Starting phenix.real_space_refine on Mon Sep 14 17:53:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pkh_13472/09_2026/7pkh_13472_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pkh_13472/09_2026/7pkh_13472.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7pkh_13472/09_2026/7pkh_13472.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pkh_13472/09_2026/7pkh_13472.map" model { file = "/net/cci-nas-00/data/ceres_data/7pkh_13472/09_2026/7pkh_13472_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pkh_13472/09_2026/7pkh_13472_trim.cif" } resolution = 3.0 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 15960 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 131 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 32420 Number of models: 1 Model: "" Number of chains: 30 Chain: "J" Number of atoms: 3226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 3226 Classifications: {'peptide': 206} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "F" Number of atoms: 3226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 3226 Classifications: {'peptide': 206} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "G" Number of atoms: 3226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 3226 Classifications: {'peptide': 206} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "H" Number of atoms: 3226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 3226 Classifications: {'peptide': 206} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "I" Number of atoms: 3226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 3226 Classifications: {'peptide': 206} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "E" Number of atoms: 3226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 3226 Classifications: {'peptide': 206} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "D" Number of atoms: 3226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 3226 Classifications: {'peptide': 206} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "C" Number of atoms: 3226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 3226 Classifications: {'peptide': 206} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "B" Number of atoms: 3226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 3226 Classifications: {'peptide': 206} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "A" Number of atoms: 3226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 3226 Classifications: {'peptide': 206} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "J" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 13 Unusual residues: {' CA': 2, ' PC': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 13 Unusual residues: {' CA': 2, ' PC': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 13 Unusual residues: {' CA': 2, ' PC': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 13 Unusual residues: {' CA': 2, ' PC': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 13 Unusual residues: {' CA': 2, ' PC': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 13 Unusual residues: {' CA': 2, ' PC': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 13 Unusual residues: {' CA': 2, ' PC': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 13 Unusual residues: {' CA': 2, ' PC': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 13 Unusual residues: {' CA': 2, ' PC': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 13 Unusual residues: {' CA': 2, ' PC': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Classifications: {'water': 1} Chain: "F" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Classifications: {'water': 1} Chain: "G" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Classifications: {'water': 1} Chain: "H" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Classifications: {'water': 1} Chain: "I" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Classifications: {'water': 1} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Classifications: {'water': 1} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Classifications: {'water': 1} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Classifications: {'water': 1} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Classifications: {'water': 1} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Classifications: {'water': 1} Time building chain proxies: 6.08, per 1000 atoms: 0.19 Number of scatterers: 32420 At special positions: 0 Unit cell: (140.448, 126.236, 110.352, 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 15960 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=2.04 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=2.04 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=2.04 Simple disulfide: pdb=" SG CYS E 36 " - pdb=" SG CYS E 97 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS B 36 " - pdb=" SG CYS B 97 " distance=2.06 Simple disulfide: pdb=" SG CYS A 36 " - pdb=" SG CYS A 97 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.08 Conformation dependent library (CDL) restraints added in 931.1 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 31 sheets defined 12.5% alpha, 38.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'J' and resid 42 through 47 removed outlier: 4.611A 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: 4.163A pdb=" N LEU J 190 " --> pdb=" O TRP J 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 46 removed outlier: 3.943A pdb=" N SER F 45 " --> pdb=" O GLU F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 148 through 151 Processing helix chain 'F' and resid 167 through 177 Processing helix chain 'F' and resid 186 through 190 removed outlier: 3.842A pdb=" N LEU F 190 " --> pdb=" O TRP F 187 " (cutoff:3.500A) Processing helix chain 'G' and resid 42 through 46 removed outlier: 4.108A 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 177 Processing helix chain 'G' and resid 186 through 190 removed outlier: 4.142A pdb=" N LEU G 190 " --> pdb=" O TRP G 187 " (cutoff:3.500A) Processing helix chain 'H' and resid 42 through 46 removed outlier: 3.579A pdb=" N SER H 45 " --> pdb=" O GLU H 42 " (cutoff:3.500A) Processing helix chain 'H' and resid 147 through 151 Processing helix chain 'H' and resid 167 through 177 Processing helix chain 'H' and resid 186 through 190 removed outlier: 4.246A pdb=" N LEU H 190 " --> pdb=" O TRP H 187 " (cutoff:3.500A) Processing helix chain 'I' and resid 42 through 46 removed outlier: 3.893A 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: 3.811A pdb=" N LEU I 190 " --> pdb=" O TRP I 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 46 removed outlier: 3.913A pdb=" N SER E 45 " --> pdb=" O GLU E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 151 Processing helix chain 'E' and resid 167 through 177 Processing helix chain 'E' and resid 186 through 190 removed outlier: 4.070A pdb=" N LEU E 190 " --> pdb=" O TRP E 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 46 removed outlier: 3.921A pdb=" N SER D 45 " --> 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: 