Starting phenix.real_space_refine on Mon Mar 18 06:29:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l3u_0826/03_2024/6l3u_0826_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l3u_0826/03_2024/6l3u_0826.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l3u_0826/03_2024/6l3u_0826.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l3u_0826/03_2024/6l3u_0826.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l3u_0826/03_2024/6l3u_0826_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l3u_0826/03_2024/6l3u_0826_trim_updated.pdb" } resolution = 2.53 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 6 9.91 5 S 66 5.16 5 C 6540 2.51 5 N 1638 2.21 5 O 1860 1.98 5 H 9588 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 4": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 7": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 13": "OE1" <-> "OE2" Residue "A ARG 15": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 16": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 32": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 75": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 172": "OE1" <-> "OE2" Residue "A ARG 184": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 220": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 4": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 7": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 13": "OE1" <-> "OE2" Residue "B ARG 15": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 16": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 32": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 75": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 172": "OE1" <-> "OE2" Residue "B ARG 184": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 220": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 4": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 7": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 13": "OE1" <-> "OE2" Residue "C ARG 15": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 16": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 32": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 75": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 172": "OE1" <-> "OE2" Residue "C ARG 184": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 220": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 4": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 7": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 13": "OE1" <-> "OE2" Residue "D ARG 15": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 16": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 32": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 75": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 172": "OE1" <-> "OE2" Residue "D ARG 184": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 220": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 4": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 7": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E GLU 13": "OE1" <-> "OE2" Residue "E ARG 15": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 16": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 32": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 75": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E GLU 172": "OE1" <-> "OE2" Residue "E ARG 184": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 220": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 4": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 7": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F GLU 13": "OE1" <-> "OE2" Residue "F ARG 15": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 16": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 32": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 75": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F GLU 172": "OE1" <-> "OE2" Residue "F ARG 184": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 220": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 19698 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 3184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 3184 Classifications: {'peptide': 201} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 190} Chain breaks: 1 Chain: "B" Number of atoms: 3184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 3184 Classifications: {'peptide': 201} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 190} Chain breaks: 1 Chain: "C" Number of atoms: 3184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 3184 Classifications: {'peptide': 201} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 190} Chain breaks: 1 Chain: "D" Number of atoms: 3184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 3184 Classifications: {'peptide': 201} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 190} Chain breaks: 1 Chain: "E" Number of atoms: 3184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 3184 Classifications: {'peptide': 201} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 190} Chain breaks: 1 Chain: "F" Number of atoms: 3184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 3184 Classifications: {'peptide': 201} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 190} Chain breaks: 1 Chain: "A" Number of atoms: 139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 139 Unusual residues: {' CA': 1, 'LMN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 70 Unusual residues: {' CA': 1, 'LMN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 70 Unusual residues: {' CA': 1, 'LMN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 70 Unusual residues: {' CA': 1, 'LMN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 70 Unusual residues: {' CA': 1, 'LMN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Chain: "B" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Chain: "C" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Chain: "D" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Chain: "E" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Chain: "F" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Time building