Starting phenix.real_space_refine (version: dev) on Sat May 14 13:46:06 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ytv_10924/05_2022/6ytv_10924.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ytv_10924/05_2022/6ytv_10924.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ytv_10924/05_2022/6ytv_10924.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ytv_10924/05_2022/6ytv_10924.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ytv_10924/05_2022/6ytv_10924.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ytv_10924/05_2022/6ytv_10924.pdb" } resolution = 4.39 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 ------------------------------------------------------------------------------- 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= 0.001 sd= 0.005 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 19560 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 1956 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 10, 'TRANS': 241} Chain breaks: 1 Chain: "B" Number of atoms: 1956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 1956 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 10, 'TRANS': 241} Chain breaks: 1 Chain: "C" Number of atoms: 1956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 1956 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 10, 'TRANS': 241} Chain breaks: 1 Chain: "D" Number of atoms: 1956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 1956 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 10, 'TRANS': 241} Chain breaks: 1 Chain: "E" Number of atoms: 1956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 1956 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 10, 'TRANS': 241} Chain breaks: 1 Chain: "F" Number of atoms: 1956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 1956 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 10, 'TRANS': 241} Chain breaks: 1 Chain: "G" Number of atoms: 1956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 1956 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 10, 'TRANS': 241} Chain breaks: 1 Chain: "H" Number of atoms: 1956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 1956 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 10, 'TRANS': 241} Chain breaks: 1 Chain: "I" Number of atoms: 1956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 1956 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 10, 'TRANS': 241} Chain breaks: 1 Chain: "J" Number of atoms: 1956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 1956 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 10, 'TRANS': 241} Chain breaks: 1 Time building chain proxies: 11.56, per 1000 atoms: 0.59 Number of scatterers: 19560 At special positions: 0 Unit cell: (140.7, 138.02, 104.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 130 16.00 O 3420 8.00 N 3250 7.00 C 12760 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=30, symmetry=0 Simple disulfide: pdb=" SG CYS A 41 " - pdb=" SG CYS A 126 " distance=2.03 Simple disulfide: pdb=" SG CYS A 43 " - pdb=" SG CYS A 155 " distance=2.04 Simple disulfide: pdb=" SG CYS A 139 " - pdb=" SG CYS A 146 " distance=2.04 Simple disulfide: pdb=" SG CYS B 41 " - pdb=" SG CYS B 126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 43 " - pdb=" SG CYS B 155 " distance=2.04 Simple disulfide: pdb=" SG CYS B 139 " - pdb=" SG CYS B 146 " distance=2.04 Simple disulfide: pdb=" SG CYS C 41 " - pdb=" SG CYS C 126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 43 " - pdb=" SG CYS C 155 " distance=2.04 Simple disulfide: pdb=" SG CYS C 139 " - pdb=" SG CYS C 146 " distance=2.04 Simple disulfide: pdb=" SG CYS D 41 " - pdb=" SG CYS D 126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 43 " - pdb=" SG CYS D 155 " distance=2.04 Simple disulfide: pdb=" SG CYS D 139 " - pdb=" SG CYS D 146 " distance=2.04 Simple disulfide: pdb=" SG CYS E 41 " - pdb=" SG CYS E 126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 43 " - pdb=" SG CYS E 155 " distance=2.04 Simple disulfide: pdb=" SG CYS E 139 " - pdb=" SG CYS E 146 " distance=2.04 Simple disulfide: pdb=" SG CYS F 41 " - pdb=" SG CYS F 126 " distance=2.03 Simple disulfide: pdb=" SG CYS F 43 " - pdb=" SG CYS F 155 " distance=2.04 Simple disulfide: pdb=" SG CYS F 139 " - pdb=" SG CYS F 146 " distance=2.03 Simple disulfide: pdb=" SG CYS G 41 " - pdb=" SG CYS G 126 " distance=2.03 Simple disulfide: pdb=" SG CYS G 43 " - pdb=" SG CYS G 155 " distance=2.04 Simple disulfide: pdb=" SG CYS G 139 " - pdb=" SG CYS G 146 " distance=2.04 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 43 " - pdb=" SG CYS H 155 " distance=2.04 Simple disulfide: pdb=" SG CYS H 139 " - pdb=" SG CYS H 146 " distance=2.04 Simple disulfide: pdb=" SG CYS I 41 " - pdb=" SG CYS I 126 " distance=2.03 Simple disulfide: pdb=" SG CYS I 43 " - pdb=" SG CYS I 155 " distance=2.04 Simple disulfide: pdb=" SG CYS I 139 " - pdb=" SG CYS I 146 " distance=2.04 Simple disulfide: pdb=" SG CYS J 41 " - pdb=" SG CYS J 126 " distance=2.03 Simple disulfide: pdb=" SG CYS J 43 " - pdb=" SG CYS J 155 " distance=2.04 Simple disulfide: pdb=" SG CYS J 139 " - pdb=" SG CYS J 146 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.95 Conformation dependent library (CDL) restraints added in 3.3 seconds 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4760 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 0 sheets defined 78.