Starting phenix.real_space_refine on Mon Jul 6 02:46:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pkd_13468/07_2026/7pkd_13468_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pkd_13468/07_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_13468/07_2026/7pkd_13468_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pkd_13468/07_2026/7pkd_13468_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7pkd_13468/07_2026/7pkd_13468.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pkd_13468/07_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-dev-6108/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, 11 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {' PC': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "F" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 11 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {' PC': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "G" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 11 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {' PC': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "H" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 11 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {' PC': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "I" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 11 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {' PC': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "E" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 11 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {' PC': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "D" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 11 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {' PC': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "C" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 11 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {' PC': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "B" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 11 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {' PC': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 11 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {' PC': 1} Classifications: {'undetermined': 1} Chain breaks: 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: 5.49, per 1000 atoms: 0.17 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: 2.96 Conformation dependent library (CDL) restraints added in 826.8 milliseconds 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: 0.83 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: 8.20 Time building geometry restraints manager: 3.81 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: 0.00 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: 4.160 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: 0.190 Extract box with map and model: 0.520 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 30.370 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.140 ------------------------------------------------------------------------------- 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 : 0.867 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: 0.3764 time to fit residues: 98.5219 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 : 0.873 ------------------------------------------------------------------------------- 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: 0.8980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 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: 0.5980 ------------------------------------------------------------------------------- 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 = 0.2795 r_free = 0.2795 target = 0.079089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2568 r_free = 0.2568 target = 0.065678 restraints weight = 75973.237| |-----------------------------------------------------------------------------| r_work (start): 0.2575 rms_B_bonded: 1.82 r_work: 0.2482 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2357 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8866 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16890 Z= 0.132 Angle : 0.742 16.063 22980 Z= 0.390 Chirality : 0.147 1.761 2470 Planarity : 0.004 0.054 2900 Dihedral : 7.452 52.869 2280 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 1.