Starting phenix.real_space_refine on Fri Mar 22 07:31:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xki_33254/03_2024/7xki_33254_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xki_33254/03_2024/7xki_33254.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xki_33254/03_2024/7xki_33254.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xki_33254/03_2024/7xki_33254.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xki_33254/03_2024/7xki_33254_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xki_33254/03_2024/7xki_33254_trim_updated.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.059 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 156 5.16 5 C 10836 2.51 5 N 2544 2.21 5 O 2748 1.98 5 H 15996 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 32280 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 2663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 2663 Classifications: {'peptide': 166} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 159} Chain breaks: 1 Chain: "B" Number of atoms: 2663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 2663 Classifications: {'peptide': 166} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 159} Chain breaks: 1 Chain: "C" Number of atoms: 2663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 2663 Classifications: {'peptide': 166} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 159} Chain breaks: 1 Chain: "D" Number of atoms: 2663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 2663 Classifications: {'peptide': 166} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 159} Chain breaks: 1 Chain: "E" Number of atoms: 2663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 2663 Classifications: {'peptide': 166} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 159} Chain breaks: 1 Chain: "F" Number of atoms: 2663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 2663 Classifications: {'peptide': 166} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 159} Chain breaks: 1 Chain: "G" Number of atoms: 2663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 2663 Classifications: {'peptide': 166} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 159} Chain breaks: 1 Chain: "H" Number of atoms: 2663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 2663 Classifications: {'peptide': 166} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 159} Chain breaks: 1 Chain: "I" Number of atoms: 2663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 2663 Classifications: {'peptide': 166} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 159} Chain breaks: 1 Chain: "J" Number of atoms: 2663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 2663 Classifications: {'peptide': 166} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 159} Chain breaks: 1 Chain: "K" Number of atoms: 2663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 2663 Classifications: {'peptide': 166} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 159} Chain breaks: 1 Chain: "L" Number of atoms: 2663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 2663 Classifications: {'peptide': 166} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 159} Chain breaks: 1 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 27 Unusual residues: {'MC3': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 157 Unresolved non-hydrogen angles: 193 Unresolved non-hydrogen dihedrals: 141 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'MC3:plan-2': 4, 'MC3:plan-1': 4} Unresolved non-hydrogen planarities: 31 Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 27 Unusual residues: {'MC3': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 157 Unresolved non-hydrogen angles: 193 Unresolved non-hydrogen dihedrals: 141 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'MC3:plan-2': 4, 'MC3:plan-1': 4} Unresolved non-hydrogen planarities: 31 Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 27 Unusual residues: {'MC3': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 157 Unresolved non-hydrogen angles: 193 Unresolved non-hydrogen dihedrals: 141 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'MC3:plan-2': 4, 'MC3:plan-1': 4} Unresolved non-hydrogen planarities: 31 Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 27 Unusual residues: {'MC3': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 157 Unresolved non-hydrogen angles: 193 Unresolved non-hydrogen dihedrals: 141 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'MC3:plan-2': 4, 'MC3:plan-1': 4} Unresolved non-hydrogen planarities: 31 Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 27 Unusual residues: {'MC3': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 157 Unresolved non-hydrogen angles: 193 Unresolved non-hydrogen dihedrals: 141 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'MC3:plan-2': 4, 'MC3:plan-1': 4} Unresolved non-hydrogen planarities: 31 Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 27 Unusual residues: {'MC3': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 157 Unresolved non-hydrogen angles: 193 Unresolved non-hydrogen dihedrals: 141 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'MC3:plan-2': 4, 'MC3:plan-1': 4} Unresolved non-hydrogen planarities: 31 Chain: "G" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 27 Unusual residues: {'MC3': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 157 Unresolved non-hydrogen angles: 193 Unresolved non-hydrogen dihedrals: 141 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'MC3:plan-2': 4, 'MC3:plan-1': 4} Unresolved non-hydrogen planarities: 31 Chain: "H" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 27 Unusual residues: {'MC3': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 157 Unresolved non-hydrogen angles: 193 Unresolved non-hydrogen dihedrals: 141 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'MC3:plan-2': 4, 'MC3:plan-1': 4} Unresolved non-hydrogen planarities: 31 Chain: "I" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 27 Unusual residues: {'MC3': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 157 Unresolved non-hydrogen angles: 193 Unresolved non-hydrogen dihedrals: 141 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'MC3:plan-2': 4, 'MC3:plan-1': 4} Unresolved non-hydrogen planarities: 31 Chain: "J" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 