Starting phenix.real_space_refine on Fri Mar 22 20:50:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lf1_23297/03_2024/7lf1_23297.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lf1_23297/03_2024/7lf1_23297.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lf1_23297/03_2024/7lf1_23297.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lf1_23297/03_2024/7lf1_23297.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lf1_23297/03_2024/7lf1_23297.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lf1_23297/03_2024/7lf1_23297.pdb" } resolution = 4.04 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= 0.010 sd= 0.057 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: 5 Type Number sf(0) Gaussians Mn 12 7.51 5 S 120 5.16 5 C 21810 2.51 5 N 5814 2.21 5 O 6762 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 180": "NH1" <-> "NH2" Residue "B ARG 180": "NH1" <-> "NH2" Residue "C ARG 180": "NH1" <-> "NH2" Residue "J ARG 180": "NH1" <-> "NH2" Residue "M ARG 180": "NH1" <-> "NH2" Residue "N ARG 180": "NH1" <-> "NH2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 34518 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 2409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2409 Classifications: {'peptide': 317} Link IDs: {'CIS': 1, 'PTRANS': 21, 'TRANS': 294} Chain: "D" Number of atoms: 1713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1713 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 2, 'PCIS': 2, 'PTRANS': 11, 'TRANS': 211} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "E" Number of atoms: 1629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1629 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 10, 'TRANS': 200} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "F" Number of atoms: 1713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1713 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 2, 'PCIS': 2, 'PTRANS': 11, 'TRANS': 211} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "G" Number of atoms: 1713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1713 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 2, 'PCIS': 2, 'PTRANS': 11, 'TRANS': 211} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "H" Number of atoms: 1629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1629 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 10, 'TRANS': 200} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "I" Number of atoms: 1629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1629 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 10, 'TRANS': 200} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "K" Number of atoms: 1713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1713 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 2, 'PCIS': 2, 'PTRANS': 11, 'TRANS': 211} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "L" Number of atoms: 1629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1629 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 10, 'TRANS': 200} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "O" Number of atoms: 1713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1713 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 2, 'PCIS': 2, 'PTRANS': 11, 'TRANS': 211} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "P" Number of atoms: 1713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1713 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 2, 'PCIS': 2, 'PTRANS': 11, 'TRANS': 211} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "Q" Number of atoms: 1629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1629 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 10, 'TRANS': 200} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "R" Number of atoms: 1629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1629 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 10, 'TRANS': 200} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 2409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2409 Classifications: {'peptide': 317} Link IDs: {'CIS': 1, 'PTRANS': 21, 'TRANS': 294} Chain: "C" Number of atoms: 2409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2409 Classifications: {'peptide': 317} Link IDs: {'CIS': 1, 'PTRANS': 21, 'TRANS': 294} Chain: "J" Number of atoms: 2409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2409 Classifications: {'peptide': 317} Link IDs: {'CIS': 1, 'PTRANS': 21, 'TRANS': 294} Chain: "M" Number of atoms: 2409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2409 Classifications: {'peptide': 317} Link IDs: {'CIS': 1, 'PTRANS': 21, 'TRANS': 294} Chain: "N" Number of atoms: 2409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2409 Classifications: {'peptide': 317} Link IDs: {'CIS': 1, 'PTRANS': 21, 'TRANS': 294} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 17.66, per 1000 atoms: 0.51 Number of scatterers: 34518 At special positions: 0 Unit cell: (116.48, 115.44, 231.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Mn 12 24.99 S 120 16.00 O 6762 8.00 N 5814 7.00 C 21810 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 152 " - pdb=" SG CYS D 208 " distance=2.02 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 134 " - pdb=" SG CYS E 194 " distance=2.02 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 152 " - pdb=" SG CYS F 208 " distance=2.02 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 152 " - pdb=" SG CYS G 208 " distance=2.02 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 134 " - pdb=" SG CYS H 194 " distance=2.02 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 134 " - pdb=" SG CYS I 194 " distance=2.02 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.03 Simple disulfide: pdb=" SG CYS K 152 " - pdb=" SG CYS K 208 " distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.02 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 96 " distance=2.03 Simple disulfide: pdb=" SG CYS O 152 " - pdb=" SG CYS O 208 " distance=2.02 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 96 " distance=2.03 Simple disulfide: pdb=" SG CYS P 152 " - pdb=" SG CYS P 208 " distance=2.02 Simple disulfide: pdb=" SG CYS Q 23 " - pdb=" SG CYS Q 88 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 134 " - pdb=" SG CYS Q 194 " distance=2.02 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 88 " distance=2.03 Simple disulfide: pdb=" SG CYS R 134 " - pdb=" SG CYS R 194 " distance=2.02 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: 13.93 Conformation dependent library (CDL) restraints added in 6.2 seconds 8976 Ramachandran restraints generated. 4488 Oldfield, 0 Emsley, 4488 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8280 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 72 sheets defined 21.9% alpha, 20.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.78 Creating SS restraints... Processing helix chain 'A' and resid 23 through 26 Processing helix chain 'A' and resid 27 through 34 Processing helix chain 'A' and resid 35 through 42 removed outlier: 3.721A pdb=" N GLU A 42 " --> pdb=" O GLU A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 90 removed outlier: 3.554A pdb=" N ASN A 90 " --> pdb=" O GLU A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 115 removed outlier: 4.286A pdb=" N GLY A 106 " --> pdb=" O SER A 102 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL A 114 " --> pdb=" O GLY A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 149 removed outlier: 3.890A pdb=" N LEU A 148 " --> pdb=" O PRO A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 153 Processing helix chain 'A' and resid 170 through 172 No H-bonds generated for 'chain 'A' and resid 170 through 172' Processing helix chain 'A' and resid 183 through 194 Processing helix chain 'A' and resid 200 through 207 Processing helix chain 'A' and resid 207 through 220 Processing helix chain 'A' and resid 253 through 268 Processing helix chain 'A' and resid 279 through 283 Processing helix chain 'A' and resid 285 through 304 removed outlier: 3.501A pdb=" N VAL A 289 " --> pdb=" O THR A 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 202 removed outlier: 3.816A pdb=" N GLY D 202 " --> pdb=" O SER D 199 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 83 removed outlier: 3.823A pdb=" N PHE E 83 " --> pdb=" O PRO E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 127 Processing helix chain 'E' and resid 183 through 188 Processing helix chain 'F' and resid 198 through 202 removed outlier: 3.816A pdb=" N GLY F 202 " --> pdb=" O SER F 199 " (cutoff:3.500A) Processing helix chain 'G' and resid 198 through 202 removed outlier: 3.817A pdb=" N GLY G 202 " --> pdb=" O SER G 199 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 83 removed outlier: 3.822A pdb=" N PHE H 83 " --> pdb=" O PRO H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 121 through 127 Processing helix chain 'H' and resid 183 through 188 Processing helix chain 'I' and resid 79 through 83 removed outlier: 3.822A pdb=" N PHE I 83 " --> pdb=" O PRO I 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 121 through 127 Processing helix chain 'I' and resid 183 through 188 Processing helix chain 'K' and resid 198 through 202 removed outlier: 3.816A pdb=" N GLY K 202 " --> pdb=" O SER K 199 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.822A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 121 through 127 Processing helix chain 'L' and resid 183 through 188 Processing helix chain 'O' and resid 198 through 202 removed outlier: 3.816A pdb=" N GLY O 202 " --> pdb=" O SER O 199 " (cutoff:3.500A) Processing helix chain 'P' and resid 198 through 202 removed outlier: 3.816A pdb=" N GLY P 202 " --> pdb=" O SER P 199 " (cutoff:3.500A) Processing helix chain 'Q' and resid 79 through 83 removed outlier: 3.822A pdb=" N PHE Q 83 " --> pdb=" O PRO Q 80 " (cutoff:3.500A) Processing helix chain 'Q' and resid 121 through 127 Processing helix chain 'Q' and resid 183 through 188 Processing helix chain 'R' and resid 79 through 83 removed outlier: 3.822A pdb=" N PHE R 83 " --> pdb=" O PRO R 80 " (cutoff:3.500A) Processing helix chain 'R' and resid 121 through 127 Processing helix chain 'R' and resid 183 through 188 Processing helix chain 'B' and resid 23 through 26 Processing helix chain 'B' and resid 27 through 34 Processing helix chain 'B' and resid 35 through 42 removed outlier: 3.721A pdb=" N GLU B 42 " --> pdb=" O GLU B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 90 removed outlier: 3.554A pdb=" N ASN B 90 " --> pdb=" O GLU B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 115 removed outlier: 4.286A pdb=" N GLY B 106 " --> pdb=" O SER B 102 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL B 114 " --> pdb=" O GLY B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 149 removed outlier: 3.890A pdb=" N LEU B 148 " --> pdb=" O PRO B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 153 Processing helix chain 'B' and resid 170 through 172 No H-bonds generated for 'chain 'B' and resid 170 through 172' Processing helix chain 'B' and resid 183 through 194 Processing helix chain 'B' and resid 200 through 207 Processing helix chain 'B' and resid 207 through 220 Processing helix chain 'B' and resid 253 through 268 Processing helix chain 'B' and resid 279 through 283 Processing helix chain 'B' and resid 285 through 304 removed outlier: 3.501A pdb=" N VAL B 289 " --> pdb=" O THR B 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 26 Processing helix chain 'C' and resid 27 