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.78 % Allowed : 3.56 % Favored : 95.67 % 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: -0.09 (0.18), residues: 2040 helix: 1.96 (0.45), residues: 110 sheet: 0.27 (0.16), residues: 890 loop : -0.51 (0.19), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 58 TYR 0.022 0.001 TYR A 54 PHE 0.016 0.001 PHE H 39 TRP 0.011 0.001 TRP H 110 HIS 0.006 0.002 HIS C 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (16880) covalent geometry : angle 0.74226 / 0.39 (22960) SS BOND : bond 0.00129 / 0.06 ( 10) SS BOND : angle 0.42991 / 0.27 ( 20) hydrogen bonds : bond 0.04688 / 2.99 ( 659) hydrogen bonds : angle 6.13918 / 4.28 ( 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 197 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 183 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 60 ASP cc_start: 0.8309 (p0) cc_final: 0.7921 (p0) REVERT: G 125 TYR cc_start: 0.8885 (t80) cc_final: 0.8532 (t80) REVERT: H 193 GLU cc_start: 0.8042 (tp30) cc_final: 0.7700 (mm-30) REVERT: I 18 SER cc_start: 0.9276 (m) cc_final: 0.8703 (p) REVERT: E 60 ASP cc_start: 0.8377 (p0) cc_final: 0.7849 (p0) REVERT: D 138 GLU cc_start: 0.7816 (tm-30) cc_final: 0.7480 (tm-30) REVERT: D 180 PHE cc_start: 0.8631 (p90) cc_final: 0.8120 (p90) REVERT: C 38 HIS cc_start: 0.9141 (OUTLIER) cc_final: 0.8859 (m-70) REVERT: C 172 ASN cc_start: 0.8514 (t0) cc_final: 0.8288 (t0) REVERT: A 138 GLU cc_start: 0.8586 (tm-30) cc_final: 0.8160 (tm-30) REVERT: A 139 GLN cc_start: 0.8550 (mt0) cc_final: 0.7919 (mt0) outliers start: 14 outliers final: 9 residues processed: 192 average time/residue: 0.3408 time to fit residues: 94.1412 Evaluate side-chains 155 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 145 time to evaluate : 0.912 ------------------------------------------------------------------------------- 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: 1.9990 chunk 16 optimal weight: 0.8980 chunk 170 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 166 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 11 optimal weight: 0.2980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.2796 r_free = 0.2796 target = 0.079163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2568 r_free = 0.2568 target = 0.065662 restraints weight = 75501.539| |-----------------------------------------------------------------------------| r_work (start): 0.2577 rms_B_bonded: 1.81 r_work: 0.2483 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2355 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8934 moved from start: 0.1843 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= 0.133 Angle : 0.688 15.797 22980 Z= 0.359 Chirality : 0.147 1.835 2470 Planarity : 0.003 0.051 2900 Dihedral : 5.975 51.817 2280 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.56 % Allowed : 5.06 % Favored : 94.39 % 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: 2.35 (0.45), residues: 110 sheet: 0.21 (0.16), residues: 890 loop : -0.39 (0.20), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 6 TYR 0.018 0.001 TYR F 54 PHE 0.012 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 0.00315 / 0.13 (16880) covalent geometry : angle 0.68857 / 0.36 (22960) SS BOND : bond 0.00185 / 0.08 ( 10) SS BOND : angle 0.41065 / 0.25 ( 20) hydrogen bonds : bond 0.04274 / 2.72 ( 659) hydrogen bonds : angle 5.69300 / 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 165 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 155 time to evaluate : 0.871 Fit side-chains REVERT: J 188 ARG cc_start: 0.8646 (mtp85) cc_final: 0.8324 (mtt-85) REVERT: G 60 ASP cc_start: 0.8344 (p0) cc_final: 0.8022 (p0) REVERT: G 125 TYR cc_start: 0.8935 (t80) cc_final: 0.8581 (t80) REVERT: G 188 ARG cc_start: 0.8575 (mmt90) cc_final: 0.8249 (mmt-90) REVERT: I 18 SER cc_start: 0.9304 (m) cc_final: 0.8853 (p) REVERT: E 3 ASP cc_start: 0.8650 (t0) cc_final: 0.8434 (t0) REVERT: D 138 GLU cc_start: 0.7865 (tm-30) cc_final: 0.7467 (tm-30) REVERT: D 180 PHE cc_start: 0.8654 (p90) cc_final: 0.8170 (p90) outliers