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'A' and resid 20 through 37 Processing helix chain 'A' and resid 47 through 71 removed outlier: 3.835A pdb=" N TYR A 51 " --> pdb=" O TRP A 47 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE A 55 " --> pdb=" O TYR A 51 " (cutoff:3.500A) Proline residue: A 59 - end of helix removed outlier: 3.781A pdb=" N SER A 71 " --> pdb=" O GLY A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 79 removed outlier: 4.206A pdb=" N TRP A 75 " --> pdb=" O SER A 71 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG A 76 " --> pdb=" O ALA A 72 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU A 77 " --> pdb=" O ARG A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 121 removed outlier: 5.549A pdb=" N ALA A 109 " --> pdb=" O ALA A 105 " (cutoff:3.500A) Proline residue: A 110 - end of helix Processing helix chain 'A' and resid 121 through 127 Processing helix chain 'A' and resid 131 through 139 removed outlier: 3.733A pdb=" N ALA A 135 " --> pdb=" O SER A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 150 removed outlier: 4.126A pdb=" N GLU A 149 " --> pdb=" O SER A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 153 No H-bonds generated for 'chain 'A' and resid 151 through 153' Processing helix chain 'A' and resid 160 through 199 removed outlier: 4.490A pdb=" N LYS A 168 " --> pdb=" O GLN A 164 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP A 169 " --> pdb=" O ASP A 165 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE A 186 " --> pdb=" O ILE A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 243 removed outlier: 3.881A pdb=" N PHE A 209 " --> pdb=" O LEU A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 260 Processing helix chain 'A' and resid 274 through 279 removed outlier: 3.595A pdb=" N LYS A 278 " --> pdb=" O SER A 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 37 Processing helix chain 'B' and resid 47 through 71 removed outlier: 3.835A pdb=" N TYR B 51 " --> pdb=" O TRP B 47 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) Proline residue: B 59 - end of helix removed outlier: 3.782A pdb=" N SER B 71 " --> pdb=" O GLY B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 79 removed outlier: 4.205A pdb=" N TRP B 75 " --> pdb=" O SER B 71 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG B 76 " --> pdb=" O ALA B 72 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU B 77 " --> pdb=" O ARG B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 121 removed outlier: 5.549A pdb=" N ALA B 109 " --> pdb=" O ALA B 105 " (cutoff:3.500A) Proline residue: B 110 - end of helix Processing helix chain 'B' and resid 121 through 127 Processing helix chain 'B' and resid 131 through 139 removed outlier: 3.733A pdb=" N ALA B 135 " --> pdb=" O SER B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 150 removed outlier: 4.126A pdb=" N GLU B 149 " --> pdb=" O SER B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 153 No H-bonds generated for 'chain 'B' and resid 151 through 153' Processing helix chain 'B' and resid 160 through 199 removed outlier: 4.490A pdb=" N LYS B 168 " --> pdb=" O GLN B 164 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP B 169 " --> pdb=" O ASP B 165 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE B 186 " --> pdb=" O ILE B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 243 removed outlier: 3.881A pdb=" N PHE B 209 " --> pdb=" O LEU B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 260 Processing helix chain 'B' and resid 274 through 279 removed outlier: 3.595A pdb=" N LYS B 278 " --> pdb=" O SER B 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 37 Processing helix chain 'C' and resid 47 through 71 removed outlier: 3.835A pdb=" N TYR C 51 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE C 55 " --> pdb=" O TYR C 51 " (cutoff:3.500A) Proline residue: C 59 - end of helix removed outlier: 3.782A pdb=" N SER C 71 " --> pdb=" O GLY C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 79 removed outlier: 4.205A pdb=" N TRP C 75 " --> pdb=" O SER C 71 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG C 76 " --> pdb=" O ALA C 72 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU C 77 " --> pdb=" O ARG C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 121 removed outlier: 5.549A pdb=" N ALA C 109 " --> pdb=" O ALA C 105 " (cutoff:3.500A) Proline residue: C 110 - end of helix Processing helix chain 'C' and resid 121 through 127 Processing helix chain 'C' and resid 131 through 139 removed outlier: 3.734A pdb=" N ALA C 135 " --> pdb=" O SER C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 150 removed outlier: 4.126A pdb=" N GLU C 149 " --> pdb=" O SER C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 153 No H-bonds generated for 'chain 'C' and resid 151 through 153' Processing helix chain 'C' and resid 160 through 199 removed outlier: 4.491A pdb=" N LYS C 168 " --> pdb=" O GLN C 164 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP C 169 " --> pdb=" O ASP C 165 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE C 186 " --> pdb=" O ILE C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 243 removed outlier: 3.881A pdb=" N PHE C 209 " --> pdb=" O LEU C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 260 Processing helix chain 'C' and resid 274 through 279 removed outlier: 3.594A pdb=" N LYS C 278 " --> pdb=" O SER C 274 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 37 Processing helix chain 'D' and resid 47 through 71 removed outlier: 3.835A pdb=" N TYR D 51 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE D 55 " --> pdb=" O TYR D 51 " (cutoff:3.500A) Proline residue: D 59 - end of helix removed outlier: 3.781A pdb=" N SER D 71 " --> pdb=" O GLY D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 79 removed outlier: 4.206A pdb=" N TRP D 75 " --> pdb=" O SER D 71 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG D 76 " --> pdb=" O ALA D 72 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU D 77 " --> pdb=" O ARG D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 121 removed outlier: 5.548A pdb=" N ALA D 109 " --> pdb=" O ALA D 105 " (cutoff:3.500A) Proline residue: D 110 - end of helix