through 34 Processing helix chain 'C' and resid 35 through 42 removed outlier: 3.721A pdb=" N GLU C 42 " --> pdb=" O GLU C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 90 removed outlier: 3.554A pdb=" N ASN C 90 " --> pdb=" O GLU C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 115 removed outlier: 4.286A pdb=" N GLY C 106 " --> pdb=" O SER C 102 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL C 114 " --> pdb=" O GLY C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 149 removed outlier: 3.890A pdb=" N LEU C 148 " --> pdb=" O PRO C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 153 Processing helix chain 'C' and resid 170 through 172 No H-bonds generated for 'chain 'C' and resid 170 through 172' Processing helix chain 'C' and resid 183 through 194 Processing helix chain 'C' and resid 200 through 207 Processing helix chain 'C' and resid 207 through 220 Processing helix chain 'C' and resid 253 through 268 Processing helix chain 'C' and resid 279 through 283 Processing helix chain 'C' and resid 285 through 304 removed outlier: 3.501A pdb=" N VAL C 289 " --> pdb=" O THR C 285 " (cutoff:3.500A) Processing helix chain 'J' and resid 23 through 26 Processing helix chain 'J' and resid 27 through 34 Processing helix chain 'J' and resid 35 through 42 removed outlier: 3.720A pdb=" N GLU J 42 " --> pdb=" O GLU J 38 " (cutoff:3.500A) Processing helix chain 'J' and resid 70 through 90 removed outlier: 3.555A pdb=" N ASN J 90 " --> pdb=" O GLU J 86 " (cutoff:3.500A) Processing helix chain 'J' and resid 102 through 115 removed outlier: 4.286A pdb=" N GLY J 106 " --> pdb=" O SER J 102 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL J 114 " --> pdb=" O GLY J 110 " (cutoff:3.500A) Processing helix chain 'J' and resid 144 through 149 removed outlier: 3.890A pdb=" N LEU J 148 " --> pdb=" O PRO J 144 " (cutoff:3.500A) Processing helix chain 'J' and resid 150 through 153 Processing helix chain 'J' and resid 170 through 172 No H-bonds generated for 'chain 'J' and resid 170 through 172' Processing helix chain 'J' and resid 183 through 194 Processing helix chain 'J' and resid 200 through 207 Processing helix chain 'J' and resid 207 through 220 Processing helix chain 'J' and resid 253 through 268 Processing helix chain 'J' and resid 279 through 283 Processing helix chain 'J' and resid 285 through 304 removed outlier: 3.501A pdb=" N VAL J 289 " --> pdb=" O THR J 285 " (cutoff:3.500A) Processing helix chain 'M' and resid 23 through 26 Processing helix chain 'M' and resid 27 through 34 Processing helix chain 'M' and resid 35 through 42 removed outlier: 3.721A pdb=" N GLU M 42 " --> pdb=" O GLU M 38 " (cutoff:3.500A) Processing helix chain 'M' and resid 70 through 90 removed outlier: 3.554A pdb=" N ASN M 90 " --> pdb=" O GLU M 86 " (cutoff:3.500A) Processing helix chain 'M' and resid 102 through 115 removed outlier: 4.286A pdb=" N GLY M 106 " --> pdb=" O SER M 102 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL M 114 " --> pdb=" O GLY M 110 " (cutoff:3.500A) Processing helix chain 'M' and resid 144 through 149 removed outlier: 3.891A pdb=" N LEU M 148 " --> pdb=" O PRO M 144 " (cutoff:3.500A) Processing helix chain 'M' and resid 150 through 153 Processing helix chain 'M' and resid 170 through 172 No H-bonds generated for 'chain 'M' and resid 170 through 172' Processing helix chain 'M' and resid 183 through 194 Processing helix chain 'M' and resid 200 through 207 Processing helix chain 'M' and resid 207 through 220 Processing helix chain 'M' and resid 253 through 268 Processing helix chain 'M' and resid 279 through 283 Processing helix chain 'M' and resid 285 through 304 removed outlier: 3.501A pdb=" N VAL M 289 " --> pdb=" O THR M 285 " (cutoff:3.500A) Processing helix chain 'N' and resid 23 through 26 Processing helix chain 'N' and resid 27 through 34 Processing helix chain 'N' and resid 35 through 42 removed outlier: 3.721A pdb=" N GLU N 42 " --> pdb=" O GLU N 38 " (cutoff:3.500A) Processing helix chain 'N' and resid 70 through 90 removed outlier: 3.554A pdb=" N ASN N 90 " --> pdb=" O GLU N 86 " (cutoff:3.500A) Processing helix chain 'N' and resid 102 through 115 removed outlier: 4.286A pdb=" N GLY N 106 " --> pdb=" O SER N 102 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL N 114 " --> pdb=" O GLY N 110 " (cutoff:3.500A) Processing helix chain 'N' and resid 144 through 149 removed outlier: 3.890A pdb=" N LEU N 148 " --> pdb=" O PRO N 144 " (cutoff:3.500A) Processing helix chain 'N' and resid 150 through 153 Processing helix chain 'N' and resid 170 through 172 No H-bonds generated for 'chain 'N' and resid 170 through 172' Processing helix chain 'N' and resid 183 through 194 Processing helix chain 'N' and resid 200 through 207 Processing helix chain 'N' and resid 207 through 220 Processing helix chain 'N' and resid 253 through 268 Processing helix chain 'N' and resid 279 through 283 Processing helix chain 'N' and resid 285 through 304 removed outlier: 3.502A pdb=" N VAL N 289 " --> pdb=" O THR N 285 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 46 through 52 removed outlier: 6.356A pdb=" N GLY A 12 " --> pdb=" O TYR A 50 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ASP A 52 " --> pdb=" O GLY A 12 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N THR A 7 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LEU A 95 " --> pdb=" O THR A 7 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N GLY A 9 " --> pdb=" O LEU A 95 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N LEU A 97 " --> pdb=" O GLY A 9 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILE A 11 " --> pdb=" O LEU A 97 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER A 94 " --> pdb=" O SER A 271 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ILE A 227 " --> pdb=" O SER A 271 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N LEU A 273 " --> pdb=" O ILE A 227 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N LEU A 229 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N ILE A 275 " --> pdb=" O LEU A 229 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N PHE A 231 " --> pdb=" O ILE A 275 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N GLY A 119 " --> pdb=" O HIS A 228 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N SER A 230 " --> pdb=" O GLY A 119 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N ILE A 121 " --> pdb=" O SER A 230 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ASP A 232 " --> pdb=" O ILE A 121 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N VAL A 123 " --> pdb=" O ASP A 232 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N VAL A 120 " --> pdb=" O VAL A 175 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N ILE A 177 " --> pdb=" O VAL A 120 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N TRP A 122 " --> pdb=" O ILE A 177 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N LEU A 179 " --> pdb=" O TRP A 122 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AA3, first strand: chain 'D' and resid 45 through 50 removed outlier: 6.479A pdb=" N TRP D 36 " --> pdb=" O MET D 48 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N SER D 50 " --> pdb=" O ILE D 34 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ILE D 34 " --> pdb=" O SER D 50 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL D 121 " --> pdb=" O ALA D 92 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 69 through 72 removed outlier: 3.782A pdb=" N THR D 69 " --> pdb=" O GLU D 82 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 150 through 151 removed outlier: 6.744A pdb=" N SER D 189 " --> pdb=" O ASP D 156 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ASP D 156 " --> pdb=" O SER D 189 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 150 through 151 removed outlier: 5.160A pdb=" N SER D 192 " --> pdb=" O PRO D 179 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N VAL D 194 " --> pdb=" O THR D 177 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N THR D 177 " --> pdb=" O VAL D 194 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 209 through 212 Processing sheet with id=AA8, first strand: chain 'E' and resid 4 through 6 Processing sheet with id=AA9, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.456A pdb=" N LEU E 11 " --> pdb=" O GLU E 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'E' and resid 46 through 48 removed outlier: 6.301A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 117 through 118 removed outlier: 3.509A pdb=" N SER E 177 " --> pdb=" O CYS E 134 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 154 through 155 removed outlier: 3.724A pdb=" N TRP E 148 " --> pdb=" O GLN E 155 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AB5, first strand: chain 'F' and resid 45 through 50 removed outlier: 6.480A pdb=" N TRP F 36 " --> pdb=" O MET F 48 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N SER F 50 " --> pdb=" O ILE F 34 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ILE F 34 " --> pdb=" O SER F 50 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL F 121 " --> pdb=" O ALA F 92 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 69 through 72 removed outlier: 3.781A pdb=" N THR F 69 " --> pdb=" O GLU F 82 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 150 through 151 removed outlier: 6.744A pdb=" N SER F 189 " --> pdb=" O ASP F 156 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ASP F 156 " --> pdb=" O SER F 189 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 150 through 151 removed outlier: 5.161A pdb=" N SER F 192 " --> pdb=" O PRO F 179 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N VAL F 194 " --> pdb=" O THR F 177 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N THR F 177 " --> pdb=" O VAL F 194 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 209 through 212 Processing sheet with id=AC1, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AC2, first strand: chain 'G' and resid 45 through 50 removed outlier: 6.480A pdb=" N TRP G 36 " --> pdb=" O MET G 48 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N SER G 50 " --> pdb=" O ILE G 34 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ILE G 34 " --> pdb=" O SER G 50 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL G 121 " --> pdb=" O ALA G 92 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 69 through 72 removed outlier: 3.782A pdb=" N THR G 69 " --> pdb=" O GLU G 82 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 150 through 151 removed outlier: 6.744A pdb=" N SER G 189 " --> pdb=" O ASP G 156 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ASP G 156 " --> pdb=" O SER G 189 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 150 through 151 removed outlier: 5.161A pdb=" N SER G 192 " --> pdb=" O PRO G 179 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N VAL G 194 " --> pdb=" O THR G 177 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N THR G 177 " --> pdb=" O VAL G 194 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 209 through 212 Processing sheet with id=AC7, first strand: chain 'H' and resid 4 through 6 Processing sheet with id=AC8, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.456A pdb=" N LEU H 11 " --> pdb=" O GLU H 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'H' and resid 46 through 48 removed outlier: 6.301A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 117 through 118 removed outlier: 3.509A pdb=" N SER H 177 " --> pdb=" O CYS H 134 