chain proxies: 8.71, per 1000 atoms: 0.44 Number of scatterers: 19698 At special positions: 0 Unit cell: (119.121, 120.467, 92.874, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 6 19.99 S 66 16.00 O 1860 8.00 N 1638 7.00 C 6540 6.00 H 9588 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 53 " - pdb=" SG CYS A 180 " distance=2.04 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 174 " distance=2.03 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 169 " distance=2.03 Simple disulfide: pdb=" SG CYS B 53 " - pdb=" SG CYS B 180 " distance=2.04 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 174 " distance=2.03 Simple disulfide: pdb=" SG CYS B 64 " - pdb=" SG CYS B 169 " distance=2.03 Simple disulfide: pdb=" SG CYS C 53 " - pdb=" SG CYS C 180 " distance=2.04 Simple disulfide: pdb=" SG CYS C 60 " - pdb=" SG CYS C 174 " distance=2.03 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 169 " distance=2.03 Simple disulfide: pdb=" SG CYS D 53 " - pdb=" SG CYS D 180 " distance=2.04 Simple disulfide: pdb=" SG CYS D 60 " - pdb=" SG CYS D 174 " distance=2.03 Simple disulfide: pdb=" SG CYS D 64 " - pdb=" SG CYS D 169 " distance=2.03 Simple disulfide: pdb=" SG CYS E 53 " - pdb=" SG CYS E 180 " distance=2.04 Simple disulfide: pdb=" SG CYS E 60 " - pdb=" SG CYS E 174 " distance=2.03 Simple disulfide: pdb=" SG CYS E 64 " - pdb=" SG CYS E 169 " distance=2.03 Simple disulfide: pdb=" SG CYS F 53 " - pdb=" SG CYS F 180 " distance=2.04 Simple disulfide: pdb=" SG CYS F 60 " - pdb=" SG CYS F 174 " distance=2.03 Simple disulfide: pdb=" SG CYS F 64 " - pdb=" SG CYS F 169 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 14.84 Conformation dependent library (CDL) restraints added in 2.0 seconds 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2172 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 54 helices and 6 sheets defined 68.2% alpha, 4.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.65 Creating SS restraints... Processing helix chain 'A' and resid 3 through 12 removed outlier: 3.552A pdb=" N ARG A 7 " --> pdb=" O GLY A 3 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG A 8 " --> pdb=" O ARG A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 22 No H-bonds generated for 'chain 'A' and resid 19 through 22' Processing helix chain 'A' and resid 24 through 44 Proline residue: A 41 - end of helix Processing helix chain 'A' and resid 60 through 68 Processing helix chain 'A' and resid 73 through 84 Processing helix chain 'A' and resid 86 through 106 removed outlier: 3.531A pdb=" N HIS A 102 " --> pdb=" O HIS A 98 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLU A 104 " --> pdb=" O ILE A 100 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LEU A 105 " --> pdb=" O TRP A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 158 Processing helix chain 'A' and resid 185 through 213 removed outlier: 3.591A pdb=" N LEU A 210 " --> pdb=" O THR A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 218 No H-bonds generated for 'chain 'A' and resid 215 through 218' Processing helix chain 'B' and resid 3 through 12 removed outlier: 3.552A pdb=" N ARG B 7 " --> pdb=" O GLY B 3 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG B 8 " --> pdb=" O ARG B 4 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 22 No H-bonds generated for 'chain 'B' and resid 19 through 22' Processing helix chain 'B' and resid 24 through 44 Proline residue: B 41 - end of helix Processing helix chain 'B' and resid 60 through 68 Processing helix chain 'B' and resid 73 through 84 Processing helix chain 'B' and resid 86 through 106 removed outlier: 3.531A pdb=" N HIS B 102 " --> pdb=" O HIS B 98 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLU B 104 " --> pdb=" O ILE B 100 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LEU B 105 " --> pdb=" O TRP B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 158 Processing helix chain 'B' and resid 185 through 213 removed outlier: 3.592A pdb=" N LEU B 210 " --> pdb=" O THR B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 218 No H-bonds generated for 'chain 'B' and resid 215 through 218' Processing helix chain 'C' and resid 3 through 12 removed outlier: 3.552A pdb=" N ARG C 7 " --> pdb=" O GLY C 3 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG C 8 " --> pdb=" O ARG C 4 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 22 No H-bonds generated for 'chain 'C' and resid 19 through 22' Processing helix chain 'C' and resid 24 through 44 Proline residue: C 41 - end of helix Processing helix chain 'C' and resid 60 through 68 Processing helix chain 'C' and resid 73 through 84 Processing helix chain 'C' and resid 86 through 106 removed outlier: 3.531A pdb=" N HIS C 102 " --> pdb=" O HIS C 98 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLU C 104 " --> pdb=" O ILE C 100 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LEU C 105 " --> pdb=" O TRP C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 158 Processing helix chain 'C' and resid 185 through 213 removed outlier: 3.592A pdb=" N LEU C 210 " --> pdb=" O THR C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 215 through 218 No H-bonds generated for 'chain 'C' and resid 215 through 218' Processing helix chain 'D' and resid 3 through 12 removed outlier: 3.552A pdb=" N ARG D 7 " --> pdb=" O GLY D 3 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG D 8 " --> pdb=" O ARG D 4 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 22 No H-bonds generated for 'chain 'D' and resid 19 through 22' Processing helix chain 'D' and resid 24 through 44 Proline residue: D 41 - end of helix Processing helix chain 'D' and resid 60 through 68 Processing helix chain 'D' and resid 73 through 84 Processing helix chain 'D' and resid 86 through 106 removed outlier: 3.532A pdb=" N HIS D 102 " --> pdb=" O HIS D 98 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLU D 104 " --> pdb=" O ILE D 100 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LEU D 105 " --> pdb=" O TRP D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 158 Processing helix