Processing helix chain 'D' and resid 121 through 127 Processing helix chain 'D' and resid 131 through 139 removed outlier: 3.733A pdb=" N ALA D 135 " --> pdb=" O SER D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 150 removed outlier: 4.126A pdb=" N GLU D 149 " --> pdb=" O SER D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 153 No H-bonds generated for 'chain 'D' and resid 151 through 153' Processing helix chain 'D' and resid 160 through 199 removed outlier: 4.491A pdb=" N LYS D 168 " --> pdb=" O GLN D 164 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP D 169 " --> pdb=" O ASP D 165 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE D 186 " --> pdb=" O ILE D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 243 removed outlier: 3.880A pdb=" N PHE D 209 " --> pdb=" O LEU D 205 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 260 Processing helix chain 'D' and resid 274 through 279 removed outlier: 3.595A pdb=" N LYS D 278 " --> pdb=" O SER D 274 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 37 Processing helix chain 'E' and resid 47 through 71 removed outlier: 3.835A pdb=" N TYR E 51 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE E 55 " --> pdb=" O TYR E 51 " (cutoff:3.500A) Proline residue: E 59 - end of helix removed outlier: 3.781A pdb=" N SER E 71 " --> pdb=" O GLY E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 79 removed outlier: 4.206A pdb=" N TRP E 75 " --> pdb=" O SER E 71 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG E 76 " --> pdb=" O ALA E 72 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU E 77 " --> pdb=" O ARG E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 121 removed outlier: 5.548A pdb=" N ALA E 109 " --> pdb=" O ALA E 105 " (cutoff:3.500A) Proline residue: E 110 - end of helix Processing helix chain 'E' and resid 121 through 127 Processing helix chain 'E' and resid 131 through 139 removed outlier: 3.732A pdb=" N ALA E 135 " --> pdb=" O SER E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 145 through 150 removed outlier: 4.126A pdb=" N GLU E 149 " --> pdb=" O SER E 145 " (cutoff:3.500A) Processing helix chain 'E' and resid 151 through 153 No H-bonds generated for 'chain 'E' and resid 151 through 153' Processing helix chain 'E' and resid 160 through 199 removed outlier: 4.491A pdb=" N LYS E 168 " --> pdb=" O GLN E 164 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP E 169 " --> pdb=" O ASP E 165 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE E 186 " --> pdb=" O ILE E 182 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 243 removed outlier: 3.881A pdb=" N PHE E 209 " --> pdb=" O LEU E 205 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 260 Processing helix chain 'E' and resid 274 through 279 removed outlier: 3.595A pdb=" N LYS E 278 " --> pdb=" O SER E 274 " (cutoff:3.500A) Processing helix chain 'F' and resid 21 through 37 Processing helix chain 'F' and resid 47 through 71 removed outlier: 3.835A pdb=" N TYR F 51 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE F 55 " --> pdb=" O TYR F 51 " (cutoff:3.500A) Proline residue: F 59 - end of helix removed outlier: 3.781A pdb=" N SER F 71 " --> pdb=" O GLY F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 71 through 79 removed outlier: 4.205A pdb=" N TRP F 75 " --> pdb=" O SER F 71 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG F 76 " --> pdb=" O ALA F 72 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU F 77 " --> pdb=" O ARG F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 95 through 121 removed outlier: 5.549A pdb=" N ALA F 109 " --> pdb=" O ALA F 105 " (cutoff:3.500A) Proline residue: F 110 - end of helix Processing helix chain 'F' and resid 121 through 127 Processing helix chain 'F' and resid 131 through 139 removed outlier: 3.733A pdb=" N ALA F 135 " --> pdb=" O SER F 131 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 150 removed outlier: 4.127A pdb=" N GLU F 149 " --> pdb=" O SER F 145 " (cutoff:3.500A) Processing helix chain 'F' and resid 151 through 153 No H-bonds generated for 'chain 'F' and resid 151 through 153' Processing helix chain 'F' and resid 160 through 199 removed outlier: 4.491A pdb=" N LYS F 168 " --> pdb=" O GLN F 164 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP F 169 " --> pdb=" O ASP F 165 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE F 186 " --> pdb=" O ILE F 182 " (cutoff:3.500A) Processing helix chain 'F' and resid 203 through 243 removed outlier: 3.881A pdb=" N PHE F 209 " --> pdb=" O LEU F 205 " (cutoff:3.500A) Processing helix chain 'F' and resid 253 through 260 Processing helix chain 'F' and resid 274 through 279 removed outlier: 3.595A pdb=" N LYS F 278 " --> pdb=" O SER F 274 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 37 Processing helix chain 'G' and resid 47 through 71 removed outlier: 3.834A pdb=" N TYR G 51 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE G 55 " --> pdb=" O TYR G 51 " (cutoff:3.500A) Proline residue: G 59 - end of helix removed outlier: 3.781A pdb=" N SER G 71 " --> pdb=" O GLY G 67 " (cutoff:3.500A) Processing helix chain 'G' and resid 71 through 79 removed outlier: 4.206A pdb=" N TRP G 75 " --> pdb=" O SER G 71 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG G 76 " --> pdb=" O ALA G 72 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU G 77 " --> pdb=" O ARG G 73 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 121 removed outlier: 5.549A pdb=" N ALA G 109 " --> pdb=" O ALA G 105 " (cutoff:3.500A) Proline residue: G 110 - end of helix Processing helix chain 'G' and resid 121 through 127 Processing helix chain 'G' and resid 131 through 139 removed outlier: 3.733A pdb=" N ALA G 135 " --> pdb=" O SER G 131 " (cutoff:3.500A) Processing helix chain 'G' and resid 145 through 150 removed