4.089A pdb=" N LEU D 190 " --> pdb=" O TRP D 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 46 removed outlier: 3.866A 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 177 Processing helix chain 'C' and resid 186 through 190 removed outlier: 3.958A pdb=" N LEU C 190 " --> pdb=" O TRP C 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 46 removed outlier: 3.884A 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 177 Processing helix chain 'B' and resid 186 through 190 removed outlier: 3.783A pdb=" N LEU B 190 " --> pdb=" O TRP B 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 46 removed outlier: 4.155A 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: 4.106A 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: 3.608A pdb=" N ILE J 106 " --> pdb=" O GLU J 101 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N THR J 34 " --> pdb=" O MET J 161 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N MET J 161 " --> pdb=" O THR J 34 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N CYS J 36 " --> pdb=" O VAL J 159 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N VAL J 159 " --> pdb=" O CYS J 36 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N ASN J 158 " --> pdb=" O LYS J 7 " (cutoff:3.500A) removed outlier: 9.999A 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: 3.552A pdb=" N TYR J 73 " --> pdb=" O PHE J 84 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N ASN J 61 " --> pdb=" O THR J 56 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N THR J 56 " --> pdb=" O ASN J 61 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N TRP J 67 " --> pdb=" O SER J 50 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N SER J 50 " --> pdb=" O TRP J 67 " (cutoff:3.500A) removed outlier: 4.027A 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: 3.684A pdb=" N ILE F 106 " --> pdb=" O GLU F 101 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N THR F 34 " --> pdb=" O MET F 161 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N MET F 161 " --> pdb=" O THR F 34 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N CYS F 36 " --> pdb=" O VAL F 159 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N VAL F 159 " --> pdb=" O CYS F 36 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N ASN F 158 " --> pdb=" O LYS F 7 " (cutoff:3.500A) removed outlier: 10.064A 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: 6.092A pdb=" N ASN F 61 " --> pdb=" O THR F 56 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N THR F 56 " --> pdb=" O ASN F 61 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N TRP F 67 " --> pdb=" O SER F 50 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N SER F 50 " --> pdb=" O TRP F 67 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ILE F 133 " --> pdb=" O LEU F 22 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 139 through 141 removed outlier: 7.370A pdb=" N GLN F 139 " --> pdb=" O PHE F 146 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N PHE F 146 " --> pdb=" O GLN F 139 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 114 through 115 Processing sheet with id=AA9, first strand: chain 'G' and resid 114 through 115 removed outlier: 3.600A pdb=" N ILE G 106 " --> pdb=" O GLU G 101 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N THR G 34 " --> pdb=" O MET G 161 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N MET G 161 " --> pdb=" O THR G 34 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N CYS G 36 " --> pdb=" O VAL G 159 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N VAL G 159 " --> pdb=" O CYS G 36 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N ASN G 158 " --> pdb=" O LYS G 7 " (cutoff:3.500A) removed outlier: 10.117A pdb=" N LYS G 7 " --> pdb=" O ASN G 158 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 80 through 85 removed outlier: 4.418A pdb=" N ASN G 61 " --> pdb=" O TYR G 54 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N TYR G 54 " --> pdb=" O ASN G 61 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ILE G 63 " --> pdb=" O PHE G 52 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N PHE G 52 " --> pdb=" O ILE G 63 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N ILE G 65 " --> pdb=" O SER G 50 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N SER G 50 " --> pdb=" O ILE G 65 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ILE G 133 " --> pdb=" O LEU G 22 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 114 through 115 Processing sheet with id=AB3, first strand: chain 'H' and resid 114 through 115 removed outlier: 3.621A pdb=" N ILE H 106 " --> pdb=" O GLU H 101 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N THR H 34 " --> pdb=" O MET H 161 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N MET H 161 " --> pdb=" O THR H 34 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N CYS H 36 " --> pdb=" O VAL H 159 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N VAL H 159 " --> pdb=" O CYS H 36 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N ASN H 158 " --> pdb=" O LYS H 7 " (cutoff:3.500A) removed outlier: 9.983A pdb=" N LYS H 7 " --> pdb=" O ASN H 158 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 80 through 85 removed outlier: 6.207A pdb=" N ASN H 61 " --> pdb=" O THR H 56 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N THR H 56 " --> pdb=" O ASN H 61 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N TRP H 67 " --> pdb=" O SER H 50 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N SER H 50 " --> pdb=" O TRP H 67 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ILE H 133 " --> pdb=" O LEU H 22 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 114 through 115 Processing sheet with id=AB6, first strand: chain 'I' and resid 114 through 115 removed outlier: 3.628A pdb=" N ILE I 106 " --> pdb=" O GLU I 101 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N THR I 34 " --> pdb=" O MET I 161 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N MET I 161 " --> pdb=" O THR I 34 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N CYS I 36 " --> pdb=" O VAL I 159 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N VAL I 159 " --> pdb=" O CYS I 36 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N ASN I 158 " --> pdb=" O LYS I 7 " (cutoff:3.500A) removed outlier: 10.189A pdb=" N LYS I 7 " --> pdb=" O ASN I 158 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 80 through 85 removed outlier: 3.547A pdb=" N TYR I 73 " --> pdb=" O PHE I 84 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ASN I 61 " --> pdb=" O TYR I 54 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N TYR I 54 " --> pdb=" O ASN I 61 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ILE I 63 " --> pdb=" O PHE I 52 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N PHE I 52 " --> pdb=" O ILE I 63 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N ILE I 65 " --> pdb=" O SER I 50 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N