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 154 through 155 removed outlier: 3.724A pdb=" N TRP H 148 " --> pdb=" O GLN H 155 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 4 through 6 Processing sheet with id=AD4, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.457A pdb=" N LEU I 11 " --> pdb=" O GLU I 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'I' and resid 46 through 48 removed outlier: 6.299A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 117 through 118 removed outlier: 3.509A pdb=" N SER I 177 " --> pdb=" O CYS I 134 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 154 through 155 removed outlier: 3.724A pdb=" N TRP I 148 " --> pdb=" O GLN I 155 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'K' and resid 3 through 7 Processing sheet with id=AD9, first strand: chain 'K' and resid 45 through 50 removed outlier: 6.479A pdb=" N TRP K 36 " --> pdb=" O MET K 48 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N SER K 50 " --> pdb=" O ILE K 34 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ILE K 34 " --> pdb=" O SER K 50 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL K 121 " --> pdb=" O ALA K 92 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'K' and resid 69 through 72 removed outlier: 3.782A pdb=" N THR K 69 " --> pdb=" O GLU K 82 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'K' and resid 150 through 151 removed outlier: 6.744A pdb=" N SER K 189 " --> pdb=" O ASP K 156 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ASP K 156 " --> pdb=" O SER K 189 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'K' and resid 150 through 151 removed outlier: 5.160A pdb=" N SER K 192 " --> pdb=" O PRO K 179 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N VAL K 194 " --> pdb=" O THR K 177 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N THR K 177 " --> pdb=" O VAL K 194 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'K' and resid 209 through 212 Processing sheet with id=AE5, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AE6, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.456A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'L' and resid 46 through 48 removed outlier: 6.300A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'L' and resid 117 through 118 removed outlier: 3.509A pdb=" N SER L 177 " --> pdb=" O CYS L 134 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'L' and resid 154 through 155 removed outlier: 3.724A pdb=" N TRP L 148 " --> pdb=" O GLN L 155 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'O' and resid 3 through 7 Processing sheet with id=AF2, first strand: chain 'O' and resid 45 through 50 removed outlier: 6.480A pdb=" N TRP O 36 " --> pdb=" O MET O 48 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N SER O 50 " --> pdb=" O ILE O 34 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ILE O 34 " --> pdb=" O SER O 50 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL O 121 " --> pdb=" O ALA O 92 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'O' and resid 69 through 72 removed outlier: 3.782A pdb=" N THR O 69 " --> pdb=" O GLU O 82 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'O' and resid 150 through 151 removed outlier: 6.744A pdb=" N SER O 189 " --> pdb=" O ASP O 156 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASP O 156 " --> pdb=" O SER O 189 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'O' and resid 150 through 151 removed outlier: 5.161A pdb=" N SER O 192 " --> pdb=" O PRO O 179 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N VAL O 194 " --> pdb=" O THR O 177 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N THR O 177 " --> pdb=" O VAL O 194 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'O' and resid 209 through 212 Processing sheet with id=AF7, first strand: chain 'P' and resid 3 through 7 Processing sheet with id=AF8, first strand: chain 'P' and resid 45 through 50 removed outlier: 6.480A pdb=" N TRP P 36 " --> pdb=" O MET P 48 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N SER P 50 " --> pdb=" O ILE P 34 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ILE P 34 " --> pdb=" O SER P 50 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL P 121 " --> pdb=" O ALA P 92 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'P' and resid 69 through 72 removed outlier: 3.781A pdb=" N THR P 69 " --> pdb=" O GLU P 82 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'P' and resid 150 through 151 removed outlier: 6.744A pdb=" N SER P 189 " --> pdb=" O ASP P 156 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASP P 156 " --> pdb=" O SER P 189 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'P' and resid 150 through 151 removed outlier: 5.161A pdb=" N SER P 192 " --> pdb=" O PRO P 179 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N VAL P 194 " --> pdb=" O THR P 177 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N THR P 177 " --> pdb=" O VAL P 194 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'P' and resid 209 through 212 Processing sheet with id=AG4, first strand: chain 'Q' and resid 4 through 6 Processing sheet with id=AG5, first strand: chain 'Q' and resid 10 through 12 removed outlier: 6.456A pdb=" N LEU Q 11 " --> pdb=" O GLU Q 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG5 Processing sheet with id=AG6, first strand: chain 'Q' and resid 46 through 48 removed outlier: 6.300A pdb=" N TRP Q 35 " --> pdb=" O LEU Q 47 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'Q' and resid 117 through 118 removed outlier: 3.509A pdb=" N SER Q 177 " --> pdb=" O CYS Q 134 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'Q' and resid 154 through 155 removed outlier: 3.724A pdb=" N TRP Q 148 " --> pdb=" O GLN Q 155 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'R' and resid 4 through 6 Processing sheet with id=AH1, first strand: chain 'R' and resid 10 through 12 removed outlier: 6.456A pdb=" N LEU R 11 " --> pdb=" O GLU R 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH1 Processing sheet with id=AH2, first strand: chain 'R' and resid 46 through 48 removed outlier: 6.300A pdb=" N TRP R 35 " --> pdb=" O LEU R 47 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'R' and resid 117 through 118 removed outlier: 3.509A pdb=" N SER R 177 " --> pdb=" O CYS R 134 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'R' and resid 154 through 155 removed outlier: 3.723A pdb=" N TRP R 148 " --> pdb=" O GLN R 155 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'B' and resid 46 through 52 removed outlier: 6.357A pdb=" N GLY B 12 " --> pdb=" O TYR B 50 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ASP B 52 " --> pdb=" O GLY B 12 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N THR B 7 " --> pdb=" O ILE B 93 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LEU B 95 " --> pdb=" O THR B 7 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N GLY B 9 " --> pdb=" O LEU B 95 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N LEU B 97 " --> pdb=" O GLY B 9 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ILE B 11 " --> pdb=" O LEU B 97 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER B 94 " --> pdb=" O SER B 271 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ILE B 227 " --> pdb=" O SER B 271 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N LEU B 273 " --> pdb=" O ILE B 227 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N LEU B 229 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N ILE B 275 " --> pdb=" O LEU B 229 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N PHE B 231 " --> pdb=" O ILE B 275 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N GLY B 119 " --> pdb=" O HIS B 228 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N SER B 230 " --> pdb=" O GLY B 119 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N ILE B 121 " --> pdb=" O SER B 230 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ASP B 232 " --> pdb=" O ILE B 121 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N VAL B 123 " --> pdb=" O ASP B 232 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N VAL B 120 " --> pdb=" O VAL B 175 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N ILE B 177 " --> pdb=" O VAL B 120 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N TRP B 122 " --> pdb=" O ILE B 177 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N LEU B 179 " --> pdb=" O TRP B 122 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'C' and resid 46 through 52 removed outlier: 6.356A pdb=" N GLY C 12 " --> pdb=" O TYR C 50 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ASP C 52 " --> pdb=" O GLY C 12 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N THR C 7 " --> pdb=" O ILE C 93 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU C 95 " --> pdb=" O THR C 7 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N GLY C 9 " --> pdb=" O LEU C 95 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N LEU C 97 " --> pdb=" O GLY C 9 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILE C 11 " --> pdb=" O LEU C 97 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER C 94 " --> pdb=" O SER C 271 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ILE C 227 " --> pdb=" O SER C 271 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N LEU C 273 " --> pdb=" O ILE C 227 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N LEU C 229 " --> pdb=" O LEU C 273 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N ILE C 275 " --> pdb=" O LEU C 229 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N PHE C 231 " --> pdb=" O ILE C 275 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N GLY C 119 " --> pdb=" O HIS C 228 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N SER C 230 " --> pdb=" O GLY C 119 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N ILE C 121 " --> pdb=" O SER C 230 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ASP C 232 " --> pdb=" O ILE C 121 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N VAL C 123 " --> pdb=" O ASP C 232 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL C 120 " --> pdb=" O VAL C 175 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N ILE C 177 " --> pdb=" O VAL C 120 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N TRP C 122 " --> pdb=" O ILE C 177 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N LEU C 179 " --> pdb=" O TRP C 122 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'J' and resid 46 through 52 removed outlier: 6.357A pdb=" N GLY J 12 " --> pdb=" O TYR J 50 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ASP J 52 " --> pdb=" O GLY J 12 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N THR J 7 " --> pdb=" O ILE J 93 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU J 95 " --> pdb=" O THR J 7 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N GLY J 9 " --> pdb=" O LEU J 95 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N LEU J 97 " --> pdb=" O GLY J 9 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ILE J 11 " --> pdb=" O LEU J 97 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER J 94 " --> pdb=" O SER J 271 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ILE J 227 " --> pdb=" O SER J 271 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N LEU J 273 " --> pdb=" O ILE J 227 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N LEU J 229 " --> pdb=" O LEU J 273 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N ILE J 275 " --> pdb=" O LEU J 229 