Starting phenix.real_space_refine on Mon Sep 14 17:47:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pkd_13468/09_2026/7pkd_13468_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pkd_13468/09_2026/7pkd_13468.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7pkd_13468/09_2026/7pkd_13468_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pkd_13468/09_2026/7pkd_13468_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7pkd_13468/09_2026/7pkd_13468.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pkd_13468/09_2026/7pkd_13468.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.002 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: 7 Type Number sf(0) Gaussians Ca 20 9.91 5 P 10 5.49 5 S 40 5.16 5 C 10630 2.51 5 N 2620 2.21 5 O 3140 1.98 5 H 15940 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 156 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 32400 Number of models: 1 Model: "" Number of chains: 30 Chain: "J" Number of atoms: 3224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 3224 Classifications: {'peptide': 206} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "F" Number of atoms: 3224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 3224 Classifications: {'peptide': 206} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "G" Number of atoms: 3224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 3224 Classifications: {'peptide': 206} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "H" Number of atoms: 3224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 3224 Classifications: {'peptide': 206} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "I" Number of atoms: 3224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 3224 Classifications: {'peptide': 206} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "E" Number of atoms: 3224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 3224 Classifications: {'peptide': 206} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "D" Number of atoms: 3224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 3224 Classifications: {'peptide': 206} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "C" Number of atoms: 3224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 3224 Classifications: {'peptide': 206} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "B" Number of atoms: 3224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 3224 Classifications: {'peptide': 206} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "A" Number of atoms: 3224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 3224 Classifications: {'peptide': 206} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "J" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 13 Unusual residues: {' CA': 2, ' PC': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 13 Unusual residues: {' CA': 2, ' PC': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 13 Unusual residues: {' CA': 2, ' PC': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 13 Unusual residues: {' CA': 2, ' PC': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 13 Unusual residues: {' CA': 2, ' PC': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 13 Unusual residues: {' CA': 2, ' PC': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 13 Unusual residues: {' CA': 2, ' PC': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 13 Unusual residues: {' CA': 2, ' PC': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 13 Unusual residues: {' CA': 2, ' PC': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 13 Unusual residues: {' CA': 2, ' PC': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Classifications: {'water': 1} Chain: "F" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Classifications: {'water': 1} Chain: "G" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Classifications: {'water': 1} Chain: "H" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Classifications: {'water': 1} Chain: "I" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Classifications: {'water': 1} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Classifications: {'water': 1} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Classifications: {'water': 1} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Classifications: {'water': 1} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Classifications: {'water': 1} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Classifications: {'water': 1} Time building chain proxies: 6.42, per 1000 atoms: 0.20 Number of scatterers: 32400 At special positions: 0 Unit cell: (119.548, 112.024, 144.628, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 20 19.99 S 40 16.00 P 10 15.00 O 3140 8.00 N 2620 7.00 C 10630 6.00 H 15940 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS J 36 " - pdb=" SG CYS J 97 " distance=2.03 Simple disulfide: pdb=" SG CYS F 36 " - pdb=" SG CYS F 97 " distance=2.03 Simple disulfide: pdb=" SG CYS G 36 " - pdb=" SG CYS G 97 " distance=2.03 Simple disulfide: pdb=" SG CYS H 36 " - pdb=" SG CYS H 97 " distance=2.03 Simple disulfide: pdb=" SG CYS I 36 " - pdb=" SG CYS I 97 " distance=2.03 Simple disulfide: pdb=" SG CYS E 36 " - pdb=" SG CYS E 97 " distance=2.03 Simple disulfide: pdb=" SG CYS D 36 " - pdb=" SG CYS D 97 " distance=2.03 Simple disulfide: pdb=" SG CYS C 36 " - pdb=" SG CYS C 97 " distance=2.03 Simple disulfide: pdb=" SG CYS B 36 " - pdb=" SG CYS B 97 " distance=2.03 Simple disulfide: pdb=" SG CYS A 36 " - pdb=" SG CYS A 97 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 3.58 Conformation dependent library (CDL) restraints added in 1.5 seconds 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3780 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 30 sheets defined 12.4% alpha, 38.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'J' and resid 42 through 47 removed outlier: 4.559A pdb=" N THR J 46 " --> pdb=" O GLU J 42 " (cutoff:3.500A) Processing helix chain 'J' and resid 147 through 151 Processing helix chain 'J' and resid 167 through 177 Processing helix chain 'J' and resid 186 through 190 removed outlier: 4.148A pdb=" N LEU J 190 " --> pdb=" O TRP J 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 46 removed outlier: 3.871A pdb=" N SER F 45 " --> pdb=" O GLU F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 147 through 151 Processing helix chain 'F' and resid 167 through 177 Processing helix chain 'F' and resid 186 through 190 removed outlier: 3.898A pdb=" N LEU F 190 " --> pdb=" O TRP F 187 " (cutoff:3.500A) Processing helix chain 'G' and resid 42 through 46 removed outlier: 3.990A pdb=" N SER G 45 " --> pdb=" O GLU G 42 " (cutoff:3.500A) Processing helix chain 'G' and resid 147 through 151 Processing helix chain 'G' and resid 167 through 176 Processing helix chain 'G' and resid 186 through 190 removed outlier: 4.198A pdb=" N LEU G 190 " --> pdb=" O TRP G 187 " (cutoff:3.500A) Processing helix chain 'H' and resid 42 through 46 Processing helix chain 'H' and resid 147 through 151 Processing helix chain 'H' and resid 167 through 