SER I 50 " --> pdb=" O ILE I 65 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ILE I 133 " --> pdb=" O LEU I 22 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 114 through 115 Processing sheet with id=AB9, first strand: chain 'E' and resid 114 through 115 removed outlier: 3.642A pdb=" N ILE E 106 " --> pdb=" O GLU E 101 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N THR E 34 " --> pdb=" O MET E 161 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N MET E 161 " --> pdb=" O THR E 34 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N CYS E 36 " --> pdb=" O VAL E 159 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N VAL E 159 " --> pdb=" O CYS E 36 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N ASN E 158 " --> pdb=" O LYS E 7 " (cutoff:3.500A) removed outlier: 9.984A pdb=" N LYS E 7 " --> pdb=" O ASN E 158 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 80 through 85 removed outlier: 6.046A pdb=" N ASN E 61 " --> pdb=" O THR E 56 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N THR E 56 " --> pdb=" O ASN E 61 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N TRP E 67 " --> pdb=" O SER E 50 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N SER E 50 " --> pdb=" O TRP E 67 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ILE E 133 " --> pdb=" O LEU E 22 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 114 through 115 Processing sheet with id=AC3, first strand: chain 'D' and resid 114 through 115 removed outlier: 3.826A pdb=" N ILE D 106 " --> pdb=" O GLU D 101 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N THR D 34 " --> pdb=" O MET D 161 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N MET D 161 " --> pdb=" O THR D 34 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N CYS D 36 " --> pdb=" O VAL D 159 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N VAL D 159 " --> pdb=" O CYS D 36 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N ASN D 158 " --> pdb=" O LYS D 7 " (cutoff:3.500A) removed outlier: 10.232A pdb=" N LYS D 7 " --> pdb=" O ASN D 158 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 80 through 85 removed outlier: 6.186A pdb=" N ASN D 61 " --> pdb=" O THR D 56 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N THR D 56 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N TRP D 67 " --> pdb=" O SER D 50 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N SER D 50 " --> pdb=" O TRP D 67 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ILE D 133 " --> pdb=" O LEU D 22 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 114 through 115 Processing sheet with id=AC6, first strand: chain 'C' and resid 114 through 115 removed outlier: 3.625A pdb=" N ILE C 106 " --> pdb=" O GLU C 101 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N HIS C 38 " --> pdb=" O ASN C 158 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N ASN C 158 " --> pdb=" O HIS C 38 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N TYR C 40 " --> pdb=" O ILE C 156 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N ILE C 156 " --> pdb=" O TYR C 40 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N ASN C 158 " --> pdb=" O LYS C 7 " (cutoff:3.500A) removed outlier: 9.911A pdb=" N LYS C 7 " --> pdb=" O ASN C 158 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 80 through 85 removed outlier: 6.261A pdb=" N ASN C 61 " --> pdb=" O THR C 56 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N THR C 56 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N TRP C 67 " --> pdb=" O SER C 50 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N SER C 50 " --> pdb=" O TRP C 67 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ILE C 133 " --> pdb=" O LEU C 22 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 114 through 115 Processing sheet with id=AC9, first strand: chain 'B' and resid 114 through 115 removed outlier: 3.644A pdb=" N ILE B 106 " --> pdb=" O GLU B 101 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N THR B 34 " --> pdb=" O MET B 161 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N MET B 161 " --> pdb=" O THR B 34 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N CYS B 36 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N VAL B 159 " --> pdb=" O CYS B 36 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N ASN B 158 " --> pdb=" O LYS B 7 " (cutoff:3.500A) removed outlier: 9.896A pdb=" N LYS B 7 " --> pdb=" O ASN B 158 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 80 through 85 removed outlier: 3.548A pdb=" N TYR B 73 " --> pdb=" O PHE B 84 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N ASN B 61 " --> pdb=" O THR B 56 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N THR B 56 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N TRP B 67 " --> pdb=" O SER B 50 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N SER B 50 " --> pdb=" O TRP B 67 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE B 133 " --> pdb=" O LEU B 22 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 114 through 115 Processing sheet with id=AD3, first strand: chain 'A' and resid 114 through 115 removed outlier: 3.643A pdb=" N ILE A 106 " --> pdb=" O GLU A 101 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N THR A 34 " --> pdb=" O MET A 161 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N MET A 161 " --> pdb=" O THR A 34 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N CYS A 36 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N VAL A 159 " --> pdb=" O CYS A 36 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N ASN A 158 " --> pdb=" O LYS A 7 " (cutoff:3.500A) removed outlier: 9.995A pdb=" N LYS A 7 " --> pdb=" O ASN A 158 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 80 through 85 removed outlier: 5.932A pdb=" N ASN A 61 " --> pdb=" O THR A 56 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N THR A 56 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N TRP A 67 " --> pdb=" O SER A 50 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N SER A 50 " --> pdb=" O TRP A 67 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ILE A 133 " --> pdb=" O LEU A 22 " (cutoff:3.500A) 682 hydrogen bonds defined for protein. 1641 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: 4.