Starting phenix.real_space_refine on Sun Oct 12 11:51:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xp1_38547/10_2025/8xp1_38547.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xp1_38547/10_2025/8xp1_38547.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8xp1_38547/10_2025/8xp1_38547.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xp1_38547/10_2025/8xp1_38547.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xp1_38547/10_2025/8xp1_38547.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xp1_38547/10_2025/8xp1_38547.map" } resolution = 4.4 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= 0.018 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: 4 Type Number sf(0) Gaussians S 108 5.16 5 C 15342 2.51 5 N 4290 2.21 5 O 4557 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24297 Number of models: 1 Model: "" Number of chains: 21 Chain: "0" Number of atoms: 675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 675 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 3, 'TRANS': 83} Chain: "C" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 224 Classifications: {'peptide': 27} Link IDs: {'PTRANS': 1, 'TRANS': 25} Chain: "S" Number of atoms: 2431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2431 Classifications: {'peptide': 301} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 279} Chain breaks: 1 Chain: "Z" Number of atoms: 2428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2428 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 6, 'TRANS': 303} Chain breaks: 1 Chain: "h" Number of atoms: 991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 991 Classifications: {'peptide': 129} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 125} Chain: "o" Number of atoms: 675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 675 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 3, 'TRANS': 83} Chain: "u" Number of atoms: 675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 675 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 3, 'TRANS': 83} Chain: "AA" Number of atoms: 675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 675 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 3, 'TRANS': 83} Chain: "D" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 224 Classifications: {'peptide': 27} Link IDs: {'PTRANS': 1, 'TRANS': 25} Chain: "T" Number of atoms: 2431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2431 Classifications: {'peptide': 301} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 279} Chain breaks: 1 Chain: "a" Number of atoms: 2428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2428 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 6, 'TRANS': 303} Chain breaks: 1 Chain: "i" Number of atoms: 991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 991 Classifications: {'peptide': 129} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 125} Chain: "p" Number of atoms: 675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 675 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 3, 'TRANS': 83} Chain: "v" Number of atoms: 675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 675 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 3, 'TRANS': 83} Chain: "AB" Number of atoms: 675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 675 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 3, 'TRANS': 83} Chain: "E" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 224 Classifications: {'peptide': 27} Link IDs: {'PTRANS': 1, 'TRANS': 25} Chain: "U" Number of atoms: 2431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2431 Classifications: {'peptide': 301} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 279} Chain breaks: 1 Chain: "b" Number of atoms: 2428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2428 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 6, 'TRANS': 303} Chain breaks: 1 Chain: "j" Number of atoms: 991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 991 Classifications: {'peptide': 129} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 125} Chain: "q" Number of atoms: 675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 675 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 3, 'TRANS': 83} Chain: "w" Number of atoms: 675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 675 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 3, 'TRANS': 83} Time building chain proxies: 6.40, per 1000 atoms: 0.26 Number of scatterers: 24297 At special positions: 0 Unit cell: (159.6, 156, 174, 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 108 16.00 O 4557 8.00 N 4290 7.00 C 15342 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.25 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 1.4 microseconds 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5820 Finding SS restraints... Secondary structure from input PDB file: 141 helices and 17 sheets defined 54.2% alpha, 22.