176 Processing helix chain 'H' and resid 186 through 190 removed outlier: 4.136A pdb=" N LEU H 190 " --> pdb=" O TRP H 187 " (cutoff:3.500A) Processing helix chain 'I' and resid 42 through 46 removed outlier: 3.935A pdb=" N SER I 45 " --> pdb=" O GLU I 42 " (cutoff:3.500A) Processing helix chain 'I' and resid 147 through 151 Processing helix chain 'I' and resid 167 through 176 Processing helix chain 'I' and resid 186 through 190 removed outlier: 4.044A pdb=" N LEU I 190 " --> pdb=" O TRP I 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 46 removed outlier: 3.999A pdb=" N SER E 45 " --> pdb=" O GLU E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 151 Processing helix chain 'E' and resid 167 through 177 Processing helix chain 'E' and resid 186 through 190 removed outlier: 4.034A pdb=" N LEU E 190 " --> pdb=" O TRP E 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 47 removed outlier: 4.431A pdb=" N THR D 46 " --> pdb=" O GLU D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 151 Processing helix chain 'D' and resid 167 through 176 Processing helix chain 'D' and resid 186 through 190 removed outlier: 3.988A pdb=" N LEU D 190 " --> pdb=" O TRP D 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 46 removed outlier: 4.187A pdb=" N SER C 45 " --> pdb=" O GLU C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 151 Processing helix chain 'C' and resid 167 through 176 Processing helix chain 'C' and resid 186 through 190 removed outlier: 4.063A pdb=" N LEU C 190 " --> pdb=" O TRP C 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 46 removed outlier: 3.626A pdb=" N SER B 45 " --> pdb=" O GLU B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 151 Processing helix chain 'B' and resid 167 through 176 Processing helix chain 'B' and resid 186 through 190 removed outlier: 3.921A pdb=" N LEU B 190 " --> pdb=" O TRP B 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 46 removed outlier: 3.992A pdb=" N SER A 45 " --> pdb=" O GLU A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 151 Processing helix chain 'A' and resid 167 through 177 Processing helix chain 'A' and resid 186 through 190 removed outlier: 3.924A pdb=" N LEU A 190 " --> pdb=" O TRP A 187 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'J' and resid 114 through 115 Processing sheet with id=AA2, first strand: chain 'J' and resid 114 through 115 removed outlier: 3.747A pdb=" N ILE J 106 " --> pdb=" O GLU J 101 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N HIS J 38 " --> pdb=" O ASN J 158 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N ASN J 158 " --> pdb=" O HIS J 38 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N TYR J 40 " --> pdb=" O ILE J 156 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N ILE J 156 " --> pdb=" O TYR J 40 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N ASN J 158 " --> pdb=" O LYS J 7 " (cutoff:3.500A) removed outlier: 10.197A pdb=" N LYS J 7 " --> pdb=" O ASN J 158 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'J' and resid 80 through 85 removed outlier: 4.582A pdb=" N ASN J 61 " --> pdb=" O TYR J 54 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N TYR J 54 " --> pdb=" O ASN J 61 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ILE J 63 " --> pdb=" O PHE J 52 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N PHE J 52 " --> pdb=" O ILE J 63 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N ILE J 65 " --> pdb=" O SER J 50 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N SER J 50 " --> pdb=" O ILE J 65 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ILE J 133 " --> pdb=" O LEU J 22 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 114 through 115 Processing sheet with id=AA5, first strand: chain 'F' and resid 114 through 115 removed outlier: 3.632A pdb=" N ILE F 106 " --> pdb=" O GLU F 101 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N THR F 34 " --> pdb=" O MET F 161 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N MET F 161 " --> pdb=" O THR F 34 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N CYS F 36 " --> pdb=" O VAL F 159 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N VAL F 159 " --> pdb=" O CYS F 36 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N ASN F 158 " --> pdb=" O LYS F 7 " (cutoff:3.500A) removed outlier: 10.120A pdb=" N LYS F 7 " --> pdb=" O ASN F 158 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 80 through 85 removed outlier: 6.004A pdb=" N ASN F 61 " --> pdb=" O THR F 56 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N THR F 56 " --> pdb=" O ASN F 61 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N TRP F 67 " --> pdb=" O SER F 50 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N SER F 50 " --> pdb=" O TRP F 67 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ILE F 133 " --> pdb=" O LEU F 22 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 114 through 115 Processing sheet with id=AA8, first strand: chain 'G' and resid 114 through 115 removed outlier: 3.850A pdb=" N ILE G 106 " --> pdb=" O GLU G 101 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU G 101 " --> pdb=" O ILE G 106 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N HIS G 38 " --> pdb=" O ASN G 158 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N ASN G 158 " --> pdb=" O HIS G 38 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N TYR G 40 " --> pdb=" O ILE G 156 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N ILE G 156 " --> pdb=" O TYR G 40 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N ASN G 158 " --> pdb=" O LYS G 7 " (cutoff:3.500A) removed outlier: 10.047A pdb=" N LYS G 7 " --> pdb=" O ASN G 158 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 80 through 85 removed outlier: 6.112A pdb=" N ASN G 61 " --> pdb=" O THR G 56 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N THR G 56 " --> pdb=" O ASN G 61 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N TRP G 67 " --> pdb=" O SER G 50 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N SER G 50 " --> pdb=" O TRP G 67 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ILE G 133 " --> pdb=" O LEU G 22 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 114 through 115 Processing sheet with id=AB2, first strand: chain 'H' and resid 114 through 115 removed outlier: 3.771A pdb=" N ILE H 106 " --> pdb=" O GLU H 101 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N THR H 34 " --> pdb=" O MET H 161 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N MET H 161 " --> pdb=" O THR H 34 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N CYS H 36 " --> pdb=" O VAL H 159 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N VAL H 159 " --> pdb=" O CYS H 36 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N ASN H 158 " --> pdb=" O LYS H 7 " (cutoff:3.500A) removed outlier: 10.275A pdb=" N LYS H 7 " --> pdb=" O ASN H 158 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 80 through 85 removed outlier: 4.404A pdb=" N ASN H 61 " --> pdb=" O TYR H 54 