chain 'D' and resid 185 through 213 removed outlier: 3.591A pdb=" N LEU D 210 " --> pdb=" O THR D 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 215 through 218 No H-bonds generated for 'chain 'D' and resid 215 through 218' Processing helix chain 'E' and resid 3 through 12 removed outlier: 3.552A pdb=" N ARG E 7 " --> pdb=" O GLY E 3 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG E 8 " --> pdb=" O ARG E 4 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 22 No H-bonds generated for 'chain 'E' and resid 19 through 22' Processing helix chain 'E' and resid 24 through 44 Proline residue: E 41 - end of helix Processing helix chain 'E' and resid 60 through 68 Processing helix chain 'E' and resid 73 through 84 Processing helix chain 'E' and resid 86 through 106 removed outlier: 3.532A pdb=" N HIS E 102 " --> pdb=" O HIS E 98 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLU E 104 " --> pdb=" O ILE E 100 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LEU E 105 " --> pdb=" O TRP E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 158 Processing helix chain 'E' and resid 185 through 213 removed outlier: 3.591A pdb=" N LEU E 210 " --> pdb=" O THR E 206 " (cutoff:3.500A) Processing helix chain 'E' and resid 215 through 218 No H-bonds generated for 'chain 'E' and resid 215 through 218' Processing helix chain 'F' and resid 3 through 12 removed outlier: 3.552A pdb=" N ARG F 7 " --> pdb=" O GLY F 3 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ARG F 8 " --> pdb=" O ARG F 4 " (cutoff:3.500A) Processing helix chain 'F' and resid 19 through 22 No H-bonds generated for 'chain 'F' and resid 19 through 22' Processing helix chain 'F' and resid 24 through 44 Proline residue: F 41 - end of helix Processing helix chain 'F' and resid 60 through 68 Processing helix chain 'F' and resid 73 through 84 Processing helix chain 'F' and resid 86 through 106 removed outlier: 3.531A pdb=" N HIS F 102 " --> pdb=" O HIS F 98 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLU F 104 " --> pdb=" O ILE F 100 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LEU F 105 " --> pdb=" O TRP F 101 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 158 Processing helix chain 'F' and resid 185 through 213 removed outlier: 3.591A pdb=" N LEU F 210 " --> pdb=" O THR F 206 " (cutoff:3.500A) Processing helix chain 'F' and resid 215 through 218 No H-bonds generated for 'chain 'F' and resid 215 through 218' Processing sheet with id= A, first strand: chain 'A' and resid 51 through 53 Processing sheet with id= B, first strand: chain 'B' and resid 51 through 53 Processing sheet with id= C, first strand: chain 'C' and resid 51 through 53 Processing sheet with id= D, first strand: chain 'D' and resid 51 through 53 Processing sheet with id= E, first strand: chain 'E' and resid 51 through 53 Processing sheet with id= F, first strand: chain 'F' and resid 51 through 53 588 hydrogen bonds defined for protein. 1746 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: 6.51 Time building geometry restraints manager: 15.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 9576 1.03 - 1.23: 12 1.23 - 1.42: 4380 1.42 - 1.62: 5760 1.62 - 1.82: 84 Bond restraints: 19812 Sorted by residual: bond pdb=" CBS LMN C 301 " pdb=" CCM LMN C 301 " ideal model delta sigma weight residual 1.529 1.614 -0.085 2.00e-02 2.50e+03 1.81e+01 bond pdb=" CBS LMN A 303 " pdb=" CCM LMN A 303 " ideal model delta sigma weight residual 1.529 1.614 -0.085 2.00e-02 2.50e+03 1.81e+01 bond pdb=" CBS LMN E 301 " pdb=" CCM LMN E 301 " ideal model delta sigma weight residual 1.529 1.614 -0.085 2.00e-02 2.50e+03 1.79e+01 bond pdb=" CBS LMN D 301 " pdb=" CCM LMN D 301 " ideal model delta sigma weight residual 1.529 1.613 -0.084 2.00e-02 2.50e+03 1.77e+01 bond pdb=" CBS LMN A 301 " pdb=" CCM LMN A 301 " ideal model delta sigma weight residual 1.529 1.613 -0.084 2.00e-02 2.50e+03 1.76e+01 ... (remaining 19807 not shown) Histogram of bond angle deviations from ideal: 99.98 - 106.81: 876 106.81 - 113.63: 22076 113.63 - 120.45: 7070 120.45 - 127.28: 5358 127.28 - 134.10: 170 Bond angle restraints: 35550 Sorted by residual: angle pdb=" N GLY E 45 " pdb=" CA GLY E 45 " pdb=" C GLY E 45 " ideal model delta sigma weight residual 112.73 117.03 -4.30 1.20e+00 6.94e-01 1.28e+01 angle pdb=" N GLY D 45 " pdb=" CA GLY D 45 " pdb=" C GLY D 45 " ideal model delta sigma weight residual 112.73 117.00 -4.27 1.20e+00 6.94e-01 1.27e+01 angle pdb=" N GLY B 45 " pdb=" CA GLY B 45 " pdb=" C GLY B 45 " ideal model delta sigma weight residual 112.73 117.00 -4.27 1.20e+00 6.94e-01 1.26e+01 angle pdb=" N GLY C 45 " pdb=" CA GLY C 45 " pdb=" C GLY C 45 " ideal model delta sigma weight residual 112.73 116.99 -4.26 1.20e+00 6.94e-01 1.26e+01 angle pdb=" N GLY F 45 " pdb=" CA GLY F 45 " pdb=" C GLY F 45 " ideal model delta sigma weight residual 112.73 116.95 -4.22 1.20e+00 6.94e-01 1.23e+01 ... (remaining 35545 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.20: 8670 17.20 - 34.41: 750 34.41 - 51.61: 284 51.61 - 68.81: 142 68.81 - 86.01: 48 Dihedral angle restraints: 9894 sinusoidal: 5592 harmonic: 4302 Sorted by residual: dihedral pdb=" CAZ LMN A 303 " pdb=" CBB LMN A 303 " pdb=" CBD LMN A 303 " pdb=" CBF LMN A 303 " ideal model delta sinusoidal sigma weight residual 180.29 94.28 86.01 1 3.00e+01 1.11e-03 9.93e+00 dihedral pdb=" CAZ LMN E 301 " pdb=" CBB LMN E 301 " pdb=" CBD LMN E 301 " pdb=" CBF LMN E 301 " ideal model delta sinusoidal sigma weight residual 180.29 94.29 86.00 1 3.00e+01 1.11e-03 9.92e+00 dihedral pdb=" CAZ LMN A 301 " pdb=" CBB LMN A 301 " pdb=" CBD LMN A 301 " pdb=" CBF LMN A 301 " ideal model delta sinusoidal sigma weight residual 180.29 94.31 85.98 1 3.00e+01 1.11e-03 9.92e+00 ... (remaining 9891 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1132 0.045 - 0.089: 352 0.089 - 0.134: 82 0.134 - 0.178: 6 0.178 - 0.223: 6 Chirality restraints: 1578 Sorted by residual: chirality pdb=" CCV LMN D 301 " pdb=" CCR LMN D 301 " pdb=" CCT LMN D 301 " pdb=" OAU LMN D 301 " both_signs ideal model delta sigma weight residual False 2.28 2.50 -0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CCV LMN E 301 " pdb=" CCR LMN E 301 " pdb=" CCT LMN E 301 " pdb=" OAU LMN E 301 " both_signs ideal model delta sigma weight residual False 2.28 2.50 -0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CCV LMN A 301 " pdb=" CCR LMN A 301 " pdb=" CCT LMN A 301 " pdb=" OAU LMN A 301 " both_signs ideal model delta sigma weight residual False 2.28 2.50 -0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 1575 not shown) Planarity restraints: 2784 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 25 " 0.027 5.00e-02 4.00e+02 4.12e-02 2.71e+00 pdb=" N PRO A 26 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 26 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 26 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU E 25 " -0.027 5.00e-02 4.00e+02 4.10e-02 2.69e+00 pdb=" N PRO E 26 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO E 26 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO E 26 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 25 " -0.027 5.00e-02 4.00e+02 4.10e-02 2.69e+00 pdb=" N PRO D 26 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO D 26 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO D 26 " -0.023 5.00e-02 4.00e+02 ... (remaining 2781 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.28: 2799 2.28 - 2.86: 40516 2.86 - 3.44: 45908 3.44 - 4.02: 64988 4.02 - 4.60: 99563 Nonbonded interactions: 253774 Sorted by model distance: nonbonded pdb="HH11 ARG F 75 " pdb=" O HOH F 405 " model vdw 1.706 1.850 nonbonded pdb="HH11 ARG C 75 " pdb=" O HOH C 405 " model vdw 1.706 1.850 nonbonded pdb=" O CYS B 202 " pdb=" HG1 THR B 206 " model vdw 1.707 1.850 nonbonded pdb=" O CYS E 202 " pdb=" HG1 THR E 206 " model vdw 1.708 1.850 nonbonded pdb=" O CYS A 202 " pdb=" HG1 THR A 206 " model vdw 1.708 1.850 ... (remaining 253769 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 2 through 221) selection = (chain 'B' and resid 2 through 221) selection = (chain 'C' and resid 2 through 221) selection = (chain 'D' and resid 2 through 221) selection = (chain 'E' and resid 2 through 221) selection = (chain 'F' and resid 2 through 221) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.300 Extract box with map and model: 7.720 Check model and map are aligned: 0.270 Set scattering table: 0.170 Process input model: 60.720 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.070 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: 0.000 Load rotamer database and sin/cos tables:12.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 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 : 0.010 0.085 10224 Z= 0.664 Angle : 0.962 8.874 13872 Z= 0.425 Chirality : 0.047 0.223 1578 Planarity : 0.006 0.041 1650 Dihedral : 17.458 86.014 4194 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 0.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.01 % Allowed : 6.63 % Favored : 90.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.86 (0.20), residues: 1182 helix: -1.90 (0.13), residues: 822 sheet: 0.71 (0.65), residues: 60 loop : -1.82 (0.34), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 103 HIS 0.004 0.001 HIS D 98 PHE 0.013 0.002 PHE F 51 TYR 0.006 0.002 TYR D 156 ARG 0.004 0.001 ARG B 7 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 160 time to evaluate : 1.414 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 ARG cc_start: 0.7914 (OUTLIER) cc_final: 0.7010 (mtt-85) REVERT: A 50 GLU cc_start: 0.8502 (mt-10) cc_final: 0.8072 (mt-10) REVERT: A 132 ARG cc_start: 0.7174 (ptp-170) cc_final: 0.6151 (tpm170) REVERT: B 16 ARG cc_start: 0.7817 (OUTLIER) cc_final: 0.6938 (mtt-85) REVERT: B 50 GLU cc_start: 0.8628 (mt-10) cc_final: 0.8366 (mt-10) REVERT: B 102 HIS cc_start: 0.7959 (m-70) cc_final: 0.7718 (m-70) REVERT: B 132 ARG cc_start: 0.7175 (ptp-170) cc_final: 0.6258 (tpm170) REVERT: B 135 TRP cc_start: 0.7514 (m-10) cc_final: 0.7122 (m100) REVERT: C 16 ARG cc_start: 0.7905 (OUTLIER) cc_final: 0.6929 (mtt-85) REVERT: C 132 ARG cc_start: 0.7169 (ptp-170) cc_final: 0.6328 (tmt170) REVERT: C 135 TRP cc_start: 0.7492 (m-10) cc_final: 0.7177 (m100) REVERT: D 16 ARG cc_start: 0.7836 (OUTLIER) cc_final: 0.7005 (mtt-85) REVERT: D 50 GLU cc_start: 0.8582 (mt-10) cc_final: 0.8191 (mt-10) REVERT: D 132 ARG cc_start: 0.7149 (ptp-170) cc_final: 0.6125 (tpm170) REVERT: D 135 TRP cc_start: 0.7529 (m-10) cc_final: 0.7228 (m100) REVERT: E 16 ARG cc_start: 0.7796 (OUTLIER) cc_final: 0.6920 (mtt-85) REVERT: E 50 GLU cc_start: 0.8630 (mt-10) cc_final: 0.8369 (mt-10) REVERT: E 102 HIS cc_start: 0.7969 (m-70) cc_final: 0.7720 (m-70) REVERT: E 132 ARG cc_start: 0.7199 (ptp-170) cc_final: 0.6250 (tpm170) REVERT: E 135 TRP cc_start: 0.7530 (m-10) cc_final: 0.7157 (m100) REVERT: F 16 ARG cc_start: 0.7882 (OUTLIER) cc_final: 0.6934 (mtt-85) REVERT: F 132 ARG cc_start: 0.7161 (ptp-170) cc_final: 0.6312 (tmt170) REVERT: F 135 TRP cc_start: 0.7503 (m-10) cc_final: 0.7191 (m100) outliers start: 30 outliers final: 6 residues processed: 178 average time/residue: 2.9595 time to fit residues: 559.7298 Evaluate side-chains 131 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 119 time to evaluate : 1.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ARG Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain B residue 16 ARG Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain C residue 16 ARG Chi-restraints excluded: chain C residue 49 SER Chi-restraints excluded: chain D residue 16 ARG Chi-restraints excluded: chain D residue 49 SER Chi-restraints excluded: chain E residue 16 ARG Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain F residue 16 ARG Chi-restraints excluded: chain F residue 49 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 50 optimal weight: 7.9990 chunk 31 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 57 optimal weight: 0.5980 chunk 70 optimal weight: 5.9990 chunk 108 optimal weight: 1.