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.05: 15960 1.05 - 1.26: 2670 1.26 - 1.48: 7237 1.48 - 1.69: 6913 1.69 - 1.91: 60 Bond restraints: 32840 Sorted by residual: bond pdb=" O2 PC D 303 " pdb=" P1 PC D 303 " ideal model delta sigma weight residual 1.733 1.599 0.134 2.00e-02 2.50e+03 4.47e+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 4.43e+01 bond pdb=" O2 PC E 303 " pdb=" P1 PC E 303 " ideal model delta sigma weight residual 1.733 1.602 0.131 2.00e-02 2.50e+03 4.29e+01 bond pdb=" O2 PC H 303 " pdb=" P1 PC H 303 " ideal model delta sigma weight residual 1.733 1.602 0.131 2.00e-02 2.50e+03 4.28e+01 bond pdb=" O2 PC A 303 " pdb=" P1 PC A 303 " ideal model delta sigma weight residual 1.733 1.603 0.130 2.00e-02 2.50e+03 4.21e+01 ... (remaining 32835 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.05: 59085 6.05 - 12.10: 99 12.10 - 18.15: 3 18.15 - 24.20: 17 24.20 - 30.25: 56 Bond angle restraints: 59260 Sorted by residual: angle pdb=" CG2 THR J 17 " pdb=" CB THR J 17 " pdb=" HB THR J 17 " ideal model delta sigma weight residual 108.00 77.75 30.25 3.00e+00 1.11e-01 1.02e+02 angle pdb=" CG2 THR A 46 " pdb=" CB THR A 46 " pdb=" HB THR A 46 " ideal model delta sigma weight residual 108.00 79.66 28.34 3.00e+00 1.11e-01 8.92e+01 angle pdb=" CA THR J 17 " pdb=" CB THR J 17 " pdb=" HB THR J 17 " ideal model delta sigma weight residual 109.00 81.03 27.97 3.00e+00 1.11e-01 8.69e+01 angle pdb=" CG2 THR J 46 " pdb=" CB THR J 46 " pdb=" HB THR J 46 " ideal model delta sigma weight residual 108.00 80.08 27.92 3.00e+00 1.11e-01 8.66e+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 80.12 27.88 3.00e+00 1.11e-01 8.64e+01 ... (remaining 59255 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 14117 17.67 - 35.35: 978 35.35 - 53.02: 310 53.02 - 70.69: 218 70.69 - 88.36: 27 Dihedral angle restraints: 15650 sinusoidal: 8280 harmonic: 7370 Sorted by residual: dihedral pdb=" CB CYS B 36 " pdb=" SG CYS B 36 " pdb=" SG CYS B 97 " pdb=" CB CYS B 97 " ideal model delta sinusoidal sigma weight residual 93.00 38.74 54.26 1 1.00e+01 1.00e-02 3.99e+01 dihedral pdb=" CA ARG H 58 " pdb=" C ARG H 58 " pdb=" N GLN H 59 " pdb=" CA GLN H 59 " ideal model delta harmonic sigma weight residual -180.00 -151.70 -28.30 0 5.00e+00 4.00e-02 3.20e+01 dihedral pdb=" CA GLU D 62 " pdb=" C GLU D 62 " pdb=" N ILE D 63 " pdb=" CA ILE D 63 " ideal model delta harmonic sigma weight residual 180.00 152.18 27.82 0 5.00e+00 4.00e-02 3.10e+01 ... (remaining 15647 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.367: 2446 0.367 - 0.733: 0 0.733 - 1.100: 1 1.100 - 1.466: 12 1.466 - 1.833: 11 Chirality restraints: 2470 Sorted by residual: chirality pdb=" CG LEU A 83 " pdb=" CB LEU A 83 " pdb=" CD1 LEU A 83 " pdb=" CD2 LEU A 83 " both_signs ideal model delta sigma weight residual False -2.59 -0.76 -1.83 2.00e-01 2.50e+01 8.40e+01 chirality pdb=" CG LEU J 83 " pdb=" CB LEU J 83 " pdb=" CD1 LEU J 83 " pdb=" CD2 LEU J 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 -0.85 -1.74 2.00e-01 2.50e+01 7.53e+01 ... (remaining 2467 not shown) Planarity restraints: 4840 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG G 58 " -0.058 9.50e-02 1.11e+02 3.87e-02 2.57e+01 pdb=" NE ARG G 58 " 0.008 2.00e-02 2.50e+03 pdb=" CZ ARG G 58 " -0.041 2.00e-02 2.50e+03 pdb=" NH1 ARG G 58 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG G 58 " 0.067 2.00e-02 2.50e+03 pdb="HH11 ARG G 58 " -0.009 2.00e-02 2.50e+03 pdb="HH12 ARG G 58 " 0.028 2.00e-02 2.50e+03 pdb="HH21 ARG G 58 " 0.002 2.00e-02 2.50e+03 pdb="HH22 ARG G 58 " -0.055 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN I 183 " -0.033 2.00e-02 2.50e+03 4.09e-02 2.50e+01 pdb=" CG ASN I 183 " 0.026 2.00e-02 2.50e+03 pdb=" OD1 ASN I 183 " 0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN I 183 " 0.066 2.00e-02 2.50e+03 pdb="HD21 ASN I 183 " 0.002 2.00e-02 2.50e+03 pdb="HD22 ASN I 183 " -0.063 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS G 38 " -0.009 2.00e-02 2.50e+03 3.11e-02 2.41e+01 pdb=" CG HIS G 38 " 0.005 2.00e-02 2.50e+03 pdb=" ND1 HIS G 38 " -0.050 2.00e-02 2.50e+03 pdb=" CD2 HIS G 38 " -0.027 2.00e-02 2.50e+03 pdb=" CE1 HIS G 38 " -0.027 2.00e-02 2.50e+03 pdb=" NE2 HIS G 38 " -0.020 2.00e-02 2.50e+03 pdb=" HD1 HIS G 38 " 0.055 2.00e-02 2.50e+03 pdb=" HD2 HIS G 38 " 0.040 2.00e-02 2.50e+03 pdb=" HE1 HIS G 38 " 0.018 2.00e-02 2.50e+03 pdb=" HE2 HIS G 38 " 0.015 2.00e-02 2.50e+03 ... (remaining 4837 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.08: 784 2.08 - 2.71: 53664 2.71 - 3.34: 94199 3.34 - 3.97: 130600 3.97 - 4.60: 202643 Nonbonded interactions: 481890 Sorted by model distance: nonbonded pdb="HE21 GLN H 139 " pdb=" O PHE H 142 " model vdw 1.448 2.450 nonbonded pdb=" H SER B 167 " pdb=" OE1 GLU B 170 " model vdw 1.504 2.450 nonbonded pdb=" HG1 THR C 41 " pdb=" O VAL C 153 " model vdw 1.507 2.450 nonbonded pdb=" HG1 THR D 41 " pdb=" O VAL D 153 " model vdw 1.511 2.450 nonbonded pdb=" HG SER B 74 " pdb=" OE2 GLU B 81 " model vdw 1.514 2.450 ... (remaining 481885 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.550 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: 0.290 Extract box with map and model: 0.550 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 31.990 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.134 16890 Z= 0.415 Angle : 1.048 19.206 22980 Z= 0.541 Chirality : 0.155 1.833 2470 Planarity : 0.006 0.074 2900 Dihedral : 13.340 88.365 6060 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % 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: -0.72 (0.18), residues: 2040 helix: -1.30 (0.38), residues: 100 sheet: -0.04 (0.16), residues: 910 loop : -0.72 (0.19), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.069 0.010 ARG G 188 TYR 0.031 0.005 TYR F 54 PHE 0.022 0.003 PHE H 66 TRP 0.030 0.006 TRP F 67 HIS 0.021 0.006 HIS G 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00959 / 0.42 (16880) covalent geometry : angle 1.04334 / 0.54 (22960) SS BOND : bond 0.00912 / 0.45 ( 10) SS BOND : angle 3.36751 / 2.08 ( 20) hydrogen bonds : bond 0.18531 / 12.20 ( 662) hydrogen bonds : angle 8.07128 / 5.60 ( 1641) *********************** 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 196 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 0.908 Fit side-chains revert: symmetry clash REVERT: D 145 ASN cc_start: 0.8573 (m110) cc_final: 0.8165 (m110) REVERT: D 172 ASN cc_start: 0.8117 (t0) cc_final: 0.7768 (t0) REVERT: C 194 VAL cc_start: 0.9091 (t) cc_final: 0.8802 (p) REVERT: A 169 ASP cc_start: 0.8182 (m-30) cc_final: 0.7927 (m-30) outliers start: 0 outliers final: 0 residues processed: 196 average time/residue: 1.4862 time to fit residues: 321.6534 Evaluate side-chains 144 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 0.930 ------------------------------------------------------------------------------- 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: 0.7980 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 172 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.093932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.077246 restraints weight = 73161.861| |-----------------------------------------------------------------------------| r_work (start): 0.2747 rms_B_bonded: 1.89 r_work: 0.2657 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2536 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 16890 Z= 0.143 Angle : 0.773 15.745 22980 Z= 0.398 Chirality : 0.156 1.787 2470 Planarity : 0.004 0.052 2900 Dihedral : 7.001 56.792 2280 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.56 % Allowed : 5.50 % Favored : 93.