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N TYR H 54 " --> pdb=" O ASN H 61 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ILE H 63 " --> pdb=" O PHE H 52 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N PHE H 52 " --> pdb=" O ILE H 63 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N ILE H 65 " --> pdb=" O SER H 50 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N SER H 50 " --> pdb=" O ILE H 65 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ILE H 133 " --> pdb=" O LEU H 22 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 114 through 120 removed outlier: 6.255A pdb=" N VAL I 111 " --> pdb=" O PRO I 115 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N VAL I 117 " --> pdb=" O PHE I 109 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N PHE I 109 " --> pdb=" O VAL I 117 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE I 106 " --> pdb=" O GLU I 101 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N THR I 34 " --> pdb=" O MET I 161 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N MET I 161 " --> pdb=" O THR I 34 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N CYS I 36 " --> pdb=" O VAL I 159 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N VAL I 159 " --> pdb=" O CYS I 36 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N ASN I 158 " --> pdb=" O LYS I 7 " (cutoff:3.500A) removed outlier: 10.247A pdb=" N LYS I 7 " --> pdb=" O ASN I 158 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 80 through 85 removed outlier: 6.149A pdb=" N ASN I 61 " --> pdb=" O THR I 56 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N THR I 56 " --> pdb=" O ASN I 61 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N TRP I 67 " --> pdb=" O SER I 50 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N SER I 50 " --> pdb=" O TRP I 67 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ILE I 133 " --> pdb=" O LEU I 22 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 114 through 115 Processing sheet with id=AB7, first strand: chain 'E' and resid 114 through 115 removed outlier: 3.543A pdb=" N ILE E 106 " --> pdb=" O GLU E 101 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N THR E 34 " --> pdb=" O MET E 161 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N MET E 161 " --> pdb=" O THR E 34 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N CYS E 36 " --> pdb=" O VAL E 159 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N VAL E 159 " --> pdb=" O CYS E 36 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ASN E 158 " --> pdb=" O LYS E 7 " (cutoff:3.500A) removed outlier: 10.193A pdb=" N LYS E 7 " --> pdb=" O ASN E 158 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 80 through 85 removed outlier: 6.113A pdb=" N ASN E 61 " --> pdb=" O THR E 56 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N THR E 56 " --> pdb=" O ASN E 61 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N TRP E 67 " --> pdb=" O SER E 50 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N SER E 50 " --> pdb=" O TRP E 67 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ILE E 133 " --> pdb=" O LEU E 22 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 139 through 141 removed outlier: 7.276A pdb=" N GLN E 139 " --> pdb=" O PHE E 146 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N PHE E 146 " --> pdb=" O GLN E 139 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 114 through 115 Processing sheet with id=AC2, first strand: chain 'D' and resid 114 through 115 removed outlier: 3.684A pdb=" N ILE D 106 " --> pdb=" O GLU D 101 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N THR D 34 " --> pdb=" O MET D 161 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N MET D 161 " --> pdb=" O THR D 34 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N CYS D 36 " --> pdb=" O VAL D 159 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N VAL D 159 " --> pdb=" O CYS D 36 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N ASN D 158 " --> pdb=" O LYS D 7 " (cutoff:3.500A) removed outlier: 10.289A pdb=" N LYS D 7 " --> pdb=" O ASN D 158 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 80 through 85 removed outlier: 6.846A pdb=" N TRP D 67 " --> pdb=" O SER D 50 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N SER D 50 " --> pdb=" O TRP D 67 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ILE D 133 " --> pdb=" O LEU D 22 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 114 through 115 Processing sheet with id=AC5, first strand: chain 'C' and resid 114 through 115 removed outlier: 3.709A pdb=" N ILE C 106 " --> pdb=" O GLU C 101 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N THR C 34 " --> pdb=" O MET C 161 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N MET C 161 " --> pdb=" O THR C 34 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N CYS C 36 " --> pdb=" O VAL C 159 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N VAL C 159 " --> pdb=" O CYS C 36 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N ASN C 158 " --> pdb=" O LYS C 7 " (cutoff:3.500A) removed outlier: 10.222A pdb=" N LYS C 7 " --> pdb=" O ASN C 158 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 80 through 85 removed outlier: 6.027A pdb=" N ASN C 61 " --> pdb=" O THR C 56 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N THR C 56 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N TRP C 67 " --> pdb=" O SER C 50 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N SER C 50 " --> pdb=" O TRP C 67 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ILE C 133 " --> pdb=" O LEU C 22 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 114 through 115 Processing sheet with id=AC8, first strand: chain 'B' and resid 114 through 115 removed outlier: 3.771A pdb=" N ILE B 106 " --> pdb=" O GLU B 101 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N THR B 34 " --> pdb=" O MET B 161 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N MET B 161 " --> pdb=" O THR B 34 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N CYS B 36 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N VAL B 159 " --> pdb=" O CYS B 36 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N ASN B 158 " --> pdb=" O LYS B 7 " (cutoff:3.500A) removed outlier: 10.311A pdb=" N LYS B 7 " --> pdb=" O ASN B 158 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 80 through 85 removed outlier: 6.023A pdb=" N ASN B 61 " --> pdb=" O THR B 56 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N THR B 56 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N TRP B 67 " --> pdb=" O SER B 50 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N SER B 50 " --> pdb=" O TRP B 67 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ILE B 133 " --> pdb=" O LEU B 22 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 114 through 115 Processing sheet with id=AD2, first strand: chain 'A' and resid 114 through 115 removed outlier: 3.587A pdb=" N ILE A 106 " --> pdb=" O GLU A 101 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N HIS A 38 " --> pdb=" O ASN A 158 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N ASN A 158 " --> pdb=" O HIS A 38 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N TYR A 40 " --> pdb=" O ILE A 156 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N ILE A 156 " --> pdb=" O TYR A 40 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N ASN A 158 " --> pdb=" O LYS A 7 " (cutoff:3.500A) removed outlier: 10.181A pdb=" N LYS A 7 " --> pdb=" O ASN A 158 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 80 through 85 removed outlier: 6.063A pdb=" N ASN A 61 " --> pdb=" O THR A 56 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N THR A 56 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N TRP A 67 " --> pdb=" O SER A 50 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N SER A 50 " --> pdb=" O TRP A 67 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ILE A 133 " --> pdb=" O LEU A 22 " (cutoff:3.500A) 677 hydrogen bonds defined for protein. 