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN B 80 GLN C 80 GLN D 80 GLN F 80 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 10224 Z= 0.226 Angle : 0.614 4.271 13872 Z= 0.314 Chirality : 0.037 0.126 1578 Planarity : 0.006 0.036 1650 Dihedral : 12.647 80.914 2106 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 1.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.51 % Allowed : 11.14 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.23), residues: 1182 helix: 0.75 (0.16), residues: 852 sheet: 0.63 (0.56), residues: 60 loop : -1.65 (0.40), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 103 HIS 0.002 0.001 HIS C 54 PHE 0.014 0.002 PHE B 94 TYR 0.009 0.002 TYR D 97 ARG 0.002 0.001 ARG F 32 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 110 time to evaluate : 1.732 Fit side-chains REVERT: A 16 ARG cc_start: 0.7939 (OUTLIER) cc_final: 0.7007 (mtt-85) REVERT: A 50 GLU cc_start: 0.8548 (mt-10) cc_final: 0.8168 (mt-10) REVERT: A 135 TRP cc_start: 0.7426 (m-10) cc_final: 0.7134 (m100) REVERT: B 16 ARG cc_start: 0.7874 (OUTLIER) cc_final: 0.7000 (mtt-85) REVERT: B 50 GLU cc_start: 0.8628 (mt-10) cc_final: 0.8391 (mt-10) REVERT: B 135 TRP cc_start: 0.7387 (m-10) cc_final: 0.7129 (m100) REVERT: C 16 ARG cc_start: 0.7954 (OUTLIER) cc_final: 0.6999 (mtt-85) REVERT: C 135 TRP cc_start: 0.7408 (m-10) cc_final: 0.7093 (m100) REVERT: D 16 ARG cc_start: 0.7950 (OUTLIER) cc_final: 0.7074 (mtt-85) REVERT: D 50 GLU cc_start: 0.8578 (mt-10) cc_final: 0.8201 (mt-10) REVERT: D 135 TRP cc_start: 0.7395 (m-10) cc_final: 0.7090 (m100) REVERT: E 16 ARG cc_start: 0.7885 (OUTLIER) cc_final: 0.7002 (mtt-85) REVERT: E 50 GLU cc_start: 0.8627 (mt-10) cc_final: 0.8394 (mt-10) REVERT: E 135 TRP cc_start: 0.7385 (m-10) cc_final: 0.7009 (m100) REVERT: F 16 ARG cc_start: 0.7943 (OUTLIER) cc_final: 0.6995 (mtt-85) REVERT: F 135 TRP cc_start: 0.7410 (m-10) cc_final: 0.7105 (m100) outliers start: 25 outliers final: 16 residues processed: 131 average time/residue: 3.4082 time to fit residues: 471.1903 Evaluate side-chains 131 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 109 time to evaluate : 1.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ARG Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain B residue 16 ARG Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain C residue 16 ARG Chi-restraints excluded: chain C residue 49 SER Chi-restraints excluded: chain C residue 166 SER Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain D residue 16 ARG Chi-restraints excluded: chain D residue 49 SER Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain E residue 16 ARG Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain F residue 16 ARG Chi-restraints excluded: chain F residue 49 SER Chi-restraints excluded: chain F residue 166 SER Chi-restraints excluded: chain F residue 178 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 60 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 90 optimal weight: 6.9990 chunk 74 optimal weight: 2.9990 chunk 30 optimal weight: 7.9990 chunk 109 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 108 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10224 Z= 0.177 Angle : 0.521 3.623 13872 Z= 0.261 Chirality : 0.034 0.114 1578 Planarity : 0.005 0.032 1650 Dihedral : 11.862 89.727 2106 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 1.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer: Outliers : 2.41 % Allowed : 11.45 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.25), residues: 1182 helix: 2.05 (0.18), residues: 852 sheet: 1.18 (0.58), residues: 60 loop : -1.61 (0.40), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 101 HIS 0.002 0.001 HIS B 98 PHE 0.011 0.002 PHE D 94 TYR 0.008 0.002 TYR D 156 ARG 0.004 0.000 ARG B 132 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 124 time to evaluate : 1.675 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 ARG cc_start: 0.7951 (OUTLIER) cc_final: 0.7090 (mtt-85) REVERT: A 50 GLU cc_start: 0.8520 (mt-10) cc_final: 0.8123 (mt-10) REVERT: A 135 TRP cc_start: 0.7366 (m-10) cc_final: 0.7083 (m100) REVERT: B 16 ARG cc_start: 0.7991 (OUTLIER) cc_final: 0.7094 (mtt-85) REVERT: B 50 GLU cc_start: 0.8618 (mt-10) cc_final: 0.8416 (mt-10) REVERT: B 102 HIS cc_start: 0.7840 (m-70) cc_final: 0.7576 (m-70) REVERT: B 135 TRP cc_start: 0.7332 (m-10) cc_final: 0.7120 (m100) REVERT: C 16 ARG cc_start: 0.7956 (OUTLIER) cc_final: 0.7070 (mtt-85) REVERT: C 102 HIS cc_start: 0.7845 (m-70) cc_final: 0.7633 (m-70) REVERT: C 135 TRP cc_start: 0.7409 (m-10) cc_final: 0.7130 (m100) REVERT: D 16 ARG cc_start: 0.7950 (OUTLIER) cc_final: 0.7108 (mtt-85) REVERT: D 50 GLU cc_start: 0.8537 (mt-10) cc_final: 0.8153 (mt-10) REVERT: D 135 TRP cc_start: 0.7322 (m-10) cc_final: 0.7041 (m100) REVERT: E 16 ARG cc_start: 0.7999 (OUTLIER) cc_final: 0.7149 (mtt-85) REVERT: E 50 GLU cc_start: 0.8618 (mt-10) cc_final: 0.8193 (mt-10) REVERT: E 102 HIS cc_start: 0.7847 (m-70) cc_final: 0.7594 (m-70) REVERT: E 135 TRP cc_start: 0.7337 (m-10) cc_final: 0.7096 (m100) REVERT: F 16 ARG cc_start: 0.7949 (OUTLIER) cc_final: 0.7059 (mtt-85) REVERT: F 135 TRP cc_start: 0.7411 (m-10) cc_final: 0.7134 (m100) outliers start: 24 outliers final: 6 residues processed: 148 average time/residue: 3.2229 time to fit residues: 505.0130 Evaluate side-chains 128 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 116 time to evaluate : 1.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ARG Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain B residue 16 ARG Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain C residue 16 ARG Chi-restraints excluded: chain C residue 49 SER Chi-restraints excluded: chain D residue 16 ARG Chi-restraints excluded: chain D residue 49 SER Chi-restraints excluded: chain E residue 16 ARG Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain F residue 16 ARG Chi-restraints excluded: chain F residue 49 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 107 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 115 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10224 Z= 0.221 Angle : 0.560 3.589 13872 Z= 0.280 Chirality : 0.036 0.115 1578 Planarity : 0.005 0.033 1650 Dihedral : 12.096 89.617 2106 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 1.