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain '0' and resid 51 through 59 Processing helix chain '0' and resid 74 through 80 Processing helix chain '0' and resid 127 through 137 Processing helix chain 'C' and resid 534 through 541 Processing helix chain 'C' and resid 543 through 558 Processing helix chain 'S' and resid 7 through 16 Processing helix chain 'S' and resid 51 through 74 Processing helix chain 'S' and resid 89 through 95 Processing helix chain 'S' and resid 119 through 131 Processing helix chain 'S' and resid 147 through 170 Processing helix chain 'S' and resid 185 through 189 Processing helix chain 'S' and resid 221 through 225 Processing helix chain 'S' and resid 227 through 233 removed outlier: 4.105A pdb=" N ASN S 233 " --> pdb=" O GLU S 229 " (cutoff:3.500A) Processing helix chain 'S' and resid 241 through 255 Processing helix chain 'S' and resid 271 through 277 Processing helix chain 'Z' and resid 5 through 17 Processing helix chain 'Z' and resid 18 through 27 Processing helix chain 'Z' and resid 30 through 43 removed outlier: 3.735A pdb=" N ASN Z 43 " --> pdb=" O THR Z 39 " (cutoff:3.500A) Processing helix chain 'Z' and resid 48 through 66 removed outlier: 4.019A pdb=" N VAL Z 55 " --> pdb=" O GLN Z 51 " (cutoff:3.500A) Processing helix chain 'Z' and resid 72 through 85 Processing helix chain 'Z' and resid 97 through 113 removed outlier: 3.637A pdb=" N ASN Z 111 " --> pdb=" O ILE Z 107 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N MET Z 113 " --> pdb=" O THR Z 109 " (cutoff:3.500A) Processing helix chain 'Z' and resid 114 through 123 Processing helix chain 'Z' and resid 126 through 136 removed outlier: 3.689A pdb=" N HIS Z 136 " --> pdb=" O THR Z 132 " (cutoff:3.500A) Processing helix chain 'Z' and resid 138 through 148 removed outlier: 3.590A pdb=" N LEU Z 148 " --> pdb=" O ASP Z 144 " (cutoff:3.500A) Processing helix chain 'Z' and resid 150 through 163 Processing helix chain 'Z' and resid 168 through 190 Processing helix chain 'Z' and resid 195 through 205 removed outlier: 3.612A pdb=" N ALA Z 199 " --> pdb=" O GLY Z 195 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU Z 205 " --> pdb=" O GLU Z 201 " (cutoff:3.500A) Processing helix chain 'Z' and resid 207 through 222 Processing helix chain 'Z' and resid 222 through 232 Processing helix chain 'Z' and resid 238 through 242 Processing helix chain 'Z' and resid 243 through 252 removed outlier: 3.576A pdb=" N GLN Z 252 " --> pdb=" O GLN Z 248 " (cutoff:3.500A) Processing helix chain 'Z' and resid 255 through 265 removed outlier: 4.267A pdb=" N GLY Z 265 " --> pdb=" O ILE Z 261 " (cutoff:3.500A) Processing helix chain 'Z' and resid 267 through 277 removed outlier: 3.547A pdb=" N ASN Z 277 " --> pdb=" O LYS Z 273 " (cutoff:3.500A) Processing helix chain 'Z' and resid 279 through 293 Processing helix chain 'Z' and resid 297 through 318 Processing helix chain 'h' and resid 14 through 28 Processing helix chain 'h' and resid 38 through 49 removed outlier: 3.545A pdb=" N ALA h 48 " --> pdb=" O ASN h 44 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLY h 49 " --> pdb=" O LYS h 45 " (cutoff:3.500A) Processing helix chain 'h' and resid 64 through 75 Processing helix chain 'h' and resid 76 through 79 removed outlier: 3.508A pdb=" N SER h 79 " --> pdb=" O SER h 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 76 through 79' Processing helix chain 'h' and resid 91 through 102 Processing helix chain 'h' and resid 112 through 127 Processing helix chain 'o' and resid 52 through 59 Processing helix chain 'o' and resid 75 through 80 Processing helix chain 'o' and resid 126 through 137 removed outlier: 3.671A pdb=" N GLU o 130 " --> pdb=" O ILE o 126 " (cutoff:3.500A) Processing helix chain 'u' and resid 52 through 59 Processing helix chain 'u' and resid 75 through 80 Processing helix chain 'u' and resid 127 through 137 Processing helix chain 'AA' and resid 52 through 59 Processing helix chain 'AA' and resid 74 through 80 Processing helix chain 'AA' and resid 127 through 137 Processing helix chain 'D' and resid 534 through 541 Processing helix chain 'D' and resid 543 through 558 Processing helix chain 'T' and resid 7 through 16 Processing helix chain 'T' and resid 51 through 74 Processing helix chain 'T' and resid 89 through 95 Processing helix chain 'T' and resid 119 through 131 Processing helix chain 'T' and resid 147 through 170 Processing helix chain 'T' and resid 185 through 189 Processing helix chain 'T' and resid 221 through 225 Processing helix chain 'T' and resid 227 through 233 removed outlier: 4.104A pdb=" N ASN T 233 " --> pdb=" O GLU T 229 " (cutoff:3.500A) Processing helix chain 'T' and resid 241 through 255 Processing helix chain 'T' and resid 271 through 277 Processing helix chain 'a' and resid 5 through 17 Processing helix chain 'a' and resid 18 through 27 Processing helix chain 'a' and resid 30 through 43 removed outlier: 3.735A pdb=" N ASN a 43 " --> pdb=" O THR a 39 " (cutoff:3.500A) Processing helix chain 'a' and resid 48 through 66 removed outlier: 4.020A pdb=" N VAL a 55 " --> pdb=" O GLN a 51 " (cutoff:3.500A) Processing helix chain 'a' and resid 72 through 85 Processing helix chain 'a' and resid 97 through 113 removed outlier: 3.637A pdb=" N ASN a 111 " --> pdb=" O ILE a 107 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N MET a 113 " --> pdb=" O THR a 109 " (cutoff:3.500A) Processing helix chain 'a' and resid 114 through 123 Processing helix chain 'a' and resid 126 through 136 removed outlier: 3.688A pdb=" N HIS a 136 " --> pdb=" O THR a 132 " (cutoff:3.500A) Processing helix chain 'a' and resid 138 through 148 removed outlier: 3.590A pdb=" N LEU a 148 " --> pdb=" O ASP a 144 " (cutoff:3.500A) Processing helix chain 'a' and resid 150 through 163 Processing helix chain 'a' and resid 168 through 190 Processing helix chain 'a' and resid 195 through 205 removed outlier: 3.612A pdb=" N ALA a 199 " --> pdb=" O GLY a 195 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU a 205 " --> pdb=" O GLU a 201 " (cutoff:3.500A) Processing helix chain 'a' and resid 207 through 222 Processing helix chain 'a' and resid 222 through 232 Processing helix chain 'a' and resid 238 through 242 Processing helix chain 'a' and resid 243 through 252 removed outlier: 