1632 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: 8.92 Time building geometry restraints manager: 4.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 15940 1.02 - 1.21: 0 1.21 - 1.41: 7107 1.41 - 1.61: 9712 1.61 - 1.80: 61 Bond restraints: 32820 Sorted by residual: bond pdb=" O2 PC A 303 " pdb=" P1 PC A 303 " ideal model delta sigma weight residual 1.733 1.599 0.134 2.00e-02 2.50e+03 4.50e+01 bond pdb=" O2 PC I 303 " pdb=" P1 PC I 303 " ideal model delta sigma weight residual 1.733 1.600 0.133 2.00e-02 2.50e+03 4.45e+01 bond pdb=" O2 PC C 303 " pdb=" P1 PC C 303 " ideal model delta sigma weight residual 1.733 1.600 0.133 2.00e-02 2.50e+03 4.41e+01 bond pdb=" O2 PC D 303 " pdb=" P1 PC D 303 " ideal model delta sigma weight residual 1.733 1.601 0.132 2.00e-02 2.50e+03 4.37e+01 bond pdb=" O2 PC G 303 " pdb=" P1 PC G 303 " ideal model delta sigma weight residual 1.733 1.602 0.131 2.00e-02 2.50e+03 4.30e+01 ... (remaining 32815 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.60: 59046 5.60 - 11.20: 107 11.20 - 16.80: 4 16.80 - 22.39: 3 22.39 - 27.99: 60 Bond angle restraints: 59220 Sorted by residual: angle pdb=" CG2 THR B 46 " pdb=" CB THR B 46 " pdb=" HB THR B 46 " ideal model delta sigma weight residual 108.00 80.01 27.99 3.00e+00 1.11e-01 8.71e+01 angle pdb=" CG2 THR D 126 " pdb=" CB THR D 126 " pdb=" HB THR D 126 " ideal model delta sigma weight residual 108.00 80.26 27.74 3.00e+00 1.11e-01 8.55e+01 angle pdb=" CG2 THR A 46 " pdb=" CB THR A 46 " pdb=" HB THR A 46 " ideal model delta sigma weight residual 108.00 80.44 27.56 3.00e+00 1.11e-01 8.44e+01 angle pdb=" CG2 THR A 173 " pdb=" CB THR A 173 " pdb=" HB THR A 173 " ideal model delta sigma weight residual 108.00 80.53 27.47 3.00e+00 1.11e-01 8.38e+01 angle pdb=" CG2 THR F 173 " pdb=" CB THR F 173 " pdb=" HB THR F 173 " ideal model delta sigma weight residual 108.00 80.60 27.40 3.00e+00 1.11e-01 8.34e+01 ... (remaining 59215 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 14153 17.97 - 35.95: 909 35.95 - 53.92: 338 53.92 - 71.89: 214 71.89 - 89.86: 16 Dihedral angle restraints: 15630 sinusoidal: 8280 harmonic: 7350 Sorted by residual: dihedral pdb=" CA SER F 80 " pdb=" C SER F 80 " pdb=" N GLU F 81 " pdb=" CA GLU F 81 " ideal model delta harmonic sigma weight residual -180.00 -151.90 -28.10 0 5.00e+00 4.00e-02 3.16e+01 dihedral pdb=" CA GLU A 62 " pdb=" C GLU A 62 " pdb=" N ILE A 63 " pdb=" CA ILE A 63 " ideal model delta harmonic sigma weight residual 180.00 152.53 27.47 0 5.00e+00 4.00e-02 3.02e+01 dihedral pdb=" CA GLU F 62 " pdb=" C GLU F 62 " pdb=" N ILE F 63 " pdb=" CA ILE F 63 " ideal model delta harmonic sigma weight residual 180.00 152.70 27.30 0 5.00e+00 4.00e-02 2.98e+01 ... (remaining 15627 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.395: 2449 0.395 - 0.790: 0 0.790 - 1.185: 0 1.185 - 1.580: 16 1.580 - 1.976: 5 Chirality restraints: 2470 Sorted by residual: chirality pdb=" CG LEU I 83 " pdb=" CB LEU I 83 " pdb=" CD1 LEU I 83 " pdb=" CD2 LEU I 83 " both_signs ideal model delta sigma weight residual False -2.59 -0.61 -1.98 2.00e-01 2.50e+01 9.76e+01 chirality pdb=" CG LEU D 83 " pdb=" CB LEU D 83 " pdb=" CD1 LEU D 83 " pdb=" CD2 LEU D 83 " both_signs ideal model delta sigma weight residual False -2.59 -0.80 -1.79 2.00e-01 2.50e+01 7.99e+01 chirality pdb=" CG LEU F 83 " pdb=" CB LEU F 83 " pdb=" CD1 LEU F 83 " pdb=" CD2 LEU F 83 " both_signs ideal model delta sigma weight residual False -2.59 -0.84 -1.75 2.00e-01 2.50e+01 7.69e+01 ... (remaining 2467 not shown) Planarity restraints: 4840 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG E 188 " 0.073 9.50e-02 1.11e+02 4.50e-02 3.28e+01 pdb=" NE ARG E 188 " -0.019 2.00e-02 2.50e+03 pdb=" CZ ARG E 188 " 0.058 2.00e-02 2.50e+03 pdb=" NH1 ARG E 188 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG E 188 " -0.069 2.00e-02 2.50e+03 pdb="HH11 ARG E 188 " 0.011 2.00e-02 2.50e+03 pdb="HH12 ARG E 188 " -0.035 2.00e-02 2.50e+03 pdb="HH21 ARG E 188 " -0.001 2.00e-02 2.50e+03 pdb="HH22 ARG E 188 " 0.054 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 58 " 0.065 9.50e-02 1.11e+02 4.25e-02 3.04e+01 pdb=" NE ARG C 58 " -0.009 2.00e-02 2.50e+03 pdb=" CZ ARG C 58 " 0.046 2.00e-02 2.50e+03 pdb=" NH1 ARG C 58 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG C 58 " -0.073 2.00e-02 2.50e+03 pdb="HH11 ARG C 58 " 0.010 2.00e-02 2.50e+03 pdb="HH12 ARG C 58 " -0.029 2.00e-02 2.50e+03 pdb="HH21 ARG C 58 " -0.002 2.00e-02 2.50e+03 pdb="HH22 ARG C 58 " 0.059 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 188 " -0.007 9.50e-02 1.11e+02 3.55e-02 2.83e+01 pdb=" NE ARG D 188 " 0.006 2.00e-02 2.50e+03 pdb=" CZ ARG D 188 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG D 188 " -0.052 2.00e-02 2.50e+03 pdb=" NH2 ARG D 188 " 0.052 2.00e-02 2.50e+03 pdb="HH11 ARG D 188 " -0.002 2.00e-02 2.50e+03 pdb="HH12 ARG D 188 " 0.057 2.00e-02 2.50e+03 pdb="HH21 ARG D 188 " 0.001 2.00e-02 2.50e+03 pdb="HH22 ARG D 188 " -0.051 2.00e-02 2.50e+03 ... (remaining 4837 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.08: 733 2.08 - 2.71: 53184 2.71 - 3.34: 93740 3.34 - 3.97: 127255 3.97 - 4.60: 199920 Nonbonded interactions: 474832 Sorted by model distance: nonbonded pdb=" OE2 GLU D 193 " pdb="HE21 GLN D 195 " model vdw 1.446 2.450 nonbonded pdb=" HG SER B 132 " pdb="HE22 GLN B 139 " model vdw 1.491 2.100 nonbonded pdb=" OE1 GLU G 197 " pdb=" HZ3 LYS H 123 " model vdw 1.534 2.450 nonbonded pdb=" HG SER H 102 " pdb=" O TYR H 125 " model vdw 1.541 2.450 nonbonded pdb=" OD1 ASP F 163 " pdb="HD22 ASN F 183 " model vdw 1.563 2.450 ... (remaining 474827 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 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' } 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: 4.650 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: 0.210 Extract box with map and model: 0.580 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 36.220 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.090 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:1.