27 Unusual residues: {'MC3': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 157 Unresolved non-hydrogen angles: 193 Unresolved non-hydrogen dihedrals: 141 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'MC3:plan-2': 4, 'MC3:plan-1': 4} Unresolved non-hydrogen planarities: 31 Chain: "K" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 27 Unusual residues: {'MC3': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 157 Unresolved non-hydrogen angles: 193 Unresolved non-hydrogen dihedrals: 141 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'MC3:plan-2': 4, 'MC3:plan-1': 4} Unresolved non-hydrogen planarities: 31 Chain: "L" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 27 Unusual residues: {'MC3': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 157 Unresolved non-hydrogen angles: 193 Unresolved non-hydrogen dihedrals: 141 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'MC3:plan-2': 4, 'MC3:plan-1': 4} Unresolved non-hydrogen planarities: 31 Time building chain proxies: 13.56, per 1000 atoms: 0.42 Number of scatterers: 32280 At special positions: 0 Unit cell: (97.1568, 99.1809, 147.759, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 156 16.00 O 2748 8.00 N 2544 7.00 C 10836 6.00 H 15996 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 55 " - pdb=" SG CYS A 242 " distance=2.03 Simple disulfide: pdb=" SG CYS A 62 " - pdb=" SG CYS A 236 " distance=2.03 Simple disulfide: pdb=" SG CYS A 66 " - pdb=" SG CYS A 231 " distance=2.03 Simple disulfide: pdb=" SG CYS B 55 " - pdb=" SG CYS B 242 " distance=2.03 Simple disulfide: pdb=" SG CYS B 62 " - pdb=" SG CYS B 236 " distance=2.03 Simple disulfide: pdb=" SG CYS B 66 " - pdb=" SG CYS B 231 " distance=2.03 Simple disulfide: pdb=" SG CYS C 55 " - pdb=" SG CYS C 242 " distance=2.03 Simple disulfide: pdb=" SG CYS C 62 " - pdb=" SG CYS C 236 " distance=2.03 Simple disulfide: pdb=" SG CYS C 66 " - pdb=" SG CYS C 231 " distance=2.03 Simple disulfide: pdb=" SG CYS D 55 " - pdb=" SG CYS D 242 " distance=2.03 Simple disulfide: pdb=" SG CYS D 62 " - pdb=" SG CYS D 236 " distance=2.03 Simple disulfide: pdb=" SG CYS D 66 " - pdb=" SG CYS D 231 " distance=2.03 Simple disulfide: pdb=" SG CYS E 55 " - pdb=" SG CYS E 242 " distance=2.03 Simple disulfide: pdb=" SG CYS E 62 " - pdb=" SG CYS E 236 " distance=2.03 Simple disulfide: pdb=" SG CYS E 66 " - pdb=" SG CYS E 231 " distance=2.03 Simple disulfide: pdb=" SG CYS F 55 " - pdb=" SG CYS F 242 " distance=2.03 Simple disulfide: pdb=" SG CYS F 62 " - pdb=" SG CYS F 236 " distance=2.03 Simple disulfide: pdb=" SG CYS F 66 " - pdb=" SG CYS F 231 " distance=2.03 Simple disulfide: pdb=" SG CYS G 55 " - pdb=" SG CYS G 242 " distance=2.03 Simple disulfide: pdb=" SG CYS G 62 " - pdb=" SG CYS G 236 " distance=2.03 Simple disulfide: pdb=" SG CYS G 66 " - pdb=" SG CYS G 231 " distance=2.03 Simple disulfide: pdb=" SG CYS H 55 " - pdb=" SG CYS H 242 " distance=2.03 Simple disulfide: pdb=" SG CYS H 62 " - pdb=" SG CYS H 236 " distance=2.03 Simple disulfide: pdb=" SG CYS H 66 " - pdb=" SG CYS H 231 " distance=2.03 Simple disulfide: pdb=" SG CYS I 55 " - pdb=" SG CYS I 242 " distance=2.03 Simple disulfide: pdb=" SG CYS I 62 " - pdb=" SG CYS I 236 " distance=2.03 Simple disulfide: pdb=" SG CYS I 66 " - pdb=" SG CYS I 231 " distance=2.03 Simple disulfide: pdb=" SG CYS J 55 " - pdb=" SG CYS J 242 " distance=2.03 Simple disulfide: pdb=" SG CYS J 62 " - pdb=" SG CYS J 236 " distance=2.03 Simple disulfide: pdb=" SG CYS J 66 " - pdb=" SG CYS J 231 " distance=2.03 Simple disulfide: pdb=" SG CYS K 55 " - pdb=" SG CYS K 242 " distance=2.03 Simple disulfide: pdb=" SG CYS K 62 " - pdb=" SG CYS K 236 " distance=2.03 Simple disulfide: pdb=" SG CYS K 66 " - pdb=" SG CYS K 231 " distance=2.03 Simple disulfide: pdb=" SG CYS L 55 " - pdb=" SG CYS L 242 " distance=2.03 Simple disulfide: pdb=" SG CYS L 62 " - pdb=" SG CYS L 236 " distance=2.03 Simple disulfide: pdb=" SG CYS L 66 " - pdb=" SG CYS L 231 " 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: 23.26 Conformation dependent library (CDL) restraints added in 3.1 seconds 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3744 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 71 helices and 12 sheets defined 68.2% alpha, 3.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.30 Creating SS restraints... Processing helix chain 'A' and resid 20 through 40 removed outlier: 4.057A pdb=" N ARG A 24 " --> pdb=" O THR A 20 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ILE A 25 " --> pdb=" O MET A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 46 No H-bonds generated for 'chain 'A' and resid 44 through 46' Processing helix chain 'A' and resid 62 through 70 Processing helix chain 'A' and resid 75 through 86 Processing helix chain 'A' and resid 88 through 100 Processing helix chain 'A' and resid 195 through 220 Processing helix chain 'A' and resid 247 through 275 Processing helix chain 'B' and resid 20 through 40 removed outlier: 3.977A pdb=" N ARG B 24 " --> pdb=" O THR B 20 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ILE B 25 " --> pdb=" O MET B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 46 No H-bonds generated for 'chain 'B' and resid 44 through 46' Processing helix chain 'B' and resid 62 through 70 Processing helix chain 'B' and resid 75 through 100 removed outlier: 3.650A pdb=" N CYS B 87 " --> pdb=" O ILE B 83 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N THR B 88 " --> pdb=" O ILE B 84 " (cutoff:3.500A) Proline residue: B 89 - end of helix Processing helix chain 'B' and resid 195 through 220 Processing helix chain 'B' and resid 247 through 275 Processing helix chain 'C' and resid 20 through 40 removed outlier: 4.014A pdb=" N ARG C 24 " --> pdb=" O THR C 20 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE C 25 " --> pdb=" O MET C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 46 No H-bonds generated for 'chain 'C' and resid 44 through 46' Processing helix chain 'C' and resid 62 through 70 Processing helix chain 'C' and resid 75 through 100 removed outlier: 3.594A pdb=" N CYS C 87 " --> pdb=" O ILE C 83 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N THR C 88 " --> pdb=" O ILE C 84 " (cutoff:3.500A) Proline residue: C 89 - end of helix Processing helix chain 'C' and resid 195 through 220 Processing helix chain 'C' and resid 247 