3.576A pdb=" N GLN a 252 " --> pdb=" O GLN a 248 " (cutoff:3.500A) Processing helix chain 'a' and resid 255 through 265 removed outlier: 4.267A pdb=" N GLY a 265 " --> pdb=" O ILE a 261 " (cutoff:3.500A) Processing helix chain 'a' and resid 267 through 277 removed outlier: 3.547A pdb=" N ASN a 277 " --> pdb=" O LYS a 273 " (cutoff:3.500A) Processing helix chain 'a' and resid 279 through 293 Processing helix chain 'a' and resid 297 through 318 Processing helix chain 'i' and resid 14 through 28 Processing helix chain 'i' and resid 38 through 49 removed outlier: 3.547A pdb=" N ALA i 48 " --> pdb=" O ASN i 44 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLY i 49 " --> pdb=" O LYS i 45 " (cutoff:3.500A) Processing helix chain 'i' and resid 64 through 75 Processing helix chain 'i' and resid 76 through 79 removed outlier: 3.508A pdb=" N SER i 79 " --> pdb=" O SER i 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 76 through 79' Processing helix chain 'i' and resid 91 through 102 Processing helix chain 'i' and resid 112 through 127 Processing helix chain 'p' and resid 52 through 59 Processing helix chain 'p' and resid 75 through 80 Processing helix chain 'p' and resid 126 through 137 removed outlier: 3.672A pdb=" N GLU p 130 " --> pdb=" O ILE p 126 " (cutoff:3.500A) Processing helix chain 'v' and resid 52 through 59 Processing helix chain 'v' and resid 75 through 80 Processing helix chain 'v' and resid 127 through 137 Processing helix chain 'AB' and resid 52 through 59 Processing helix chain 'AB' and resid 74 through 80 Processing helix chain 'AB' and resid 127 through 137 Processing helix chain 'E' and resid 534 through 541 Processing helix chain 'E' and resid 543 through 558 Processing helix chain 'U' and resid 7 through 16 Processing helix chain 'U' and resid 51 through 74 Processing helix chain 'U' and resid 89 through 95 Processing helix chain 'U' and resid 119 through 131 Processing helix chain 'U' and resid 147 through 170 Processing helix chain 'U' and resid 185 through 189 Processing helix chain 'U' and resid 221 through 225 Processing helix chain 'U' and resid 227 through 233 removed outlier: 4.104A pdb=" N ASN U 233 " --> pdb=" O GLU U 229 " (cutoff:3.500A) Processing helix chain 'U' and resid 241 through 255 Processing helix chain 'U' and resid 271 through 277 Processing helix chain 'b' and resid 5 through 17 Processing helix chain 'b' and resid 18 through 27 Processing helix chain 'b' and resid 30 through 43 removed outlier: 3.735A pdb=" N ASN b 43 " --> pdb=" O THR b 39 " (cutoff:3.500A) Processing helix chain 'b' and resid 48 through 66 removed outlier: 4.020A pdb=" N VAL b 55 " --> pdb=" O GLN b 51 " (cutoff:3.500A) Processing helix chain 'b' and resid 72 through 85 Processing helix chain 'b' and resid 97 through 113 removed outlier: 3.638A pdb=" N ASN b 111 " --> pdb=" O ILE b 107 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N MET b 113 " --> pdb=" O THR b 109 " (cutoff:3.500A) Processing helix chain 'b' and resid 114 through 123 Processing helix chain 'b' and resid 126 through 136 removed outlier: 3.688A pdb=" N HIS b 136 " --> pdb=" O THR b 132 " (cutoff:3.500A) Processing helix chain 'b' and resid 138 through 148 removed outlier: 3.591A pdb=" N LEU b 148 " --> pdb=" O ASP b 144 " (cutoff:3.500A) Processing helix chain 'b' and resid 150 through 163 Processing helix chain 'b' and resid 168 through 190 Processing helix chain 'b' and resid 195 through 205 removed outlier: 3.613A pdb=" N ALA b 199 " --> pdb=" O GLY b 195 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU b 205 " --> pdb=" O GLU b 201 " (cutoff:3.500A) Processing helix chain 'b' and resid 207 through 222 Processing helix chain 'b' and resid 222 through 232 Processing helix chain 'b' and resid 238 through 242 Processing helix chain 'b' and resid 243 through 252 removed outlier: 3.576A pdb=" N GLN b 252 " --> pdb=" O GLN b 248 " (cutoff:3.500A) Processing helix chain 'b' and resid 255 through 265 removed outlier: 4.267A pdb=" N GLY b 265 " --> pdb=" O ILE b 261 " (cutoff:3.500A) Processing helix chain 'b' and resid 267 through 277 removed outlier: 3.547A pdb=" N ASN b 277 " --> pdb=" O LYS b 273 " (cutoff:3.500A) Processing helix chain 'b' and resid 279 through 293 Processing helix chain 'b' and resid 297 through 318 Processing helix chain 'j' and resid 14 through 28 Processing helix chain 'j' and resid 38 through 49 removed outlier: 3.546A pdb=" N ALA j 48 " --> pdb=" O ASN j 44 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLY j 49 " --> pdb=" O LYS j 45 " (cutoff:3.500A) Processing helix chain 'j' and resid 64 through 75 Processing helix chain 'j' and resid 76 through 79 removed outlier: 3.508A pdb=" N SER j 79 " --> pdb=" O SER j 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'j' and resid 76 through 79' Processing helix chain 'j' and resid 91 through 102 Processing helix chain 'j' and resid 112 through 127 Processing helix chain 'q' and resid 52 through 59 Processing helix chain 'q' and resid 75 through 80 Processing helix chain 'q' and resid 126 through 137 removed outlier: 3.671A pdb=" N GLU q 130 " --> pdb=" O ILE q 126 " (cutoff:3.500A) Processing helix chain 'w' and resid 52 through 59 Processing helix chain 'w' and resid 75 through 80 Processing helix chain 'w' and resid 127 through 137 Processing sheet with id=AA1, first strand: chain '0' and resid 86 through 92 removed outlier: 5.319A pdb=" N TYR u 118 " --> pdb=" O LEU 0 89 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N GLN u 108 " --> pdb=" O THR u 123 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N ILE u 125 " --> pdb=" O ILE u 106 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N ILE u 106 " --> pdb=" O ILE u 125 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N LEU u 105 " --> pdb=" O ILE u 101 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ILE u 101 " --> pdb=" O LEU u 105 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASP u 98 " --> pdb=" O GLU u 67 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY 0 69 " --> pdb=" O VAL u 66 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N LEU u 68 " --> pdb=" O GLU 0 67 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N GLU 0 67 " --> pdb=" O LEU u 68 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N ARG u 70 " --> pdb=" O THR 0 65 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N THR 0 65 " --> pdb=" O ARG u 70 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N ARG u 72 " --> pdb=" O LYS 0 63 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N LYS 0 63 " --> pdb=" O ARG u 72 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N THR u 74 " --> pdb=" O PRO 0 61 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASP 0 98 " --> pdb=" O GLU 0 67 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ILE 0 101 " --> pdb=" O LEU 0 105 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N LEU 0 105 " --> pdb=" O ILE 0 101 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N ILE 0 106 " --> pdb=" O ILE 0 125 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N ILE 0 125 " --> pdb=" O ILE 0 106 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N GLN 0 108 " --> pdb=" O THR 0 123 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '0' and resid 86 through 92 removed outlier: 5.319A pdb=" N TYR u 118 " --> pdb=" O LEU 0 89 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N GLN u 108 " --> pdb=" O THR u 123 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N ILE u 125 " --> pdb=" O ILE u 106 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N ILE u 106 " --> pdb=" O ILE u 125 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'S' and resid 35 through 37 removed outlier: 7.675A pdb=" N ILE w 106 " --> pdb=" O ILE w 125 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N ILE w 125 " --> pdb=" O ILE w 106 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N GLN w 108 " --> pdb=" O THR w 123 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N TYR w 118 " --> pdb=" O LEUAB 89 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'S' and resid 35 through 37 removed outlier: 5.438A pdb=" N LEU w 105 " --> pdb=" O ILE w 101 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ILE w 101 " --> pdb=" O LEU w 105 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASP w 98 " --> pdb=" O GLU w 67 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLYAB 69 " --> pdb=" O VAL w 66 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N LEU w 68 " --> pdb=" O GLUAB 67 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N GLUAB 67 " --> pdb=" O LEU w 68 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N ARG w 70 " --> pdb=" O THRAB 65 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N THRAB 65 " --> pdb=" O ARG w 70 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N ARG w 72 " --> pdb=" O LYSAB 63 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N LYSAB 63 " --> pdb=" O ARG w 72 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N THR w 74 " --> pdb=" O PROAB 61 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASPAB 98 " --> pdb=" O GLUAB 67 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ILEAB 101 " --> pdb=" O LEUAB 105 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N LEUAB 105 " --> pdb=" O ILEAB 101 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N ILEAB 106 " --> pdb=" O ILEAB 125 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N ILEAB 125 " --> pdb=" O ILEAB 106 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N GLNAB 108 " --> pdb=" O THRAB 123 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'S' and resid 77 through 81 removed outlier: 3.532A pdb=" N GLN S 87 " --> pdb=" O VAL S 199 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'S' and resid 77 through 81 removed outlier: 3.625A pdb=" N ARG S 181 " --> pdb=" O LEU S 104 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N HIS S 106 " --> pdb=" O TYR S 179 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N TYR S 179 " --> pdb=" O HIS S 106 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N LYS S 108 " --> pdb=" O VAL S 177 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N VAL S 177 " --> pdb=" O LYS S 108 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'S' and resid 283 through 285 removed outlier: 6.981A pdb=" N GLN o 108 " --> pdb=" O THR o 123 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N LEU o 105 " --> pdb=" O ILE o 101 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ILE o 101 " --> pdb=" O LEU o 105 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASP o 98 " --> pdb=" O GLU o 67 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N LYS o 63 " --> pdb=" O PRO S 269 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N THR o 65 " --> pdb=" O ASP S 267 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N ASP S 267 " --> pdb=" O THR o 65 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N GLU o 67 " --> pdb=" O PHE S 265 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N PHE S 265 " --> pdb=" O GLU o 67 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLY o 69 " --> pdb=" O ALA S 263 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ALA S 