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8877 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 : 0.009 0.134 16890 Z= 0.398 Angle : 0.947 15.349 22980 Z= 0.479 Chirality : 0.147 1.976 2470 Planarity : 0.005 0.051 2900 Dihedral : 13.290 89.862 6060 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.18), residues: 2040 helix: -0.09 (0.39), residues: 110 sheet: -0.16 (0.17), residues: 810 loop : -0.84 (0.18), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.066 0.009 ARG E 188 TYR 0.026 0.005 TYR F 54 PHE 0.027 0.003 PHE G 66 TRP 0.022 0.004 TRP B 187 HIS 0.030 0.004 HIS J 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00901 / 0.40 (16880) covalent geometry : angle 0.94730 / 0.48 (22960) SS BOND : bond 0.00198 / 0.09 ( 10) SS BOND : angle 0.64307 / 0.43 ( 20) hydrogen bonds : bond 0.18614 / 12.15 ( 659) hydrogen bonds : angle 8.36300 / 5.81 ( 1632) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 180 PHE cc_start: 0.8529 (p90) cc_final: 0.8167 (p90) outliers start: 0 outliers final: 0 residues processed: 188 average time/residue: 0.3875 time to fit residues: 101.6890 Evaluate side-chains 140 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.1980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 0.2980 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 38 HIS G 38 HIS G 195 GLN H 38 HIS H 95 HIS H 139 GLN H 186 ASN D 38 HIS D 95 HIS D 145 ASN C 38 HIS B 38 HIS B 59 GLN B 95 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.079101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2565 r_free = 0.2565 target = 0.065444 restraints weight = 76046.430| |-----------------------------------------------------------------------------| r_work (start): 0.2574 rms_B_bonded: 1.90 r_work: 0.2480 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2352 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8922 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16890 Z= 0.128 Angle : 0.734 16.028 22980 Z= 0.386 Chirality : 0.147 1.761 2470 Planarity : 0.004 0.054 2900 Dihedral : 6.223 31.468 2280 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 1.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 0.72 % Allowed : 3.22 % Favored : 96.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.18), residues: 2040 helix: 2.00 (0.45), residues: 110 sheet: 0.29 (0.16), residues: 890 loop : -0.52 (0.19), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 6 TYR 0.022 0.001 TYR A 54 PHE 0.017 0.001 PHE H 39 TRP 0.011 0.001 TRP H 110 HIS 0.005 0.002 HIS C 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (16880) covalent geometry : angle 0.73447 / 0.39 (22960) SS BOND : bond 0.00124 / 0.06 ( 10) SS BOND : angle 0.42041 / 0.26 ( 20) hydrogen bonds : bond 0.04659 / 2.97 ( 659) hydrogen bonds : angle 6.11336 / 4.26 ( 1632) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 177 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 125 TYR cc_start: 0.8928 (t80) cc_final: 0.8591 (t80) REVERT: H 193 GLU cc_start: 0.8043 (tp30) cc_final: 0.7730 (mm-30) REVERT: I 18 SER cc_start: 0.9299 (m) cc_final: 0.8740 (p) REVERT: E 145 ASN cc_start: 0.8558 (m-40) cc_final: 0.8261 (m110) REVERT: D 180 PHE cc_start: 0.8652 (p90) cc_final: 0.8179 (p90) REVERT: C 38 HIS cc_start: 0.9177 (OUTLIER) cc_final: 0.8903 (m-70) REVERT: C 172 ASN cc_start: 0.8624 (t0) cc_final: 0.8404 (t0) outliers start: 13 outliers final: 9 residues processed: 186 average time/residue: 0.3301 time to fit residues: 88.2916 Evaluate side-chains 150 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 140 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 38 HIS Chi-restraints excluded: chain J residue 193 GLU Chi-restraints excluded: chain F residue 15 SER Chi-restraints excluded: chain F residue 98 THR Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 104 SER Chi-restraints excluded: chain C residue 38 HIS Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain B residue 99 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 95 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 170 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 166 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 11 optimal weight: 0.5980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 95 HIS G 95 HIS E 95 HIS D 145 ASN C 38 HIS C 95 HIS A 38 HIS A 95 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.077880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2545 r_free = 0.2545 target = 0.064459 restraints weight = 76164.572| |-----------------------------------------------------------------------------| r_work (start): 0.2556 rms_B_bonded: 1.85 r_work: 0.2460 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2333 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8944 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 16890 Z= 0.153 Angle : 0.695 15.797 22980 Z= 0.363 Chirality : 0.147 1.832 2470 Planarity : 0.003 0.049 2900 Dihedral : 5.666 30.561 2280 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 2.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.67 % Allowed : 4.67 % Favored : 94.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.18), residues: 2040 helix: 2.30 (0.45), residues: 110 sheet: 0.22 (0.16), residues: 890 loop : -0.40 (0.20), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 6 TYR 0.022 0.001 TYR F 54 PHE 0.011 0.001 PHE H 39 TRP 0.009 0.001 TRP C 110 HIS 0.010 0.002 HIS C 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.15 (16880) covalent geometry : angle 0.69518 / 0.36 (22960) SS BOND : bond 0.00177 / 0.08 ( 10) SS BOND : angle 0.40773 / 0.25 ( 20) hydrogen bonds : bond 0.04383 / 2.79 ( 659) hydrogen bonds : angle 5.69856 / 3.99 ( 1632) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 152 time to evaluate : 0.665 Fit side-chains REVERT: J 188 ARG cc_start: 0.8655 (mtp85) cc_final: 0.8321 (mtt-85) REVERT: G 125 TYR cc_start: 0.8941 (t80) cc_final: 0.8596 (t80) REVERT: I 18 SER cc_start: 0.9335 (m) cc_final: 0.8888 (p) REVERT: D 180 PHE cc_start: 0.8652 (p90) cc_final: 0.8177 (p90) outliers start: 12 outliers final: 10 residues processed: 162 average time/residue: 0.3409 time to fit residues: 78.9975 Evaluate side-chains 147 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 137 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 15 SER Chi-restraints excluded: chain F residue 98 THR Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 197 GLU Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 104 SER Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain A residue 76 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 158 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 145 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 185 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 82 optimal weight: 0.3980 chunk 107 optimal weight: 3.9990 chunk 106 optimal weight: 0.7980 chunk 190 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 38 HIS E 38 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.076204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2520 r_free = 0.2520 target = 0.063165 restraints weight = 76298.323| |-----------------------------------------------------------------------------| r_work (start): 0.2528 rms_B_bonded: 1.77 r_work: 0.2435 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2311 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.2311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8960 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 16890 Z= 0.191 Angle : 0.696 15.724 22980 Z= 0.363 Chirality : 0.147 1.830 2470 Planarity : 0.003 0.049 2900 Dihedral : 5.660 40.655 2280 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 2.