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N PHE J 231 " --> pdb=" O ILE J 275 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N GLY J 119 " --> pdb=" O HIS J 228 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N SER J 230 " --> pdb=" O GLY J 119 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N ILE J 121 " --> pdb=" O SER J 230 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ASP J 232 " --> pdb=" O ILE J 121 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N VAL J 123 " --> pdb=" O ASP J 232 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N VAL J 120 " --> pdb=" O VAL J 175 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N ILE J 177 " --> pdb=" O VAL J 120 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N TRP J 122 " --> pdb=" O ILE J 177 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N LEU J 179 " --> pdb=" O TRP J 122 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'M' and resid 46 through 52 removed outlier: 6.357A pdb=" N GLY M 12 " --> pdb=" O TYR M 50 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ASP M 52 " --> pdb=" O GLY M 12 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N THR M 7 " --> pdb=" O ILE M 93 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LEU M 95 " --> pdb=" O THR M 7 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N GLY M 9 " --> pdb=" O LEU M 95 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N LEU M 97 " --> pdb=" O GLY M 9 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILE M 11 " --> pdb=" O LEU M 97 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER M 94 " --> pdb=" O SER M 271 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ILE M 227 " --> pdb=" O SER M 271 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N LEU M 273 " --> pdb=" O ILE M 227 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N LEU M 229 " --> pdb=" O LEU M 273 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N ILE M 275 " --> pdb=" O LEU M 229 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N PHE M 231 " --> pdb=" O ILE M 275 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N GLY M 119 " --> pdb=" O HIS M 228 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N SER M 230 " --> pdb=" O GLY M 119 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N ILE M 121 " --> pdb=" O SER M 230 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ASP M 232 " --> pdb=" O ILE M 121 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N VAL M 123 " --> pdb=" O ASP M 232 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N VAL M 120 " --> pdb=" O VAL M 175 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N ILE M 177 " --> pdb=" O VAL M 120 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N TRP M 122 " --> pdb=" O ILE M 177 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N LEU M 179 " --> pdb=" O TRP M 122 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'N' and resid 46 through 52 removed outlier: 6.356A pdb=" N GLY N 12 " --> pdb=" O TYR N 50 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ASP N 52 " --> pdb=" O GLY N 12 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N THR N 7 " --> pdb=" O ILE N 93 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU N 95 " --> pdb=" O THR N 7 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N GLY N 9 " --> pdb=" O LEU N 95 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N LEU N 97 " --> pdb=" O GLY N 9 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILE N 11 " --> pdb=" O LEU N 97 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER N 94 " --> pdb=" O SER N 271 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ILE N 227 " --> pdb=" O SER N 271 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N LEU N 273 " --> pdb=" O ILE N 227 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N LEU N 229 " --> pdb=" O LEU N 273 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N ILE N 275 " --> pdb=" O LEU N 229 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N PHE N 231 " --> pdb=" O ILE N 275 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N GLY N 119 " --> pdb=" O HIS N 228 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N SER N 230 " --> pdb=" O GLY N 119 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N ILE N 121 " --> pdb=" O SER N 230 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ASP N 232 " --> pdb=" O ILE N 121 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N VAL N 123 " --> pdb=" O ASP N 232 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL N 120 " --> pdb=" O VAL N 175 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N ILE N 177 " --> pdb=" O VAL N 120 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N TRP N 122 " --> pdb=" O ILE N 177 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N LEU N 179 " --> pdb=" O TRP N 122 " (cutoff:3.500A) 1002 hydrogen bonds defined for protein. 2718 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: 12.43 Time building geometry restraints manager: 14.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 11050 1.34 - 1.46: 7306 1.46 - 1.58: 16756 1.58 - 1.69: 0 1.69 - 1.81: 162 Bond restraints: 35274 Sorted by residual: bond pdb=" C LYS G 13 " pdb=" N PRO G 14 " ideal model delta sigma weight residual 1.334 1.390 -0.056 2.34e-02 1.83e+03 5.66e+00 bond pdb=" C LYS P 13 " pdb=" N PRO P 14 " ideal model delta sigma weight residual 1.334 1.389 -0.055 2.34e-02 1.83e+03 5.60e+00 bond pdb=" C LYS D 13 " pdb=" N PRO D 14 " ideal model delta sigma weight residual 1.334 1.389 -0.055 2.34e-02 1.83e+03 5.54e+00 bond pdb=" C LYS F 13 " pdb=" N PRO F 14 " ideal model delta sigma weight residual 1.334 1.389 -0.055 2.34e-02 1.83e+03 5.52e+00 bond pdb=" C LYS K 13 " pdb=" N PRO K 14 " ideal model delta sigma weight residual 1.334 1.389 -0.055 2.34e-02 1.83e+03 5.48e+00 ... (remaining 35269 not shown) Histogram of bond angle deviations from ideal: 99.70 - 106.57: 1380 106.57 - 113.43: 19720 113.43 - 120.29: 12134 120.29 - 127.16: 14260 127.16 - 134.02: 446 Bond angle restraints: 47940 Sorted by residual: angle pdb=" C PHE P 112 " pdb=" N ASP P 113 " pdb=" CA ASP P 113 " ideal model delta sigma weight residual 123.21 113.64 9.57 1.19e+00 7.06e-01 6.47e+01 angle pdb=" C PHE G 112 " pdb=" N ASP G 113 " pdb=" CA ASP G 113 " ideal model delta sigma weight residual 123.21 113.65 9.56 1.19e+00 7.06e-01 6.45e+01 angle pdb=" C PHE O 112 " pdb=" N ASP O 113 " pdb=" CA ASP O 113 " ideal model delta sigma weight residual 123.21 113.68 9.53 1.19e+00 7.06e-01 6.42e+01 angle pdb=" C PHE K 112 " pdb=" N ASP K 113 " pdb=" CA ASP K 113 " ideal model delta sigma weight residual 123.21 113.68 9.53 1.19e+00 7.06e-01 6.41e+01 angle pdb=" C PHE F 112 " pdb=" N ASP F 113 " pdb=" CA ASP F 113 " ideal model delta sigma weight residual 123.21 113.71 9.50 1.19e+00 7.06e-01 6.37e+01 ... (remaining 47935 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.91: 19332 11.91 - 23.83: 1392 23.83 - 35.74: 354 35.74 - 47.65: 90 47.65 - 59.57: 12 Dihedral angle restraints: 21180 sinusoidal: 8190 harmonic: 12990 Sorted by residual: dihedral pdb=" CA PRO P 114 " pdb=" C PRO P 114 " pdb=" N TRP P 115 " pdb=" CA TRP P 115 " ideal model delta harmonic sigma weight residual 180.00 -134.66 -45.34 0 5.00e+00 4.00e-02 8.22e+01 dihedral pdb=" CA PRO F 114 " pdb=" C PRO F 114 " pdb=" N TRP F 115 " pdb=" CA TRP F 115 " ideal model delta harmonic sigma weight residual 180.00 -134.68 -45.32 0 5.00e+00 4.00e-02 8.22e+01 dihedral pdb=" CA PRO D 114 " pdb=" C PRO D 114 " pdb=" N TRP D 115 " pdb=" CA TRP D 115 " ideal model delta harmonic sigma weight residual 180.00 -134.69 -45.31 0 5.00e+00 4.00e-02 8.21e+01 ... (remaining 21177 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 3940 0.053 - 0.105: 1116 0.105 - 0.158: 314 0.158 - 0.211: 78 0.211 - 0.263: 6 Chirality restraints: 5454 Sorted by residual: chirality pdb=" CB ILE L 48 " pdb=" CA ILE L 48 " pdb=" CG1 ILE L 48 " pdb=" CG2 ILE L 48 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CB ILE Q 48 " pdb=" CA ILE Q 48 " pdb=" CG1 ILE Q 48 " pdb=" CG2 ILE Q 48 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" CB ILE I 48 " pdb=" CA ILE I 48 " pdb=" CG1 ILE I 48 " pdb=" CG2 ILE I 48 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.71e+00 ... (remaining 5451 not shown) Planarity restraints: 6144 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS D 13 " 0.068 5.00e-02 4.00e+02 1.04e-01 1.74e+01 pdb=" N PRO D 14 " -0.180 5.00e-02 4.00e+02 pdb=" CA PRO D 14 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO D 14 " 0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS G 13 " -0.068 5.00e-02 4.00e+02 1.04e-01 1.74e+01 pdb=" N PRO G 14 " 0.180 5.00e-02 4.00e+02 pdb=" CA PRO G 14 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO G 14 " -0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS K 13 " 0.068 5.00e-02 4.00e+02 1.04e-01 1.74e+01 pdb=" N PRO K 14 " -0.180 5.00e-02 4.00e+02 pdb=" CA PRO K 14 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO K 14 " 0.058 5.00e-02 4.00e+02 ... (remaining 6141 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.25: 54 2.25 - 2.92: 14748 2.92 - 3.58: 52644 3.58 - 4.24: 90343 4.24 - 4.90: 144355 Nonbonded interactions: 302144 Sorted by model distance: nonbonded pdb=" ND1 HIS M 126 " pdb="MN MN M1002 " model vdw 1.592 2.400 nonbonded pdb=" ND1 HIS J 126 " pdb="MN MN J1002 " model vdw 1.592 2.400 nonbonded pdb=" ND1 HIS C 126 " pdb="MN MN C1002 " model vdw 1.592 2.400 nonbonded pdb=" ND1 HIS A 126 " pdb="MN MN A1002 " model vdw 1.593 2.400 nonbonded pdb=" ND1 HIS B 126 " pdb="MN MN B1002 " model vdw 1.593 2.400 ... (remaining 302139 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'J' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'G' selection = chain 'K' selection = chain 'O' selection = chain 'P' } ncs_group { reference = chain 'E' selection = chain 'H' selection = chain 'I' selection = chain 'L' selection = chain 'Q' selection = chain 'R' } 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 group one per residue 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: 1.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 8.840 Check model and map are aligned: 0.490 Set scattering table: 0.310 Process input model: 88.000 Find NCS groups from input model: 2.370 Set up NCS constraints: 0.300 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 105.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6618 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 : 0.006 0.066 35274 Z= 0.426 Angle : 1.073 13.848 47940 Z= 0.582 Chirality : 0.055 0.263 5454 Planarity : 0.009 0.104 6144 Dihedral : 9.387 59.568 12828 Min Nonbonded Distance : 1.592 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.40 % Allowed : 12.88 % Favored : 86.72 % Rotamer: Outliers : 0.16 % Allowed : 2.51 % Favored : 97.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.57 % Twisted Proline : 2.17 % Twisted General : 1.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.16 (0.11), residues: 4488 helix: -1.83 (0.14), residues: 792 sheet: -3.35 (0.12), residues: 1302 loop : -2.73 (0.12), residues: 2394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.004 TRP P 47 HIS 0.018 0.004 HIS E 91 PHE 0.048 0.004 PHE O 178 TYR 0.032 0.003 TYR R 49 ARG 0.007 0.001 ARG C 180 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8976 Ramachandran restraints generated. 4488 Oldfield, 0 Emsley, 4488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8976 Ramachandran restraints generated. 