start: 10 outliers final: 8 residues processed: 163 average time/residue: 0.3691 time to fit residues: 85.1780 Evaluate side-chains 147 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 139 time to evaluate : 0.886 ------------------------------------------------------------------------------- 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 E residue 98 THR Chi-restraints excluded: chain E residue 104 SER 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=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: 3.9990 chunk 124 optimal weight: 2.9990 chunk 185 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 82 optimal weight: 0.0670 chunk 107 optimal weight: 3.9990 chunk 106 optimal weight: 0.6980 chunk 190 optimal weight: 2.9990 chunk 89 optimal weight: 0.0670 overall best weight: 0.7458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 38 HIS D 145 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.078958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2563 r_free = 0.2563 target = 0.065422 restraints weight = 75064.699| |-----------------------------------------------------------------------------| r_work (start): 0.2570 rms_B_bonded: 1.86 r_work: 0.2476 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2349 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8920 moved from start: 0.2134 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= 0.123 Angle : 0.672 15.720 22980 Z= 0.349 Chirality : 0.146 1.813 2470 Planarity : 0.003 0.048 2900 Dihedral : 5.584 59.014 2280 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.72 % Allowed : 5.78 % Favored : 93.50 % 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: -0.04 (0.18), residues: 2040 helix: 2.41 (0.46), residues: 110 sheet: 0.18 (0.16), residues: 890 loop : -0.39 (0.20), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 58 TYR 0.017 0.001 TYR F 54 PHE 0.011 0.001 PHE H 39 TRP 0.009 0.001 TRP C 110 HIS 0.008 0.002 HIS C 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.12 (16880) covalent geometry : angle 0.67190 / 0.35 (22960) SS BOND : bond 0.00159 / 0.07 ( 10) SS BOND : angle 0.39526 / 0.25 ( 20) hydrogen bonds : bond 0.03814 / 2.43 ( 659) hydrogen bonds : angle 5.41457 / 3.80 ( 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: 13 poor density : 160 time to evaluate : 0.916 Fit side-chains revert: symmetry clash REVERT: J 80 SER cc_start: 0.8334 (t) cc_final: 0.7908 (m) REVERT: F 60 ASP cc_start: 0.8458 (p0) cc_final: 0.8171 (p0) REVERT: G 125 TYR cc_start: 0.8907 (t80) cc_final: 0.8532 (t80) REVERT: G 188 ARG cc_start: 0.8612 (mmt90) cc_final: 0.8267 (mpt-90) REVERT: I 18 SER cc_start: 0.9309 (m) cc_final: 0.8821 (p) REVERT: E 3 ASP cc_start: 0.8681 (t0) cc_final: 0.8450 (t0) REVERT: E 60 ASP cc_start: 0.8256 (p0) cc_final: 0.7971 (p0) REVERT: D 138 GLU cc_start: 0.7849 (tm-30) cc_final: 0.7334 (tm-30) outliers start: 13 outliers final: 12 residues processed: 170 average time/residue: 0.3508 time to fit residues: 85.3098 Evaluate side-chains 161 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 149 time to evaluate : 0.895 ------------------------------------------------------------------------------- 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 6 optimal weight: 2.9990 chunk 117 optimal weight: 0.9980 chunk 158 optimal weight: 1.9990 chunk 186 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 175 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 170 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 38 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.075293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2502 r_free = 0.2502 target = 0.062213 restraints weight = 76572.444| |-----------------------------------------------------------------------------| r_work (start): 0.2513 rms_B_bonded: 1.79 r_work: 0.2419 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2294 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8970 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 16890 Z= 0.232 Angle : 0.704 15.708 22980 Z= 0.368 Chirality : 0.147 1.767 2470 Planarity : 0.004 0.048 2900 Dihedral : 5.820 50.753 2280 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.94 % Allowed : 6.89 % Favored : 92.17 % 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: -0.33 (0.18), residues: 2040 helix: 2.05 (0.46), residues: 110 sheet: 0.07 (0.17), residues: 890 loop : -0.66 (0.19), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 58 TYR 0.021 0.002 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 0.00556 / 0.23 (16880) covalent geometry : angle 0.70412 / 0.37 (22960) SS BOND : bond 0.00192 / 0.09 ( 10) SS BOND : angle 0.25428 / 0.16 ( 20) hydrogen bonds : bond 0.04269 / 2.73 ( 659) hydrogen bonds : angle 5.45824 / 3.83 ( 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 163 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 146 time to evaluate : 0.889 Fit side-chains REVERT: J 80 SER cc_start: 0.8317 (t) cc_final: 0.7884 (m) REVERT: F 60 ASP cc_start: 0.8439 (p0) cc_final: 0.8163 (p0) REVERT: G 125 TYR cc_start: 0.8938 (t80) cc_final: 0.8615 (t80) REVERT: I 18 SER cc_start: 0.9387 (m) cc_final: 0.8878 (p) REVERT: E 94 VAL cc_start: 0.9132 (OUTLIER) cc_final: 0.8898 (p) REVERT: D 38 HIS cc_start: 0.9153 (OUTLIER) cc_final: 0.8778 (m90) REVERT: D 138 GLU cc_start: 0.7943 (tm-30) cc_final: 0.7292 (tm-30) REVERT: D 163 ASP cc_start: 0.8821 (p0) cc_final: 0.8559 (p0) REVERT: A 175 TYR cc_start: 0.9323 (t80) cc_final: 0.9111 (t80) outliers start: 17 outliers final: 13 residues processed: 161 average time/residue: 0.3514 time to fit residues: 81.7380 Evaluate side-chains 152 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 137 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 38 HIS Chi-restraints excluded: chain J residue 89 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 125 optimal weight: 2.9990 chunk 77 optimal weight: 0.4980 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: 0.6980 overall best weight: 1.4386 ------------------------------------------------------------------------------- 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 = 0.2740 r_free = 0.2740 target = 0.075973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2508 r_free = 0.2508 target = 0.062527 restraints weight = 76042.081| |-----------------------------------------------------------------------------| r_work (start): 0.2552 rms_B_bonded: 1.87 r_work: 0.2458 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2331 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9018 moved from start: 0.2432 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= 0.185 Angle : 0.681 15.637 22980 Z= 0.354 Chirality : 0.146 1.752 2470 Planarity : 0.004 0.060 2900 Dihedral : 5.665 48.054 2280 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.94 % Allowed : 7.44 % Favored : 91.61 % 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: -0.36 (0.18), residues: 2040 helix: 2.18 (0.46), residues: 110 sheet: 0.05 (0.17), residues: 890 loop : -0.71 (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 0.011 0.001 PHE E 52 TRP 0.008 0.001 TRP C 110 HIS 0.008 0.002 HIS C 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.19 (16880) covalent geometry : angle 0.68166 / 0.35 (22960) SS BOND : bond 0.00172 / 0.08 ( 10) SS BOND : angle 0.30712 / 0.18 ( 20) hydrogen bonds : bond 0.03894 / 2.50 ( 659) hydrogen bonds : angle 5.39029 / 3.79 ( 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 165 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 148 time to evaluate : 0.825 Fit side-chains REVERT: J 80 SER cc_start: 0.8401 (t) cc_final: 0.7984 (m) REVERT: F 60 ASP cc_start: 0.8450 (p0) cc_final: 0.8249 (p0) REVERT: G 125 TYR cc_start: 0.8965 (t80) cc_final: 0.8674 (t80) REVERT: I 18 SER cc_start: 0.9383 (m) cc_final: 0.8881 (p) REVERT: E 94 VAL cc_start: 0.9155 (OUTLIER) cc_final: 0.8932 (p) REVERT: D 38 HIS cc_start: 0.9194 (OUTLIER) cc_final: 0.8850 (m90) REVERT: D 138 GLU cc_start: 0.7973 (tm-30) cc_final: 0.7406 (tm-30) REVERT: A 175 TYR cc_start: 0.9376 (t80) cc_final: 0.9156 (t80) outliers start: 17 outliers final: 13 residues processed: 161 average time/residue: 0.3420 time to fit residues: 79.8867 Evaluate side-chains 154 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 139 time to evaluate : 0.889 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 72 optimal weight: 1.9990 chunk 171 optimal weight: 1.9990 chunk 146 optimal weight: 1.9990 chunk 152 optimal weight: 3.9990 chunk 163 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 114 optimal weight: 4.9990 chunk 124 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 182 optimal weight: 2.