final: 0.8297 (tptt) REVERT: F 207 ASP cc_start: 0.8347 (m-30) cc_final: 0.7916 (m-30) REVERT: F 222 ASN cc_start: 0.8826 (t0) cc_final: 0.7998 (t0) REVERT: I 33 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7885 (tm-30) REVERT: I 243 ASP cc_start: 0.8305 (OUTLIER) cc_final: 0.7831 (t0) REVERT: J 201 MET cc_start: 0.8776 (ttt) cc_final: 0.8408 (ttt) REVERT: L 116 THR cc_start: 0.8722 (t) cc_final: 0.8497 (p) REVERT: L 158 MET cc_start: 0.8911 (OUTLIER) cc_final: 0.8564 (mtm) REVERT: L 173 ASN cc_start: 0.8737 (m110) cc_final: 0.8342 (m110) REVERT: N 9 ARG cc_start: 0.8370 (tpp80) cc_final: 0.7838 (ttp80) REVERT: N 56 MET cc_start: 0.7919 (OUTLIER) cc_final: 0.7622 (mtm) REVERT: N 221 GLN cc_start: 0.7807 (mm110) cc_final: 0.7540 (mm110) REVERT: O 201 ARG cc_start: 0.8086 (tpp-160) cc_final: 0.7838 (tpp-160) REVERT: P 212 ASP cc_start: 0.8750 (m-30) cc_final: 0.8484 (m-30) REVERT: Q 30 GLU cc_start: 0.7341 (pm20) cc_final: 0.6716 (pm20) REVERT: Q 129 MET cc_start: 0.7839 (OUTLIER) cc_final: 0.6606 (mmt) REVERT: Q 224 LEU cc_start: 0.7989 (tp) cc_final: 0.7751 (pt) outliers start: 46 outliers final: 23 residues processed: 304 average time/residue: 1.6004 time to fit residues: 563.9187 Evaluate side-chains 300 residues out of total 3140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 272 time to evaluate : 3.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 154 HIS Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 78 MET Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 112 ASP Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain I residue 33 GLU Chi-restraints excluded: chain I residue 243 ASP Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 187 THR Chi-restraints excluded: chain L residue 88 MET Chi-restraints excluded: chain L residue 158 MET Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 28 MET Chi-restraints excluded: chain M residue 39 SER Chi-restraints excluded: chain M residue 148 THR Chi-restraints excluded: chain M residue 150 THR Chi-restraints excluded: chain N residue 56 MET Chi-restraints excluded: chain N residue 130 LYS Chi-restraints excluded: chain N residue 187 VAL Chi-restraints excluded: chain O residue 233 GLU Chi-restraints excluded: chain P residue 101 ASP Chi-restraints excluded: chain Q residue 66 ASP Chi-restraints excluded: chain Q residue 129 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 220 optimal weight: 0.8980 chunk 142 optimal weight: 10.0000 chunk 212 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 226 optimal weight: 1.9990 chunk 242 optimal weight: 0.4980 chunk 175 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 279 optimal weight: 4.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 ASN A 169 ASN G 224 ASN ** H 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 148 GLN J 229 GLN P 83 ASN P 230 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.1319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 29643 Z= 0.138 Angle : 0.453 7.513 40044 Z= 0.240 Chirality : 0.041 0.163 4515 Planarity : 0.004 0.060 5137 Dihedral : 3.812 30.716 4088 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.35 % Allowed : 14.85 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.14), residues: 3663 helix: 2.67 (0.15), residues: 1281 sheet: 0.80 (0.18), residues: 820 loop : -1.02 (0.15), residues: 1562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 114 HIS 0.006 0.001 HIS M 132 PHE 0.020 0.001 PHE M 137 TYR 0.023 0.001 TYR L 147 ARG 0.012 0.000 ARG K 186 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 3140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 276 time to evaluate : 3.741 Fit side-chains REVERT: B 140 ASP cc_start: 0.7991 (t0) cc_final: 0.7698 (t0) REVERT: C 23 GLN cc_start: 0.7913 (tm-30) cc_final: 0.7509 (tm-30) REVERT: E 217 LYS cc_start: 0.8486 (ttpt) cc_final: 0.8272 (tptt) REVERT: F 207 ASP cc_start: 0.8288 (m-30) cc_final: 0.7854 (m-30) REVERT: F 222 ASN cc_start: 0.8819 (t0) cc_final: 0.7994 (t0) REVERT: I 33 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7881 (tm-30) REVERT: I 243 ASP cc_start: 0.8287 (OUTLIER) cc_final: 0.7828 (t0) REVERT: J 201 MET cc_start: 0.8757 (ttt) cc_final: 0.8401 (ttt) REVERT: L 116 THR cc_start: 0.8721 (t) cc_final: 0.8501 (p) REVERT: L 158 MET cc_start: 0.8808 (OUTLIER) cc_final: 0.8562 (mtt) REVERT: L 165 GLU cc_start: 0.8648 (pm20) cc_final: 0.8272 (pm20) REVERT: L 173 ASN cc_start: 0.8682 (m110) cc_final: 0.8245 (m110) REVERT: M 174 ASN cc_start: 0.7170 (p0) cc_final: 0.6793 (p0) REVERT: N 9 ARG cc_start: 0.8362 (tpp80) cc_final: 0.7834 (ttp80) REVERT: N 56 MET cc_start: 0.7920 (OUTLIER) cc_final: 0.7623 (mtm) REVERT: N 92 LYS cc_start: 0.6723 (mmpt) cc_final: 0.6035 (mttt) REVERT: N 221 GLN cc_start: 0.7793 (mm110) cc_final: 0.7516 (mm110) REVERT: P 212 ASP cc_start: 0.8754 (m-30) cc_final: 0.8490 (m-30) REVERT: Q 224 LEU cc_start: 0.7961 (tp) cc_final: 0.7753 (pt) outliers start: 42 outliers final: 27 residues processed: 303 average time/residue: 1.7342 time to fit residues: 618.1074 Evaluate side-chains 300 residues out of total 3140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 269 time to evaluate : 3.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 154 HIS Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 78 MET Chi-restraints excluded: chain D residue 214 ASN Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain E residue 183 ASN Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 112 ASP Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain I residue 33 GLU Chi-restraints excluded: chain I residue 243 ASP Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 187 THR Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 88 MET Chi-restraints excluded: chain L residue 158 MET Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 28 MET Chi-restraints excluded: chain M residue 39 SER Chi-restraints excluded: chain M residue 148 THR Chi-restraints excluded: chain M residue 192 ASP Chi-restraints excluded: chain N residue 56 MET Chi-restraints excluded: chain N residue 130 LYS Chi-restraints excluded: chain N residue 187 VAL Chi-restraints excluded: chain O residue 233 GLU Chi-restraints excluded: chain P residue 101 ASP Chi-restraints excluded: chain Q residue 66 ASP Chi-restraints excluded: chain Q residue 222 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 323 optimal weight: 4.9990 chunk 340 optimal weight: 0.5980 chunk 310 optimal weight: 10.0000 chunk 331 optimal weight: 1.9990 chunk 199 optimal weight: 0.9990 chunk 144 optimal weight: 5.9990 chunk 260 optimal weight: 2.9990 chunk 101 optimal weight: 5.9990 chunk 299 optimal weight: 10.0000 chunk 313 optimal weight: 8.9990 chunk 330 optimal weight: 6.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 224 ASN ** H 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 148 GLN J 229 GLN O 174 GLN P 83 ASN P 230 ASN Q 41 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.1288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 29643 Z= 0.200 Angle : 0.475 6.999 40044 Z= 0.251 Chirality : 0.042 0.166 4515 Planarity : 0.004 0.062 5137 Dihedral : 3.835 29.473 4088 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.41 % Allowed : 15.07 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.14), residues: 3663 helix: 2.64 (0.15), residues: 1283 sheet: 0.79 (0.18), residues: 820 loop : -1.02 (0.15), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 102 HIS 0.006 0.001 HIS M 132 PHE 0.023 0.001 PHE O 163 TYR 0.021 0.001 TYR P 189 ARG 0.013 0.000 ARG K 186 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 3140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 272 time to