outlier: 4.126A pdb=" N GLU G 149 " --> pdb=" O SER G 145 " (cutoff:3.500A) Processing helix chain 'G' and resid 151 through 153 No H-bonds generated for 'chain 'G' and resid 151 through 153' Processing helix chain 'G' and resid 160 through 199 removed outlier: 4.491A pdb=" N LYS G 168 " --> pdb=" O GLN G 164 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASP G 169 " --> pdb=" O ASP G 165 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE G 186 " --> pdb=" O ILE G 182 " (cutoff:3.500A) Processing helix chain 'G' and resid 203 through 243 removed outlier: 3.881A pdb=" N PHE G 209 " --> pdb=" O LEU G 205 " (cutoff:3.500A) Processing helix chain 'G' and resid 253 through 260 Processing helix chain 'G' and resid 274 through 279 removed outlier: 3.595A pdb=" N LYS G 278 " --> pdb=" O SER G 274 " (cutoff:3.500A) Processing helix chain 'H' and resid 21 through 37 Processing helix chain 'H' and resid 47 through 71 removed outlier: 3.835A pdb=" N TYR H 51 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE H 55 " --> pdb=" O TYR H 51 " (cutoff:3.500A) Proline residue: H 59 - end of helix removed outlier: 3.781A pdb=" N SER H 71 " --> pdb=" O GLY H 67 " (cutoff:3.500A) Processing helix chain 'H' and resid 71 through 79 removed outlier: 4.206A pdb=" N TRP H 75 " --> pdb=" O SER H 71 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG H 76 " --> pdb=" O ALA H 72 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU H 77 " --> pdb=" O ARG H 73 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 121 removed outlier: 5.549A pdb=" N ALA H 109 " --> pdb=" O ALA H 105 " (cutoff:3.500A) Proline residue: H 110 - end of helix Processing helix chain 'H' and resid 121 through 127 Processing helix chain 'H' and resid 131 through 139 removed outlier: 3.733A pdb=" N ALA H 135 " --> pdb=" O SER H 131 " (cutoff:3.500A) Processing helix chain 'H' and resid 145 through 150 removed outlier: 4.126A pdb=" N GLU H 149 " --> pdb=" O SER H 145 " (cutoff:3.500A) Processing helix chain 'H' and resid 151 through 153 No H-bonds generated for 'chain 'H' and resid 151 through 153' Processing helix chain 'H' and resid 160 through 199 removed outlier: 4.490A pdb=" N LYS H 168 " --> pdb=" O GLN H 164 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP H 169 " --> pdb=" O ASP H 165 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE H 186 " --> pdb=" O ILE H 182 " (cutoff:3.500A) Processing helix chain 'H' and resid 203 through 243 removed outlier: 3.880A pdb=" N PHE H 209 " --> pdb=" O LEU H 205 " (cutoff:3.500A) Processing helix chain 'H' and resid 253 through 260 Processing helix chain 'H' and resid 274 through 279 removed outlier: 3.595A pdb=" N LYS H 278 " --> pdb=" O SER H 274 " (cutoff:3.500A) Processing helix chain 'I' and resid 21 through 37 Processing helix chain 'I' and resid 47 through 71 removed outlier: 3.835A pdb=" N TYR I 51 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE I 55 " --> pdb=" O TYR I 51 " (cutoff:3.500A) Proline residue: I 59 - end of helix removed outlier: 3.781A pdb=" N SER I 71 " --> pdb=" O GLY I 67 " (cutoff:3.500A) Processing helix chain 'I' and resid 71 through 79 removed outlier: 4.206A pdb=" N TRP I 75 " --> pdb=" O SER I 71 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG I 76 " --> pdb=" O ALA I 72 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU I 77 " --> pdb=" O ARG I 73 " (cutoff:3.500A) Processing helix chain 'I' and resid 95 through 121 removed outlier: 5.549A pdb=" N ALA I 109 " --> pdb=" O ALA I 105 " (cutoff:3.500A) Proline residue: I 110 - end of helix Processing helix chain 'I' and resid 121 through 127 Processing helix chain 'I' and resid 131 through 139 removed outlier: 3.734A pdb=" N ALA I 135 " --> pdb=" O SER I 131 " (cutoff:3.500A) Processing helix chain 'I' and resid 145 through 150 removed outlier: 4.126A pdb=" N GLU I 149 " --> pdb=" O SER I 145 " (cutoff:3.500A) Processing helix chain 'I' and resid 151 through 153 No H-bonds generated for 'chain 'I' and resid 151 through 153' Processing helix chain 'I' and resid 160 through 199 removed outlier: 4.491A pdb=" N LYS I 168 " --> pdb=" O GLN I 164 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP I 169 " --> pdb=" O ASP I 165 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE I 186 " --> pdb=" O ILE I 182 " (cutoff:3.500A) Processing helix chain 'I' and resid 203 through 243 removed outlier: 3.880A pdb=" N PHE I 209 " --> pdb=" O LEU I 205 " (cutoff:3.500A) Processing helix chain 'I' and resid 253 through 260 Processing helix chain 'I' and resid 274 through 279 removed outlier: 3.594A pdb=" N LYS I 278 " --> pdb=" O SER I 274 " (cutoff:3.500A) Processing helix chain 'J' and resid 21 through 37 Processing helix chain 'J' and resid 47 through 71 removed outlier: 3.835A pdb=" N TYR J 51 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE J 55 " --> pdb=" O TYR J 51 " (cutoff:3.500A) Proline residue: J 59 - end of helix removed outlier: 3.781A pdb=" N SER J 71 " --> pdb=" O GLY J 67 " (cutoff:3.500A) Processing helix chain 'J' and resid 71 through 79 removed outlier: 4.205A pdb=" N TRP J 75 " --> pdb=" O SER J 71 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG J 76 " --> pdb=" O ALA J 72 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU J 77 " --> pdb=" O ARG J 73 " (cutoff:3.500A) Processing helix chain 'J' and resid 95 through 121 removed outlier: 5.549A pdb=" N ALA J 109 " --> pdb=" O ALA J 105 " (cutoff:3.500A) Proline residue: J 110 - end of helix Processing helix chain 'J' and resid 121 through 127 Processing helix chain 'J' and resid 131 through 139 removed outlier: 3.733A pdb=" N ALA J 135 " --> pdb=" O SER J 131 " (cutoff:3.500A) Processing helix chain 'J' and resid 145 through 150 removed outlier: 4.126A pdb=" N GLU J 149 " --> pdb=" O SER J 145 " (cutoff:3.500A) Processing helix chain 'J' and resid 151 through 153 No H-bonds generated for 'chain 'J' and resid 151 through 153' Processing helix chain 'J' and resid 160 through 199 removed outlier: 4.491A pdb=" N LYS J 168 " --> pdb=" O GLN J 164 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP J 169 " --> pdb=" O ASP J 165 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE J 186 " --> pdb=" O ILE J 182 " (cutoff:3.500A) Processing helix chain 'J' and resid 203 through 243 removed outlier: 3.881A pdb=" N PHE J 209 " --> pdb=" O LEU J 205 " (cutoff:3.500A) Processing helix chain 'J' and resid 253 through 260 Processing helix chain 'J' and resid 274 through 279 removed outlier: 3.594A pdb=" N LYS J 278 " --> pdb=" O SER J 274 " (cutoff:3.500A) 1311 hydrogen bonds defined for protein. 