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.18), residues: 2040 helix: 1.09 (0.40), residues: 110 sheet: 0.25 (0.16), residues: 890 loop : -0.53 (0.19), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J 58 TYR 0.018 0.001 TYR D 54 PHE 0.014 0.001 PHE D 180 TRP 0.009 0.001 TRP A 110 HIS 0.006 0.002 HIS A 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.14 (16880) covalent geometry : angle 0.76981 / 0.40 (22960) SS BOND : bond 0.00538 / 0.26 ( 10) SS BOND : angle 2.57136 / 1.54 ( 20) hydrogen bonds : bond 0.04707 / 3.05 ( 662) hydrogen bonds : angle 6.08779 / 4.20 ( 1641) *********************** 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 180 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 170 time to evaluate : 0.924 Fit side-chains revert: symmetry clash REVERT: H 18 SER cc_start: 0.8381 (m) cc_final: 0.8148 (p) REVERT: I 188 ARG cc_start: 0.8177 (mpt-90) cc_final: 0.7900 (mmt-90) REVERT: D 145 ASN cc_start: 0.8528 (m110) cc_final: 0.8033 (m110) REVERT: D 163 ASP cc_start: 0.7955 (p0) cc_final: 0.7621 (p0) REVERT: D 172 ASN cc_start: 0.8318 (t0) cc_final: 0.7907 (t0) REVERT: C 80 SER cc_start: 0.8731 (m) cc_final: 0.8445 (t) outliers start: 10 outliers final: 2 residues processed: 177 average time/residue: 1.3736 time to fit residues: 269.9568 Evaluate side-chains 143 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 141 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 181 SER Chi-restraints excluded: chain E residue 80 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 19 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 136 optimal weight: 1.9990 chunk 172 optimal weight: 4.9990 chunk 25 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 109 optimal weight: 0.9980 chunk 123 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 145 ASN H 172 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.090363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.073035 restraints weight = 73776.334| |-----------------------------------------------------------------------------| r_work (start): 0.2766 rms_B_bonded: 1.98 r_work: 0.2675 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2552 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8835 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 16890 Z= 0.146 Angle : 0.734 15.640 22980 Z= 0.376 Chirality : 0.156 1.796 2470 Planarity : 0.004 0.057 2900 Dihedral : 6.521 62.237 2280 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.67 % Allowed : 7.39 % Favored : 91.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.18), residues: 2040 helix: 1.96 (0.44), residues: 110 sheet: 0.31 (0.16), residues: 890 loop : -0.51 (0.19), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG J 6 TYR 0.018 0.001 TYR J 54 PHE 0.013 0.001 PHE D 180 TRP 0.009 0.001 TRP A 110 HIS 0.005 0.001 HIS G 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 (16880) covalent geometry : angle 0.73091 / 0.38 (22960) SS BOND : bond 0.00530 / 0.25 ( 10) SS BOND : angle 2.36639 / 1.42 ( 20) hydrogen bonds : bond 0.04248 / 2.76 ( 662) hydrogen bonds : angle 5.69683 / 3.92 ( 1641) *********************** 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: 12 poor density : 153 time to evaluate : 0.864 Fit side-chains revert: symmetry clash REVERT: J 70 ASP cc_start: 0.7739 (m-30) cc_final: 0.7485 (t0) REVERT: H 18 SER cc_start: 0.8405 (m) cc_final: 0.8195 (p) REVERT: I 114 LYS cc_start: 0.8598 (mmpt) cc_final: 0.8305 (mmpt) REVERT: D 145 ASN cc_start: 0.8506 (m110) cc_final: 0.8007 (m110) REVERT: D 163 ASP cc_start: 0.8133 (p0) cc_final: 0.7773 (p0) REVERT: D 172 ASN cc_start: 0.8348 (t0) cc_final: 0.7990 (t0) REVERT: C 80 SER cc_start: 0.8715 (m) cc_final: 0.8397 (t) REVERT: C 88 GLU cc_start: 0.7740 (pp20) cc_final: 0.6999 (pm20) outliers start: 12 outliers final: 2 residues processed: 159 average time/residue: 1.3888 time to fit residues: 245.1274 Evaluate side-chains 144 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 142 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 80 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 196 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 148 optimal weight: 0.9980 chunk 127 optimal weight: 2.9990 chunk 197 optimal weight: 0.5980 chunk 161 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 186 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.089570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.072071 restraints weight = 73909.353| |-----------------------------------------------------------------------------| r_work (start): 0.2773 rms_B_bonded: 2.02 r_work: 0.2679 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2556 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8842 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 16890 Z= 0.160 Angle : 0.728 15.410 22980 Z= 0.373 Chirality : 0.156 1.772 2470 Planarity : 0.004 0.068 2900 Dihedral : 6.525 71.874 2280 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 2.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.61 % Allowed : 8.39 % Favored : 91.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.18), residues: 2040 helix: 2.06 (0.45), residues: 110 sheet: 0.32 (0.17), residues: 890 loop : -0.54 (0.19), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J 58 TYR 0.018 0.001 TYR J 54 PHE 0.015 0.001 PHE D 180 TRP 0.009 0.001 TRP A 110 HIS 0.005 0.001 HIS G 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.16 (16880) covalent geometry : angle 0.72541 / 0.37 (22960) SS BOND : bond 0.00531 / 0.26 ( 10) SS BOND : angle 2.29197 / 1.37 ( 20) hydrogen bonds : bond 0.03916 / 2.54 ( 662) hydrogen bonds : angle 5.56563 / 3.83 ( 1641) *********************** 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 157 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 146 time to evaluate : 0.925 Fit side-chains revert: symmetry clash REVERT: J 197 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.6697 (pp20) REVERT: G 138 GLU cc_start: 0.7904 (tm-30) cc_final: 0.7599 (tm-30) REVERT: H 18 SER cc_start: 0.8406 (m) cc_final: 0.8188 (p) REVERT: I 114 LYS cc_start: 0.8570 (mmpt) cc_final: 0.8276 (mmpt) REVERT: D 145 ASN cc_start: 0.8570 (m110) cc_final: 0.8118 (m110) REVERT: D 163 ASP cc_start: 0.8114 (p0) cc_final: 0.7825 (p0) REVERT: D 172 ASN cc_start: 0.8354 (t0) cc_final: 0.8005 (t0) REVERT: C 80 SER cc_start: 0.8662 (m) cc_final: 0.8334 (t) REVERT: C 88 GLU cc_start: 0.7674 (pp20) cc_final: 0.6925 (pm20) outliers start: 11 outliers final: 3 residues processed: 153 average time/residue: 1.4536 time to fit residues: 246.2827 Evaluate side-chains 142 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 138 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 197 GLU Chi-restraints excluded: chain F residue 98 THR Chi-restraints excluded: chain E residue 80 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 140 optimal weight: 3.9990 chunk 157 optimal weight: 0.6980 chunk 113 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 135 optimal weight: 0.9990 chunk 150 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 172 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.088365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.070948 