Starting phenix.real_space_refine (version: 1.21rc1) on Wed Aug 16 09:29:13 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l3u_0826/08_2023/6l3u_0826_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l3u_0826/08_2023/6l3u_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_0826/08_2023/6l3u_0826.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l3u_0826/08_2023/6l3u_0826.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l3u_0826/08_2023/6l3u_0826_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l3u_0826/08_2023/6l3u_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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/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: 8.70, 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: 14.79 Conformation dependent library (CDL) restraints added in 1.6 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: 2.10 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: 7.32 Time building geometry restraints manager: 15.46 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: 7084 17.20 - 34.41: 602 34.41 - 51.61: 146 51.61 - 68.81: 46 68.81 - 86.01: 36 Dihedral angle restraints: 7914 sinusoidal: 3612 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 7911 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: 2.030 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: 0.320 Extract box with map and model: 8.760 Check model and map are aligned: 0.280 Set scattering table: 0.190 Process input model: 61.370 Find NCS groups from input model: 1.190 Set up NCS constraints: 0.100 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:11.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.790 ------------------------------------------------------------------------------- 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 : 16.879 86.014 3558 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 % 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 *********************** 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 : 1.509 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 6 residues processed: 178 average time/residue: 3.0013 time to fit residues: 567.4782 Evaluate side-chains 128 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 122 time to evaluate : 1.611 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 6 residues processed: 0 time to fit residues: 1.9074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 3.9990 chunk 90 optimal weight: 6.9990 chunk 50 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 57 optimal weight: 0.7980 chunk 70 optimal weight: 5.9990 chunk 108 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN C 80 GLN D 80 GLN F 80 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.020 10224 Z= 0.206 Angle : 0.612 4.085 13872 Z= 0.314 Chirality : 0.037 0.109 1578 Planarity : 0.006 0.034 1650 Dihedral : 8.975 68.549 1440 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer Outliers : 2.91 % 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: 0.44 (0.24), residues: 1182 helix: 0.92 (0.17), residues: 852 sheet: 0.63 (0.56), residues: 60 loop : -1.67 (0.39), residues: 270 *********************** 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 144 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 115 time to evaluate : 1.690 Fit side-chains outliers start: 29 outliers final: 16 residues processed: 132 average time/residue: 3.4189 time to fit residues: 476.9816 Evaluate side-chains 124 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 108 time to evaluate : 1.540 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 12 residues processed: 4 average time/residue: 0.2670 time to fit residues: 3.6089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 60 optimal weight: 0.4980 chunk 33 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 109 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 108 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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: 0.8284 moved from start: 0.2483 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= 0.179 Angle : 0.524 3.687 13872 Z= 0.261 Chirality : 0.034 0.115 1578 Planarity : 0.004 0.032 1650 Dihedral : 9.124 89.145 1440 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 1.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer Outliers : 1.51 % 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: 1.75 (0.25), residues: 1182 helix: 1.99 (0.18), residues: 852 sheet: 1.18 (0.58), residues: 60 loop : -1.65 (0.40), residues: 270 *********************** 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 135 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 120 time to evaluate : 1.716 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 8 residues processed: 135 average time/residue: 3.0984 time to fit residues: 443.9426 Evaluate side-chains 120 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 112 time to evaluate : 1.406 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 8 residues processed: 0 time to fit residues: 1.7427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 107 optimal weight: 0.6980 chunk 82 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 115 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- 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: 0.8321 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 10224 Z= 0.235 Angle : 0.578 3.684 13872 Z= 0.288 Chirality : 0.036 0.118 1578 Planarity : 0.005 0.033 1650 Dihedral : 9.260 88.704 1440 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 1.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer Outliers : 1.91 % 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: 1.86 (0.25), residues: 1182 helix: 2.10 (0.17), residues: 852 sheet: 1.35 (0.59), residues: 60 loop : -1.76 (0.39), residues: 270 *********************** 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 134 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 115 time to evaluate : 1.509 Fit side-chains outliers start: 19 outliers final: 13 residues processed: 133 average time/residue: 3.2463 time to fit residues: 457.4285 Evaluate side-chains 127 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 114 time to evaluate : 1.548 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 13 residues processed: 0 time to fit residues: 1.8754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 96 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 86 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 104 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- 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: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.019 10224 Z= 0.139 Angle : 0.479 3.718 13872 Z= 0.241 Chirality : 0.033 0.114 1578 Planarity : 0.004 0.029 1650 Dihedral : 8.799 89.511 1440 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 1.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer Outliers : 1.71 % 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: 2.25 (0.25), residues: 1182 helix: 2.32 (0.18), residues: 858 sheet: 1.56 (0.60), residues: 60 loop : -1.46 (0.38), residues: 264 *********************** 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 132 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 115 time to evaluate : 1.758 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 14 residues processed: 132 average time/residue: 3.2556 time to fit residues: 456.1447 Evaluate side-chains 128 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 114 time to evaluate : 1.595 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 14 residues processed: 0 time to fit residues: 1.9199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7980 chunk 28 optimal weight: 1.9990 chunk 116 optimal weight: 0.0870 chunk 96 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 overall best weight: 1.1764 ------------------------------------------------------------------------------- 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: 0.8287 moved from start: 0.3072 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= 0.147 Angle : 0.474 3.708 13872 Z= 0.236 Chirality : 0.033 0.139 1578 Planarity : 0.004 0.028 1650 Dihedral : 8.201 82.532 1440 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 1.