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Rotamer: Outliers : 2.21 % Allowed : 12.65 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.25), residues: 1182 helix: 2.09 (0.18), residues: 858 sheet: 1.42 (0.59), residues: 60 loop : -1.53 (0.38), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 103 HIS 0.003 0.001 HIS F 98 PHE 0.013 0.002 PHE C 51 TYR 0.010 0.002 TYR C 156 ARG 0.002 0.000 ARG E 4 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 118 time to evaluate : 1.680 Fit side-chains REVERT: A 16 ARG cc_start: 0.7937 (OUTLIER) cc_final: 0.7293 (mtt-85) REVERT: A 50 GLU cc_start: 0.8549 (mt-10) cc_final: 0.8189 (mt-10) REVERT: A 135 TRP cc_start: 0.7411 (m-10) cc_final: 0.7133 (m100) REVERT: B 16 ARG cc_start: 0.8014 (OUTLIER) cc_final: 0.7278 (mtt-85) REVERT: B 50 GLU cc_start: 0.8638 (mt-10) cc_final: 0.8247 (mt-10) REVERT: B 102 HIS cc_start: 0.7867 (m-70) cc_final: 0.7614 (m-70) REVERT: B 135 TRP cc_start: 0.7355 (m-10) cc_final: 0.7136 (m100) REVERT: C 16 ARG cc_start: 0.7988 (OUTLIER) cc_final: 0.7197 (mtt-85) REVERT: C 135 TRP cc_start: 0.7435 (m-10) cc_final: 0.7176 (m100) REVERT: D 16 ARG cc_start: 0.7935 (OUTLIER) cc_final: 0.7279 (mtt-85) REVERT: D 50 GLU cc_start: 0.8564 (mt-10) cc_final: 0.8205 (mt-10) REVERT: D 135 TRP cc_start: 0.7400 (m-10) cc_final: 0.7119 (m100) REVERT: E 16 ARG cc_start: 0.8015 (OUTLIER) cc_final: 0.7316 (mtt-85) REVERT: E 50 GLU cc_start: 0.8631 (mt-10) cc_final: 0.8242 (mt-10) REVERT: E 102 HIS cc_start: 0.7879 (m-70) cc_final: 0.7633 (m-70) REVERT: E 135 TRP cc_start: 0.7351 (m-10) cc_final: 0.7119 (m100) REVERT: F 16 ARG cc_start: 0.7985 (OUTLIER) cc_final: 0.7204 (mtt-85) REVERT: F 135 TRP cc_start: 0.7434 (m-10) cc_final: 0.7180 (m100) outliers start: 22 outliers final: 12 residues processed: 139 average time/residue: 3.3838 time to fit residues: 497.2502 Evaluate side-chains 135 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 117 time to evaluate : 1.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ARG Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain B residue 16 ARG Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain C residue 16 ARG Chi-restraints excluded: chain C residue 49 SER Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain D residue 16 ARG Chi-restraints excluded: chain D residue 49 SER Chi-restraints excluded: chain D residue 69 HIS Chi-restraints excluded: chain E residue 16 ARG Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 69 HIS Chi-restraints excluded: chain F residue 16 ARG Chi-restraints excluded: chain F residue 49 SER Chi-restraints excluded: chain F residue 69 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 96 optimal weight: 0.7980 chunk 65 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 86 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 chunk 104 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10224 Z= 0.190 Angle : 0.517 3.501 13872 Z= 0.260 Chirality : 0.035 0.137 1578 Planarity : 0.005 0.040 1650 Dihedral : 10.406 89.485 2106 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 2.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Rotamer: Outliers : 1.71 % Allowed : 13.55 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.24 (0.25), residues: 1182 helix: 2.29 (0.18), residues: 858 sheet: 1.68 (0.61), residues: 60 loop : -1.41 (0.39), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 103 HIS 0.003 0.001 HIS A 102 PHE 0.012 0.002 PHE F 51 TYR 0.010 0.002 TYR F 156 ARG 0.003 0.000 ARG B 8 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 118 time to evaluate : 1.833 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8549 (mt-10) cc_final: 0.8178 (mt-10) REVERT: A 135 TRP cc_start: 0.7381 (m-10) cc_final: 0.7104 (m100) REVERT: A 220 ARG cc_start: 0.2645 (OUTLIER) cc_final: 0.2045 (tpm170) REVERT: B 16 ARG cc_start: 0.8054 (OUTLIER) cc_final: 0.7367 (mtt-85) REVERT: B 50 GLU cc_start: 0.8630 (mt-10) cc_final: 0.8234 (mt-10) REVERT: B 102 HIS cc_start: 0.7851 (m-70) cc_final: 0.7614 (m-70) REVERT: B 135 TRP cc_start: 0.7355 (m-10) cc_final: 0.7116 (m100) REVERT: B 220 ARG cc_start: 0.2632 (OUTLIER) cc_final: 0.1985 (tpm170) REVERT: C 135 TRP cc_start: 0.7455 (m-10) cc_final: 0.7188 (m100) REVERT: D 50 GLU cc_start: 0.8561 (mt-10) cc_final: 0.8189 (mt-10) REVERT: D 135 TRP cc_start: 0.7404 (m-10) cc_final: 0.7138 (m100) REVERT: D 220 ARG cc_start: 0.2608 (OUTLIER) cc_final: 0.1974 (tpm170) REVERT: E 16 ARG cc_start: 0.8072 (OUTLIER) cc_final: 0.7400 (mtt-85) REVERT: E 50 GLU cc_start: 0.8625 (mt-10) cc_final: 0.8232 (mt-10) REVERT: E 102 HIS cc_start: 0.7857 (m-70) cc_final: 0.7617 (m-70) REVERT: E 135 TRP cc_start: 0.7341 (m-10) cc_final: 0.7108 (m100) REVERT: E 220 ARG cc_start: 0.2579 (OUTLIER) cc_final: 0.1944 (tpm170) REVERT: F 135 TRP cc_start: 0.7452 (m-10) cc_final: 0.7182 (m100) outliers start: 17 outliers final: 6 residues processed: 135 average time/residue: 3.6080 time to fit residues: 513.0493 Evaluate side-chains 130 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 118 time to evaluate : 1.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain A residue 220 ARG Chi-restraints excluded: chain B residue 16 ARG Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain B residue 220 ARG Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain D residue 69 HIS Chi-restraints excluded: chain D residue 220 ARG Chi-restraints excluded: chain E residue 16 ARG Chi-restraints excluded: chain E residue 69 HIS Chi-restraints excluded: chain E residue 220 ARG Chi-restraints excluded: chain F residue 69 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 39 optimal weight: 5.9990 chunk 104 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 116 optimal weight: 0.6980 chunk 96 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 10224 Z= 0.150 Angle : 0.476 3.492 13872 Z= 0.240 Chirality : 0.034 0.138 1578 Planarity : 0.004 0.032 1650 Dihedral : 9.025 87.152 2084 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 1.