restraints weight = 74133.913| |-----------------------------------------------------------------------------| r_work (start): 0.2724 rms_B_bonded: 1.99 r_work: 0.2631 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2508 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8869 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 16890 Z= 0.202 Angle : 0.741 15.650 22980 Z= 0.380 Chirality : 0.156 1.786 2470 Planarity : 0.005 0.075 2900 Dihedral : 6.588 89.732 2280 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.06 % Allowed : 9.28 % Favored : 89.67 % 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: -0.20 (0.18), residues: 2040 helix: 1.90 (0.45), residues: 110 sheet: 0.28 (0.17), residues: 890 loop : -0.69 (0.19), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG J 58 TYR 0.019 0.001 TYR J 54 PHE 0.014 0.001 PHE D 180 TRP 0.009 0.001 TRP A 110 HIS 0.006 0.002 HIS G 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00486 / 0.20 (16880) covalent geometry : angle 0.73773 / 0.38 (22960) SS BOND : bond 0.00588 / 0.28 ( 10) SS BOND : angle 2.29063 / 1.37 ( 20) hydrogen bonds : bond 0.04044 / 2.62 ( 662) hydrogen bonds : angle 5.61522 / 3.86 ( 1641) *********************** 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 162 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 143 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 197 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.6735 (pp20) REVERT: H 18 SER cc_start: 0.8444 (m) cc_final: 0.8202 (p) REVERT: I 114 LYS cc_start: 0.8574 (mmpt) cc_final: 0.8315 (mmpt) REVERT: D 145 ASN cc_start: 0.8562 (m110) cc_final: 0.8138 (m110) REVERT: D 163 ASP cc_start: 0.8177 (p0) cc_final: 0.7891 (p0) REVERT: D 172 ASN cc_start: 0.8357 (t0) cc_final: 0.8022 (t0) REVERT: C 80 SER cc_start: 0.8650 (m) cc_final: 0.8305 (t) REVERT: C 88 GLU cc_start: 0.7669 (pp20) cc_final: 0.6924 (pm20) REVERT: B 7 LYS cc_start: 0.8943 (OUTLIER) cc_final: 0.8476 (mttt) outliers start: 19 outliers final: 11 residues processed: 156 average time/residue: 1.4243 time to fit residues: 245.9718 Evaluate side-chains 151 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 138 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 197 GLU Chi-restraints excluded: chain F residue 98 THR Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain G residue 181 SER Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain E residue 80 SER Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain B residue 7 LYS Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain A residue 13 LYS Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 169 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 4 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 115 optimal weight: 1.9990 chunk 162 optimal weight: 0.1980 chunk 186 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 195 optimal weight: 1.9990 chunk 160 optimal weight: 2.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** J 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 150 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.088917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.071431 restraints weight = 73881.546| |-----------------------------------------------------------------------------| r_work (start): 0.2692 rms_B_bonded: 2.01 r_work: 0.2598 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2477 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8856 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 16890 Z= 0.165 Angle : 0.721 15.585 22980 Z= 0.368 Chirality : 0.155 1.767 2470 Planarity : 0.004 0.081 2900 Dihedral : 6.278 79.097 2280 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.72 % Allowed : 10.39 % Favored : 88.89 % 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: -0.22 (0.18), residues: 2040 helix: 2.06 (0.46), residues: 110 sheet: 0.26 (0.17), residues: 890 loop : -0.71 (0.19), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG J 58 TYR 0.018 0.001 TYR J 54 PHE 0.012 0.001 PHE D 180 TRP 0.008 0.001 TRP A 110 HIS 0.005 0.001 HIS G 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.17 (16880) covalent geometry : angle 0.71848 / 0.37 (22960) SS BOND : bond 0.00554 / 0.27 ( 10) SS BOND : angle 2.21452 / 1.32 ( 20) hydrogen bonds : bond 0.03759 / 2.43 ( 662) hydrogen bonds : angle 5.51669 / 3.80 ( 1641) *********************** 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 156 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 143 time to evaluate : 0.558 Fit side-chains revert: symmetry clash REVERT: J 197 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.6739 (pp20) REVERT: G 88 GLU cc_start: 0.7093 (pm20) cc_final: 0.6827 (pm20) REVERT: G 89 VAL cc_start: 0.7999 (OUTLIER) cc_final: 0.7729 (p) REVERT: G 138 GLU cc_start: 0.7911 (tm-30) cc_final: 0.7585 (tm-30) REVERT: H 18 SER cc_start: 0.8425 (m) cc_final: 0.8179 (p) REVERT: I 114 LYS cc_start: 0.8568 (mmpt) cc_final: 0.8308 (mmpt) REVERT: D 145 ASN cc_start: 0.8554 (m110) cc_final: 0.8135 (m110) REVERT: D 163 ASP cc_start: 0.8133 (p0) cc_final: 0.7850 (p0) REVERT: D 172 ASN cc_start: 0.8358 (t0) cc_final: 0.8025 (t0) REVERT: C 80 SER cc_start: 0.8555 (m) cc_final: 0.8212 (t) REVERT: C 88 GLU cc_start: 0.7688 (pp20) cc_final: 0.6940 (pm20) REVERT: B 7 LYS cc_start: 0.8924 (OUTLIER) cc_final: 0.8462 (mttt) outliers start: 13 outliers final: 7 residues processed: 155 average time/residue: 1.3710 time to fit residues: 235.8411 Evaluate side-chains 143 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 133 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 197 GLU Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 98 THR Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain E residue 80 SER Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain B residue 7 LYS 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 73 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 192 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 chunk 138 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 141 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 51 optimal weight: 0.5980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** J 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.088078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2683 r_free = 0.2683 target = 0.070488 restraints weight = 74438.991| |-----------------------------------------------------------------------------| r_work (start): 0.2684 rms_B_bonded: 2.02 r_work: 0.2590 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2468 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8858 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 16890 Z= 0.175 Angle : 0.725 15.748 22980 Z= 0.371 Chirality : 0.156 1.773 2470 Planarity : 0.004 0.089 2900 Dihedral : 6.250 67.968 2280 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.06 % Allowed : 10.44 % Favored : 88.50 % 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: -0.29 (0.18), residues: 