through 275 Processing helix chain 'D' and resid 20 through 41 removed outlier: 4.053A pdb=" N ARG D 24 " --> pdb=" O THR D 20 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE D 25 " --> pdb=" O MET D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 46 No H-bonds generated for 'chain 'D' and resid 44 through 46' Processing helix chain 'D' and resid 62 through 70 Processing helix chain 'D' and resid 75 through 100 removed outlier: 3.630A pdb=" N CYS D 87 " --> pdb=" O ILE D 83 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N THR D 88 " --> pdb=" O ILE D 84 " (cutoff:3.500A) Proline residue: D 89 - end of helix Processing helix chain 'D' and resid 195 through 221 Processing helix chain 'D' and resid 247 through 275 Processing helix chain 'E' and resid 20 through 40 removed outlier: 4.022A pdb=" N ARG E 24 " --> pdb=" O THR E 20 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ILE E 25 " --> pdb=" O MET E 21 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 70 Processing helix chain 'E' and resid 75 through 100 removed outlier: 3.675A pdb=" N CYS E 87 " --> pdb=" O ILE E 83 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N THR E 88 " --> pdb=" O ILE E 84 " (cutoff:3.500A) Proline residue: E 89 - end of helix Processing helix chain 'E' and resid 195 through 220 Processing helix chain 'E' and resid 247 through 275 Processing helix chain 'F' and resid 20 through 40 removed outlier: 3.971A pdb=" N ARG F 24 " --> pdb=" O THR F 20 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ILE F 25 " --> pdb=" O MET F 21 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 70 Processing helix chain 'F' and resid 75 through 100 removed outlier: 3.612A pdb=" N CYS F 87 " --> pdb=" O ILE F 83 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR F 88 " --> pdb=" O ILE F 84 " (cutoff:3.500A) Proline residue: F 89 - end of helix Processing helix chain 'F' and resid 195 through 220 Processing helix chain 'F' and resid 247 through 275 Processing helix chain 'G' and resid 20 through 40 removed outlier: 4.102A pdb=" N ARG G 24 " --> pdb=" O THR G 20 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE G 25 " --> pdb=" O MET G 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 44 through 46 No H-bonds generated for 'chain 'G' and resid 44 through 46' Processing helix chain 'G' and resid 62 through 70 Processing helix chain 'G' and resid 75 through 100 removed outlier: 3.631A pdb=" N CYS G 87 " --> pdb=" O ILE G 83 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N THR G 88 " --> pdb=" O ILE G 84 " (cutoff:3.500A) Proline residue: G 89 - end of helix Processing helix chain 'G' and resid 195 through 220 Processing helix chain 'G' and resid 247 through 275 Processing helix chain 'H' and resid 20 through 40 removed outlier: 4.066A pdb=" N ARG H 24 " --> pdb=" O THR H 20 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE H 25 " --> pdb=" O MET H 21 " (cutoff:3.500A) Processing helix chain 'H' and resid 44 through 46 No H-bonds generated for 'chain 'H' and resid 44 through 46' Processing helix chain 'H' and resid 62 through 70 Processing helix chain 'H' and resid 75 through 100 removed outlier: 3.624A pdb=" N CYS H 87 " --> pdb=" O ILE H 83 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N THR H 88 " --> pdb=" O ILE H 84 " (cutoff:3.500A) Proline residue: H 89 - end of helix Processing helix chain 'H' and resid 195 through 220 Processing helix chain 'H' and resid 247 through 275 Processing helix chain 'I' and resid 22 through 40 Processing helix chain 'I' and resid 44 through 46 No H-bonds generated for 'chain 'I' and resid 44 through 46' Processing helix chain 'I' and resid 62 through 70 Processing helix chain 'I' and resid 75 through 100 removed outlier: 3.681A pdb=" N CYS I 87 " --> pdb=" O ILE I 83 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N THR I 88 " --> pdb=" O ILE I 84 " (cutoff:3.500A) Proline residue: I 89 - end of helix Processing helix chain 'I' and resid 195 through 220 Processing helix chain 'I' and resid 247 through 275 Processing helix chain 'J' and resid 20 through 40 removed outlier: 4.012A pdb=" N ARG J 24 " --> pdb=" O THR J 20 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ILE J 25 " --> pdb=" O MET J 21 " (cutoff:3.500A) Processing helix chain 'J' and resid 44 through 46 No H-bonds generated for 'chain 'J' and resid 44 through 46' Processing helix chain 'J' and resid 62 through 70 Processing helix chain 'J' and resid 75 through 100 removed outlier: 3.621A pdb=" N CYS J 87 " --> pdb=" O ILE J 83 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N THR J 88 " --> pdb=" O ILE J 84 " (cutoff:3.500A) Proline residue: J 89 - end of helix Processing helix chain 'J' and resid 195 through 220 Processing helix chain 'J' and resid 247 through 275 Processing helix chain 'K' and resid 20 through 40 removed outlier: 3.926A pdb=" N ARG K 24 " --> pdb=" O THR K 20 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ILE K 25 " --> pdb=" O MET K 21 " (cutoff:3.500A) Processing helix chain 'K' and resid 44 through 46 No H-bonds generated for 'chain 'K' and resid 44 through 46' Processing helix chain 'K' and resid 62 through 70 Processing helix chain 'K' and resid 75 through 100 removed outlier: 3.581A pdb=" N CYS K 87 " --> pdb=" O ILE K 83 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N THR K 88 " --> pdb=" O ILE K 84 " (cutoff:3.500A) Proline residue: K 89 - end of helix Processing helix chain 'K' and resid 195 through 220 Processing helix chain 'K' and resid 247 through 275 Processing helix chain 'L' and resid 22 through 40 Processing helix chain 'L' and resid 44 through 46 No H-bonds generated for 'chain 'L' and resid 44 through 46' Processing helix chain 'L' and resid 62 through 70 Processing helix chain 'L' and resid 75 through 100 removed outlier: 3.644A pdb=" N CYS L 87 " --> pdb=" O ILE L 83 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N THR L 88 " --> pdb=" O ILE L 84 " (cutoff:3.500A) Proline residue: L 89 - end of helix Processing helix chain 'L' and resid 195 through 220 Processing helix chain 'L' and resid 247 through 275 Processing sheet with id= A, first strand: chain 'A' and resid 228 through 231 Processing sheet with id= B, first strand: chain 'B' and resid 228 through 231 Processing sheet with id= C, first strand: chain 'C' and resid 228 through 231 Processing sheet with id= D, first strand: chain 'D' and resid 228 through 231 Processing sheet with id= E, first strand: chain 'E' and resid 228 through 231 Processing sheet with id= F, first strand: chain 'F' and resid 228 through 231 Processing sheet with id= G, first strand: chain 'G' and resid 228 through 231 Processing sheet with id= H, first strand: chain 'H' and resid 228 through 231 Processing sheet with id= I, first strand: chain 'I' and resid 228 through 231 Processing sheet with id= J, first strand: chain 'J' and resid 228 through 231 Processing sheet with id= K, first strand: chain 'K' and resid 228 through 231 Processing sheet with id= L, first strand: chain 'L' and resid 228 through 231 1058 hydrogen bonds defined for protein. 