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.08 % Favored : 99.92 % Rotamer: Outliers : 1.31 % Allowed : 13.86 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.57 (0.25), residues: 1182 helix: 2.49 (0.18), residues: 864 sheet: 1.87 (0.63), residues: 60 loop : -1.21 (0.40), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 103 HIS 0.002 0.001 HIS C 98 PHE 0.010 0.001 PHE C 51 TYR 0.008 0.002 TYR A 156 ARG 0.002 0.000 ARG F 8 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 118 time to evaluate : 1.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8537 (mt-10) cc_final: 0.8145 (mt-10) REVERT: A 135 TRP cc_start: 0.7360 (m-10) cc_final: 0.7093 (m100) REVERT: B 16 ARG cc_start: 0.8061 (OUTLIER) cc_final: 0.7360 (mtt-85) REVERT: B 50 GLU cc_start: 0.8620 (mt-10) cc_final: 0.8226 (mt-10) REVERT: B 135 TRP cc_start: 0.7335 (m-10) cc_final: 0.7107 (m100) REVERT: C 135 TRP cc_start: 0.7429 (m-10) cc_final: 0.7148 (m100) REVERT: D 50 GLU cc_start: 0.8548 (mt-10) cc_final: 0.8160 (mt-10) REVERT: D 135 TRP cc_start: 0.7369 (m-10) cc_final: 0.7103 (m100) REVERT: E 16 ARG cc_start: 0.8060 (OUTLIER) cc_final: 0.7356 (mtt-85) REVERT: E 50 GLU cc_start: 0.8617 (mt-10) cc_final: 0.8222 (mt-10) REVERT: E 135 TRP cc_start: 0.7325 (m-10) cc_final: 0.7100 (m100) REVERT: F 135 TRP cc_start: 0.7434 (m-10) cc_final: 0.7156 (m100) outliers start: 13 outliers final: 9 residues processed: 130 average time/residue: 3.5069 time to fit residues: 480.5590 Evaluate side-chains 129 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 118 time to evaluate : 1.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ARG Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain B residue 16 ARG Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain D residue 16 ARG Chi-restraints excluded: chain D residue 69 HIS Chi-restraints excluded: chain E residue 16 ARG Chi-restraints excluded: chain E residue 69 HIS Chi-restraints excluded: chain F residue 16 ARG Chi-restraints excluded: chain F residue 69 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 111 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 84 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 115 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10224 Z= 0.184 Angle : 0.509 3.442 13872 Z= 0.255 Chirality : 0.035 0.137 1578 Planarity : 0.005 0.039 1650 Dihedral : 9.017 86.571 2084 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 1.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Rotamer: Outliers : 1.31 % Allowed : 13.86 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.54 (0.25), residues: 1182 helix: 2.46 (0.18), residues: 864 sheet: 1.98 (0.65), residues: 60 loop : -1.25 (0.40), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 103 HIS 0.003 0.001 HIS E 102 PHE 0.013 0.002 PHE C 51 TYR 0.010 0.002 TYR E 156 ARG 0.002 0.000 ARG F 15 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 118 time to evaluate : 1.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8553 (mt-10) cc_final: 0.8193 (mt-10) REVERT: A 135 TRP cc_start: 0.7403 (m-10) cc_final: 0.7127 (m100) REVERT: B 50 GLU cc_start: 0.8623 (mt-10) cc_final: 0.8230 (mt-10) REVERT: B 102 HIS cc_start: 0.7817 (m-70) cc_final: 0.7564 (m-70) REVERT: B 135 TRP cc_start: 0.7343 (m-10) cc_final: 0.7120 (m100) REVERT: C 135 TRP cc_start: 0.7456 (m-10) cc_final: 0.7173 (m100) REVERT: D 50 GLU cc_start: 0.8557 (mt-10) cc_final: 0.8180 (mt-10) REVERT: D 135 TRP cc_start: 0.7380 (m-10) cc_final: 0.7122 (m100) REVERT: E 50 GLU cc_start: 0.8620 (mt-10) cc_final: 0.8227 (mt-10) REVERT: E 102 HIS cc_start: 0.7831 (m-70) cc_final: 0.7586 (m-70) REVERT: E 135 TRP cc_start: 0.7346 (m-10) cc_final: 0.7122 (m100) REVERT: F 135 TRP cc_start: 0.7455 (m-10) cc_final: 0.7151 (m100) outliers start: 13 outliers final: 9 residues processed: 130 average time/residue: 3.5506 time to fit residues: 486.5635 Evaluate side-chains 127 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 118 time to evaluate : 1.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ARG Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain D residue 16 ARG Chi-restraints excluded: chain D residue 69 HIS Chi-restraints excluded: chain E residue 69 HIS Chi-restraints excluded: chain F residue 16 ARG Chi-restraints excluded: chain F residue 69 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 71 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 10 optimal weight: 10.0000 chunk 90 optimal weight: 10.0000 chunk 105 optimal weight: 4.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.2995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10224 Z= 0.250 Angle : 0.577 3.472 13872 Z= 0.289 Chirality : 0.037 0.140 1578 Planarity : 0.005 0.037 1650 Dihedral : 9.385 86.416 2076 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 1.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.00 % Allowed : 14.26 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.27 (0.25), residues: 1182 helix: 2.27 (0.17), residues: 864 sheet: 1.81 (0.64), residues: 60 loop : -1.35 (0.39), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 103 HIS 0.003 0.001 HIS A 102 PHE 0.016 0.002 PHE F 51 TYR 0.012 0.003 TYR D 156 ARG 0.002 0.000 ARG D 15 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 117 time to evaluate : 1.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 TRP cc_start: 0.7402 (m-10) cc_final: 0.7128 (m100) REVERT: B 50 GLU cc_start: 0.8629 (mt-10) cc_final: 0.8256 (mt-10) REVERT: B 135 TRP cc_start: 0.7370 (m-10) cc_final: 0.7150 (m100) REVERT: C 135 TRP cc_start: 0.7472 (m-10) cc_final: 0.7170 (m100) REVERT: D 135 TRP cc_start: 0.7389 (m-10) cc_final: 0.7125 (m100) REVERT: E 50 GLU cc_start: 0.8626 (mt-10) cc_final: 0.8277 (mt-10) REVERT: E 135 TRP cc_start: 0.7366 (m-10) cc_final: 0.7154 (m100) REVERT: F 135 TRP cc_start: 0.7465 (m-10) cc_final: 0.7150 (m100) outliers start: 10 outliers final: 10 residues processed: 127 average time/residue: 3.5431 time to fit residues: 474.8715 Evaluate side-chains 127 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 117 time to evaluate : 1.