2040 helix: 1.95 (0.45), residues: 110 sheet: 0.22 (0.17), residues: 890 loop : -0.77 (0.19), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG J 58 TYR 0.018 0.001 TYR J 54 PHE 0.012 0.001 PHE D 180 TRP 0.008 0.001 TRP D 162 HIS 0.005 0.001 HIS G 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.18 (16880) covalent geometry : angle 0.72244 / 0.37 (22960) SS BOND : bond 0.00588 / 0.28 ( 10) SS BOND : angle 2.25475 / 1.35 ( 20) hydrogen bonds : bond 0.03810 / 2.46 ( 662) hydrogen bonds : angle 5.52990 / 3.81 ( 1641) *********************** 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 160 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 141 time to evaluate : 0.778 Fit side-chains revert: symmetry clash REVERT: J 197 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.6758 (pp20) REVERT: G 89 VAL cc_start: 0.8014 (OUTLIER) cc_final: 0.7740 (p) REVERT: G 138 GLU cc_start: 0.7926 (tm-30) cc_final: 0.7555 (tm-30) REVERT: H 18 SER cc_start: 0.8412 (m) cc_final: 0.8153 (p) REVERT: I 114 LYS cc_start: 0.8561 (mmpt) cc_final: 0.8301 (mmpt) REVERT: E 94 VAL cc_start: 0.9356 (OUTLIER) cc_final: 0.9153 (p) REVERT: D 139 GLN cc_start: 0.8491 (pt0) cc_final: 0.8231 (pt0) REVERT: D 145 ASN cc_start: 0.8576 (m110) cc_final: 0.8140 (m110) REVERT: D 163 ASP cc_start: 0.8164 (p0) cc_final: 0.7890 (p0) REVERT: D 172 ASN cc_start: 0.8370 (t0) cc_final: 0.8034 (t0) REVERT: C 80 SER cc_start: 0.8547 (m) cc_final: 0.8187 (t) REVERT: C 88 GLU cc_start: 0.7725 (pp20) cc_final: 0.6946 (pm20) REVERT: B 7 LYS cc_start: 0.8912 (OUTLIER) cc_final: 0.8428 (mttt) REVERT: A 3 ASP cc_start: 0.8883 (t0) cc_final: 0.8563 (t0) outliers start: 19 outliers final: 13 residues processed: 157 average time/residue: 1.3128 time to fit residues: 230.9088 Evaluate side-chains 148 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 131 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 197 GLU Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 98 THR Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain G residue 181 SER Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain E residue 80 SER Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain B residue 7 LYS Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 169 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 95 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 131 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 155 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** J 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.087442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2673 r_free = 0.2673 target = 0.069950 restraints weight = 74492.739| |-----------------------------------------------------------------------------| r_work (start): 0.2703 rms_B_bonded: 2.01 r_work: 0.2609 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2488 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8870 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 16890 Z= 0.206 Angle : 0.739 15.765 22980 Z= 0.379 Chirality : 0.156 1.779 2470 Planarity : 0.005 0.099 2900 Dihedral : 6.449 57.765 2280 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.22 % Allowed : 10.72 % Favored : 88.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.18), residues: 2040 helix: 1.88 (0.45), residues: 110 sheet: 0.09 (0.17), residues: 910 loop : -0.87 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG J 58 TYR 0.018 0.001 TYR J 54 PHE 0.012 0.001 PHE J 52 TRP 0.008 0.001 TRP A 110 HIS 0.006 0.002 HIS G 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00494 / 0.21 (16880) covalent geometry : angle 0.73600 / 0.38 (22960) SS BOND : bond 0.00604 / 0.29 ( 10) SS BOND : angle 2.25200 / 1.35 ( 20) hydrogen bonds : bond 0.03946 / 2.55 ( 662) hydrogen bonds : angle 5.56910 / 3.84 ( 1641) *********************** 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 157 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 135 time to evaluate : 0.885 Fit side-chains revert: symmetry clash REVERT: J 197 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.6771 (pp20) REVERT: G 89 VAL cc_start: 0.8060 (OUTLIER) cc_final: 0.7794 (p) REVERT: H 18 SER cc_start: 0.8475 (m) cc_final: 0.8190 (p) REVERT: I 114 LYS cc_start: 0.8587 (mmpt) cc_final: 0.8331 (mmpt) REVERT: D 139 GLN cc_start: 0.8499 (pt0) cc_final: 0.8238 (pt0) REVERT: D 145 ASN cc_start: 0.8533 (m110) cc_final: 0.8128 (m110) REVERT: D 163 ASP cc_start: 0.8205 (p0) cc_final: 0.7956 (p0) REVERT: D 172 ASN cc_start: 0.8354 (t0) cc_final: 0.8015 (t0) REVERT: D 191 LYS cc_start: 0.8380 (mttm) cc_final: 0.8053 (mmmt) REVERT: C 80 SER cc_start: 0.8563 (m) cc_final: 0.8165 (t) REVERT: C 188 ARG cc_start: 0.8527 (OUTLIER) cc_final: 0.7989 (mtm-85) REVERT: B 7 LYS cc_start: 0.8919 (OUTLIER) cc_final: 0.8444 (mttt) outliers start: 22 outliers final: 12 residues processed: 154 average time/residue: 1.3461 time to fit residues: 231.2352 Evaluate side-chains 145 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 129 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 197 GLU Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 98 THR Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain G residue 181 SER Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain E residue 80 SER Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 188 ARG Chi-restraints excluded: chain B residue 7 LYS Chi-restraints excluded: chain B residue 76 THR 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 39 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 164 optimal weight: 1.9990 chunk 180 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 129 optimal weight: 0.0670 chunk 88 optimal weight: 0.8980 chunk 69 optimal weight: 0.6980 chunk 133 optimal weight: 2.9990 chunk 168 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 overall best weight: 1.1322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** J 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.088477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2695 r_free = 0.2695 target = 0.071134 restraints weight = 74051.382| |-----------------------------------------------------------------------------| r_work (start): 0.2680 rms_B_bonded: 2.00 r_work: 0.2587 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2467 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8854 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 16890 Z= 0.160 Angle : 0.721 15.702 22980 Z= 0.368 Chirality : 0.156 1.760 2470 Planarity : 0.004 0.103 2900 Dihedral : 6.225 58.380 2280 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.06 % Allowed : 11.22 % Favored : 87.72 % 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: 1.98 (0.45), residues: 110 sheet: 0.21 (0.17), residues: 890 loop : -0.81 (0.19), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG J 58 TYR 0.017 0.001 TYR J 54 PHE 0.011 0.001 PHE D 180 TRP 0.007 0.001 TRP D 162 HIS 0.005 0.002 HIS H 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.16 (16880) covalent geometry : angle 