3138 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.48 Time building geometry restraints manager: 24.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 15960 1.03 - 1.23: 192 1.23 - 1.43: 6840 1.43 - 1.62: 9420 1.62 - 1.82: 204 Bond restraints: 32616 Sorted by residual: bond pdb=" N LYS G 238 " pdb=" CA LYS G 238 " ideal model delta sigma weight residual 1.471 1.456 0.014 1.74e-02 3.30e+03 6.66e-01 bond pdb=" N LYS E 238 " pdb=" CA LYS E 238 " ideal model delta sigma weight residual 1.471 1.457 0.014 1.74e-02 3.30e+03 6.44e-01 bond pdb=" N LYS I 238 " pdb=" CA LYS I 238 " ideal model delta sigma weight residual 1.471 1.457 0.014 1.74e-02 3.30e+03 6.23e-01 bond pdb=" N LYS L 238 " pdb=" CA LYS L 238 " ideal model delta sigma weight residual 1.471 1.457 0.014 1.74e-02 3.30e+03 6.20e-01 bond pdb=" N LYS C 238 " pdb=" CA LYS C 238 " ideal model delta sigma weight residual 1.471 1.457 0.014 1.74e-02 3.30e+03 6.06e-01 ... (remaining 32611 not shown) Histogram of bond angle deviations from ideal: 100.81 - 107.44: 931 107.44 - 114.07: 37635 114.07 - 120.70: 12616 120.70 - 127.33: 7218 127.33 - 133.96: 124 Bond angle restraints: 58524 Sorted by residual: angle pdb=" C LYS C 238 " pdb=" CA LYS C 238 " pdb=" CB LYS C 238 " ideal model delta sigma weight residual 116.34 111.69 4.65 1.40e+00 5.10e-01 1.10e+01 angle pdb=" C LYS D 238 " pdb=" CA LYS D 238 " pdb=" CB LYS D 238 " ideal model delta sigma weight residual 116.34 111.74 4.60 1.40e+00 5.10e-01 1.08e+01 angle pdb=" C LYS H 238 " pdb=" CA LYS H 238 " pdb=" CB LYS H 238 " ideal model delta sigma weight residual 116.34 111.81 4.53 1.40e+00 5.10e-01 1.05e+01 angle pdb=" C LYS J 238 " pdb=" CA LYS J 238 " pdb=" CB LYS J 238 " ideal model delta sigma weight residual 116.34 111.82 4.52 1.40e+00 5.10e-01 1.04e+01 angle pdb=" C LYS L 238 " pdb=" CA LYS L 238 " pdb=" CB LYS L 238 " ideal model delta sigma weight residual 116.34 111.89 4.45 1.40e+00 5.10e-01 1.01e+01 ... (remaining 58519 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 14240 17.99 - 35.97: 982 35.97 - 53.96: 315 53.96 - 71.94: 27 71.94 - 89.93: 12 Dihedral angle restraints: 15576 sinusoidal: 8304 harmonic: 7272 Sorted by residual: dihedral pdb=" CB CYS I 62 " pdb=" SG CYS I 62 " pdb=" SG CYS I 236 " pdb=" CB CYS I 236 " ideal model delta sinusoidal sigma weight residual 93.00 125.71 -32.71 1 1.00e+01 1.00e-02 1.52e+01 dihedral pdb=" CB CYS L 62 " pdb=" SG CYS L 62 " pdb=" SG CYS L 236 " pdb=" CB CYS L 236 " ideal model delta sinusoidal sigma weight residual 93.00 125.58 -32.58 1 1.00e+01 1.00e-02 1.51e+01 dihedral pdb=" CB CYS H 62 " pdb=" SG CYS H 62 " pdb=" SG CYS H 236 " pdb=" CB CYS H 236 " ideal model delta sinusoidal sigma weight residual 93.00 125.07 -32.07 1 1.00e+01 1.00e-02 1.47e+01 ... (remaining 15573 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1701 0.027 - 0.054: 379 0.054 - 0.081: 396 0.081 - 0.109: 103 0.109 - 0.136: 25 Chirality restraints: 2604 Sorted by residual: chirality pdb=" CA ILE L 73 " pdb=" N ILE L 73 " pdb=" C ILE L 73 " pdb=" CB ILE L 73 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.60e-01 chirality pdb=" CA ILE B 73 " pdb=" N ILE B 73 " pdb=" C ILE B 73 " pdb=" CB ILE B 73 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.19e-01 chirality pdb=" CA ILE J 73 " pdb=" N ILE J 73 " pdb=" C ILE J 73 " pdb=" CB ILE J 73 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.18e-01 ... (remaining 2601 not shown) Planarity restraints: 4644 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG L 246 " -0.015 5.00e-02 4.00e+02 2.34e-02 8.78e-01 pdb=" N PRO L 247 " 0.041 5.00e-02 4.00e+02 pdb=" CA PRO L 247 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO L 247 " -0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG I 246 " 0.014 5.00e-02 4.00e+02 2.17e-02 7.55e-01 pdb=" N PRO I 247 " -0.038 5.00e-02 4.00e+02 pdb=" CA PRO I 247 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO I 247 " 0.012 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG G 246 " -0.014 5.00e-02 4.00e+02 2.16e-02 7.46e-01 pdb=" N PRO G 247 " 0.037 5.00e-02 4.00e+02 pdb=" CA PRO G 247 " -0.011 5.00e-02 4.00e+02 pdb=" CD PRO G 247 " -0.012 5.00e-02 4.00e+02 ... (remaining 4641 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.24: 2885 2.24 - 2.83: 68053 2.83 - 3.42: 76934 3.42 - 4.01: 103612 4.01 - 4.60: 157943 Nonbonded interactions: 409427 Sorted by model distance: nonbonded pdb=" O ILE B 73 " pdb=" HH TYR B 221 " model vdw 1.652 1.850 nonbonded pdb=" O ILE D 73 " pdb=" HH TYR D 221 " model vdw 1.656 1.850 nonbonded pdb=" O ILE E 73 " pdb=" HH TYR E 221 " model vdw 1.656 1.850 nonbonded pdb=" O ILE H 73 " pdb=" HH TYR H 221 " model vdw 1.659 1.850 nonbonded pdb=" O ILE F 73 " pdb=" HH TYR F 221 " model vdw 1.660 1.850 ... (remaining 409422 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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: 11.070 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: 0.500 Extract box with map and model: 31.010 Check model and map are aligned: 0.440 Set scattering table: 0.270 Process input model: 92.530 Find NCS groups from input model: 1.410 Set up NCS constraints: 0.210 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 140.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 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 : 0.002 0.020 16620 Z= 0.135 Angle : 0.410 4.653 22452 Z= 0.225 Chirality : 0.038 0.136 2604 Planarity : 0.003 0.023 2748 Dihedral : 13.459 89.926 5928 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 1.