4488 Oldfield, 0 Emsley, 4488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 686 residues out of total 3858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 680 time to evaluate : 4.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 ASP cc_start: 0.6879 (p0) cc_final: 0.6349 (p0) REVERT: A 127 THR cc_start: 0.8662 (p) cc_final: 0.7985 (p) REVERT: A 176 TYR cc_start: 0.7851 (m-80) cc_final: 0.7379 (m-80) REVERT: A 254 TYR cc_start: 0.9080 (t80) cc_final: 0.8613 (t80) REVERT: A 274 ASP cc_start: 0.6846 (m-30) cc_final: 0.6299 (t0) REVERT: A 277 GLU cc_start: 0.8368 (mm-30) cc_final: 0.7090 (mt-10) REVERT: A 279 ASN cc_start: 0.8416 (t0) cc_final: 0.8171 (t0) REVERT: F 206 TYR cc_start: 0.6688 (m-80) cc_final: 0.6465 (m-80) REVERT: G 21 SER cc_start: 0.8358 (m) cc_final: 0.8136 (p) REVERT: G 145 GLU cc_start: 0.6642 (mt-10) cc_final: 0.6252 (tm-30) REVERT: K 45 LEU cc_start: 0.3893 (mp) cc_final: 0.2745 (mp) REVERT: K 90 ASP cc_start: 0.6628 (m-30) cc_final: 0.5915 (m-30) REVERT: K 211 ASP cc_start: 0.8327 (m-30) cc_final: 0.7932 (t0) REVERT: L 35 TRP cc_start: 0.7849 (m100) cc_final: 0.7002 (m100) REVERT: L 47 LEU cc_start: 0.8993 (mt) cc_final: 0.8724 (mt) REVERT: O 37 VAL cc_start: 0.9206 (OUTLIER) cc_final: 0.8854 (p) REVERT: O 90 ASP cc_start: 0.5867 (m-30) cc_final: 0.5173 (m-30) REVERT: O 121 VAL cc_start: 0.7523 (t) cc_final: 0.6347 (t) REVERT: O 211 ASP cc_start: 0.8170 (m-30) cc_final: 0.7679 (t0) REVERT: P 36 TRP cc_start: 0.7766 (m100) cc_final: 0.6846 (m100) REVERT: P 89 ASP cc_start: 0.7538 (p0) cc_final: 0.7274 (p0) REVERT: P 112 PHE cc_start: 0.6773 (m-80) cc_final: 0.6298 (m-80) REVERT: P 211 ASP cc_start: 0.8740 (m-30) cc_final: 0.8485 (t0) REVERT: Q 32 TYR cc_start: 0.6993 (m-10) cc_final: 0.5976 (m-80) REVERT: Q 35 TRP cc_start: 0.7582 (m100) cc_final: 0.6040 (m100) REVERT: Q 36 TYR cc_start: 0.7770 (m-80) cc_final: 0.6413 (m-80) REVERT: Q 48 ILE cc_start: 0.8527 (mt) cc_final: 0.8322 (tp) REVERT: Q 87 TYR cc_start: 0.9052 (m-80) cc_final: 0.8679 (m-80) REVERT: R 32 TYR cc_start: 0.7276 (m-10) cc_final: 0.6845 (m-80) REVERT: R 35 TRP cc_start: 0.7574 (m100) cc_final: 0.6502 (m100) REVERT: R 36 TYR cc_start: 0.7954 (m-80) cc_final: 0.7652 (m-80) REVERT: R 47 LEU cc_start: 0.8771 (mt) cc_final: 0.8275 (mt) REVERT: B 100 ASP cc_start: 0.6464 (p0) cc_final: 0.5962 (p0) REVERT: B 127 THR cc_start: 0.8719 (p) cc_final: 0.7948 (p) REVERT: B 176 TYR cc_start: 0.7795 (m-80) cc_final: 0.7198 (m-80) REVERT: B 200 MET cc_start: 0.7900 (mmm) cc_final: 0.7660 (mmt) REVERT: B 274 ASP cc_start: 0.7120 (m-30) cc_final: 0.6583 (t0) REVERT: B 277 GLU cc_start: 0.8672 (mm-30) cc_final: 0.7183 (mt-10) REVERT: B 279 ASN cc_start: 0.8627 (t0) cc_final: 0.8307 (t0) REVERT: C 50 TYR cc_start: 0.7724 (m-80) cc_final: 0.7373 (m-10) REVERT: C 103 LEU cc_start: 0.9096 (mt) cc_final: 0.8847 (mt) REVERT: C 200 MET cc_start: 0.7802 (mmm) cc_final: 0.7037 (tpp) REVERT: C 277 GLU cc_start: 0.8444 (mm-30) cc_final: 0.7173 (mt-10) REVERT: C 279 ASN cc_start: 0.8277 (t0) cc_final: 0.7917 (t0) REVERT: J 108 ILE cc_start: 0.7597 (mt) cc_final: 0.7249 (mt) REVERT: N 108 ILE cc_start: 0.7683 (mt) cc_final: 0.7264 (mt) outliers start: 6 outliers final: 0 residues processed: 684 average time/residue: 0.5253 time to fit residues: 552.3499 Evaluate side-chains 311 residues out of total 3858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 310 time to evaluate : 4.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 374 optimal weight: 3.9990 chunk 336 optimal weight: 0.7980 chunk 186 optimal weight: 7.9990 chunk 114 optimal weight: 9.9990 chunk 227 optimal weight: 6.9990 chunk 179 optimal weight: 9.9990 chunk 348 optimal weight: 5.9990 chunk 134 optimal weight: 7.9990 chunk 211 optimal weight: 6.9990 chunk 259 optimal weight: 7.9990 chunk 403 optimal weight: 30.0000 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN A 319 ASN D 39 GLN ** D 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 38 GLN E 160 GLN F 39 GLN ** F 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 GLN ** G 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 38 GLN ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 183 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 160 GLN ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 183 GLN ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 183 GLN ** Q 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 ASN B 319 ASN ** C 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 126 HIS ** C 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 294 ASN C 319 ASN J 90 ASN J 319 ASN M 90 ASN M 319 ASN N 90 ASN N 319 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6792 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 35274 Z= 0.429 Angle : 0.835 9.794 47940 Z= 0.434 Chirality : 0.048 0.192 5454 Planarity : 0.007 0.094 6144 Dihedral : 7.397 39.014 4878 Min Nonbonded Distance : 1.330 Molprobity Statistics. All-atom Clashscore : 26.95 Ramachandran Plot: Outliers : 0.20 % Allowed : 11.32 % Favored : 88.48 % Rotamer: Outliers : 0.21 % Allowed : 2.46 % Favored : 97.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.57 % Twisted Proline : 2.17 % Twisted General : 0.50 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.43 (0.12), residues: 4488 helix: -0.64 (0.17), residues: 804 sheet: -2.98 (0.13), residues: 1308 loop : -2.42 (0.12), residues: 2376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP O 47 HIS 0.013 0.002 HIS L 91 PHE 0.034 0.003 PHE B 64 TYR 0.035 0.002 TYR K 102 ARG 0.010 0.001 ARG O 38 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8976 Ramachandran restraints generated. 4488 Oldfield, 0 Emsley, 4488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8976 Ramachandran restraints generated. 4488 Oldfield, 0 Emsley, 4488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 3858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 395 time to evaluate : 3.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 TYR cc_start: 0.8456 (m-80) cc_final: 0.7683 (m-80) REVERT: A 277 GLU cc_start: 0.8807 (mm-30) cc_final: 0.6817 (mt-10) REVERT: A 279 ASN cc_start: 0.8277 (t0) cc_final: 0.7852 (t0) REVERT: D 81 MET cc_start: 0.8776 (tmm) cc_final: 0.8440 (tmm) REVERT: D 206 TYR cc_start: 0.7381 (m-80) cc_final: 0.6938 (m-80) REVERT: E 49 TYR cc_start: 0.7165 (p90) cc_final: 0.6695 (p90) REVERT: E 70 ASP cc_start: 0.8317 (p0) cc_final: 0.7627 (p0) REVERT: F 81 MET cc_start: 0.8786 (tmm) cc_final: 0.8558 (tmm) REVERT: F 99 GLU cc_start: 0.7853 (pt0) cc_final: 0.7608 (pt0) REVERT: F 206 TYR cc_start: 0.7045 (m-80) cc_final: 0.6818 (m-80) REVERT: G 145 GLU cc_start: 0.6655 (mt-10) cc_final: 0.6204 (tm-30) REVERT: H 49 TYR cc_start: 0.7591 (OUTLIER) cc_final: 0.7288 (p90) REVERT: I 49 TYR cc_start: 0.7652 (OUTLIER) cc_final: 0.7310 (p90) REVERT: K 45 LEU cc_start: 0.3605 (mp) cc_final: 0.3172 (mp) REVERT: K 90 ASP cc_start: 0.5633 (m-30) cc_final: 0.5113 (m-30) REVERT: K 211 ASP cc_start: 0.8296 (m-30) cc_final: 0.7837 (t0) REVERT: L 35 TRP cc_start: 0.7701 (m100) cc_final: 0.6537 (m100) REVERT: O 45 LEU cc_start: 0.4569 (mp) cc_final: 0.4348 (mp) REVERT: O 89 ASP cc_start: 0.8733 (p0) cc_final: 0.8273 (p0) REVERT: O 90 ASP cc_start: 0.4912 (m-30) cc_final: 0.3538 (m-30) REVERT: O 112 PHE cc_start: 0.7189 (m-80) cc_final: 0.6839 (m-80) REVERT: O 211 ASP cc_start: 0.8384 (m-30) cc_final: 0.7887 (t0) REVERT: P 89 ASP cc_start: 0.7475 (p0) cc_final: 0.7098 (p0) REVERT: P 112 PHE cc_start: 0.6669 (m-80) cc_final: 0.6375 (m-80) REVERT: P 211 ASP cc_start: 0.8624 (m-30) cc_final: 0.8341 (t0) REVERT: Q 35 TRP cc_start: 0.6788 (m100) cc_final: 0.6168 (m100) REVERT: Q 36 TYR cc_start: 0.6704 (m-80) cc_final: 0.6492 (m-80) REVERT: Q 87 TYR cc_start: 0.9205 (m-80) cc_final: 0.8991 (m-80) REVERT: R 35 TRP cc_start: 0.7363 (m100) cc_final: 0.6285 (m100) REVERT: R 71 PHE cc_start: 0.6995 (m-80) cc_final: 0.6012 (m-80) REVERT: B 100 ASP cc_start: 0.7072 (p0) cc_final: 0.6693 (p0) REVERT: B 176 TYR cc_start: 0.8504 (m-80) cc_final: 0.7506 (m-80) REVERT: B 200 MET cc_start: 0.8469 (mmm) cc_final: 0.8252 (tpp) REVERT: B 277 GLU cc_start: 0.8814 (mm-30) cc_final: 0.6679 (mt-10) REVERT: B 279 ASN cc_start: 0.8326 (t0) cc_final: 0.7896 (t0) REVERT: C 100 ASP cc_start: 0.7753 (p0) cc_final: 0.6884 (m-30) REVERT: C 200 MET cc_start: 0.8353 (mmm) cc_final: 0.8083 (tpp) REVERT: C 214 GLU cc_start: 0.9157 (mt-10) cc_final: 0.8660 (mt-10) REVERT: C 237 ASP cc_start: 0.8595 (t0) cc_final: 0.8295 (t0) REVERT: C 274 ASP cc_start: 0.7970 (m-30) cc_final: 0.7627 (m-30) REVERT: C 279 ASN cc_start: 0.8140 (t0) cc_final: 0.7643 (t0) REVERT: J 95 LEU cc_start: 0.7623 (tt) cc_final: 0.7273 (mm) outliers start: 8 outliers final: 1 residues processed: 403 average time/residue: 0.4979 time to fit residues: 318.1613 Evaluate side-chains 248 residues out of total 3858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 245 time to evaluate : 3.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 224 optimal weight: 1.9990 chunk 125 optimal weight: 4.9990 chunk 335 optimal weight: 0.8980 chunk 274 optimal weight: 20.0000 chunk 111 optimal weight: 9.9990 chunk 403 optimal weight: 40.0000 chunk 436 optimal weight: 0.8980 chunk 359 optimal weight: 30.0000 chunk 400 optimal weight: 10.0000 chunk 137 optimal weight: 5.9990 chunk 324 optimal weight: 7.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 141 HIS ** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 38 GLN ** F 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 6 GLN P 6 GLN P 110 ASN Q 160 GLN ** R 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 126 HIS B 141 HIS ** B 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 141 HIS ** C 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 228 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6778 moved from start: 0.3073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 35274 Z= 0.288 Angle : 0.714 12.355 47940 Z= 0.368 Chirality : 0.046 0.192 5454 Planarity : 0.006 0.096 6144 Dihedral : 6.957 36.947 4878 Min Nonbonded Distance : 1.367 Molprobity Statistics. All-atom Clashscore : 22.15 Ramachandran Plot: Outliers : 0.16 % Allowed : 11.39 % Favored : 88.46 % Rotamer: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.57 % Twisted Proline : 2.17 % Twisted General : 0.28 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.94 (0.12), residues: 4488 helix: 0.17 (0.18), residues: 780 sheet: -2.76 (0.13), residues: 1290 loop : -2.20 (0.13), residues: 2418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP O 47 HIS 0.013 0.001 HIS L 91 PHE 0.025 0.002 PHE L 62 TYR 0.027 0.002 TYR K 102 ARG 0.026 0.001 ARG L 61 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8976 Ramachandran restraints generated. 4488 Oldfield, 0 Emsley, 4488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8976 Ramachandran restraints generated. 4488 Oldfield, 0 Emsley, 4488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 3858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 363 time to evaluate : 3.