0.71791 / 0.37 (22960) SS BOND : bond 0.00572 / 0.28 ( 10) SS BOND : angle 2.19982 / 1.31 ( 20) hydrogen bonds : bond 0.03714 / 2.40 ( 662) hydrogen bonds : angle 5.47536 / 3.78 ( 1641) *********************** 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 155 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 136 time to evaluate : 0.990 Fit side-chains revert: symmetry clash REVERT: J 197 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.6710 (pp20) REVERT: G 89 VAL cc_start: 0.8050 (OUTLIER) cc_final: 0.7779 (p) REVERT: H 18 SER cc_start: 0.8411 (m) cc_final: 0.8146 (p) REVERT: I 114 LYS cc_start: 0.8548 (mmpt) cc_final: 0.8296 (mmpt) REVERT: D 139 GLN cc_start: 0.8475 (pt0) cc_final: 0.8202 (pt0) REVERT: D 145 ASN cc_start: 0.8562 (m110) cc_final: 0.8137 (m110) REVERT: D 163 ASP cc_start: 0.8159 (p0) cc_final: 0.7889 (p0) REVERT: D 172 ASN cc_start: 0.8369 (t0) cc_final: 0.8029 (t0) REVERT: D 191 LYS cc_start: 0.8427 (mttm) cc_final: 0.8004 (mmmt) REVERT: C 80 SER cc_start: 0.8547 (m) cc_final: 0.8138 (t) REVERT: B 7 LYS cc_start: 0.8874 (OUTLIER) cc_final: 0.8404 (mttt) REVERT: A 3 ASP cc_start: 0.8857 (t0) cc_final: 0.8515 (t0) outliers start: 19 outliers final: 12 residues processed: 154 average time/residue: 1.3918 time to fit residues: 239.9380 Evaluate side-chains 142 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 127 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 197 GLU Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 98 THR Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain G residue 181 SER Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain E residue 80 SER Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain B residue 7 LYS Chi-restraints excluded: chain B residue 76 THR 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 22 optimal weight: 3.9990 chunk 128 optimal weight: 0.9990 chunk 109 optimal weight: 0.9990 chunk 199 optimal weight: 2.9990 chunk 195 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 148 optimal weight: 0.9980 chunk 130 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 chunk 110 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** J 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.088262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.070755 restraints weight = 74472.465| |-----------------------------------------------------------------------------| r_work (start): 0.2693 rms_B_bonded: 2.02 r_work: 0.2599 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2478 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8858 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 16890 Z= 0.161 Angle : 0.721 15.757 22980 Z= 0.368 Chirality : 0.156 1.745 2470 Planarity : 0.004 0.109 2900 Dihedral : 6.168 58.138 2280 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.94 % Allowed : 11.28 % Favored : 87.78 % 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: -0.33 (0.18), residues: 2040 helix: 2.00 (0.45), residues: 110 sheet: 0.21 (0.17), residues: 890 loop : -0.81 (0.19), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG J 58 TYR 0.017 0.001 TYR J 54 PHE 0.010 0.001 PHE J 52 TRP 0.007 0.001 TRP D 162 HIS 0.006 0.001 HIS H 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.16 (16880) covalent geometry : angle 0.71858 / 0.37 (22960) SS BOND : bond 0.00557 / 0.27 ( 10) SS BOND : angle 2.18182 / 1.30 ( 20) hydrogen bonds : bond 0.03709 / 2.39 ( 662) hydrogen bonds : angle 5.45364 / 3.77 ( 1641) ********************** 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 145 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 128 time to evaluate : 0.950 Fit side-chains revert: symmetry clash REVERT: J 197 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.6718 (pp20) REVERT: G 89 VAL cc_start: 0.8015 (OUTLIER) cc_final: 0.7768 (p) REVERT: H 18 SER cc_start: 0.8409 (m) cc_final: 0.8156 (p) REVERT: I 58 ARG cc_start: 0.6746 (pmm150) cc_final: 0.6372 (pmt170) REVERT: I 114 LYS cc_start: 0.8553 (mmpt) cc_final: 0.8301 (mmpt) REVERT: D 139 GLN cc_start: 0.8488 (pt0) cc_final: 0.8218 (pt0) REVERT: D 145 ASN cc_start: 0.8513 (m110) cc_final: 0.8102 (m110) REVERT: D 163 ASP cc_start: 0.8157 (p0) cc_final: 0.7890 (p0) REVERT: D 172 ASN cc_start: 0.8376 (t0) cc_final: 0.8040 (t0) REVERT: D 191 LYS cc_start: 0.8388 (mttm) cc_final: 0.7993 (mmmt) REVERT: C 80 SER cc_start: 0.8554 (m) cc_final: 0.8151 (t) REVERT: B 7 LYS cc_start: 0.8867 (OUTLIER) cc_final: 0.8403 (mttt) REVERT: A 3 ASP cc_start: 0.8848 (t0) cc_final: 0.8532 (t0) REVERT: A 197 GLU cc_start: 0.7839 (mt-10) cc_final: 0.7627 (tt0) outliers start: 17 outliers final: 12 residues processed: 143 average time/residue: 1.2720 time to fit residues: 203.6149 Evaluate side-chains 137 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 122 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 197 GLU Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 98 THR Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain G residue 181 SER Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain E residue 80 SER Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain B residue 7 LYS Chi-restraints excluded: chain B residue 76 THR 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 56 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 chunk 119 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 159 optimal weight: 1.9990 chunk 149 optimal weight: 0.6980 chunk 199 optimal weight: 2.9990 chunk 99 optimal weight: 0.0980 chunk 26 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 172 ASN A 1 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.089378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.071883 restraints weight = 74043.604| |-----------------------------------------------------------------------------| r_work (start): 0.2707 rms_B_bonded: 2.02 r_work: 0.2614 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2494 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8842 moved from start: 0.2836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 16890 Z= 0.124 Angle : 0.705 15.694 22980 Z= 0.358 Chirality : 0.155 1.737 2470 Planarity : 0.004 0.109 2900 Dihedral : 5.780 58.714 2280 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.89 % Allowed : 11.56 % Favored : 87.56 % 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: -0.24 (0.18), residues: 2040 helix: 2.20 (0.45), residues: 110 sheet: 0.25 (0.17), residues: 890 loop : -0.74 (0.19), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG J 58 TYR 0.016 0.001 TYR J 54 PHE 0.012 0.001 PHE D 180 TRP 0.007 0.001 TRP A 162 HIS 0.006 0.001 HIS H 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.12 (16880) covalent geometry : angle 0.70207 / 0.36 (22960) SS BOND : bond 0.00520 / 0.25 ( 10) SS BOND : angle 2.13384 / 1.27 ( 20) hydrogen bonds : bond 0.03458 / 2.23 ( 662) hydrogen bonds : angle 5.33580 / 3.70 ( 1641) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8986.26 seconds wall clock time: 152 minutes 50.06 seconds (9170.06 seconds total)