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 5.17 (0.19), residues: 1944 helix: 4.78 (0.12), residues: 1332 sheet: 2.58 (0.39), residues: 120 loop : -0.68 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP F 79 HIS 0.002 0.000 HIS J 274 PHE 0.007 0.001 PHE L 256 TYR 0.005 0.001 TYR F 199 ARG 0.004 0.000 ARG L 77 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 422 time to evaluate : 2.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.4497 (mmm) cc_final: 0.4022 (pmm) REVERT: B 21 MET cc_start: 0.4579 (mmm) cc_final: 0.4179 (pmm) REVERT: C 21 MET cc_start: 0.4535 (mmm) cc_final: 0.4152 (pmm) REVERT: D 21 MET cc_start: 0.4580 (mmm) cc_final: 0.4033 (pmm) REVERT: G 21 MET cc_start: 0.4691 (mmm) cc_final: 0.4324 (pmm) REVERT: H 21 MET cc_start: 0.4739 (mmm) cc_final: 0.4096 (pmm) REVERT: I 21 MET cc_start: 0.4363 (mmm) cc_final: 0.3753 (pmm) REVERT: L 21 MET cc_start: 0.4703 (mmm) cc_final: 0.3401 (pmm) REVERT: L 93 PHE cc_start: 0.7234 (t80) cc_final: 0.6978 (t80) outliers start: 0 outliers final: 0 residues processed: 422 average time/residue: 0.5862 time to fit residues: 374.0036 Evaluate side-chains 232 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 232 time to evaluate : 2.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 0.8980 chunk 145 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 98 optimal weight: 0.0570 chunk 77 optimal weight: 1.9990 chunk 150 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 112 optimal weight: 5.9990 chunk 174 optimal weight: 1.9990 overall best weight: 1.3904 ------------------------------------------------------------------------------- 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: 0.7625 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 16620 Z= 0.224 Angle : 0.476 4.421 22452 Z= 0.255 Chirality : 0.039 0.129 2604 Planarity : 0.003 0.033 2748 Dihedral : 5.023 36.547 2364 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.11 % Allowed : 8.00 % Favored : 89.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 4.58 (0.19), residues: 1944 helix: 4.31 (0.13), residues: 1332 sheet: 2.74 (0.41), residues: 120 loop : -0.92 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 79 HIS 0.003 0.001 HIS E 274 PHE 0.024 0.001 PHE L 256 TYR 0.005 0.001 TYR H 199 ARG 0.005 0.000 ARG K 197 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 244 time to evaluate : 2.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.4412 (mmm) cc_final: 0.3911 (pmm) REVERT: B 21 MET cc_start: 0.4453 (mmm) cc_final: 0.4008 (pmm) REVERT: C 21 MET cc_start: 0.4520 (mmm) cc_final: 0.3961 (pmm) REVERT: D 21 MET cc_start: 0.4545 (mmm) cc_final: 0.4139 (pmm) REVERT: G 21 MET cc_start: 0.4730 (mmm) cc_final: 0.4310 (pmm) REVERT: H 21 MET cc_start: 0.4629 (mmm) cc_final: 0.4036 (pmm) REVERT: I 21 MET cc_start: 0.4460 (mmm) cc_final: 0.3901 (pmm) REVERT: L 21 MET cc_start: 0.4691 (mmm) cc_final: 0.3440 (pmm) REVERT: L 93 PHE cc_start: 0.7330 (t80) cc_final: 0.7040 (t80) outliers start: 38 outliers final: 33 residues processed: 265 average time/residue: 0.5463 time to fit residues: 229.9872 Evaluate side-chains 244 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 211 time to evaluate : 2.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 199 TYR Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain D residue 199 TYR Chi-restraints excluded: chain D residue 261 SER Chi-restraints excluded: chain E residue 199 TYR Chi-restraints excluded: chain E residue 261 SER Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain F residue 261 SER Chi-restraints excluded: chain G residue 32 ILE Chi-restraints excluded: chain G residue 261 SER Chi-restraints excluded: chain G residue 265 VAL Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain H residue 261 SER Chi-restraints excluded: chain H residue 265 VAL Chi-restraints excluded: chain I residue 261 SER Chi-restraints excluded: chain I residue 265 VAL Chi-restraints excluded: chain J residue 261 SER Chi-restraints excluded: chain J residue 265 VAL Chi-restraints excluded: chain K residue 32 ILE Chi-restraints excluded: chain K residue 261 SER Chi-restraints excluded: chain K residue 265 VAL Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 261 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 96 optimal weight: 10.0000 chunk 54 optimal weight: 2.9990 chunk 145 optimal weight: 4.9990 chunk 118 optimal weight: 2.9990 chunk 48 optimal weight: 8.9990 chunk 174 optimal weight: 1.9990 chunk 188 optimal weight: 0.0770 chunk 155 optimal weight: 0.0010 chunk 173 optimal weight: 0.6980 chunk 59 optimal weight: 0.7980 chunk 140 optimal weight: 0.8980 overall best weight: 0.4944 ------------------------------------------------------------------------------- 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: 0.7564 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 16620 Z= 0.123 Angle : 0.408 5.122 22452 Z= 0.212 Chirality : 0.037 0.132 2604 Planarity : 0.003 0.027 2748 Dihedral : 4.213 40.303 2364 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 2.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.17 % Allowed : 10.61 % Favored : 88.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 4.97 (0.19), residues: 1944 helix: 4.59 (0.13), residues: 1332 sheet: 2.87 (0.41), residues: 120 loop : -0.73 (0.30), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP L 79 HIS 0.002 0.000 HIS E 274 PHE 0.015 0.001 PHE L 256 TYR 0.004 0.001 TYR H 199 ARG 0.003 0.000 ARG K 197 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 212 time to evaluate : 2.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.4347 (mmm) cc_final: 0.3891 (pmm) REVERT: B 21 MET cc_start: 0.4379 (mmm) cc_final: 0.3996 (pmm) REVERT: C 21 MET cc_start: 0.4407 (mmm) cc_final: 0.3859 (pmm) REVERT: D 21 MET cc_start: 0.4452 (mmm) cc_final: 0.4133 (pmm) REVERT: E 21 MET cc_start: 0.4589 (mmt) cc_final: 0.3406 (pmm) REVERT: E 29 VAL cc_start: 0.8210 (t) cc_final: 0.7904 (p) REVERT: G 21 MET cc_start: 0.4717 (mmm) cc_final: 0.4277 (pmm) REVERT: H 21 MET cc_start: 0.4561 (mmm) cc_final: 0.3864 (pmm) REVERT: I 21 MET cc_start: 0.4381 (mmm) cc_final: 0.3828 (pmm) REVERT: L 21 MET cc_start: 0.4683 (mmm) cc_final: 0.3477 (pmm) REVERT: L 93 PHE cc_start: 0.7265 (t80) cc_final: 0.6974 (t80) outliers start: 21 outliers final: 20 residues processed: 222 average time/residue: 0.4499 time to fit residues: 165.5067 Evaluate side-chains 224 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 204 time to evaluate : 2.