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ARG Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain C residue 16 ARG Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain D residue 16 ARG Chi-restraints excluded: chain D residue 69 HIS Chi-restraints excluded: chain E residue 69 HIS Chi-restraints excluded: chain F residue 16 ARG Chi-restraints excluded: chain F residue 69 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 110 optimal weight: 7.9990 chunk 101 optimal weight: 6.9990 chunk 107 optimal weight: 0.3980 chunk 64 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 70 optimal weight: 0.6980 chunk 113 optimal weight: 0.5980 chunk 69 optimal weight: 2.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 10224 Z= 0.164 Angle : 0.497 3.470 13872 Z= 0.250 Chirality : 0.035 0.137 1578 Planarity : 0.005 0.033 1650 Dihedral : 8.657 88.751 2076 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 1.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Rotamer: Outliers : 0.90 % Allowed : 14.56 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.51 (0.25), residues: 1182 helix: 2.44 (0.18), residues: 864 sheet: 1.86 (0.64), residues: 60 loop : -1.23 (0.39), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 103 HIS 0.002 0.001 HIS D 102 PHE 0.011 0.001 PHE F 51 TYR 0.009 0.002 TYR C 156 ARG 0.001 0.000 ARG A 15 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 121 time to evaluate : 1.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8552 (mt-10) cc_final: 0.8167 (mt-10) REVERT: A 135 TRP cc_start: 0.7373 (m-10) cc_final: 0.7108 (m100) REVERT: B 50 GLU cc_start: 0.8632 (mt-10) cc_final: 0.8234 (mt-10) REVERT: B 135 TRP cc_start: 0.7348 (m-10) cc_final: 0.6989 (m100) REVERT: C 135 TRP cc_start: 0.7444 (m-10) cc_final: 0.7134 (m100) REVERT: D 50 GLU cc_start: 0.8561 (mt-10) cc_final: 0.8193 (mt-10) REVERT: D 132 ARG cc_start: 0.6958 (ptm160) cc_final: 0.6646 (ptm160) REVERT: D 135 TRP cc_start: 0.7366 (m-10) cc_final: 0.7102 (m100) REVERT: E 50 GLU cc_start: 0.8626 (mt-10) cc_final: 0.8224 (mt-10) REVERT: E 135 TRP cc_start: 0.7348 (m-10) cc_final: 0.6990 (m100) REVERT: F 135 TRP cc_start: 0.7454 (m-10) cc_final: 0.7140 (m100) outliers start: 9 outliers final: 9 residues processed: 130 average time/residue: 3.4446 time to fit residues: 473.9188 Evaluate side-chains 127 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 118 time to evaluate : 1.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ARG Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain D residue 16 ARG Chi-restraints excluded: chain D residue 69 HIS Chi-restraints excluded: chain E residue 69 HIS Chi-restraints excluded: chain F residue 16 ARG Chi-restraints excluded: chain F residue 69 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 54 optimal weight: 2.9990 chunk 79 optimal weight: 6.9990 chunk 119 optimal weight: 6.9990 chunk 110 optimal weight: 9.9990 chunk 95 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 101 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.3051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 10224 Z= 0.320 Angle : 0.631 3.688 13872 Z= 0.316 Chirality : 0.040 0.137 1578 Planarity : 0.006 0.053 1650 Dihedral : 9.595 85.438 2076 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 1.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.00 % Allowed : 14.46 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.10 (0.24), residues: 1182 helix: 2.16 (0.17), residues: 864 sheet: 1.77 (0.64), residues: 60 loop : -1.46 (0.38), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP F 77 HIS 0.003 0.001 HIS B 98 PHE 0.018 0.002 PHE C 51 TYR 0.013 0.004 TYR D 156 ARG 0.003 0.001 ARG D 15 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 117 time to evaluate : 1.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 TRP cc_start: 0.7426 (m-10) cc_final: 0.7142 (m100) REVERT: B 50 GLU cc_start: 0.8644 (mt-10) cc_final: 0.8302 (mt-10) REVERT: B 135 TRP cc_start: 0.7403 (m-10) cc_final: 0.7065 (m100) REVERT: C 135 TRP cc_start: 0.7491 (m-10) cc_final: 0.7181 (m100) REVERT: D 135 TRP cc_start: 0.7411 (m-10) cc_final: 0.7140 (m100) REVERT: E 50 GLU cc_start: 0.8631 (mt-10) cc_final: 0.8287 (mt-10) REVERT: E 135 TRP cc_start: 0.7413 (m-10) cc_final: 0.7072 (m100) REVERT: F 135 TRP cc_start: 0.7489 (m-10) cc_final: 0.7179 (m100) outliers start: 10 outliers final: 10 residues processed: 127 average time/residue: 3.5660 time to fit residues: 477.3079 Evaluate side-chains 127 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 117 time to evaluate : 1.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ARG Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain C residue 16 ARG Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain D residue 16 ARG Chi-restraints excluded: chain D residue 69 HIS Chi-restraints excluded: chain E residue 69 HIS Chi-restraints excluded: chain F residue 16 ARG Chi-restraints excluded: chain F residue 69 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 87 optimal weight: 0.8980 chunk 14 optimal weight: 0.2980 chunk 26 optimal weight: 0.7980 chunk 95 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.153483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.119650 restraints weight = 25316.951| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 1.23 r_work: 0.3059 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 10224 Z= 0.140 Angle : 0.479 3.544 13872 Z= 0.242 Chirality : 0.034 0.141 1578 Planarity : 0.005 0.050 1650 Dihedral : 8.469 89.956 2076 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 1.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Rotamer: Outliers : 1.00 % Allowed : 14.36 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.60 (0.25), residues: 1182 helix: 2.55 (0.18), residues: 858 sheet: 1.85 (0.64), residues: 60 loop : -1.27 (0.39), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 103 HIS 0.002 0.001 HIS C 54 PHE 0.009 0.001 PHE F 51 TYR 0.008 0.001 TYR C 156 ARG 0.001 0.000 ARG A 7 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8199.18 seconds wall clock time: 142 minutes 42.41 seconds (8562.41 seconds total)