3933 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: 5.60 Time building geometry restraints manager: 9.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6040 1.34 - 1.46: 4782 1.46 - 1.58: 9038 1.58 - 1.70: 0 1.70 - 1.82: 150 Bond restraints: 20010 Sorted by residual: bond pdb=" C LEU I 150 " pdb=" N PRO I 151 " ideal model delta sigma weight residual 1.334 1.356 -0.022 2.34e-02 1.83e+03 9.06e-01 bond pdb=" C LEU B 150 " pdb=" N PRO B 151 " ideal model delta sigma weight residual 1.334 1.356 -0.022 2.34e-02 1.83e+03 8.98e-01 bond pdb=" C LEU J 150 " pdb=" N PRO J 151 " ideal model delta sigma weight residual 1.334 1.356 -0.022 2.34e-02 1.83e+03 8.90e-01 bond pdb=" C LEU H 150 " pdb=" N PRO H 151 " ideal model delta sigma weight residual 1.334 1.356 -0.022 2.34e-02 1.83e+03 8.89e-01 bond pdb=" C LEU E 150 " pdb=" N PRO E 151 " ideal model delta sigma weight residual 1.334 1.356 -0.022 2.34e-02 1.83e+03 8.79e-01 ... (remaining 20005 not shown) Histogram of bond angle deviations from ideal: 100.73 - 107.40: 666 107.40 - 114.07: 11494 114.07 - 120.74: 9025 120.74 - 127.41: 5795 127.41 - 134.08: 220 Bond angle restraints: 27200 Sorted by residual: angle pdb=" CA LEU A 190 " pdb=" CB LEU A 190 " pdb=" CG LEU A 190 " ideal model delta sigma weight residual 116.30 106.69 9.61 3.50e+00 8.16e-02 7.54e+00 angle pdb=" CA LEU B 190 " pdb=" CB LEU B 190 " pdb=" CG LEU B 190 " ideal model delta sigma weight residual 116.30 106.69 9.61 3.50e+00 8.16e-02 7.54e+00 angle pdb=" CA LEU J 190 " pdb=" CB LEU J 190 " pdb=" CG LEU J 190 " ideal model delta sigma weight residual 116.30 106.70 9.60 3.50e+00 8.16e-02 7.52e+00 angle pdb=" CA LEU D 190 " pdb=" CB LEU D 190 " pdb=" CG LEU D 190 " ideal model delta sigma weight residual 116.30 106.71 9.59 3.50e+00 8.16e-02 7.51e+00 angle pdb=" CA LEU G 190 " pdb=" CB LEU G 190 " pdb=" CG LEU G 190 " ideal model delta sigma weight residual 116.30 106.71 9.59 3.50e+00 8.16e-02 7.51e+00 ... (remaining 27195 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 10562 17.73 - 35.46: 1128 35.46 - 53.19: 200 53.19 - 70.93: 20 70.93 - 88.66: 20 Dihedral angle restraints: 11930 sinusoidal: 4570 harmonic: 7360 Sorted by residual: dihedral pdb=" CB CYS E 43 " pdb=" SG CYS E 43 " pdb=" SG CYS E 155 " pdb=" CB CYS E 155 " ideal model delta sinusoidal sigma weight residual -86.00 -20.20 -65.80 1 1.00e+01 1.00e-02 5.67e+01 dihedral pdb=" CB CYS J 43 " pdb=" SG CYS J 43 " pdb=" SG CYS J 155 " pdb=" CB CYS J 155 " ideal model delta sinusoidal sigma weight residual -86.00 -20.21 -65.79 1 1.00e+01 1.00e-02 5.66e+01 dihedral pdb=" CB CYS C 43 " pdb=" SG CYS C 43 " pdb=" SG CYS C 155 " pdb=" CB CYS C 155 " ideal model delta sinusoidal sigma weight residual -86.00 -20.22 -65.78 1 1.00e+01 1.00e-02 5.66e+01 ... (remaining 11927 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 2561 0.051 - 0.102: 557 0.102 - 0.153: 42 0.153 - 0.203: 0 0.203 - 0.254: 10 Chirality restraints: 3170 Sorted by residual: chirality pdb=" CG LEU C 190 " pdb=" CB LEU C 190 " pdb=" CD1 LEU C 190 " pdb=" CD2 LEU C 190 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" CG LEU E 190 " pdb=" CB LEU E 190 " pdb=" CD1 LEU E 190 " pdb=" CD2 LEU E 190 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" CG LEU G 190 " pdb=" CB LEU G 190 " pdb=" CD1 LEU G 190 " pdb=" CD2 LEU G 190 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.60e+00 ... (remaining 3167 not shown) Planarity restraints: 3350 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN F 173 " -0.009 2.00e-02 2.50e+03 1.90e-02 3.61e+00 pdb=" C GLN F 173 " 0.033 2.00e-02 2.50e+03 pdb=" O GLN F 173 " -0.012 2.00e-02 2.50e+03 pdb=" N SER F 174 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN H 173 " 0.009 2.00e-02 2.50e+03 1.90e-02 3.59e+00 pdb=" C GLN H 173 " -0.033 2.00e-02 2.50e+03 pdb=" O GLN H 173 " 0.012 2.00e-02 2.50e+03 pdb=" N SER H 174 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 173 " 0.009 2.00e-02 2.50e+03 1.89e-02 3.58e+00 pdb=" C GLN A 173 " -0.033 2.00e-02 2.50e+03 pdb=" O GLN A 173 " 0.012 2.00e-02 2.50e+03 pdb=" N SER A 174 " 0.011 2.00e-02 2.50e+03 ... (remaining 3347 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 1407 2.73 - 3.27: 22326 3.27 - 3.81: 31951 3.81 - 4.36: 34735 4.36 - 4.90: 57513 Nonbonded interactions: 147932 Sorted by model distance: nonbonded pdb=" O PRO C 42 " pdb=" ND2 ASN C 48 " model vdw 2.183 2.520 nonbonded pdb=" O PRO I 42 " pdb=" ND2 ASN I 48 " model vdw 2.184 2.520 nonbonded pdb=" O PRO D 42 " pdb=" ND2 ASN D 48 " model vdw 2.184 2.520 nonbonded pdb=" O PRO G 42 " pdb=" ND2 ASN G 48 " model vdw 2.184 2.520 nonbonded pdb=" O PRO H 42 " pdb=" ND2 ASN H 48 " model vdw 2.184 2.520 ... (remaining 147927 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 130 5.16 5 C 12760 2.51 5 N 3250 2.21 5 O 3420 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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 group one per residue 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: 0.380 