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 ASP cc_start: 0.7687 (p0) cc_final: 0.7468 (p0) REVERT: A 181 ASP cc_start: 0.7981 (t0) cc_final: 0.7642 (t0) REVERT: A 261 THR cc_start: 0.7779 (p) cc_final: 0.7451 (p) REVERT: A 276 MET cc_start: 0.7803 (mpp) cc_final: 0.7013 (mpp) REVERT: A 277 GLU cc_start: 0.8664 (mm-30) cc_final: 0.6716 (mt-10) REVERT: A 279 ASN cc_start: 0.8378 (t0) cc_final: 0.7912 (t0) REVERT: D 81 MET cc_start: 0.8873 (tmm) cc_final: 0.8455 (tmm) REVERT: D 206 TYR cc_start: 0.7126 (m-80) cc_final: 0.6778 (m-80) REVERT: E 4 MET cc_start: 0.8328 (mmm) cc_final: 0.8116 (mmm) REVERT: F 81 MET cc_start: 0.8908 (tmm) cc_final: 0.8431 (tmm) REVERT: F 99 GLU cc_start: 0.7764 (pt0) cc_final: 0.7501 (pt0) REVERT: G 70 MET cc_start: 0.9083 (mtm) cc_final: 0.8680 (mtm) REVERT: G 81 MET cc_start: 0.9292 (tmm) cc_final: 0.8959 (tmm) REVERT: G 145 GLU cc_start: 0.6549 (mt-10) cc_final: 0.6233 (tm-30) REVERT: K 45 LEU cc_start: 0.3936 (mp) cc_final: 0.3453 (mp) REVERT: K 62 GLN cc_start: 0.8981 (tp40) cc_final: 0.8601 (tm-30) REVERT: K 90 ASP cc_start: 0.5861 (m-30) cc_final: 0.4683 (m-30) REVERT: K 211 ASP cc_start: 0.8322 (m-30) cc_final: 0.7901 (t0) REVERT: L 35 TRP cc_start: 0.7948 (m100) cc_final: 0.6781 (m100) REVERT: L 47 LEU cc_start: 0.8218 (mt) cc_final: 0.7785 (mt) REVERT: L 87 TYR cc_start: 0.9168 (m-10) cc_final: 0.8919 (m-80) REVERT: O 45 LEU cc_start: 0.5792 (mp) cc_final: 0.4852 (mp) REVERT: O 89 ASP cc_start: 0.8723 (p0) cc_final: 0.8466 (p0) REVERT: O 211 ASP cc_start: 0.8441 (m-30) cc_final: 0.7999 (t0) REVERT: P 45 LEU cc_start: 0.3082 (mp) cc_final: 0.2309 (mp) REVERT: P 211 ASP cc_start: 0.8646 (m-30) cc_final: 0.8385 (t0) REVERT: Q 35 TRP cc_start: 0.7134 (m100) cc_final: 0.6263 (m100) REVERT: Q 36 TYR cc_start: 0.7333 (m-80) cc_final: 0.7082 (m-80) REVERT: Q 47 LEU cc_start: 0.8269 (mt) cc_final: 0.7974 (mp) REVERT: R 35 TRP cc_start: 0.7524 (m100) cc_final: 0.6380 (m100) REVERT: R 47 LEU cc_start: 0.8548 (mt) cc_final: 0.8257 (mt) REVERT: R 71 PHE cc_start: 0.7944 (m-10) cc_final: 0.7414 (m-10) REVERT: R 87 TYR cc_start: 0.9225 (m-10) cc_final: 0.8917 (m-80) REVERT: B 100 ASP cc_start: 0.6833 (p0) cc_final: 0.6446 (p0) REVERT: B 200 MET cc_start: 0.8414 (mmm) cc_final: 0.7653 (mpp) REVERT: B 277 GLU cc_start: 0.8651 (mm-30) cc_final: 0.6605 (mt-10) REVERT: B 279 ASN cc_start: 0.8384 (t0) cc_final: 0.7886 (t0) REVERT: C 200 MET cc_start: 0.8366 (mmm) cc_final: 0.7974 (tpp) REVERT: C 274 ASP cc_start: 0.7865 (m-30) cc_final: 0.7561 (m-30) REVERT: C 277 GLU cc_start: 0.8704 (mm-30) cc_final: 0.7737 (mm-30) REVERT: C 279 ASN cc_start: 0.8302 (t0) cc_final: 0.7572 (t0) outliers start: 0 outliers final: 0 residues processed: 363 average time/residue: 0.4614 time to fit residues: 270.0051 Evaluate side-chains 254 residues out of total 3858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 254 time to evaluate : 4.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 399 optimal weight: 20.0000 chunk 303 optimal weight: 2.9990 chunk 209 optimal weight: 8.9990 chunk 44 optimal weight: 10.0000 chunk 192 optimal weight: 10.0000 chunk 271 optimal weight: 50.0000 chunk 405 optimal weight: 1.9990 chunk 429 optimal weight: 40.0000 chunk 211 optimal weight: 1.9990 chunk 384 optimal weight: 9.9990 chunk 115 optimal weight: 30.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 126 HIS ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 GLN ** G 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 38 GLN I 38 GLN ** I 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 294 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6853 moved from start: 0.3715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.098 35274 Z= 0.429 Angle : 0.796 9.257 47940 Z= 0.410 Chirality : 0.047 0.211 5454 Planarity : 0.007 0.087 6144 Dihedral : 6.942 36.443 4878 Min Nonbonded Distance : 1.293 Molprobity Statistics. All-atom Clashscore : 26.43 Ramachandran Plot: Outliers : 0.18 % Allowed : 12.21 % Favored : 87.61 % Rotamer: Outliers : 0.08 % Allowed : 3.47 % Favored : 96.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.57 % Twisted Proline : 0.72 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.85 (0.12), residues: 4488 helix: 0.16 (0.18), residues: 780 sheet: -2.58 (0.14), residues: 1182 loop : -2.25 (0.12), residues: 2526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 115 HIS 0.014 0.002 HIS L 91 PHE 0.033 0.003 PHE I 71 TYR 0.038 0.002 TYR E 49 ARG 0.027 0.001 ARG K 38 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8976 Ramachandran restraints generated. 4488 Oldfield, 0 Emsley, 4488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8976 Ramachandran restraints generated. 4488 Oldfield, 0 Emsley, 4488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 3858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 325 time to evaluate : 4.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 ASP cc_start: 0.8423 (t0) cc_final: 0.8194 (t0) REVERT: A 277 GLU cc_start: 0.8735 (mm-30) cc_final: 0.7779 (mm-30) REVERT: A 279 ASN cc_start: 0.8393 (t0) cc_final: 0.7921 (t0) REVERT: D 89 ASP cc_start: 0.9235 (p0) cc_final: 0.9023 (p0) REVERT: F 57 GLU cc_start: 0.8349 (mt-10) cc_final: 0.8135 (mt-10) REVERT: F 104 TYR cc_start: 0.8068 (t80) cc_final: 0.7867 (t80) REVERT: G 145 GLU cc_start: 0.6713 (mt-10) cc_final: 0.6268 (tm-30) REVERT: K 45 LEU cc_start: 0.3840 (mp) cc_final: 0.3340 (mp) REVERT: K 50 SER cc_start: 0.7189 (p) cc_final: 0.6523 (t) REVERT: K 62 GLN cc_start: 0.9052 (tp40) cc_final: 0.8846 (tm-30) REVERT: K 109 GLN cc_start: 0.4340 (mt0) cc_final: 0.4112 (pm20) REVERT: K 211 ASP cc_start: 0.8353 (m-30) cc_final: 0.7941 (t0) REVERT: L 35 TRP cc_start: 0.7957 (m100) cc_final: 0.6934 (m100) REVERT: L 36 TYR cc_start: 0.8042 (m-10) cc_final: 0.7586 (m-80) REVERT: L 87 TYR cc_start: 0.9144 (m-10) cc_final: 0.8864 (m-80) REVERT: O 45 LEU cc_start: 0.5767 (mp) cc_final: 0.4486 (mp) REVERT: O 67 ARG cc_start: 0.6269 (mtm110) cc_final: 0.5905 (mtp-110) REVERT: O 89 ASP cc_start: 0.8770 (p0) cc_final: 0.8562 (p0) REVERT: O 211 ASP cc_start: 0.8393 (m-30) cc_final: 0.7968 (t0) REVERT: P 211 ASP cc_start: 0.8611 (m-30) cc_final: 0.8344 (t0) REVERT: Q 35 TRP cc_start: 0.7382 (m100) cc_final: 0.6536 (m100) REVERT: R 35 TRP cc_start: 0.7558 (m100) cc_final: 0.6355 (m100) REVERT: R 36 TYR cc_start: 0.8149 (m-80) cc_final: 0.7925 (m-80) REVERT: B 176 TYR cc_start: 0.8352 (m-80) cc_final: 0.7425 (m-80) REVERT: B 181 ASP cc_start: 0.8376 (t0) cc_final: 0.8049 (t0) REVERT: B 200 MET cc_start: 0.8500 (mmm) cc_final: 0.8279 (tpp) REVERT: B 277 GLU cc_start: 0.8562 (mm-30) cc_final: 0.7791 (mm-30) REVERT: B 279 ASN cc_start: 0.8251 (t0) cc_final: 0.7752 (t0) REVERT: C 181 ASP cc_start: 0.8552 (t0) cc_final: 0.8302 (t0) REVERT: C 200 MET cc_start: 0.8525 (mmm) cc_final: 0.8320 (tpp) REVERT: C 274 ASP cc_start: 0.8141 (m-30) cc_final: 0.7801 (m-30) REVERT: C 277 GLU cc_start: 0.8696 (mm-30) cc_final: 0.7871 (mm-30) REVERT: C 279 ASN cc_start: 0.8292 (t0) cc_final: 0.7736 (t0) outliers start: 3 outliers final: 2 residues processed: 327 average time/residue: 0.4748 time to fit residues: 254.2695 Evaluate side-chains 233 residues out of total 3858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 231 time to evaluate : 3.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 357 optimal weight: 8.9990 chunk 243 optimal weight: 10.0000 chunk 6 optimal weight: 0.9980 chunk 319 optimal weight: 0.8980 chunk 177 optimal weight: 30.0000 chunk 366 optimal weight: 6.9990 chunk 296 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 219 optimal weight: 20.0000 chunk 385 optimal weight: 20.0000 chunk 108 optimal weight: 7.9990 overall best weight: 3.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 GLN ** B 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 294 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6820 moved from start: 0.3885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 35274 Z= 0.296 Angle : 0.717 11.509 47940 Z= 0.368 Chirality : 0.046 0.255 5454 Planarity : 0.006 0.089 6144 Dihedral : 6.764 37.472 4878 Min Nonbonded Distance : 1.391 Molprobity Statistics. All-atom Clashscore : 23.71 Ramachandran Plot: Outliers : 0.13 % Allowed : 11.68 % Favored : 88.19 % Rotamer: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.57 % Twisted Proline : 0.36 % Twisted General : 0.33 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.62 (0.12), residues: 4488 helix: 0.29 (0.18), residues: 804 sheet: -2.39 (0.14), residues: 1182 loop : -2.11 (0.13), residues: 2502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP P 36 HIS 0.010 0.001 HIS H 91 PHE 0.033 0.002 PHE O 29 TYR 0.025 0.002 TYR K 102 ARG 0.011 0.001 ARG P 98 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8976 Ramachandran restraints generated. 4488 Oldfield, 0 Emsley, 4488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8976 Ramachandran restraints generated. 4488 Oldfield, 0 Emsley, 4488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 3858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 328 time to evaluate : 3.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 THR cc_start: 0.8011 (p) cc_final: 0.7723 (p) REVERT: A 277 GLU cc_start: 0.8692 (mm-30) cc_final: 0.7808 (mm-30) REVERT: A 279 ASN cc_start: 0.8423 (t0) cc_final: 0.7964 (t0) REVERT: D 89 ASP cc_start: 0.9206 (p0) cc_final: 0.8994 (p0) REVERT: F 57 GLU cc_start: 0.8328 (mt-10) cc_final: 0.8106 (mt-10) REVERT: G 48 MET cc_start: 0.8545 (mtm) cc_final: 0.8056 (mtm) REVERT: G 145 GLU cc_start: 0.6660 (mt-10) cc_final: 0.6221 (tm-30) REVERT: K 45 LEU cc_start: 0.3655 (mp) cc_final: 0.3082 (mp) REVERT: K 62 GLN cc_start: 0.8881 (tp40) cc_final: 0.8652 (tm-30) REVERT: K 109 GLN cc_start: 0.4435 (mt0) cc_final: 0.4218 (pm20) REVERT: K 211 ASP cc_start: 0.8354 (m-30) cc_final: 0.7946 (t0) REVERT: L 35 TRP cc_start: 0.8224 (m100) cc_final: 0.7032 (m100) REVERT: L 36 TYR cc_start: 0.8052 (m-10) cc_final: 0.7664 (m-80) REVERT: L 87 TYR cc_start: 0.9122 (m-10) cc_final: 0.8835 (m-80) REVERT: O 64 LEU cc_start: 0.7878 (pt) cc_final: 0.7172 (pp) REVERT: O 67 ARG cc_start: 0.6354 (mtm110) cc_final: 0.5559 (mtp-110) REVERT: O 89 ASP cc_start: 0.8786 (p0) cc_final: 0.8427 (p0) REVERT: O 109 GLN cc_start: 0.4541 (mt0) cc_final: 0.3856 (pm20) REVERT: O 112 PHE cc_start: 0.7588 (m-80) cc_final: 0.6991 (m-10) REVERT: O 211 ASP cc_start: 0.8397 (m-30) cc_final: 0.7971 (t0) REVERT: P 45 LEU cc_start: 0.3889 (mp) cc_final: 0.2524 (mp) REVERT: P 211 ASP cc_start: 0.8644 (m-30) cc_final: 0.8382 (t0) REVERT: Q 35 TRP cc_start: 0.7446 (m100) cc_final: 0.6267 (m100) REVERT: Q 36 TYR cc_start: 0.7801 (m-80) cc_final: 0.6979 (m-80) REVERT: Q 47 LEU cc_start: 0.8116 (mt) cc_final: 0.7876 (mt) REVERT: R 35 TRP cc_start: 0.7704 (m100) cc_final: 0.6368 (m100) REVERT: R 36 TYR cc_start: 0.8320 (m-80) cc_final: 0.7814 (m-80) REVERT: B 176 TYR cc_start: 0.8303 (m-80) cc_final: 0.7343 (m-80) REVERT: B 200 MET cc_start: 0.8457 (mmm) cc_final: 0.8213 (tpp) REVERT: B 212 MET cc_start: 0.9176 (mmm) cc_final: 0.8938 (mmm) REVERT: B 261 THR cc_start: 0.7754 (p) cc_final: 0.7487 (p) REVERT: B 277 GLU cc_start: 0.8501 (mm-30) cc_final: 0.7788 (mm-30) REVERT: B 279 ASN cc_start: 0.8273 (t0) cc_final: 0.7759 (t0) REVERT: C 181 ASP cc_start: 0.8442 (t0) cc_final: 0.8111 (t0) REVERT: C 200 MET cc_start: 0.8542 (mmm) cc_final: 0.8228 (tpp) REVERT: C 274 ASP cc_start: 0.8058 (m-30) cc_final: 0.7703 (m-30) REVERT: C 277 GLU cc_start: 0.8638 (mm-30) cc_final: 0.7840 (mm-30) REVERT: C 279 ASN cc_start: 0.8372 (t0) cc_final: 0.7786 (t0) outliers start: 0 outliers final: 0 residues processed: 328 average time/residue: 0.4650 time to fit residues: 249.3687 Evaluate side-chains 241 residues out of total 3858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 241 time to evaluate : 3.