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 38 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.074401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2479 r_free = 0.2479 target = 0.061083 restraints weight = 76936.996| |-----------------------------------------------------------------------------| r_work (start): 0.2490 rms_B_bonded: 1.86 r_work: 0.2394 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2267 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8985 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 16890 Z= 0.253 Angle : 0.703 15.667 22980 Z= 0.367 Chirality : 0.147 1.757 2470 Planarity : 0.004 0.046 2900 Dihedral : 5.860 45.211 2280 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.39 % Allowed : 7.94 % Favored : 90.67 % 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: -0.75 (0.18), residues: 2040 helix: 1.95 (0.46), residues: 110 sheet: -0.33 (0.18), residues: 790 loop : -0.81 (0.18), residues: 1140 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 0.014 0.001 PHE E 52 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 0.00607 / 0.25 (16880) covalent geometry : angle 0.70351 / 0.37 (22960) SS BOND : bond 0.00196 / 0.09 ( 10) SS BOND : angle 0.25755 / 0.14 ( 20) hydrogen bonds : bond 0.04192 / 2.70 ( 659) hydrogen bonds : angle 5.46265 / 3.84 ( 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 167 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 142 time to evaluate : 0.896 Fit side-chains REVERT: J 80 SER cc_start: 0.8306 (t) cc_final: 0.7909 (m) REVERT: F 60 ASP cc_start: 0.8399 (p0) cc_final: 0.8140 (p0) REVERT: G 125 TYR cc_start: 0.8967 (t80) cc_final: 0.8616 (t80) REVERT: I 18 SER cc_start: 0.9433 (m) cc_final: 0.8913 (p) REVERT: E 94 VAL cc_start: 0.9109 (OUTLIER) cc_final: 0.8872 (p) REVERT: D 38 HIS cc_start: 0.9173 (OUTLIER) cc_final: 0.8770 (m90) outliers start: 25 outliers final: 17 residues processed: 164 average time/residue: 0.3102 time to fit residues: 74.0433 Evaluate side-chains 155 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 136 time to evaluate : 0.882 ------------------------------------------------------------------------------- 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 89 VAL 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: 0.7980 chunk 186 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 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: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 1 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.076204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2512 r_free = 0.2512 target = 0.062757 restraints weight = 75947.678| |-----------------------------------------------------------------------------| r_work (start): 0.2544 rms_B_bonded: 1.90 r_work: 0.2450 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2323 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8968 moved from start: 0.2652 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= 0.128 Angle : 0.669 15.621 22980 Z= 0.347 Chirality : 0.146 1.747 2470 Planarity : 0.003 0.047 2900 Dihedral : 5.582 50.982 2280 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.00 % Allowed : 8.44 % Favored : 90.56 % 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: -0.62 (0.18), residues: 2040 helix: 2.19 (0.47), residues: 110 sheet: -0.27 (0.18), residues: 790 loop : -0.72 (0.18), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 58 TYR 0.016 0.001 TYR F 54 PHE 0.010 0.001 PHE E 52 TRP 0.008 0.001 TRP J 162 HIS 0.006 0.002 HIS C 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 (16880) covalent geometry : angle 0.66922 / 0.35 (22960) SS BOND : bond 0.00156 / 0.07 ( 10) SS BOND : angle 0.35587 / 0.20 ( 20) hydrogen bonds : bond 0.03626 / 2.33 ( 659) hydrogen bonds : angle 5.35802 / 3.78 ( 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: 18 poor density : 148 time to evaluate : 1.024 Fit side-chains revert: symmetry clash REVERT: J 80 SER cc_start: 0.8267 (t) cc_final: 0.7879 (m) REVERT: F 60 ASP cc_start: 0.8406 (p0) cc_final: 0.8183 (p0) REVERT: G 125 TYR cc_start: 0.8961 (t80) cc_final: 0.8670 (t80) REVERT: I 18 SER cc_start: 0.9390 (m) cc_final: 0.8877 (p) REVERT: E 60 ASP cc_start: 0.8186 (p0) cc_final: 0.7896 (p0) REVERT: E 94 VAL cc_start: 0.9097 (OUTLIER) cc_final: 0.8875 (p) REVERT: D 38 HIS cc_start: 0.9154 (OUTLIER) cc_final: 0.8806 (m90) REVERT: A 175 TYR cc_start: 0.9324 (t80) cc_final: 0.9096 (t80) outliers start: 18 outliers final: 14 residues processed: 163 average time/residue: 0.3263 time to fit residues: 76.9486 Evaluate side-chains 158 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 142 time to evaluate : 1.322 ------------------------------------------------------------------------------- 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 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: 0.8980 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: 2.9990 chunk 77 optimal weight: 0.7980 chunk 161 optimal weight: 0.5980 chunk 8 optimal weight: 0.6980 chunk 104 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.2767 r_free = 0.2767 target = 0.077510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2534 r_free = 0.2534 target = 0.063931 restraints weight = 75335.407| |-----------------------------------------------------------------------------| r_work (start): 0.2539 rms_B_bonded: 1.87 r_work: 0.2444 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2317 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8921 moved from start: 0.2769 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= 0.121 Angle : 0.661 15.619 22980 Z= 0.342 Chirality : 0.146 1.747 2470 Planarity : 0.003 0.060 2900 Dihedral : 5.383 57.476 2280 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.89 % Allowed : 8.94 % Favored : 90.17 % 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: 2.29 (0.47), residues: 110 sheet: -0.23 (0.18), residues: 790 loop : -0.69 (0.18), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 58 TYR 0.016 0.001 TYR F 54 PHE 0.010 0.001 PHE A 66 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 0.00294 / 0.12 (16880) covalent geometry : angle 0.66104 / 0.34 (22960) SS BOND : bond 0.00169 / 0.08 ( 10) SS BOND : angle 0.38131 / 0.22 ( 20) hydrogen bonds : bond 0.03477 / 2.22 ( 659) hydrogen bonds : angle 5.25470 / 3.70 ( 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 169 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 153 time to evaluate : 0.798 Fit side-chains revert: symmetry clash REVERT: J 80 SER cc_start: 0.8260 (t) cc_final: 0.7874 (m) REVERT: J 88 GLU cc_start: 0.7996 (tt0) cc_final: 0.7747 (tp30) REVERT: G 125 TYR cc_start: 0.8965 (t80) cc_final: 0.8675 (t80) REVERT: H 60 ASP cc_start: 0.7779 (p0) cc_final: 0.7553 (p0) REVERT: I 18 SER cc_start: 0.9369 (m) cc_final: 0.8843 (p) REVERT: E 1 GLN cc_start: 0.6899 (mt0) cc_final: 0.6640 (mt0) REVERT: E 60 ASP cc_start: 0.8154 (p0) cc_final: 0.7701 (p0) REVERT: E 94 VAL cc_start: 0.9042 (OUTLIER) cc_final: 0.8819 (p) REVERT: D 38 HIS cc_start: 0.9105 (OUTLIER) cc_final: 0.8732 (m90) REVERT: D 138 GLU cc_start: 0.7865 (tm-30) cc_final: 0.7147 (tm-30) REVERT: A 60 ASP cc_start: 0.8574 (p0) cc_final: 0.8111 (p0) REVERT: A 175 TYR cc_start: 0.9254 (t80) cc_final: 0.9023 (t80) outliers start: 16 outliers final: 14 residues processed: 166 average time/residue: 0.3081 time to fit residues: 74.0761 Evaluate side-chains 159 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 143 time to evaluate : 0.780 ------------------------------------------------------------------------------- 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 12 optimal weight: 3.9990 chunk 117 optimal weight: 0.0270 chunk 83 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 185 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 56 optimal weight: 0.5980 chunk 115 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 95 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.077765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2537 r_free = 0.2537 target = 0.064165 restraints weight = 