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain C residue 263 ILE Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain G residue 32 ILE Chi-restraints excluded: chain G residue 265 VAL Chi-restraints excluded: chain H residue 265 VAL Chi-restraints excluded: chain I residue 265 VAL Chi-restraints excluded: chain J residue 86 VAL Chi-restraints excluded: chain J residue 265 VAL Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 263 ILE Chi-restraints excluded: chain K residue 265 VAL Chi-restraints excluded: chain L residue 86 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 172 optimal weight: 0.6980 chunk 131 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 117 optimal weight: 0.9980 chunk 175 optimal weight: 4.9990 chunk 185 optimal weight: 4.9990 chunk 91 optimal weight: 0.8980 chunk 166 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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: 0.7650 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 16620 Z= 0.210 Angle : 0.457 4.615 22452 Z= 0.247 Chirality : 0.038 0.131 2604 Planarity : 0.003 0.035 2748 Dihedral : 4.980 37.963 2364 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.11 % Allowed : 11.28 % Favored : 87.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 4.63 (0.19), residues: 1944 helix: 4.31 (0.13), residues: 1332 sheet: 3.47 (0.46), residues: 120 loop : -1.03 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 79 HIS 0.002 0.001 HIS B 274 PHE 0.027 0.001 PHE I 256 TYR 0.006 0.001 TYR G 199 ARG 0.002 0.000 ARG B 77 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 235 time to evaluate : 2.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.4310 (mmm) cc_final: 0.3875 (pmm) REVERT: B 21 MET cc_start: 0.4435 (mmm) cc_final: 0.4035 (pmm) REVERT: C 21 MET cc_start: 0.4497 (mmm) cc_final: 0.3916 (pmm) REVERT: D 21 MET cc_start: 0.4552 (mmm) cc_final: 0.4220 (pmm) REVERT: E 29 VAL cc_start: 0.8164 (t) cc_final: 0.7659 (p) REVERT: G 21 MET cc_start: 0.4692 (mmm) cc_final: 0.4287 (pmm) REVERT: H 21 MET cc_start: 0.4605 (mmm) cc_final: 0.3905 (pmm) REVERT: I 21 MET cc_start: 0.4439 (mmm) cc_final: 0.3872 (pmm) REVERT: L 21 MET cc_start: 0.4697 (mmm) cc_final: 0.3555 (pmm) REVERT: L 93 PHE cc_start: 0.7321 (t80) cc_final: 0.7018 (t80) outliers start: 20 outliers final: 20 residues processed: 242 average time/residue: 0.4559 time to fit residues: 180.7576 Evaluate side-chains 238 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 218 time to evaluate : 2.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 265 VAL Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 265 VAL Chi-restraints excluded: chain I residue 265 VAL Chi-restraints excluded: chain J residue 86 VAL Chi-restraints excluded: chain J residue 265 VAL Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 265 VAL Chi-restraints excluded: chain L residue 86 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 154 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 138 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 158 optimal weight: 2.9990 chunk 128 optimal weight: 4.9990 chunk 0 optimal weight: 10.9990 chunk 94 optimal weight: 2.9990 chunk 166 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.3637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 16620 Z= 0.361 Angle : 0.557 4.931 22452 Z= 0.311 Chirality : 0.040 0.135 2604 Planarity : 0.004 0.044 2748 Dihedral : 6.449 58.432 2364 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.28 % Allowed : 10.56 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 3.51 (0.19), residues: 1944 helix: 3.38 (0.13), residues: 1344 sheet: 3.83 (0.49), residues: 120 loop : -1.52 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 79 HIS 0.003 0.001 HIS I 75 PHE 0.024 0.002 PHE L 256 TYR 0.008 0.001 TYR G 199 ARG 0.003 0.000 ARG K 77 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 249 time to evaluate : 2.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.4323 (mmm) cc_final: 0.3880 (pmm) REVERT: B 21 MET cc_start: 0.4473 (mmm) cc_final: 0.4025 (pmm) REVERT: C 21 MET cc_start: 0.4529 (mmm) cc_final: 0.3944 (pmm) REVERT: D 21 MET cc_start: 0.4508 (mmm) cc_final: 0.4183 (pmm) REVERT: G 21 MET cc_start: 0.4627 (mmm) cc_final: 0.4156 (pmm) REVERT: H 21 MET cc_start: 0.4559 (mmm) cc_final: 0.3904 (pmm) REVERT: I 21 MET cc_start: 0.4400 (mmm) cc_final: 0.3741 (pmm) REVERT: I 93 PHE cc_start: 0.6916 (t80) cc_final: 0.6698 (t80) REVERT: L 21 MET cc_start: 0.4756 (mmm) cc_final: 0.3611 (pmm) REVERT: L 93 PHE cc_start: 0.7358 (t80) cc_final: 0.6988 (t80) outliers start: 41 outliers final: 34 residues processed: 264 average time/residue: 0.4811 time to fit residues: 205.8865 Evaluate side-chains 263 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 229 time to evaluate : 2.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 265 VAL Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 265 VAL Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain I residue 86 VAL Chi-restraints excluded: chain I residue 265 VAL Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 86 VAL Chi-restraints excluded: chain J residue 265 VAL Chi-restraints excluded: chain K residue 44 THR Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 265 VAL Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 101 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 62 optimal weight: 2.9990 chunk 167 optimal weight: 3.9990 chunk 36 optimal weight: 0.0020 chunk 108 optimal weight: 0.1980 chunk 45 optimal weight: 0.9990 chunk 185 optimal weight: 5.9990 chunk 154 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 61 optimal weight: 0.5980 chunk 97 optimal weight: 3.9990 overall best weight: 0.5590 ------------------------------------------------------------------------------- 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: 0.7635 moved from start: 0.3416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 16620 Z= 0.135 Angle : 0.442 5.859 22452 Z= 0.233 Chirality : 0.037 0.126 2604 Planarity : 0.003 0.036 2748 Dihedral : 3.598 56.104 2364 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.11 % Allowed : 11.94 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 4.34 (0.20), residues: 1944 helix: 3.98 (0.13), residues: 1344 sheet: 3.63 (0.48), residues: 120 loop : -0.96 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP D 79 HIS 0.003 0.000 HIS E 274 PHE 0.013 0.001 PHE L 256 TYR 0.006 0.001 TYR C 199 ARG 0.002 0.000 ARG G 77 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 226 time to evaluate : 2.461 Fit side-chains revert: symmetry clash REVERT: A 21 MET cc_start: 0.4246 (mmm) cc_final: 0.3792 (pmm) REVERT: B 21 MET cc_start: 0.4353 (mmm) cc_final: 0.3923 (pmm) REVERT: B 29 VAL cc_start: 0.8045 (t) cc_final: 0.7754 (p) REVERT: C 21 MET cc_start: 0.4456 (mmm) cc_final: 0.3856 (pmm) REVERT: C 267 LEU cc_start: 0.7548 (mt) cc_final: 0.7323 (tt) REVERT: D 21 MET cc_start: 0.4346 (mmm) cc_final: 0.3899 (pmm) REVERT: E 29 VAL cc_start: 0.8138 (t) cc_final: 0.7823 (p) REVERT: G 21 MET cc_start: 0.4545 (mmm) cc_final: 0.4050 (pmm) REVERT: H 21 MET cc_start: 0.4623 (mmm) cc_final: 0.3888 (pmm) REVERT: I 21 MET cc_start: 0.4310 (mmm) cc_final: 0.3716 (pmm) REVERT: L 21 MET cc_start: 0.4675 (mmm) cc_final: 0.3520 (pmm) REVERT: L 93 PHE cc_start: 0.7246 (t80) cc_final: 0.6905 (t80) outliers start: 20 outliers final: 13 residues processed: 241 average time/residue: 0.4332 time to fit residues: 173.0223 Evaluate side-chains 221 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 208 time to evaluate : 2.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain F residue 263 ILE Chi-restraints excluded: chain G residue 265 VAL Chi-restraints excluded: chain H residue 265 VAL Chi-restraints excluded: chain I residue 265 VAL Chi-restraints excluded: chain J residue 265 VAL Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 265 VAL Chi-restraints excluded: chain L residue 86 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 179 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 105 optimal weight: 5.9990 chunk 135 optimal weight: 2.9990 chunk 156 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 chunk 185 optimal weight: 5.9990 chunk 115 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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: 0.7699 moved from start: 0.3695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 16620 Z= 0.240 Angle : 0.483 4.662 22452 Z= 0.262 Chirality : 0.039 0.144 2604 Planarity : 0.004 0.038 2748 Dihedral : 3.800 15.655 2364 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 1.17 % Allowed : 12.61 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 4.09 (0.20), residues: 1944 helix: 3.81 (0.13), residues: 1344 sheet: 3.60 (0.49), residues: 120 loop : -1.14 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP F 79 HIS 0.003 0.001 HIS E 274 PHE 0.026 0.001 PHE L 256 TYR 0.006 0.001 TYR A 199 ARG 0.004 0.000 ARG C 77 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 220 time to evaluate : 2.465 Fit side-chains revert: symmetry clash REVERT: A 21 MET cc_start: 0.4462 (mmm) cc_final: 0.3897 (pmm) REVERT: B 21 MET cc_start: 0.4377 (mmm) cc_final: 0.3936 (pmm) REVERT: C 21 MET cc_start: 0.4410 (mmm) cc_final: 0.3780 (pmm) REVERT: D 21 MET cc_start: 0.4398 (mmm) cc_final: 0.3896 (pmm) REVERT: E 29 VAL cc_start: 0.8044 (t) cc_final: 0.7715 (p) REVERT: G 21 MET cc_start: 0.4485 (mmm) cc_final: 0.3996 (pmm) REVERT: H 21 MET cc_start: 0.4580 (mmm) cc_final: 0.3802 (pmm) REVERT: I 21 MET cc_start: 0.4327 (mmm) cc_final: 0.3739 (pmm) REVERT: L 21 MET cc_start: 0.4640 (mmm) cc_final: 0.3467 (pmm) REVERT: L 93 PHE cc_start: 0.7309 (t80) cc_final: 0.6936 (t80) outliers start: 21 outliers final: 20 residues processed: 232 average time/residue: 0.4603 time to fit residues: 175.5463 Evaluate side-chains 232 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 212 time to evaluate : 2.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain G residue 265 VAL Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 220 LEU Chi-restraints excluded: chain H residue 265 VAL Chi-restraints excluded: chain I residue 86 VAL Chi-restraints excluded: chain I residue 265 VAL Chi-restraints excluded: chain J residue 86 VAL Chi-restraints excluded: chain J residue 265 VAL Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 220 LEU Chi-restraints excluded: chain K residue 265 VAL Chi-restraints excluded: chain L residue 25 ILE Chi-restraints excluded: chain L residue 86 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 73 optimal weight: 4.9990 chunk 110 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 145 optimal weight: 0.7980 chunk 168 optimal weight: 6.9990 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: 0.7708 moved from start: 0.3846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 16620 Z= 0.238 Angle : 0.496 7.098 22452 Z= 0.268 Chirality : 0.039 0.165 2604 Planarity : 0.004 0.041 2748 Dihedral : 3.754 13.949 2364 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.17 % Allowed : 13.11 % Favored : 85.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 3.96 (0.20), residues: 1944 helix: 3.70 (0.13), residues: 1344 sheet: 3.57 (0.48), residues: 120 loop : -1.13 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP L 79 HIS 0.003 0.001 HIS E 274 PHE 0.027 0.001 PHE F 256 TYR 0.007 0.001 TYR A 199 ARG 0.004 0.000 ARG C 77 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 217 time to evaluate : 2.443 Fit side-chains REVERT: A 21 MET cc_start: 0.4409 (mmm) cc_final: 0.3866 (pmm) REVERT: B 21 MET cc_start: 0.4411 (mmm) cc_final: 0.3818 (pmm) REVERT: C 21 MET cc_start: 0.4382 (mmm) cc_final: 0.3802 (pmm) REVERT: D 21 MET cc_start: 0.4391 (mmm) cc_final: 0.3874 (pmm) REVERT: E 29 VAL cc_start: 0.8037 (t) cc_final: 0.7709 (p) REVERT: G 21 MET cc_start: 0.4433 (mmm) cc_final: 0.3967 (pmm) REVERT: H 21 MET cc_start: 0.4527 (mmm) cc_final: 0.3801 (pmm) REVERT: I 21 MET cc_start: 0.4259 (mmm) cc_final: 0.3678 (pmm) REVERT: L 21 MET cc_start: 0.4532 (mmm) cc_final: 0.3589 (pmm) REVERT: L 93 PHE cc_start: 0.7325 (t80) cc_final: 0.6916 (t80) outliers start: 21 outliers final: 21 residues processed: 228 average time/residue: 0.5019 time to fit residues: 189.5517 Evaluate side-chains 231 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 210 time to evaluate : 2.