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 144 optimal weight: 4.9990 chunk 386 optimal weight: 9.9990 chunk 84 optimal weight: 0.9990 chunk 251 optimal weight: 5.9990 chunk 105 optimal weight: 3.9990 chunk 429 optimal weight: 6.9990 chunk 356 optimal weight: 6.9990 chunk 198 optimal weight: 6.9990 chunk 35 optimal weight: 9.9990 chunk 142 optimal weight: 1.9990 chunk 225 optimal weight: 20.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 138 ASN ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 294 ASN M 143 GLN N 294 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6843 moved from start: 0.4151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 35274 Z= 0.318 Angle : 0.722 9.576 47940 Z= 0.369 Chirality : 0.046 0.186 5454 Planarity : 0.006 0.083 6144 Dihedral : 6.654 36.898 4878 Min Nonbonded Distance : 1.294 Molprobity Statistics. All-atom Clashscore : 24.45 Ramachandran Plot: Outliers : 0.11 % Allowed : 11.97 % Favored : 87.92 % Rotamer: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.57 % Twisted Proline : 0.72 % Twisted General : 0.28 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.54 (0.12), residues: 4488 helix: 0.39 (0.18), residues: 810 sheet: -2.38 (0.14), residues: 1224 loop : -2.05 (0.13), residues: 2454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP F 115 HIS 0.009 0.001 HIS C 126 PHE 0.046 0.002 PHE B 64 TYR 0.027 0.002 TYR H 49 ARG 0.008 0.001 ARG P 98 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8976 Ramachandran restraints generated. 4488 Oldfield, 0 Emsley, 4488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8976 Ramachandran restraints generated. 4488 Oldfield, 0 Emsley, 4488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 3858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 322 time to evaluate : 3.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 THR cc_start: 0.8003 (p) cc_final: 0.7694 (p) REVERT: A 277 GLU cc_start: 0.8650 (mm-30) cc_final: 0.7897 (mm-30) REVERT: A 279 ASN cc_start: 0.8353 (t0) cc_final: 0.7900 (t0) REVERT: D 206 TYR cc_start: 0.7300 (m-80) cc_final: 0.6994 (m-80) REVERT: F 57 GLU cc_start: 0.8354 (mt-10) cc_final: 0.8098 (mt-10) REVERT: G 145 GLU cc_start: 0.6673 (mt-10) cc_final: 0.6232 (tm-30) REVERT: K 45 LEU cc_start: 0.3760 (mp) cc_final: 0.3052 (mp) REVERT: K 62 GLN cc_start: 0.8934 (tp40) cc_final: 0.8684 (tm-30) REVERT: K 211 ASP cc_start: 0.8373 (m-30) cc_final: 0.7963 (t0) REVERT: L 35 TRP cc_start: 0.7835 (m100) cc_final: 0.7018 (m100) REVERT: L 36 TYR cc_start: 0.8145 (m-10) cc_final: 0.7742 (m-80) REVERT: L 75 ILE cc_start: 0.9285 (mm) cc_final: 0.9007 (mm) REVERT: L 87 TYR cc_start: 0.9171 (m-10) cc_final: 0.8850 (m-80) REVERT: O 45 LEU cc_start: 0.6600 (mp) cc_final: 0.4692 (mp) REVERT: O 67 ARG cc_start: 0.5918 (mtm110) cc_final: 0.5623 (mtp-110) REVERT: O 109 GLN cc_start: 0.4594 (mt0) cc_final: 0.3889 (pm20) REVERT: O 112 PHE cc_start: 0.6733 (m-80) cc_final: 0.6500 (m-80) REVERT: O 211 ASP cc_start: 0.8421 (m-30) cc_final: 0.8007 (t0) REVERT: P 45 LEU cc_start: 0.3908 (mp) cc_final: 0.2362 (mp) REVERT: P 48 MET cc_start: 0.8273 (mpp) cc_final: 0.7864 (mpp) REVERT: P 211 ASP cc_start: 0.8645 (m-30) cc_final: 0.8385 (t0) REVERT: Q 35 TRP cc_start: 0.7261 (m100) cc_final: 0.6417 (m100) REVERT: Q 47 LEU cc_start: 0.8070 (mt) cc_final: 0.7600 (mt) REVERT: Q 87 TYR cc_start: 0.8995 (m-80) cc_final: 0.8689 (m-80) REVERT: R 35 TRP cc_start: 0.7693 (m100) cc_final: 0.6687 (m100) REVERT: R 36 TYR cc_start: 0.8312 (m-80) cc_final: 0.8065 (m-80) REVERT: R 47 LEU cc_start: 0.8476 (mt) cc_final: 0.8221 (mt) REVERT: B 176 TYR cc_start: 0.8283 (m-80) cc_final: 0.7373 (m-80) REVERT: B 200 MET cc_start: 0.8473 (mmm) cc_final: 0.8225 (tpp) REVERT: B 261 THR cc_start: 0.7755 (p) cc_final: 0.7459 (p) REVERT: B 277 GLU cc_start: 0.8439 (mm-30) cc_final: 0.7633 (mm-30) REVERT: B 279 ASN cc_start: 0.8239 (t0) cc_final: 0.7735 (t0) REVERT: C 100 ASP cc_start: 0.7594 (p0) cc_final: 0.7386 (p0) REVERT: C 176 TYR cc_start: 0.8247 (m-80) cc_final: 0.7502 (m-80) REVERT: C 274 ASP cc_start: 0.8097 (m-30) cc_final: 0.7795 (m-30) REVERT: C 279 ASN cc_start: 0.8322 (t0) cc_final: 0.7744 (t0) REVERT: N 105 ILE cc_start: 0.7992 (mp) cc_final: 0.7575 (pt) outliers start: 0 outliers final: 0 residues processed: 322 average time/residue: 0.4626 time to fit residues: 244.5304 Evaluate side-chains 225 residues out of total 3858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 225 time to evaluate : 3.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 414 optimal weight: 10.0000 chunk 48 optimal weight: 8.9990 chunk 244 optimal weight: 30.0000 chunk 313 optimal weight: 6.9990 chunk 243 optimal weight: 5.9990 chunk 361 optimal weight: 20.0000 chunk 239 optimal weight: 9.9990 chunk 427 optimal weight: 0.0670 chunk 267 optimal weight: 20.0000 chunk 260 optimal weight: 40.0000 chunk 197 optimal weight: 30.0000 overall best weight: 6.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 39 GLN ** D 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 38 GLN ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 143 GLN J 294 ASN N 294 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6899 moved from start: 0.4610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 35274 Z= 0.496 Angle : 0.823 9.482 47940 Z= 0.425 Chirality : 0.049 0.245 5454 Planarity : 0.007 0.106 6144 Dihedral : 6.936 36.606 4878 Min Nonbonded Distance : 1.246 Molprobity Statistics. All-atom Clashscore : 30.15 Ramachandran Plot: Outliers : 0.16 % Allowed : 13.41 % Favored : 86.43 % Rotamer: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.57 % Twisted Proline : 1.09 % Twisted General : 0.31 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.71 (0.12), residues: 4488 helix: 0.10 (0.18), residues: 810 sheet: -2.40 (0.13), residues: 1308 loop : -2.11 (0.13), residues: 2370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP D 115 HIS 0.011 0.002 HIS H 91 PHE 0.057 0.003 PHE B 64 TYR 0.041 0.003 TYR H 49 ARG 0.011 0.001 ARG D 98 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8976 Ramachandran restraints generated. 4488 Oldfield, 0 Emsley, 4488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8976 Ramachandran restraints generated. 4488 Oldfield, 0 Emsley, 4488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 3858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 303 time to evaluate : 4.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 ASP cc_start: 0.8404 (t0) cc_final: 0.8166 (t0) REVERT: G 48 MET cc_start: 0.9030 (mtm) cc_final: 0.8821 (mtm) REVERT: K 45 LEU cc_start: 0.3979 (mp) cc_final: 0.3229 (mp) REVERT: K 62 GLN cc_start: 0.8869 (tp40) cc_final: 0.8593 (tm-30) REVERT: K 81 MET cc_start: 0.9076 (ppp) cc_final: 0.8712 (ppp) REVERT: K 211 ASP cc_start: 0.8392 (m-30) cc_final: 0.7976 (t0) REVERT: L 35 TRP cc_start: 0.8170 (m100) cc_final: 0.7005 (m100) REVERT: L 87 TYR cc_start: 0.9205 (m-80) cc_final: 0.8955 (m-80) REVERT: O 109 GLN cc_start: 0.4471 (mt0) cc_final: 0.3611 (pm20) REVERT: O 112 PHE cc_start: 0.6879 (m-80) cc_final: 0.6392 (m-80) REVERT: O 211 ASP cc_start: 0.8385 (m-30) cc_final: 0.7965 (t0) REVERT: P 45 LEU cc_start: 0.3573 (mp) cc_final: 0.2514 (mp) REVERT: P 48 MET cc_start: 0.8290 (mpp) cc_final: 0.7901 (mpp) REVERT: P 94 TYR cc_start: 0.7984 (m-10) cc_final: 0.7601 (m-10) REVERT: P 98 ARG cc_start: 0.5842 (tmm160) cc_final: 0.5617 (tmm160) REVERT: P 211 ASP cc_start: 0.8652 (m-30) cc_final: 0.8410 (t0) REVERT: Q 35 TRP cc_start: 0.7332 (m100) cc_final: 0.6151 (m100) REVERT: Q 48 ILE cc_start: 0.8038 (pt) cc_final: 0.7798 (pt) REVERT: Q 71 PHE cc_start: 0.6405 (m-80) cc_final: 0.6183 (m-80) REVERT: R 35 TRP cc_start: 0.7648 (m100) cc_final: 0.6615 (m100) REVERT: R 36 TYR cc_start: 0.8369 (m-80) cc_final: 0.8159 (m-80) REVERT: R 87 TYR cc_start: 0.9183 (m-10) cc_final: 0.8831 (m-80) REVERT: B 176 TYR cc_start: 0.8383 (m-80) cc_final: 0.7470 (m-80) REVERT: B 200 MET cc_start: 0.8479 (mmm) cc_final: 0.7712 (mpp) REVERT: B 277 GLU cc_start: 0.8644 (mm-30) cc_final: 0.7716 (mm-30) REVERT: C 100 ASP cc_start: 0.7614 (p0) cc_final: 0.7391 (p0) REVERT: C 176 TYR cc_start: 0.8297 (m-80) cc_final: 0.7505 (m-80) REVERT: C 200 MET cc_start: 0.8232 (tpp) cc_final: 0.7927 (mpp) REVERT: C 274 ASP cc_start: 0.8106 (m-30) cc_final: 0.7779 (m-30) REVERT: J 304 PHE cc_start: 0.7243 (m-80) cc_final: 0.6652 (m-80) outliers start: 0 outliers final: 0 residues processed: 303 average time/residue: 0.4472 time to fit residues: 223.0940 Evaluate side-chains 215 residues out of total 3858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 215 time to evaluate : 4.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 264 optimal weight: 30.0000 chunk 170 optimal weight: 8.9990 chunk 255 optimal weight: 6.9990 chunk 128 optimal weight: 7.9990 chunk 84 optimal weight: 0.6980 chunk 82 optimal weight: 4.9990 chunk 272 optimal weight: 8.9990 chunk 291 optimal weight: 0.7980 chunk 211 optimal weight: 9.9990 chunk 39 optimal weight: 5.9990 chunk 336 optimal weight: 2.9990 overall best weight: 3.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 53 ASN ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 176 HIS ** Q 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 294 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6853 moved from start: 0.4679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 35274 Z= 0.291 Angle : 0.721 10.047 47940 Z= 0.368 Chirality : 0.047 0.289 5454 Planarity : 0.006 0.092 6144 Dihedral : 6.688 39.023 4878 Min Nonbonded Distance : 1.336 Molprobity Statistics. All-atom Clashscore : 24.83 Ramachandran Plot: Outliers : 0.07 % Allowed : 12.25 % Favored : 87.68 % Rotamer: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.57 % Twisted Proline : 0.72 % Twisted General : 0.28 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.46 (0.13), residues: 4488 helix: 0.37 (0.18), residues: 810 sheet: -2.29 (0.14), residues: 1326 loop : -1.94 (0.13), residues: 2352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP O 47 HIS 0.007 0.001 HIS H 91 PHE 0.050 0.003 PHE B 64 TYR 0.025 0.002 TYR H 32 ARG 0.014 0.001 ARG I 24 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8976 Ramachandran restraints generated. 4488 Oldfield, 0 Emsley, 4488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8976 Ramachandran restraints generated. 4488 Oldfield, 0 Emsley, 4488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 3858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 314 time to evaluate : 3.