75839.327| |-----------------------------------------------------------------------------| r_work (start): 0.2545 rms_B_bonded: 1.89 r_work: 0.2450 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2323 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8918 moved from start: 0.2856 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= 0.117 Angle : 0.663 15.625 22980 Z= 0.342 Chirality : 0.146 1.749 2470 Planarity : 0.003 0.060 2900 Dihedral : 5.273 54.977 2280 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.89 % Allowed : 9.33 % 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: -0.50 (0.18), residues: 2040 helix: 2.37 (0.47), residues: 110 sheet: -0.22 (0.18), residues: 790 loop : -0.64 (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 0.009 0.001 PHE H 39 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 0.00286 / 0.12 (16880) covalent geometry : angle 0.66272 / 0.34 (22960) SS BOND : bond 0.00175 / 0.08 ( 10) SS BOND : angle 0.38474 / 0.21 ( 20) hydrogen bonds : bond 0.03416 / 2.18 ( 659) hydrogen bonds : angle 5.21231 / 3.67 ( 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 159 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 143 time to evaluate : 0.701 Fit side-chains revert: symmetry clash REVERT: J 80 SER cc_start: 0.8288 (t) cc_final: 0.7901 (m) REVERT: J 88 GLU cc_start: 0.7997 (tt0) cc_final: 0.7751 (tp30) REVERT: G 125 TYR cc_start: 0.8964 (t80) cc_final: 0.8684 (t80) REVERT: H 60 ASP cc_start: 0.7711 (p0) cc_final: 0.7486 (p0) REVERT: I 18 SER cc_start: 0.9378 (m) cc_final: 0.8850 (p) REVERT: E 1 GLN cc_start: 0.6943 (mt0) cc_final: 0.6692 (mt0) REVERT: E 60 ASP cc_start: 0.8166 (p0) cc_final: 0.7725 (p0) REVERT: E 94 VAL cc_start: 0.9047 (OUTLIER) cc_final: 0.8824 (p) REVERT: D 38 HIS cc_start: 0.9105 (OUTLIER) cc_final: 0.8729 (m90) REVERT: D 138 GLU cc_start: 0.7859 (tm-30) cc_final: 0.7129 (tm-30) REVERT: C 1 GLN cc_start: 0.7581 (mp10) cc_final: 0.7321 (mt0) REVERT: C 197 GLU cc_start: 0.8170 (mm-30) cc_final: 0.7661 (mt-10) REVERT: A 60 ASP cc_start: 0.8578 (p0) cc_final: 0.8117 (p0) outliers start: 16 outliers final: 14 residues processed: 156 average time/residue: 0.3148 time to fit residues: 71.0965 Evaluate side-chains 157 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 141 time to evaluate : 0.844 ------------------------------------------------------------------------------- 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: 3.9990 chunk 107 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 164 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 191 optimal weight: 0.9980 chunk 77 optimal weight: 0.1980 chunk 115 optimal weight: 0.9990 chunk 82 optimal weight: 0.1980 chunk 120 optimal weight: 3.9990 chunk 155 optimal weight: 2.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 = 0.2758 r_free = 0.2758 target = 0.077068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2535 r_free = 0.2535 target = 0.064008 restraints weight = 75747.707| |-----------------------------------------------------------------------------| r_work (start): 0.2558 rms_B_bonded: 1.79 r_work: 0.2465 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2339 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.2339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8971 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16890 Z= 0.134 Angle : 0.664 15.641 22980 Z= 0.343 Chirality : 0.146 1.759 2470 Planarity : 0.003 0.059 2900 Dihedral : 5.220 41.819 2280 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.89 % Allowed : 9.33 % 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: -0.53 (0.18), residues: 2040 helix: 2.34 (0.47), residues: 110 sheet: -0.25 (0.18), residues: 790 loop : -0.65 (0.18), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 58 TYR 0.016 0.001 TYR F 54 PHE 0.009 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 0.00326 / 0.13 (16880) covalent geometry : angle 0.66382 / 0.34 (22960) SS BOND : bond 0.00169 / 0.08 ( 10) SS BOND : angle 0.36888 / 0.20 ( 20) hydrogen bonds : bond 0.03485 / 2.23 ( 659) hydrogen bonds : angle 5.20543 / 3.67 ( 1632) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6653.98 seconds wall clock time: 113 minutes 48.31 seconds (6828.31 seconds total)