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: 0.010 Extract box with map and model: 3.600 Check model and map are aligned: 0.300 Convert atoms to be neutral: 0.170 Process input model: 53.050 Find NCS groups from input model: 1.390 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Set scattering table: 0.020 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:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 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 : 0.004 0.036 20010 Z= 0.275 Angle : 0.779 9.611 27200 Z= 0.413 Chirality : 0.043 0.254 3170 Planarity : 0.005 0.031 3350 Dihedral : 14.562 88.658 7080 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 16.16 Ramachandran Plot: Outliers : 0.40 % Allowed : 6.05 % Favored : 93.55 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.16), residues: 2480 helix: -0.63 (0.11), residues: 1880 sheet: None (None), residues: 0 loop : -3.55 (0.22), residues: 600 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 785 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 785 time to evaluate : 2.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 785 average time/residue: 0.3170 time to fit residues: 366.9361 Evaluate side-chains 608 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 608 time to evaluate : 2.358 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 211 optimal weight: 9.9990 chunk 189 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 127 optimal weight: 4.9990 chunk 101 optimal weight: 5.9990 chunk 195 optimal weight: 2.9990 chunk 75 optimal weight: 0.6980 chunk 119 optimal weight: 2.9990 chunk 145 optimal weight: 6.9990 chunk 227 optimal weight: 0.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 GLN A 206 GLN A 216 GLN ** A 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 HIS A 277 HIS B 175 GLN B 206 GLN B 216 GLN B 245 HIS ** B 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 175 GLN C 206 GLN C 216 GLN ** C 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 245 HIS ** C 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 175 GLN ** D 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 216 GLN D 236 ASN ** D 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 206 GLN E 216 GLN E 258 GLN E 277 HIS F 175 GLN F 206 GLN F 216 GLN ** F 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 277 HIS ** G 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 206 GLN G 216 GLN ** G 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 175 GLN H 206 GLN H 216 GLN ** H 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 175 GLN I 206 GLN I 216 GLN I 258 GLN ** I 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 175 GLN J 206 GLN J 216 GLN J 236 ASN J 258 GLN J 277 HIS Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 20010 Z= 0.239 Angle : 0.712 7.650 27200 Z= 0.359 Chirality : 0.040 0.199 3170 Planarity : 0.005 0.046 3350 Dihedral : 5.302 23.957 2690 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.40 % Allowed : 5.85 % Favored : 93.75 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.17), residues: 2480 helix: 0.35 (0.12), residues: 1890 sheet: None (None), residues: 0 loop : -3.59 (0.23), residues: 590 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 699 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 699 time to evaluate : 2.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 699 average time/residue: 0.2988 time to fit residues: 320.2278 Evaluate side-chains 578 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 578 time to evaluate : 2.369 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 126 optimal weight: 3.9990 chunk 70 optimal weight: 0.9980 chunk 188 optimal weight: 1.9990 chunk 154 optimal weight: 0.9990 chunk 62 optimal weight: 0.0870 chunk 227 optimal weight: 0.9980 chunk 245 optimal weight: 0.9990 chunk 202 optimal weight: 7.9990 chunk 225 optimal weight: 6.9990 chunk 77 optimal weight: 7.9990 chunk 182 optimal weight: 0.9980 overall best weight: 0.8160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 175 GLN ** D 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 258 GLN E 236 ASN ** F 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 175 GLN G 206 GLN ** G 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 206 GLN ** H 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 206 GLN ** I 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.2752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 20010 Z= 0.187 Angle : 0.692 9.532 27200 Z= 0.342 Chirality : 0.040 0.269 3170 Planarity : 0.005 0.065 3350 Dihedral : 4.972 24.227 2690 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.40 % Allowed : 6.45 % Favored : 93.15 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.17), residues: 2480 helix: 0.79 (0.12), residues: 1890 sheet: None (None), residues: 0 loop : -3.67 (0.21), residues: 590 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 732 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 732 time to evaluate : 2.