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 THR cc_start: 0.8044 (p) cc_final: 0.7775 (p) REVERT: A 279 ASN cc_start: 0.8268 (t0) cc_final: 0.7917 (t0) REVERT: D 35 SER cc_start: 0.9279 (p) cc_final: 0.9023 (m) REVERT: G 48 MET cc_start: 0.8935 (mtm) cc_final: 0.8615 (mtm) REVERT: K 45 LEU cc_start: 0.3847 (mp) cc_final: 0.2634 (mp) REVERT: K 62 GLN cc_start: 0.8844 (tp40) cc_final: 0.8534 (tm-30) REVERT: K 211 ASP cc_start: 0.8388 (m-30) cc_final: 0.7969 (t0) REVERT: L 35 TRP cc_start: 0.8054 (m100) cc_final: 0.6917 (m100) REVERT: L 36 TYR cc_start: 0.8119 (m-10) cc_final: 0.7750 (m-80) REVERT: L 47 LEU cc_start: 0.8171 (mt) cc_final: 0.7897 (mt) REVERT: L 87 TYR cc_start: 0.9248 (m-80) cc_final: 0.8974 (m-80) REVERT: O 45 LEU cc_start: 0.6584 (mp) cc_final: 0.5613 (mp) REVERT: O 112 PHE cc_start: 0.7009 (m-80) cc_final: 0.6553 (m-80) REVERT: O 211 ASP cc_start: 0.8399 (m-30) cc_final: 0.7971 (t0) REVERT: P 45 LEU cc_start: 0.3698 (mp) cc_final: 0.2493 (mp) REVERT: P 48 MET cc_start: 0.8214 (mpp) cc_final: 0.7845 (mpp) REVERT: P 94 TYR cc_start: 0.7991 (m-10) cc_final: 0.7640 (m-10) REVERT: P 211 ASP cc_start: 0.8648 (m-30) cc_final: 0.8408 (t0) REVERT: Q 35 TRP cc_start: 0.7165 (m100) cc_final: 0.6081 (m100) REVERT: Q 36 TYR cc_start: 0.7511 (m-80) cc_final: 0.7196 (m-80) REVERT: Q 48 ILE cc_start: 0.8100 (pt) cc_final: 0.7847 (pt) REVERT: R 35 TRP cc_start: 0.7690 (m100) cc_final: 0.6733 (m100) REVERT: R 47 LEU cc_start: 0.8284 (mt) cc_final: 0.7778 (mt) REVERT: R 71 PHE cc_start: 0.8576 (m-10) cc_final: 0.8100 (m-80) REVERT: R 87 TYR cc_start: 0.9236 (m-10) cc_final: 0.8887 (m-80) REVERT: B 100 ASP cc_start: 0.7550 (p0) cc_final: 0.7300 (p0) REVERT: B 176 TYR cc_start: 0.8387 (m-80) cc_final: 0.7524 (m-80) REVERT: B 200 MET cc_start: 0.8457 (mmm) cc_final: 0.7700 (mpp) REVERT: B 261 THR cc_start: 0.7816 (p) cc_final: 0.7512 (p) REVERT: B 277 GLU cc_start: 0.8429 (mm-30) cc_final: 0.7682 (mm-30) REVERT: C 100 ASP cc_start: 0.7638 (p0) cc_final: 0.7378 (p0) REVERT: C 176 TYR cc_start: 0.8194 (m-80) cc_final: 0.7457 (m-80) REVERT: C 200 MET cc_start: 0.8169 (tpp) cc_final: 0.7866 (mpp) REVERT: C 274 ASP cc_start: 0.8036 (m-30) cc_final: 0.7738 (m-30) REVERT: C 279 ASN cc_start: 0.8055 (t0) cc_final: 0.7548 (t0) REVERT: J 105 ILE cc_start: 0.8184 (mp) cc_final: 0.7733 (pt) REVERT: J 304 PHE cc_start: 0.7164 (m-80) cc_final: 0.6465 (m-80) REVERT: N 122 TRP cc_start: 0.5647 (t-100) cc_final: 0.5401 (t-100) outliers start: 0 outliers final: 0 residues processed: 314 average time/residue: 0.4425 time to fit residues: 231.5353 Evaluate side-chains 220 residues out of total 3858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 220 time to evaluate : 3.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 389 optimal weight: 10.0000 chunk 409 optimal weight: 6.9990 chunk 374 optimal weight: 20.0000 chunk 398 optimal weight: 20.0000 chunk 240 optimal weight: 8.9990 chunk 173 optimal weight: 50.0000 chunk 313 optimal weight: 9.9990 chunk 122 optimal weight: 3.9990 chunk 360 optimal weight: 30.0000 chunk 377 optimal weight: 1.9990 chunk 397 optimal weight: 30.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 39 GLN ** F 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 38 GLN ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 294 ASN N 143 GLN N 294 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6920 moved from start: 0.5077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.068 35274 Z= 0.503 Angle : 0.852 12.510 47940 Z= 0.437 Chirality : 0.050 0.300 5454 Planarity : 0.007 0.091 6144 Dihedral : 6.993 38.138 4878 Min Nonbonded Distance : 1.237 Molprobity Statistics. All-atom Clashscore : 31.33 Ramachandran Plot: Outliers : 0.20 % Allowed : 14.19 % Favored : 85.61 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.57 % Twisted Proline : 0.36 % Twisted General : 0.31 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.81 (0.12), residues: 4488 helix: -0.29 (0.17), residues: 846 sheet: -2.33 (0.14), residues: 1296 loop : -2.17 (0.13), residues: 2346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.003 TRP D 115 HIS 0.011 0.002 HIS H 91 PHE 0.055 0.003 PHE B 64 TYR 0.040 0.003 TYR E 49 ARG 0.010 0.001 ARG L 24 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8976 Ramachandran restraints generated. 4488 Oldfield, 0 Emsley, 4488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8976 Ramachandran restraints generated. 4488 Oldfield, 0 Emsley, 4488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 3858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 286 time to evaluate : 4.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 ASP cc_start: 0.8326 (t0) cc_final: 0.8073 (t0) REVERT: A 276 MET cc_start: 0.7602 (mpp) cc_final: 0.7349 (mpp) REVERT: D 70 MET cc_start: 0.8992 (mtp) cc_final: 0.8777 (mtm) REVERT: K 45 LEU cc_start: 0.3908 (mp) cc_final: 0.3105 (mp) REVERT: K 211 ASP cc_start: 0.8311 (m-30) cc_final: 0.7853 (t0) REVERT: L 35 TRP cc_start: 0.8315 (m100) cc_final: 0.6805 (m100) REVERT: L 36 TYR cc_start: 0.8160 (m-10) cc_final: 0.7557 (m-80) REVERT: L 72 THR cc_start: 0.8392 (p) cc_final: 0.8185 (p) REVERT: L 87 TYR cc_start: 0.9228 (m-80) cc_final: 0.8964 (m-80) REVERT: O 112 PHE cc_start: 0.6805 (m-80) cc_final: 0.6306 (m-80) REVERT: O 211 ASP cc_start: 0.8211 (m-30) cc_final: 0.7780 (t0) REVERT: P 36 TRP cc_start: 0.6072 (m100) cc_final: 0.5334 (m100) REVERT: P 45 LEU cc_start: 0.3705 (mp) cc_final: 0.3000 (mp) REVERT: P 94 TYR cc_start: 0.7964 (m-10) cc_final: 0.7125 (m-10) REVERT: P 211 ASP cc_start: 0.8632 (m-30) cc_final: 0.8385 (t0) REVERT: Q 35 TRP cc_start: 0.7239 (m100) cc_final: 0.6156 (m100) REVERT: Q 48 ILE cc_start: 0.7969 (pt) cc_final: 0.7739 (pt) REVERT: R 35 TRP cc_start: 0.7742 (m100) cc_final: 0.6492 (m100) REVERT: R 36 TYR cc_start: 0.8358 (m-80) cc_final: 0.7958 (m-80) REVERT: R 75 ILE cc_start: 0.8879 (mm) cc_final: 0.8639 (mm) REVERT: R 87 TYR cc_start: 0.9256 (m-10) cc_final: 0.9025 (m-80) REVERT: B 100 ASP cc_start: 0.7459 (p0) cc_final: 0.7251 (p0) REVERT: B 176 TYR cc_start: 0.8500 (m-80) cc_final: 0.7626 (m-80) REVERT: B 200 MET cc_start: 0.8548 (mmm) cc_final: 0.8053 (mpp) REVERT: C 100 ASP cc_start: 0.7624 (p0) cc_final: 0.7407 (p0) REVERT: C 176 TYR cc_start: 0.8246 (m-80) cc_final: 0.7484 (m-80) REVERT: J 122 TRP cc_start: 0.6326 (t-100) cc_final: 0.6089 (t-100) outliers start: 0 outliers final: 0 residues processed: 286 average time/residue: 0.4403 time to fit residues: 209.7913 Evaluate side-chains 199 residues out of total 3858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 199 time to evaluate : 3.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 261 optimal weight: 30.0000 chunk 421 optimal weight: 20.0000 chunk 257 optimal weight: 0.2980 chunk 200 optimal weight: 30.0000 chunk 293 optimal weight: 0.9990 chunk 442 optimal weight: 4.9990 chunk 407 optimal weight: 9.9990 chunk 352 optimal weight: 10.0000 chunk 36 optimal weight: 1.9990 chunk 272 optimal weight: 0.0010 chunk 215 optimal weight: 40.0000 overall best weight: 1.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 6 GLN ** P 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 111 HIS N 294 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6836 moved from start: 0.5020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 35274 Z= 0.227 Angle : 0.716 14.415 47940 Z= 0.363 Chirality : 0.047 0.359 5454 Planarity : 0.006 0.087 6144 Dihedral : 6.595 41.056 4878 Min Nonbonded Distance : 1.396 Molprobity Statistics. All-atom Clashscore : 23.46 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.72 % Favored : 88.19 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.57 % Twisted Proline : 0.36 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.13), residues: 4488 helix: 0.30 (0.18), residues: 810 sheet: -2.29 (0.14), residues: 1266 loop : -1.80 (0.13), residues: 2412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP O 47 HIS 0.007 0.001 HIS E 91 PHE 0.042 0.002 PHE B 64 TYR 0.028 0.002 TYR P 32 ARG 0.022 0.001 ARG Q 96 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8976 Ramachandran restraints generated. 4488 Oldfield, 0 Emsley, 4488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8976 Ramachandran restraints generated. 4488 Oldfield, 0 Emsley, 4488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 3858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 307 time to evaluate : 4.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 THR cc_start: 0.7430 (p) cc_final: 0.7134 (p) REVERT: A 276 MET cc_start: 0.7564 (mpp) cc_final: 0.7320 (mpp) REVERT: D 35 SER cc_start: 0.9271 (p) cc_final: 0.9045 (m) REVERT: F 70 MET cc_start: 0.8640 (mtm) cc_final: 0.8360 (ptp) REVERT: K 45 LEU cc_start: 0.3449 (mp) cc_final: 0.2515 (mp) REVERT: K 211 ASP cc_start: 0.8289 (m-30) cc_final: 0.7838 (t0) REVERT: L 35 TRP cc_start: 0.7982 (m100) cc_final: 0.7142 (m100) REVERT: L 36 TYR cc_start: 0.8152 (m-10) cc_final: 0.7853 (m-80) REVERT: L 47 LEU cc_start: 0.8068 (mt) cc_final: 0.7762 (mp) REVERT: L 87 TYR cc_start: 0.9214 (m-80) cc_final: 0.8961 (m-80) REVERT: O 45 LEU cc_start: 0.6745 (mp) cc_final: 0.5744 (mp) REVERT: O 112 PHE cc_start: 0.6821 (m-80) cc_final: 0.6143 (m-80) REVERT: O 211 ASP cc_start: 0.8400 (m-30) cc_final: 0.7976 (t0) REVERT: P 45 LEU cc_start: 0.3829 (mp) cc_final: 0.2943 (mp) REVERT: P 48 MET cc_start: 0.8133 (mpp) cc_final: 0.7822 (mpp) REVERT: P 81 MET cc_start: 0.9003 (ppp) cc_final: 0.8345 (tpt) REVERT: P 211 ASP cc_start: 0.8633 (m-30) cc_final: 0.8393 (t0) REVERT: Q 35 TRP cc_start: 0.7015 (m100) cc_final: 0.6119 (m100) REVERT: Q 47 LEU cc_start: 0.7862 (mt) cc_final: 0.7433 (mp) REVERT: Q 48 ILE cc_start: 0.8040 (pt) cc_final: 0.7814 (pt) REVERT: R 35 TRP cc_start: 0.7526 (m100) cc_final: 0.6594 (m100) REVERT: R 47 LEU cc_start: 0.8386 (mt) cc_final: 0.8162 (mt) REVERT: R 87 TYR cc_start: 0.9245 (m-10) cc_final: 0.8888 (m-80) REVERT: B 100 ASP cc_start: 0.7430 (p0) cc_final: 0.7186 (p0) REVERT: B 176 TYR cc_start: 0.8335 (m-80) cc_final: 0.7504 (m-80) REVERT: B 276 MET cc_start: 0.7818 (mpp) cc_final: 0.7615 (mpp) REVERT: B 277 GLU cc_start: 0.8591 (mm-30) cc_final: 0.7719 (mm-30) REVERT: C 176 TYR cc_start: 0.8219 (m-80) cc_final: 0.7518 (m-80) REVERT: J 95 LEU cc_start: 0.7778 (tt) cc_final: 0.7461 (mm) REVERT: J 122 TRP cc_start: 0.6203 (t-100) cc_final: 0.5989 (t-100) REVERT: J 304 PHE cc_start: 0.7207 (m-80) cc_final: 0.6007 (m-80) REVERT: M 105 ILE cc_start: 0.7962 (mp) cc_final: 0.7473 (pt) REVERT: N 122 TRP cc_start: 0.5701 (t-100) cc_final: 0.5461 (t-100) outliers start: 0 outliers final: 0 residues processed: 307 average time/residue: 0.4393 time to fit residues: 224.6194 Evaluate side-chains 206 residues out of total 3858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 206 time to evaluate : 3.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 279 optimal weight: 10.0000 chunk 375 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 324 optimal weight: 1.9990 chunk 52 optimal weight: 10.0000 chunk 97 optimal weight: 0.7980 chunk 352 optimal weight: 20.0000 chunk 147 optimal weight: 1.9990 chunk 362 optimal weight: 30.0000 chunk 44 optimal weight: 3.9990 chunk 64 optimal weight: 9.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 294 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.114188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.088036 restraints weight = 157410.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.086411 restraints weight = 78145.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.087309 restraints weight = 51698.624| |-----------------------------------------------------------------------------| r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.5093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 35274 Z= 0.234 Angle : 0.705 14.060 47940 Z= 0.356 Chirality : 0.047 0.312 5454 Planarity : 0.006 0.083 6144 Dihedral : 6.450 40.847 4878 Min Nonbonded Distance : 1.344 Molprobity Statistics. All-atom Clashscore : 22.54 Ramachandran Plot: Outliers : 0.07 % Allowed : 12.52 % Favored : 87.41 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.57 % Twisted Proline : 0.36 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.25 (0.13), residues: 4488 helix: 0.41 (0.18), residues: 810 sheet: -2.19 (0.14), residues: 1266 loop : -1.74 (0.13), residues: 2412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP G 111 HIS 0.008 0.001 HIS H 91 PHE 0.042 0.002 PHE B 64 TYR 0.021 0.002 TYR P 102 ARG 0.016 0.001 ARG K 38 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6348.04 seconds wall clock time: 118 minutes 37.13 seconds (7117.13 seconds total)