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.06 % Allowed : 5.94 % Favored : 93.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.18), residues: 2040 helix: 2.18 (0.46), residues: 110 sheet: 0.13 (0.17), residues: 890 loop : -0.53 (0.20), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 58 TYR 0.021 0.001 TYR F 54 PHE 0.011 0.001 PHE D 66 TRP 0.010 0.001 TRP C 110 HIS 0.010 0.002 HIS C 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.19 (16880) covalent geometry : angle 0.69609 / 0.36 (22960) SS BOND : bond 0.00158 / 0.07 ( 10) SS BOND : angle 0.33252 / 0.21 ( 20) hydrogen bonds : bond 0.04150 / 2.65 ( 659) hydrogen bonds : angle 5.49794 / 3.86 ( 1632) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 154 time to evaluate : 0.895 Fit side-chains REVERT: J 80 SER cc_start: 0.8334 (t) cc_final: 0.7905 (m) REVERT: F 38 HIS cc_start: 0.9224 (OUTLIER) cc_final: 0.8253 (m90) REVERT: G 125 TYR cc_start: 0.8918 (t80) cc_final: 0.8603 (t80) REVERT: I 18 SER cc_start: 0.9376 (m) cc_final: 0.8905 (p) REVERT: E 94 VAL cc_start: 0.9114 (OUTLIER) cc_final: 0.8883 (p) REVERT: D 38 HIS cc_start: 0.9138 (OUTLIER) cc_final: 0.8808 (m90) REVERT: D 180 PHE cc_start: 0.8657 (p90) cc_final: 0.8425 (p90) outliers start: 19 outliers final: 15 residues processed: 170 average time/residue: 0.3420 time to fit residues: 83.6979 Evaluate side-chains 157 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 139 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 38 HIS Chi-restraints excluded: chain J residue 193 GLU Chi-restraints excluded: chain F residue 38 HIS Chi-restraints excluded: chain F residue 98 THR Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 197 GLU Chi-restraints excluded: chain H residue 45 SER Chi-restraints excluded: chain I residue 38 HIS Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 104 SER Chi-restraints excluded: chain D residue 38 HIS Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 155 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 6 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 158 optimal weight: 0.8980 chunk 186 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 175 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 170 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.076483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2521 r_free = 0.2521 target = 0.063151 restraints weight = 76279.346| |-----------------------------------------------------------------------------| r_work (start): 0.2526 rms_B_bonded: 1.85 r_work: 0.2431 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2306 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8959 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 16890 Z= 0.156 Angle : 0.676 15.658 22980 Z= 0.351 Chirality : 0.146 1.746 2470 Planarity : 0.003 0.048 2900 Dihedral : 5.512 47.133 2280 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.78 % Allowed : 7.28 % Favored : 91.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.18), residues: 2040 helix: 2.24 (0.46), residues: 110 sheet: 0.12 (0.17), residues: 890 loop : -0.56 (0.19), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 58 TYR 0.018 0.001 TYR F 54 PHE 0.010 0.001 PHE H 39 TRP 0.008 0.001 TRP A 162 HIS 0.007 0.002 HIS C 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 (16880) covalent geometry : angle 0.67620 / 0.35 (22960) SS BOND : bond 0.00159 / 0.07 ( 10) SS BOND : angle 0.35131 / 0.20 ( 20) hydrogen bonds : bond 0.03874 / 2.48 ( 659) hydrogen bonds : angle 5.40059 / 3.80 ( 1632) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 147 time to evaluate : 0.891 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 80 SER cc_start: 0.8324 (t) cc_final: 0.7892 (m) REVERT: G 125 TYR cc_start: 0.8927 (t80) cc_final: 0.8616 (t80) REVERT: I 18 SER cc_start: 0.9360 (m) cc_final: 0.8865 (p) REVERT: D 38 HIS cc_start: 0.9140 (OUTLIER) cc_final: 0.8826 (m90) outliers start: 14 outliers final: 13 residues processed: 158 average time/residue: 0.3266 time to fit residues: 75.4924 Evaluate side-chains 155 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 141 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 38 HIS Chi-restraints excluded: chain J residue 74 SER Chi-restraints excluded: chain J residue 193 GLU Chi-restraints excluded: chain F residue 98 THR Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 45 SER Chi-restraints excluded: chain I residue 38 HIS Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 104 SER Chi-restraints excluded: chain D residue 38 HIS Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain A residue 76 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 125 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 171 optimal weight: 1.9990 chunk 182 optimal weight: 2.9990 chunk 152 optimal weight: 3.9990 chunk 82 optimal weight: 0.5980 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.074994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2493 r_free = 0.2493 target = 0.061783 restraints weight = 76814.051| |-----------------------------------------------------------------------------| r_work (start): 0.2503 rms_B_bonded: 1.84 r_work: 0.2408 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2282 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.2282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8982 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 16890 Z= 0.219 Angle : 0.696 15.635 22980 Z= 0.363 Chirality : 0.147 1.751 2470 Planarity : 0.004 0.048 2900 Dihedral : 5.818 55.866 2280 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.17 % Allowed : 7.78 % Favored : 91.