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Rotamer Outliers : 1.61 % 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: 2.55 (0.18), residues: 858 sheet: 1.89 (0.62), residues: 60 loop : -1.39 (0.39), residues: 264 *********************** 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 130 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 114 time to evaluate : 1.599 Fit side-chains outliers start: 16 outliers final: 13 residues processed: 130 average time/residue: 3.1740 time to fit residues: 438.0158 Evaluate side-chains 126 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 113 time to evaluate : 1.562 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 13 residues processed: 0 time to fit residues: 1.9187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 111 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 65 optimal weight: 0.2980 chunk 97 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 115 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 70 optimal weight: 0.0070 chunk 53 optimal weight: 3.9990 overall best weight: 1.0202 ------------------------------------------------------------------------------- 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: 0.8279 moved from start: 0.3140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.019 10224 Z= 0.131 Angle : 0.453 3.722 13872 Z= 0.227 Chirality : 0.033 0.136 1578 Planarity : 0.004 0.042 1650 Dihedral : 7.650 72.721 1440 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 1.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer Outliers : 1.61 % 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: 2.70 (0.25), residues: 1182 helix: 2.65 (0.18), residues: 858 sheet: 2.04 (0.65), residues: 60 loop : -1.37 (0.38), residues: 264 *********************** 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 130 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 114 time to evaluate : 1.534 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 13 residues processed: 129 average time/residue: 3.2570 time to fit residues: 445.2501 Evaluate side-chains 127 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 114 time to evaluate : 1.600 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 13 residues processed: 0 time to fit residues: 1.9395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 71 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 10 optimal weight: 9.9990 chunk 90 optimal weight: 10.0000 chunk 105 optimal weight: 0.0770 overall best weight: 2.4146 ------------------------------------------------------------------------------- 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: 0.3147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 10224 Z= 0.232 Angle : 0.557 3.646 13872 Z= 0.276 Chirality : 0.036 0.134 1578 Planarity : 0.004 0.037 1650 Dihedral : 8.010 74.138 1440 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 1.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer Outliers : 1.51 % 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: 2.46 (0.25), residues: 1182 helix: 2.37 (0.17), residues: 870 sheet: 1.89 (0.64), residues: 60 loop : -1.21 (0.39), residues: 252 *********************** 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 129 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 114 time to evaluate : 1.711 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 13 residues processed: 129 average time/residue: 3.2760 time to fit residues: 448.2080 Evaluate side-chains 127 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 114 time to evaluate : 1.578 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 13 residues processed: 0 time to fit residues: 1.9309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 110 optimal weight: 6.9990 chunk 101 optimal weight: 6.9990 chunk 107 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 70 optimal weight: 0.6980 chunk 113 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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: 0.8302 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.023 10224 Z= 0.163 Angle : 0.489 4.039 13872 Z= 0.245 Chirality : 0.034 0.139 1578 Planarity : 0.004 0.049 1650 Dihedral : 7.538 65.558 1440 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 1.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer Outliers : 1.31 % 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: 2.55 (0.25), residues: 1182 helix: 2.48 (0.18), residues: 864 sheet: 1.96 (0.65), residues: 60 loop : -1.30 (0.39), residues: 258 *********************** 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 127 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 114 time to evaluate : 1.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 13 residues processed: 127 average time/residue: 3.3582 time to fit residues: 452.4867 Evaluate side-chains 127 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 114 time to evaluate : 1.581 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 13 residues processed: 0 time to fit residues: 1.9237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 54 optimal weight: 0.9990 chunk 79 optimal weight: 4.9990 chunk 119 optimal weight: 3.9990 chunk 110 optimal weight: 8.9990 chunk 95 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 75 optimal weight: 1.9990 chunk 101 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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: 0.8329 moved from start: 0.3215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 10224 Z= 0.248 Angle : 0.568 4.058 13872 Z= 0.282 Chirality : 0.037 0.137 1578 Planarity : 0.005 0.036 1650 Dihedral : 7.772 67.768 1440 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 1.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer Outliers : 1.31 % 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: 2.36 (0.25), residues: 1182 helix: 2.29 (0.17), residues: 870 sheet: 1.88 (0.65), residues: 60 loop : -1.24 (0.38), residues: 252 ********************** 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: 13 poor density : 114 time to evaluate : 1.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 13 residues processed: 127 average time/residue: 3.3252 time to fit residues: 447.3375 Evaluate side-chains 127 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 114 time to evaluate : 1.636 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 13 residues processed: 0 time to fit residues: 1.8822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 87 optimal weight: 0.4980 chunk 14 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 95 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 = 0.3725 r_free = 0.3725 target = 0.155621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.116706 restraints weight = 25269.918| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 1.37 r_work: 0.3035 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.3276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.021 10224 Z= 0.147 Angle : 0.475 3.790 13872 Z= 0.239 Chirality : 0.034 0.139 1578 Planarity : 0.004 0.034 1650 Dihedral : 7.230 56.018 1440 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 1.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Rotamer Outliers : 1.41 % 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: 2.52 (0.18), residues: 864 sheet: 2.00 (0.65), residues: 60 loop : -1.27 (0.39), residues: 258 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7817.55 seconds wall clock time: 136 minutes 55.58 seconds (8215.58 seconds total)