263 " --> pdb=" O GLY o 69 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ILE S 293 " --> pdb=" O ASN S 264 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU S 302 " --> pdb=" O ALA S 294 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N VAL S 296 " --> pdb=" O PRO S 300 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N VAL S 301 " --> pdb=" O LEU S 320 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N LEU S 320 " --> pdb=" O VAL S 301 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N THR S 303 " --> pdb=" O GLU S 318 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N TYR S 313 " --> pdb=" O LEU o 89 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU S 315 " --> pdb=" O VAL o 87 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL o 87 " --> pdb=" O LEU S 315 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'h' and resid 33 through 36 removed outlier: 6.491A pdb=" N ILE h 54 " --> pdb=" O LEU h 84 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N VAL h 86 " --> pdb=" O ILE h 54 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N SER h 56 " --> pdb=" O VAL h 86 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N VAL h 83 " --> pdb=" O GLY h 105 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N VAL h 107 " --> pdb=" O VAL h 83 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N MET h 85 " --> pdb=" O VAL h 107 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'AA' and resid 86 through 92 removed outlier: 5.319A pdb=" N TYR v 118 " --> pdb=" O LEUAA 89 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N GLN v 108 " --> pdb=" O THR v 123 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N ILE v 125 " --> pdb=" O ILE v 106 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N ILE v 106 " --> pdb=" O ILE v 125 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N LEU v 105 " --> pdb=" O ILE v 101 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ILE v 101 " --> pdb=" O LEU v 105 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASP v 98 " --> pdb=" O GLU v 67 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLYAA 69 " --> pdb=" O VAL v 66 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N LEU v 68 " --> pdb=" O GLUAA 67 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N GLUAA 67 " --> pdb=" O LEU v 68 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N ARG v 70 " --> pdb=" O THRAA 65 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N THRAA 65 " --> pdb=" O ARG v 70 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N ARG v 72 " --> pdb=" O LYSAA 63 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N LYSAA 63 " --> pdb=" O ARG v 72 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N THR v 74 " --> pdb=" O PROAA 61 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASPAA 98 " --> pdb=" O GLUAA 67 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ILEAA 101 " --> pdb=" O LEUAA 105 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N LEUAA 105 " --> pdb=" O ILEAA 101 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N ILEAA 106 " --> pdb=" O ILEAA 125 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N ILEAA 125 " --> pdb=" O ILEAA 106 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N GLNAA 108 " --> pdb=" O THRAA 123 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'T' and resid 77 through 81 removed outlier: 3.532A pdb=" N GLN T 87 " --> pdb=" O VAL T 199 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'T' and resid 77 through 81 removed outlier: 3.625A pdb=" N ARG T 181 " --> pdb=" O LEU T 104 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N HIS T 106 " --> pdb=" O TYR T 179 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N TYR T 179 " --> pdb=" O HIS T 106 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N LYS T 108 " --> pdb=" O VAL T 177 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N VAL T 177 " --> pdb=" O LYS T 108 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'T' and resid 283 through 285 removed outlier: 6.981A pdb=" N GLN p 108 " --> pdb=" O THR p 123 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N LEU p 105 " --> pdb=" O ILE p 101 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ILE p 101 " --> pdb=" O LEU p 105 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASP p 98 " --> pdb=" O GLU p 67 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N LYS p 63 " --> pdb=" O PRO T 269 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N THR p 65 " --> pdb=" O ASP T 267 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N ASP T 267 " --> pdb=" O THR p 65 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N GLU p 67 " --> pdb=" O PHE T 265 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N PHE T 265 " --> pdb=" O GLU p 67 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLY p 69 " --> pdb=" O ALA T 263 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ALA T 263 " --> pdb=" O GLY p 69 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ILE T 293 " --> pdb=" O ASN T 264 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU T 302 " --> pdb=" O ALA T 294 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N VAL T 296 " --> pdb=" O PRO T 300 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N VAL T 301 " --> pdb=" O LEU T 320 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N LEU T 320 " --> pdb=" O VAL T 301 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N THR T 303 " --> pdb=" O GLU T 318 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N TYR T 313 " --> pdb=" O LEU p 89 