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 732 average time/residue: 0.2876 time to fit residues: 323.3304 Evaluate side-chains 603 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 603 time to evaluate : 2.458 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 224 optimal weight: 8.9990 chunk 170 optimal weight: 5.9990 chunk 118 optimal weight: 3.9990 chunk 25 optimal weight: 10.0000 chunk 108 optimal weight: 0.9980 chunk 152 optimal weight: 4.9990 chunk 228 optimal weight: 0.0870 chunk 241 optimal weight: 6.9990 chunk 119 optimal weight: 0.9990 chunk 216 optimal weight: 6.9990 chunk 65 optimal weight: 0.8980 overall best weight: 1.3962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 GLN ** A 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 GLN ** B 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 206 GLN ** C 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 175 GLN ** D 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 175 GLN E 206 GLN ** E 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 206 GLN ** G 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 277 HIS ** H 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 277 HIS J 206 GLN ** J 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 20010 Z= 0.214 Angle : 0.707 7.928 27200 Z= 0.350 Chirality : 0.039 0.195 3170 Planarity : 0.005 0.079 3350 Dihedral : 4.917 24.153 2690 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.02 % Favored : 92.70 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.17), residues: 2480 helix: 0.87 (0.12), residues: 1890 sheet: None (None), residues: 0 loop : -3.79 (0.21), residues: 590 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 713 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 713 time to evaluate : 2.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 713 average time/residue: 0.2881 time to fit residues: 318.1286 Evaluate side-chains 589 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 589 time to evaluate : 2.406 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 201 optimal weight: 4.9990 chunk 137 optimal weight: 0.0970 chunk 3 optimal weight: 0.8980 chunk 179 optimal weight: 4.9990 chunk 99 optimal weight: 0.0770 chunk 206 optimal weight: 6.9990 chunk 167 optimal weight: 0.9990 chunk 0 optimal weight: 9.9990 chunk 123 optimal weight: 0.6980 chunk 216 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 overall best weight: 0.4936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 48 ASN ** B 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 277 HIS ** C 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 277 HIS ** E 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 236 ASN ** H 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 277 HIS I 175 GLN ** I 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.3476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 20010 Z= 0.175 Angle : 0.674 9.189 27200 Z= 0.329 Chirality : 0.038 0.168 3170 Planarity : 0.005 0.054 3350 Dihedral : 4.690 23.116 2690 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.49 % Favored : 93.35 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.17), residues: 2480 helix: 1.04 (0.12), residues: 1890 sheet: None (None), residues: 0 loop : -3.75 (0.20), residues: 590 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 742 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 741 time to evaluate : 2.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 742 average time/residue: 0.3021 time to fit residues: 349.8722 Evaluate side-chains 612 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 611 time to evaluate : 2.737 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2438 time to fit residues: 4.2248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 81 optimal weight: 8.9990 chunk 217 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 141 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 241 optimal weight: 5.9990 chunk 200 optimal weight: 9.9990 chunk 111 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 48 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.3466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.055 20010 Z= 0.269 Angle : 0.741 8.896 27200 Z= 0.372 Chirality : 0.041 0.176 3170 Planarity : 0.005 0.075 3350 Dihedral : 4.893 24.452 2690 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.36 % Allowed : 8.23 % Favored : 91.41 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.17), residues: 2480 helix: 0.93 (0.12), residues: 1890 sheet: None (None), residues: 0 loop : -3.72 (0.21), residues: 590 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 705 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 705 time to evaluate : 2.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 705 average time/residue: 0.2873 time to fit residues: 312.6998 Evaluate side-chains 578 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 578 time to evaluate : 2.406 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 233 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 chunk 137 optimal weight: 0.8980 chunk 176 optimal weight: 6.9990 chunk 136 optimal weight: 5.9990 chunk 203 optimal weight: 2.9990 chunk 135 optimal weight: 5.9990 chunk 240 optimal weight: 0.9980 chunk 150 optimal weight: 8.9990 chunk 146 optimal weight: 2.9990 chunk 111 optimal weight: 9.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 48 ASN ** B 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 236 ASN F 236 ASN ** H 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 48 ASN J 236 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.3637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 20010 Z= 0.226 Angle : 0.719 9.968 27200 Z= 0.359 Chirality : 0.040 0.255 3170 Planarity : 0.005 0.068 3350 Dihedral : 4.832 22.534 2690 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.18 % Favored : 92.54 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.17), residues: 2480 helix: 0.97 (0.12), residues: 1890 sheet: None (None), residues: 0 loop : -3.64 (0.21), residues: 590 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 699 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 698 time to evaluate : 2.