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.18), residues: 2040 helix: 2.04 (0.46), residues: 110 sheet: 0.00 (0.17), residues: 890 loop : -0.73 (0.19), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 58 TYR 0.020 0.001 TYR F 54 PHE 0.018 0.001 PHE D 180 TRP 0.009 0.001 TRP J 110 HIS 0.009 0.002 HIS C 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00526 / 0.22 (16880) covalent geometry : angle 0.69616 / 0.36 (22960) SS BOND : bond 0.00175 / 0.08 ( 10) SS BOND : angle 0.25378 / 0.15 ( 20) hydrogen bonds : bond 0.04098 / 2.63 ( 659) hydrogen bonds : angle 5.43524 / 3.83 ( 1632) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 143 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 80 SER cc_start: 0.8293 (t) cc_final: 0.7884 (m) REVERT: I 18 SER cc_start: 0.9425 (m) cc_final: 0.8913 (p) REVERT: E 94 VAL cc_start: 0.9106 (OUTLIER) cc_final: 0.8863 (p) REVERT: D 38 HIS cc_start: 0.9176 (OUTLIER) cc_final: 0.8819 (m90) REVERT: D 163 ASP cc_start: 0.8812 (p0) cc_final: 0.8565 (p0) outliers start: 21 outliers final: 14 residues processed: 161 average time/residue: 0.3228 time to fit residues: 75.7140 Evaluate side-chains 150 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 134 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 38 HIS Chi-restraints excluded: chain J residue 74 SER Chi-restraints excluded: chain J residue 193 GLU Chi-restraints excluded: chain F residue 98 THR Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 45 SER Chi-restraints excluded: chain I residue 38 HIS Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 104 SER Chi-restraints excluded: chain D residue 38 HIS Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 155 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 72 optimal weight: 2.9990 chunk 171 optimal weight: 1.9990 chunk 146 optimal weight: 2.9990 chunk 152 optimal weight: 2.9990 chunk 163 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 182 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 38 HIS E 1 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2695 r_free = 0.2695 target = 0.073383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2467 r_free = 0.2467 target = 0.060535 restraints weight = 77686.033| |-----------------------------------------------------------------------------| r_work (start): 0.2474 rms_B_bonded: 1.77 r_work: 0.2381 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2258 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.2258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9006 moved from start: 0.2519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.047 16890 Z= 0.318 Angle : 0.732 15.643 22980 Z= 0.384 Chirality : 0.148 1.759 2470 Planarity : 0.004 0.050 2900 Dihedral : 6.264 59.066 2280 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.11 % Allowed : 8.61 % Favored : 90.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.18), residues: 2040 helix: 1.76 (0.46), residues: 110 sheet: -0.40 (0.18), residues: 790 loop : -0.91 (0.18), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 58 TYR 0.021 0.002 TYR I 54 PHE 0.016 0.002 PHE E 52 TRP 0.009 0.001 TRP B 100 HIS 0.010 0.002 HIS C 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00762 / 0.32 (16880) covalent geometry : angle 0.73278 / 0.38 (22960) SS BOND : bond 0.00196 / 0.09 ( 10) SS BOND : angle 0.24184 / 0.14 ( 20) hydrogen bonds : bond 0.04457 / 2.88 ( 659) hydrogen bonds : angle 5.54724 / 3.91 ( 1632) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 138 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 18 SER cc_start: 0.9452 (m) cc_final: 0.8959 (p) REVERT: E 94 VAL cc_start: 0.9123 (OUTLIER) cc_final: 0.8882 (p) REVERT: D 38 HIS cc_start: 0.9188 (OUTLIER) cc_final: 0.8798 (m90) REVERT: D 163 ASP cc_start: 0.8794 (p0) cc_final: 0.8540 (p0) outliers start: 20 outliers final: 16 residues processed: 156 average time/residue: 0.3250 time to fit residues: 73.6771 Evaluate side-chains 149 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 131 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 38 HIS Chi-restraints excluded: chain J residue 74 SER Chi-restraints excluded: chain J residue 193 GLU Chi-restraints excluded: chain F residue 98 THR Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 45 SER Chi-restraints excluded: chain I residue 38 HIS Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 104 SER Chi-restraints excluded: chain D residue 38 HIS Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 155 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 149 optimal weight: 0.8980 chunk 186 optimal weight: 0.4980 chunk 58 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 196 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 179 optimal weight: 0.7980 chunk 54 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.075730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2513 r_free = 0.2513 target = 0.062846 restraints weight = 76573.152| |-----------------------------------------------------------------------------| r_work (start): 0.2523 rms_B_bonded: 1.78 r_work: 0.2430 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2307 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.2307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8966 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16890 Z= 0.130 Angle : 0.671 15.619 22980 Z= 0.348 Chirality : 0.146 1.754 2470 Planarity : 0.003 0.050 2900 Dihedral : 5.806 53.281 2280 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.17 % Allowed : 8.83 % Favored : 90.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.18), residues: 2040 helix: 2.13 (0.47), residues: 110 sheet: -0.30 (0.18), residues: 790 loop : -0.75 (0.18), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 58 TYR 0.016 0.001 TYR F 54 PHE 0.011 0.001 PHE A 66 TRP 0.008 0.001 TRP A 162 HIS 0.007 0.002 HIS B 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 (16880) covalent geometry : angle 0.67110 / 0.35 (22960) SS BOND : bond 0.00153 / 0.07 ( 10) SS BOND : angle 0.34352 / 0.19 ( 20) hydrogen bonds : bond 0.03633 / 2.34 ( 659) hydrogen bonds : angle 5.38007 / 3.79 ( 1632) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 145 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 18 SER cc_start: 0.9397 (m) cc_final: 0.8895 (p) REVERT: I 163 ASP cc_start: 0.8639 (p0) cc_final: 0.8409 (p0) REVERT: E 1 GLN cc_start: 0.6910 (mt0) cc_final: 0.6663 (mt0) REVERT: E 94 VAL cc_start: 0.9070 (OUTLIER) cc_final: 0.8845 (p) REVERT: D 38 HIS cc_start: 0.9152 (OUTLIER) cc_final: 0.8806 (m90) REVERT: C 1 GLN cc_start: 0.7741 (mp10) cc_final: 0.7394 (mm-40) outliers start: 21 outliers final: 15 residues processed: 163 average time/residue: 0.3238 time to fit residues: 76.6944 Evaluate side-chains 157 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 140 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 38 HIS Chi-restraints excluded: chain J residue 74 SER Chi-restraints excluded: chain J residue 193 GLU Chi-restraints excluded: chain F residue 98 THR Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 45 SER Chi-restraints excluded: chain I residue 38 HIS Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 104 SER Chi-restraints excluded: chain D residue 38 HIS Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 133 ILE Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain A residue 76 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 150 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 131 optimal weight: 0.8980 chunk 82 optimal weight: 0.5980 chunk 146 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 161 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 104 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.076051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2515 r_free = 0.2515 target = 0.062937 restraints weight = 76385.027| |-----------------------------------------------------------------------------| r_work (start): 0.2532 rms_B_bonded: 1.84 r_work: 0.2438 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2311 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.2311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8966 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16890 Z= 0.131 Angle : 0.664 15.634 22980 Z= 0.344 Chirality : 0.146 1.747 2470 Planarity : 0.003 0.046 2900 Dihedral : 5.672 58.199 2280 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.94 % Allowed : 9.28 % Favored : 89.