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU T 315 " --> pdb=" O VAL p 87 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL p 87 " --> pdb=" O LEU T 315 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'i' and resid 33 through 36 removed outlier: 6.492A pdb=" N ILE i 54 " --> pdb=" O LEU i 84 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N VAL i 86 " --> pdb=" O ILE i 54 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N SER i 56 " --> pdb=" O VAL i 86 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N VAL i 83 " --> pdb=" O GLY i 105 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N VAL i 107 " --> pdb=" O VAL i 83 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N MET i 85 " --> pdb=" O VAL i 107 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'U' and resid 77 through 81 removed outlier: 3.532A pdb=" N GLN U 87 " --> pdb=" O VAL U 199 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'U' and resid 77 through 81 removed outlier: 3.624A pdb=" N ARG U 181 " --> pdb=" O LEU U 104 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N HIS U 106 " --> pdb=" O TYR U 179 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N TYR U 179 " --> pdb=" O HIS U 106 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N LYS U 108 " --> pdb=" O VAL U 177 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N VAL U 177 " --> pdb=" O LYS U 108 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'U' and resid 283 through 285 removed outlier: 6.981A pdb=" N GLN q 108 " --> pdb=" O THR q 123 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N LEU q 105 " --> pdb=" O ILE q 101 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ILE q 101 " --> pdb=" O LEU q 105 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASP q 98 " --> pdb=" O GLU q 67 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N LYS q 63 " --> pdb=" O PRO U 269 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N THR q 65 " --> pdb=" O ASP U 267 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N ASP U 267 " --> pdb=" O THR q 65 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N GLU q 67 " --> pdb=" O PHE U 265 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N PHE U 265 " --> pdb=" O GLU q 67 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLY q 69 " --> pdb=" O ALA U 263 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ALA U 263 " --> pdb=" O GLY q 69 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ILE U 293 " --> pdb=" O ASN U 264 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU U 302 " --> pdb=" O ALA U 294 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N VAL U 296 " --> pdb=" O PRO U 300 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N VAL U 301 " --> pdb=" O LEU U 320 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N LEU U 320 " --> pdb=" O VAL U 301 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N THR U 303 " --> pdb=" O GLU U 318 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N TYR U 313 " --> pdb=" O LEU q 89 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU U 315 " --> pdb=" O VAL q 87 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL q 87 " --> pdb=" O LEU U 315 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'j' and resid 33 through 36 removed outlier: 6.491A pdb=" N ILE j 54 " --> pdb=" O LEU j 84 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N VAL j 86 " --> pdb=" O ILE j 54 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N SER j 56 " --> pdb=" O VAL j 86 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N VAL j 83 " --> pdb=" O GLY j 105 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N VAL j 107 " --> pdb=" O VAL j 83 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N MET j 85 " --> pdb=" O VAL j 107 " (cutoff:3.500A) 1412 hydrogen bonds defined for protein. 4089 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: 5.00 Time building geometry restraints manager: 2.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6480 1.33 - 1.45: 3397 1.45 - 1.57: 14498 1.57 - 1.69: 0 1.69 - 1.81: 213 Bond restraints: 24588 Sorted by residual: bond pdb=" N ILE o 60 " pdb=" CA ILE o 60 " ideal model delta sigma weight residual 1.460 1.503 -0.043 9.30e-03 1.16e+04 2.11e+01 bond pdb=" N ILE q 60 " pdb=" CA ILE q 60 " ideal model delta sigma weight residual 1.460 1.502 -0.042 9.30e-03 1.16e+04 2.05e+01 bond pdb=" N ILE p 60 " pdb=" CA ILE p 60 " ideal model delta sigma weight residual 1.460 1.502 -0.042 9.30e-03 1.16e+04 2.05e+01 bond pdb=" N VAL T 232 " pdb=" CA VAL T 232 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.25e-02 6.40e+03 9.61e+00 bond pdb=" N ILE o 126 " pdb=" CA ILE o 126 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.25e-02 6.40e+03 9.46e+00 ... (remaining 24583 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 32280 1.60 - 3.20: 802 3.20 - 4.80: 117 4.80 - 6.40: 32 6.40 - 8.00: 3 Bond angle restraints: 33234 Sorted by residual: angle pdb=" N PRO v 128 " pdb=" CA PRO v 128 " pdb=" C PRO v 128 " ideal model delta sigma weight residual 113.57 121.57 -8.00 1.31e+00 5.83e-01 3.73e+01 angle pdb=" N PRO u 128 " pdb=" CA PRO u 128 " pdb=" C PRO u 128 " ideal model delta sigma weight residual 113.57 121.54 -7.97 1.31e+00 5.83e-01 3.70e+01 angle pdb=" N PRO w 128 " pdb=" CA PRO w 128 " pdb=" C PRO w 128 " ideal model delta sigma weight residual 113.57 121.54 -7.97 1.31e+00 5.83e-01 3.70e+01 angle pdb=" N ILE o 60 " pdb=" CA ILE o 60 " pdb=" C ILE o 60 " ideal model delta sigma weight residual 107.73 113.69 -5.96 1.14e+00 7.69e-01 2.73e+01 angle pdb=" N ILE p 60 " pdb=" CA ILE p 60 " pdb=" C