evaluate : 3.730 Fit side-chains REVERT: B 140 ASP cc_start: 0.8038 (t0) cc_final: 0.7737 (t0) REVERT: C 23 GLN cc_start: 0.7909 (tm-30) cc_final: 0.7492 (tm-30) REVERT: E 217 LYS cc_start: 0.8481 (ttpt) cc_final: 0.8208 (tptm) REVERT: F 207 ASP cc_start: 0.8314 (m-30) cc_final: 0.7882 (m-30) REVERT: F 222 ASN cc_start: 0.8838 (t0) cc_final: 0.8016 (t0) REVERT: I 33 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7873 (tm-30) REVERT: I 243 ASP cc_start: 0.8299 (OUTLIER) cc_final: 0.7833 (t0) REVERT: J 201 MET cc_start: 0.8789 (ttt) cc_final: 0.8449 (ttt) REVERT: L 116 THR cc_start: 0.8730 (t) cc_final: 0.8513 (p) REVERT: L 173 ASN cc_start: 0.8673 (m110) cc_final: 0.8233 (m110) REVERT: M 174 ASN cc_start: 0.7190 (p0) cc_final: 0.6839 (p0) REVERT: N 9 ARG cc_start: 0.8349 (tpp80) cc_final: 0.7839 (ttp80) REVERT: N 56 MET cc_start: 0.7933 (OUTLIER) cc_final: 0.7638 (mtm) REVERT: N 221 GLN cc_start: 0.7800 (mm110) cc_final: 0.7523 (mm110) REVERT: P 212 ASP cc_start: 0.8753 (m-30) cc_final: 0.8500 (m-30) outliers start: 44 outliers final: 26 residues processed: 296 average time/residue: 1.5940 time to fit residues: 545.5461 Evaluate side-chains 300 residues out of total 3140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 271 time to evaluate : 3.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 154 HIS Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 78 MET Chi-restraints excluded: chain D residue 214 ASN Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 112 ASP Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain I residue 33 GLU Chi-restraints excluded: chain I residue 243 ASP Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 187 THR Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 88 MET Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 28 MET Chi-restraints excluded: chain M residue 39 SER Chi-restraints excluded: chain M residue 148 THR Chi-restraints excluded: chain M residue 150 THR Chi-restraints excluded: chain M residue 192 ASP Chi-restraints excluded: chain N residue 56 MET Chi-restraints excluded: chain N residue 130 LYS Chi-restraints excluded: chain N residue 187 VAL Chi-restraints excluded: chain N residue 199 ASP Chi-restraints excluded: chain P residue 101 ASP Chi-restraints excluded: chain Q residue 66 ASP Chi-restraints excluded: chain Q residue 222 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 217 optimal weight: 7.9990 chunk 350 optimal weight: 0.9980 chunk 213 optimal weight: 8.9990 chunk 166 optimal weight: 20.0000 chunk 243 optimal weight: 5.9990 chunk 367 optimal weight: 20.0000 chunk 338 optimal weight: 0.7980 chunk 292 optimal weight: 20.0000 chunk 30 optimal weight: 0.8980 chunk 226 optimal weight: 8.9990 chunk 179 optimal weight: 10.0000 overall best weight: 3.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 224 ASN ** H 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 148 GLN J 229 GLN P 83 ASN P 230 ASN Q 41 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.1283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 29643 Z= 0.266 Angle : 0.507 10.157 40044 Z= 0.267 Chirality : 0.042 0.168 4515 Planarity : 0.004 0.062 5137 Dihedral : 3.930 29.914 4088 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.15 % Allowed : 15.33 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.14), residues: 3663 helix: 2.58 (0.15), residues: 1284 sheet: 0.69 (0.18), residues: 834 loop : -1.04 (0.15), residues: 1545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 13 HIS 0.006 0.001 HIS M 132 PHE 0.025 0.001 PHE L 69 TYR 0.023 0.001 TYR L 147 ARG 0.013 0.000 ARG K 186 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 3140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 271 time to evaluate : 3.635 Fit side-chains REVERT: B 140 ASP cc_start: 0.8084 (t0) cc_final: 0.7766 (t0) REVERT: C 23 GLN cc_start: 0.7900 (tm-30) cc_final: 0.7453 (tm-30) REVERT: E 217 LYS cc_start: 0.8490 (ttpt) cc_final: 0.8214 (tptm) REVERT: F 207 ASP cc_start: 0.8340 (m-30) cc_final: 0.7901 (m-30) REVERT: F 222 ASN cc_start: 0.8855 (t0) cc_final: 0.8037 (t0) REVERT: I 33 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7873 (tm-30) REVERT: I 243 ASP cc_start: 0.8325 (OUTLIER) cc_final: 0.7836 (t0) REVERT: J 201 MET cc_start: 0.8812 (ttt) cc_final: 0.8505 (ttt) REVERT: L 116 THR cc_start: 0.8736 (t) cc_final: 0.8518 (p) REVERT: L 173 ASN cc_start: 0.8686 (m110) cc_final: 0.8254 (m110) REVERT: M 174 ASN cc_start: 0.7226 (p0) cc_final: 0.6871 (p0) REVERT: N 9 ARG cc_start: 0.8357 (tpp80) cc_final: 0.7846 (ttp80) REVERT: N 56 MET cc_start: 0.7940 (OUTLIER) cc_final: 0.7628 (mtm) REVERT: N 221 GLN cc_start: 0.7803 (mm110) cc_final: 0.7526 (mm110) REVERT: P 212 ASP cc_start: 0.8732 (m-30) cc_final: 0.8466 (m-30) outliers start: 36 outliers final: 25 residues processed: 295 average time/residue: 1.6654 time to fit residues: 568.1904 Evaluate side-chains 297 residues out of total 3140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 269 time to evaluate : 3.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 154 HIS Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 78 MET Chi-restraints excluded: chain D residue 214 ASN Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 112 ASP Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain I residue 33 GLU Chi-restraints excluded: chain I residue 243 ASP Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 187 THR Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 88 MET Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 28 MET Chi-restraints excluded: chain M residue 39 SER Chi-restraints excluded: chain M residue 148 THR Chi-restraints excluded: chain M residue 150 THR Chi-restraints excluded: chain M residue 192 ASP Chi-restraints excluded: chain N residue 56 MET Chi-restraints excluded: chain N residue 130 LYS Chi-restraints excluded: chain N residue 187 VAL Chi-restraints excluded: chain P residue 101 ASP Chi-restraints excluded: chain Q residue 66 ASP Chi-restraints excluded: chain Q residue 222 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 232 optimal weight: 10.0000 chunk 311 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 269 optimal weight: 10.0000 chunk 43 optimal weight: 9.9990 chunk 81 optimal weight: 0.8980 chunk 293 optimal weight: 0.4980 chunk 122 optimal weight: 1.9990 chunk 301 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 54 optimal weight: 10.0000 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 224 ASN ** H 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 148 GLN J 229 GLN P 83 ASN P 230 ASN Q 41 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.092276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.065917 restraints weight = 56859.445| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 2.73 r_work: 0.2746 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2619 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.1311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 29643 Z= 0.198 Angle : 0.486 9.969 40044 Z= 0.257 Chirality : 0.042 0.189 4515 Planarity : 0.004 0.062 5137 Dihedral : 3.880 29.925 4088 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.15 % Allowed : 15.49 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.14), residues: 3663 helix: 2.62 (0.15), residues: 1284 sheet: 0.75 (0.18), residues: 822 loop : -1.02 (0.15), residues: 1557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 102 HIS 0.006 0.001 HIS M 132 PHE 0.024 0.001 PHE O 163 TYR 0.022 0.001 TYR P 189 ARG 0.013 0.000 ARG K 186 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9730.67 seconds wall clock time: 175 minutes 21.48 seconds (10521.48 seconds total)