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 699 average time/residue: 0.2864 time to fit residues: 308.7208 Evaluate side-chains 581 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 581 time to evaluate : 2.395 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.0958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 149 optimal weight: 0.4980 chunk 96 optimal weight: 0.9990 chunk 143 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 153 optimal weight: 0.0670 chunk 164 optimal weight: 3.9990 chunk 119 optimal weight: 0.9980 chunk 22 optimal weight: 0.3980 chunk 189 optimal weight: 1.9990 overall best weight: 0.5920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 206 GLN ** H 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 175 GLN I 206 GLN ** I 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 175 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.3931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 20010 Z= 0.183 Angle : 0.714 9.627 27200 Z= 0.347 Chirality : 0.040 0.290 3170 Planarity : 0.005 0.067 3350 Dihedral : 4.677 21.470 2690 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.26 % Favored : 92.42 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.17), residues: 2480 helix: 1.04 (0.12), residues: 1900 sheet: None (None), residues: 0 loop : -3.62 (0.22), residues: 580 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 723 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 723 time to evaluate : 2.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 723 average time/residue: 0.2808 time to fit residues: 313.9532 Evaluate side-chains 608 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 608 time to evaluate : 2.284 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.0423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 219 optimal weight: 6.9990 chunk 230 optimal weight: 5.9990 chunk 210 optimal weight: 0.7980 chunk 224 optimal weight: 1.9990 chunk 135 optimal weight: 0.7980 chunk 97 optimal weight: 0.8980 chunk 176 optimal weight: 7.9990 chunk 68 optimal weight: 0.9990 chunk 202 optimal weight: 3.9990 chunk 212 optimal weight: 0.8980 chunk 223 optimal weight: 6.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 48 ASN ** C 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 175 GLN ** E 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 175 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.4083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 20010 Z= 0.189 Angle : 0.717 9.411 27200 Z= 0.348 Chirality : 0.040 0.249 3170 Planarity : 0.005 0.072 3350 Dihedral : 4.636 21.515 2690 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.98 % Favored : 92.82 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.17), residues: 2480 helix: 1.03 (0.12), residues: 1900 sheet: None (None), residues: 0 loop : -3.56 (0.22), residues: 580 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 731 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 731 time to evaluate : 2.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 731 average time/residue: 0.2766 time to fit residues: 313.9404 Evaluate side-chains 599 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 599 time to evaluate : 2.242 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.9980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 147 optimal weight: 4.9990 chunk 237 optimal weight: 6.9990 chunk 144 optimal weight: 1.9990 chunk 112 optimal weight: 0.0470 chunk 165 optimal weight: 0.9980 chunk 249 optimal weight: 3.9990 chunk 229 optimal weight: 0.9990 chunk 198 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 153 optimal weight: 0.0970 chunk 121 optimal weight: 0.8980 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 175 GLN H 175 GLN ** H 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.4307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 20010 Z= 0.179 Angle : 0.710 8.943 27200 Z= 0.343 Chirality : 0.039 0.226 3170 Planarity : 0.005 0.064 3350 Dihedral : 4.565 22.643 2690 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.22 % Favored : 92.46 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.17), residues: 2480 helix: 1.01 (0.12), residues: 1920 sheet: None (None), residues: 0 loop : -3.70 (0.22), residues: 560 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 732 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 732 time to evaluate : 2.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 732 average time/residue: 0.2873 time to fit residues: 326.1677 Evaluate side-chains 605 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 605 time to evaluate : 2.456 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.3111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 157 optimal weight: 6.9990 chunk 211 optimal weight: 9.9990 chunk 60 optimal weight: 5.9990 chunk 182 optimal weight: 6.9990 chunk 29 optimal weight: 0.7980 chunk 55 optimal weight: 7.9990 chunk 198 optimal weight: 0.0870 chunk 83 optimal weight: 0.6980 chunk 203 optimal weight: 0.0470 chunk 25 optimal weight: 0.7980 chunk 36 optimal weight: 20.0000 overall best weight: 0.4856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.145602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.126539 restraints weight = 35350.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.130005 restraints weight = 21154.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.132544 restraints weight = 14339.955| |-----------------------------------------------------------------------------| r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.4499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.062 20010 Z= 0.177 Angle : 0.705 8.553 27200 Z= 0.342 Chirality : 0.039 0.211 3170 Planarity : 0.005 0.090 3350 Dihedral : 4.539 23.010 2690 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.06 % Favored : 92.70 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.17), residues: 2480 helix: 1.04 (0.12), residues: 1920 sheet: None (None), residues: 0 loop : -3.52 (0.23), residues: 560 =============================================================================== Job complete usr+sys time: 5049.00 seconds wall clock time: 91 minutes 51.81 seconds (5511.81 seconds total)