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.18), residues: 2040 helix: 2.21 (0.47), residues: 110 sheet: -0.29 (0.18), residues: 790 loop : -0.68 (0.18), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 58 TYR 0.015 0.001 TYR F 54 PHE 0.011 0.001 PHE A 66 TRP 0.008 0.001 TRP A 162 HIS 0.006 0.002 HIS C 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.13 (16880) covalent geometry : angle 0.66411 / 0.34 (22960) SS BOND : bond 0.00169 / 0.08 ( 10) SS BOND : angle 0.36069 / 0.20 ( 20) hydrogen bonds : bond 0.03562 / 2.28 ( 659) hydrogen bonds : angle 5.29625 / 3.74 ( 1632) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 146 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 80 SER cc_start: 0.8309 (t) cc_final: 0.7931 (m) REVERT: I 18 SER cc_start: 0.9395 (m) cc_final: 0.8879 (p) REVERT: E 1 GLN cc_start: 0.6948 (mt0) cc_final: 0.6673 (mt0) REVERT: E 94 VAL cc_start: 0.9084 (OUTLIER) cc_final: 0.8857 (p) REVERT: D 38 HIS cc_start: 0.9144 (OUTLIER) cc_final: 0.8773 (m90) REVERT: C 1 GLN cc_start: 0.7797 (mp10) cc_final: 0.7536 (mm-40) outliers start: 17 outliers final: 15 residues processed: 159 average time/residue: 0.3352 time to fit residues: 76.8650 Evaluate side-chains 156 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 139 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 38 HIS Chi-restraints excluded: chain J residue 74 SER Chi-restraints excluded: chain J residue 163 ASP Chi-restraints excluded: chain F residue 98 THR Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 45 SER Chi-restraints excluded: chain I residue 38 HIS Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 104 SER Chi-restraints excluded: chain D residue 38 HIS Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 133 ILE Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain A residue 76 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 12 optimal weight: 3.9990 chunk 117 optimal weight: 0.9990 chunk 83 optimal weight: 0.6980 chunk 93 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 185 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 56 optimal weight: 0.8980 chunk 115 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.076156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2517 r_free = 0.2517 target = 0.063055 restraints weight = 76701.412| |-----------------------------------------------------------------------------| r_work (start): 0.2534 rms_B_bonded: 1.85 r_work: 0.2440 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2313 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8967 moved from start: 0.2800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16890 Z= 0.134 Angle : 0.666 15.634 22980 Z= 0.345 Chirality : 0.146 1.754 2470 Planarity : 0.003 0.062 2900 Dihedral : 5.659 57.004 2280 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.00 % Allowed : 9.50 % Favored : 89.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.18), residues: 2040 helix: 2.27 (0.47), residues: 110 sheet: -0.26 (0.18), residues: 790 loop : -0.66 (0.18), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 58 TYR 0.015 0.001 TYR F 54 PHE 0.010 0.001 PHE A 66 TRP 0.008 0.001 TRP A 162 HIS 0.006 0.002 HIS C 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.13 (16880) covalent geometry : angle 0.66637 / 0.35 (22960) SS BOND : bond 0.00167 / 0.08 ( 10) SS BOND : angle 0.33377 / 0.19 ( 20) hydrogen bonds : bond 0.03540 / 2.27 ( 659) hydrogen bonds : angle 5.26697 / 3.72 ( 1632) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 140 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 80 SER cc_start: 0.8329 (t) cc_final: 0.7954 (m) REVERT: I 18 SER cc_start: 0.9401 (m) cc_final: 0.8886 (p) REVERT: E 1 GLN cc_start: 0.6926 (mt0) cc_final: 0.6641 (mt0) REVERT: E 94 VAL cc_start: 0.9088 (OUTLIER) cc_final: 0.8860 (p) REVERT: D 38 HIS cc_start: 0.9143 (OUTLIER) cc_final: 0.8766 (m90) REVERT: C 1 GLN cc_start: 0.7896 (mp10) cc_final: 0.7628 (mm-40) outliers start: 18 outliers final: 14 residues processed: 155 average time/residue: 0.3315 time to fit residues: 74.7728 Evaluate side-chains 155 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 139 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 38 HIS Chi-restraints excluded: chain J residue 74 SER Chi-restraints excluded: chain F residue 98 THR Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 45 SER Chi-restraints excluded: chain I residue 38 HIS Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 104 SER Chi-restraints excluded: chain D residue 38 HIS Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 133 ILE Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain A residue 76 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 147 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 164 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 191 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 115 optimal weight: 0.7980 chunk 82 optimal weight: 0.9990 chunk 120 optimal weight: 3.9990 chunk 155 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.075221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2504 r_free = 0.2504 target = 0.062437 restraints weight = 76951.245| |-----------------------------------------------------------------------------| r_work (start): 0.2519 rms_B_bonded: 1.77 r_work: 0.2426 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2302 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8976 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 16890 Z= 0.180 Angle : 0.677 15.639 22980 Z= 0.352 Chirality : 0.146 1.755 2470 Planarity : 0.004 0.072 2900 Dihedral : 5.794 59.804 2280 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.89 % Allowed : 9.89 % Favored : 89.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.18), residues: 2040 helix: 2.14 (0.47), residues: 110 sheet: -0.31 (0.18), residues: 790 loop : -0.73 (0.18), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG I 188 TYR 0.016 0.001 TYR F 54 PHE 0.011 0.001 PHE E 52 TRP 0.007 0.001 TRP A 162 HIS 0.006 0.002 HIS C 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.18 (16880) covalent geometry : angle 0.67754 / 0.35 (22960) SS BOND : bond 0.00174 / 0.08 ( 10) SS BOND : angle 0.29440 / 0.16 ( 20) hydrogen bonds : bond 0.03754 / 2.41 ( 659) hydrogen bonds : angle 5.31222 / 3.75 ( 1632) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6081.55 seconds wall clock time: 104 minutes 7.27 seconds (6247.27 seconds total)