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain G residue 265 VAL Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 220 LEU Chi-restraints excluded: chain H residue 265 VAL Chi-restraints excluded: chain I residue 86 VAL Chi-restraints excluded: chain I residue 265 VAL Chi-restraints excluded: chain J residue 86 VAL Chi-restraints excluded: chain J residue 265 VAL Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 220 LEU Chi-restraints excluded: chain K residue 265 VAL Chi-restraints excluded: chain L residue 25 ILE Chi-restraints excluded: chain L residue 86 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 177 optimal weight: 0.9980 chunk 161 optimal weight: 2.9990 chunk 172 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 155 optimal weight: 0.7980 chunk 163 optimal weight: 1.9990 chunk 171 optimal weight: 0.9980 chunk 113 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.3787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 16620 Z= 0.161 Angle : 0.467 9.205 22452 Z= 0.243 Chirality : 0.038 0.172 2604 Planarity : 0.003 0.037 2748 Dihedral : 3.253 13.390 2364 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.94 % Allowed : 13.78 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 4.27 (0.20), residues: 1944 helix: 4.02 (0.13), residues: 1332 sheet: 3.54 (0.48), residues: 120 loop : -1.12 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 79 HIS 0.003 0.000 HIS E 274 PHE 0.023 0.001 PHE L 256 TYR 0.005 0.001 TYR C 199 ARG 0.003 0.000 ARG C 77 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 225 time to evaluate : 2.636 Fit side-chains REVERT: A 21 MET cc_start: 0.4425 (mmm) cc_final: 0.3894 (pmm) REVERT: B 21 MET cc_start: 0.4381 (mmm) cc_final: 0.3808 (pmm) REVERT: C 21 MET cc_start: 0.4402 (mmm) cc_final: 0.3760 (pmm) REVERT: C 267 LEU cc_start: 0.7552 (mt) cc_final: 0.7166 (tt) REVERT: D 21 MET cc_start: 0.4305 (mmm) cc_final: 0.3842 (pmm) REVERT: E 29 VAL cc_start: 0.8055 (t) cc_final: 0.7727 (p) REVERT: G 21 MET cc_start: 0.4358 (mmm) cc_final: 0.3855 (pmm) REVERT: H 21 MET cc_start: 0.4466 (mmm) cc_final: 0.3732 (pmm) REVERT: I 21 MET cc_start: 0.4261 (mmm) cc_final: 0.3669 (pmm) REVERT: L 21 MET cc_start: 0.4521 (mmm) cc_final: 0.3569 (pmm) REVERT: L 93 PHE cc_start: 0.7224 (t80) cc_final: 0.6831 (t80) outliers start: 17 outliers final: 16 residues processed: 236 average time/residue: 0.4474 time to fit residues: 174.7408 Evaluate side-chains 218 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 202 time to evaluate : 2.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain G residue 265 VAL Chi-restraints excluded: chain H residue 220 LEU Chi-restraints excluded: chain H residue 265 VAL Chi-restraints excluded: chain I residue 265 VAL Chi-restraints excluded: chain J residue 265 VAL Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 220 LEU Chi-restraints excluded: chain K residue 265 VAL Chi-restraints excluded: chain L residue 25 ILE Chi-restraints excluded: chain L residue 86 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 182 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 chunk 86 optimal weight: 0.7980 chunk 126 optimal weight: 1.9990 chunk 191 optimal weight: 2.9990 chunk 176 optimal weight: 1.9990 chunk 152 optimal weight: 8.9990 chunk 15 optimal weight: 0.9990 chunk 117 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 120 optimal weight: 10.0000 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.3973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 16620 Z= 0.239 Angle : 0.497 6.699 22452 Z= 0.267 Chirality : 0.039 0.175 2604 Planarity : 0.004 0.039 2748 Dihedral : 3.794 15.232 2364 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 0.89 % Allowed : 14.11 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 4.03 (0.20), residues: 1944 helix: 3.76 (0.13), residues: 1344 sheet: 3.49 (0.48), residues: 120 loop : -1.10 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP L 79 HIS 0.003 0.001 HIS E 274 PHE 0.024 0.001 PHE L 256 TYR 0.007 0.001 TYR A 199 ARG 0.004 0.000 ARG L 77 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 207 time to evaluate : 2.577 Fit side-chains REVERT: A 21 MET cc_start: 0.4456 (mmm) cc_final: 0.3939 (pmm) REVERT: B 21 MET cc_start: 0.4379 (mmm) cc_final: 0.3837 (pmm) REVERT: C 21 MET cc_start: 0.4417 (mmm) cc_final: 0.3817 (pmm) REVERT: D 21 MET cc_start: 0.4386 (mmm) cc_final: 0.3908 (pmm) REVERT: G 21 MET cc_start: 0.4340 (mmm) cc_final: 0.3833 (pmm) REVERT: H 21 MET cc_start: 0.4461 (mmm) cc_final: 0.3731 (pmm) REVERT: I 21 MET cc_start: 0.4286 (mmm) cc_final: 0.3699 (pmm) REVERT: L 21 MET cc_start: 0.4568 (mmm) cc_final: 0.3665 (pmm) REVERT: L 93 PHE cc_start: 0.7269 (t80) cc_final: 0.6854 (t80) outliers start: 16 outliers final: 16 residues processed: 217 average time/residue: 0.4585 time to fit residues: 164.6289 Evaluate side-chains 220 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 204 time to evaluate : 2.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain G residue 265 VAL Chi-restraints excluded: chain H residue 220 LEU Chi-restraints excluded: chain H residue 265 VAL Chi-restraints excluded: chain I residue 265 VAL Chi-restraints excluded: chain J residue 265 VAL Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 220 LEU Chi-restraints excluded: chain K residue 265 VAL Chi-restraints excluded: chain L residue 25 ILE Chi-restraints excluded: chain L residue 86 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 140 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 152 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 156 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 133 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.199884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.153988 restraints weight = 58025.370| |-----------------------------------------------------------------------------| r_work (start): 0.3851 rms_B_bonded: 2.71 r_work: 0.3696 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.3876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 16620 Z= 0.159 Angle : 0.460 7.489 22452 Z= 0.240 Chirality : 0.038 0.178 2604 Planarity : 0.003 0.037 2748 Dihedral : 3.200 12.165 2364 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.94 % Allowed : 14.11 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 4.31 (0.20), residues: 1944 helix: 4.05 (0.13), residues: 1332 sheet: 3.49 (0.48), residues: 120 loop : -1.12 (0.30), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP D 79 HIS 0.003 0.000 HIS E 274 PHE 0.022 0.001 PHE L 256 TYR 0.005 0.001 TYR C 199 ARG 0.003 0.000 ARG L 77 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6580.31 seconds wall clock time: 117 minutes 15.76 seconds (7035.76 seconds total)