ILE p 60 " ideal model delta sigma weight residual 107.73 113.69 -5.96 1.14e+00 7.69e-01 2.73e+01 ... (remaining 33229 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.57: 14671 16.57 - 33.15: 452 33.15 - 49.72: 132 49.72 - 66.30: 33 66.30 - 82.87: 3 Dihedral angle restraints: 15291 sinusoidal: 6375 harmonic: 8916 Sorted by residual: dihedral pdb=" CD ARG q 131 " pdb=" NE ARG q 131 " pdb=" CZ ARG q 131 " pdb=" NH1 ARG q 131 " ideal model delta sinusoidal sigma weight residual 0.00 -30.83 30.83 1 1.00e+01 1.00e-02 1.36e+01 dihedral pdb=" CD ARG o 131 " pdb=" NE ARG o 131 " pdb=" CZ ARG o 131 " pdb=" NH1 ARG o 131 " ideal model delta sinusoidal sigma weight residual 0.00 -30.82 30.82 1 1.00e+01 1.00e-02 1.36e+01 dihedral pdb=" CD ARG p 131 " pdb=" NE ARG p 131 " pdb=" CZ ARG p 131 " pdb=" NH1 ARG p 131 " ideal model delta sinusoidal sigma weight residual 0.00 -30.80 30.80 1 1.00e+01 1.00e-02 1.35e+01 ... (remaining 15288 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 2981 0.038 - 0.075: 550 0.075 - 0.113: 311 0.113 - 0.150: 89 0.150 - 0.188: 47 Chirality restraints: 3978 Sorted by residual: chirality pdb=" CA ARGAA 134 " pdb=" N ARGAA 134 " pdb=" C ARGAA 134 " pdb=" CB ARGAA 134 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.81e-01 chirality pdb=" CA LEU p 135 " pdb=" N LEU p 135 " pdb=" C LEU p 135 " pdb=" CB LEU p 135 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.80e-01 chirality pdb=" CA ARG 0 134 " pdb=" N ARG 0 134 " pdb=" C ARG 0 134 " pdb=" CB ARG 0 134 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.75e-01 ... (remaining 3975 not shown) Planarity restraints: 4308 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG o 131 " 0.544 9.50e-02 1.11e+02 2.44e-01 3.64e+01 pdb=" NE ARG o 131 " -0.034 2.00e-02 2.50e+03 pdb=" CZ ARG o 131 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG o 131 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG o 131 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG q 131 " 0.543 9.50e-02 1.11e+02 2.44e-01 3.63e+01 pdb=" NE ARG q 131 " -0.034 2.00e-02 2.50e+03 pdb=" CZ ARG q 131 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG q 131 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG q 131 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG p 131 " 0.543 9.50e-02 1.11e+02 2.43e-01 3.63e+01 pdb=" NE ARG p 131 " -0.034 2.00e-02 2.50e+03 pdb=" CZ ARG p 131 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG p 131 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG p 131 " 0.017 2.00e-02 2.50e+03 ... (remaining 4305 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.78: 4636 2.78 - 3.31: 24069 3.31 - 3.84: 39047 3.84 - 4.37: 45347 4.37 - 4.90: 77441 Nonbonded interactions: 190540 Sorted by model distance: nonbonded pdb=" O ILE v 126 " pdb=" OG1 THR v 127 " model vdw 2.256 3.040 nonbonded pdb=" O ILE u 126 " pdb=" OG1 THR u 127 " model vdw 2.256 3.040 nonbonded pdb=" O ILE w 126 " pdb=" OG1 THR w 127 " model vdw 2.256 3.040 nonbonded pdb=" O ILEAA 126 " pdb=" OG1 THRAA 127 " model vdw 2.256 3.040 nonbonded pdb=" O ILEAB 126 " pdb=" OG1 THRAB 127 " model vdw 2.257 3.040 ... (remaining 190535 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain '0' selection = chain 'AA' selection = chain 'AB' selection = chain 'o' selection = chain 'p' selection = chain 'q' selection = chain 'u' selection = chain 'v' selection = chain 'w' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'S' selection = chain 'T' selection = chain 'U' } ncs_group { reference = chain 'Z' selection = chain 'a' selection = chain 'b' } ncs_group { reference = 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 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: 21.750 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: 0.030 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 24.350 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5914 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 : 0.003 0.043 24588 Z= 0.240 Angle : 0.579 8.003 33234 Z= 0.401 Chirality : 0.045 0.188 3978 Planarity : 0.013 0.244 4308 Dihedral : 9.244 82.869 9471 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 1.19 % Allowed : 2.97 % Favored : 95.84 % Rotamer: Outliers : 3.35 % Allowed : 3.35 % Favored : 93.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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 aren not related in a simple way. whole: 1.85 (0.16), residues: 3030 helix: 1.86 (0.13), residues: 1605 sheet: 1.29 (0.30), residues: 324 loop : 0.37 (0.20), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARGAA 131 TYR 0.008 0.001 TYR S 165 PHE 0.011 0.001 PHE T 61 TRP 0.004 0.001 TRP S 246 HIS 0.003 0.001 HIS Z 155 Details of bonding type rmsd covalent geometry : bond 0.00331 (24588) covalent geometry : angle 0.57906 (33234) hydrogen bonds : bond 0.18891 ( 1388) hydrogen bonds : angle 6.11266 ( 4089) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1001 residues out of total 2685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 911 time to evaluate : 1.083 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 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 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 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 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 97 LEU cc_start: 0.9417 (mt) cc_final: 0.9193 (mp) REVERT: S 157 MET cc_start: 0.8887 (mtp) cc_final: 0.8661 (mtm) REVERT: S 165 TYR cc_start: 0.9182 (t80) cc_final: 0.8901 (t80) REVERT: Z 132 THR cc_start: 0.8110 (m) cc_final: 0.7882 (p) REVERT: Z 134 LEU cc_start: 0.9115 (mt) cc_final: 0.8875 (mt) REVERT: Z 176 THR cc_start: 0.8685 (m) cc_final: 0.8173 (p) REVERT: h 54 ILE cc_start: 0.8215 (mt) cc_final: 0.7327 (mt) REVERT: h 78 MET cc_start: 0.5601 (mtm) cc_final: 0.5217 (mtt) REVERT: h 86 VAL cc_start: 0.7977 (t) cc_final: 0.7751 (t) REVERT: o 98 ASP cc_start: 0.5209 (m-30) cc_final: 0.4953 (m-30) REVERT: o 99 ILE cc_start: 0.8477 (mt) cc_final: 0.8129 (mt) REVERT: o 106 ILE cc_start: 0.8909 (OUTLIER) cc_final: 0.8630 (tp) REVERT: AA 106 ILE cc_start: 0.4503 (OUTLIER) cc_final: 0.3879 (mm) REVERT: T 286 ILE cc_start: 0.9234 (OUTLIER) cc_final: 0.8956 (pt) REVERT: a 100 THR cc_start: 0.6826 (OUTLIER) cc_final: 0.6585 (m) REVERT: i 22 ARG cc_start: 0.7009 (ttm170) cc_final: 0.6733 (ttm170) REVERT: i 45 LYS cc_start: 0.7977 (mttt) cc_final: 0.7751 (ptpt) REVERT: i 84 LEU cc_start: 0.8604 (tp) cc_final: 0.8189 (tp) REVERT: v 66 VAL cc_start: 0.8188 (t) cc_final: 0.7850 (p) REVERT: v 97 LEU cc_start: 0.6682 (mt) cc_final: 0.6384 (mp) REVERT: AB 59 ASP cc_start: 0.7917 (m-30) cc_final: 0.7627 (p0) REVERT: U 177 VAL cc_start: 0.8937 (t) cc_final: 0.8549 (t) REVERT: U 231 LEU cc_start: 0.8815 (mt) cc_final: 0.8354 (mt) REVERT: U 254 VAL cc_start: 0.9150 (t) cc_final: 0.8833 (p) REVERT: U 297 ASP cc_start: 0.6791 (t0) cc_final: 0.6143 (t0) REVERT: j 10 VAL cc_start: 0.9223 (t) cc_final: 0.8826 (p) REVERT: j 28 LEU cc_start: 0.9178 (mt) cc_final: 0.8822 (tp) REVERT: j 38 ASP cc_start: 0.7979 (p0) cc_final: 0.7391 (p0) REVERT: j 54 ILE cc_start: 0.8938 (mt) cc_final: 0.8090 (mt) REVERT: j 64 ASP cc_start: 0.6465 (p0) cc_final: 0.6144 (p0) REVERT: j 116 LEU cc_start: 0.9122 (tp) cc_final: 0.8774 (tp) REVERT: j 119 LYS cc_start: 0.8079 (mmtt) cc_final: 0.7662 (tttt) REVERT: q 56 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8644 (mt) REVERT: q 68 LEU cc_start: 0.7905 (tp) cc_final: 0.7684 (tt) REVERT: q 106 ILE cc_start: 0.8926 (OUTLIER) cc_final: 0.8367 (tp) REVERT: q 122 ILE cc_start: 0.8264 (mm) cc_final: 0.8044 (mm) REVERT: w 99 ILE cc_start: 0.9012 (mt) cc_final: 0.8791 (mt) outliers start: 90 outliers final: 18 residues processed: 963 average time/residue: 0.2196 time to fit residues: 300.2281 Evaluate side-chains 485 residues out of total 2685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 461 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 20.0000 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 5.9990 chunk 111 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 542 ASN S 129 ASN Z 28 HIS Z 61 GLN Z 186 GLN ** u 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 542 ASN T 52 GLN T 71 ASN ** T 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 95 ASN T 295 HIS ** a 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 70 ASN ** a 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 186 GLN v 52 GLN E 542 ASN ** U 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 295 HIS b 61 GLN b 186 GLN ** w 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.084558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.062724 restraints weight = 165226.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.064158 restraints weight = 101223.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.065086 restraints weight = 73013.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.065655 restraints weight = 58930.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.066013 restraints weight = 51638.767| |-----------------------------------------------------------------------------| r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.5807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 24588 Z= 0.321 Angle : 0.894 11.711 33234 Z= 0.463 Chirality : 0.049 0.263 3978 Planarity : 0.007 0.063 4308 Dihedral : 5.074 23.890 3336 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 21.47 Ramachandran Plot: Outliers : 0.69 % Allowed : 4.06 % Favored : 95.25 % Rotamer: Outliers : 0.15 % Allowed : 4.54 % Favored : 95.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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 aren not related in a simple way. whole: 0.67 (0.15), residues: 3030 helix: 0.77 (0.12), residues: 1641 sheet: 1.00 (0.32), residues: 273 loop : -0.01 (0.19), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG Z 314 TYR 0.027 0.004 TYR o 104 PHE 0.029 0.003 PHE T 221 TRP 0.015 0.002 TRP T 246 HIS 0.010 0.002 HIS S 256 Details of bonding type rmsd covalent geometry : bond 0.00682 (24588) covalent geometry : angle 0.89413 (33234) hydrogen bonds : bond 0.05306 ( 1388) hydrogen bonds : angle 5.67734 ( 4089) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 2685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 469 time to evaluate : 0.942 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 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 54 LEU cc_start: 0.9411 (tp) cc_final: 0.9177 (tp) REVERT: S 165 TYR cc_start: 0.9552 (t80) cc_final: 0.9117 (t80) REVERT: S 231 LEU cc_start: 0.9373 (mt) cc_final: 0.9159 (mt) REVERT: Z 132 THR cc_start: 0.9178 (m) cc_final: 0.8954 (p) REVERT: h 12 ASP cc_start: 0.7759 (t0) cc_final: 0.7338 (t0) REVERT: h 15 SER cc_start: 0.9177 (p) cc_final: 0.8894 (m) REVERT: h 19 ARG cc_start: 0.8403 (tpp80) cc_final: 0.8157 (mmm160) REVERT: h 57 ASP cc_start: 0.7670 (t70) cc_final: 0.7379 (t0) REVERT: h 85 MET cc_start: 0.9152 (tpt) cc_final: 0.8881 (tpp) REVERT: o 73 MET cc_start: 0.7921 (ptm) cc_final: 0.7543 (ppp) REVERT: u 73 MET cc_start: 0.8530 (ppp) cc_final: 0.8273 (tmm) REVERT: AA 76 LYS cc_start: 0.9189 (tttt) cc_final: 0.8951 (tptp) REVERT: D 532 MET cc_start: 0.4836 (pmm) cc_final: 0.4537 (mtm) REVERT: a 188 LEU cc_start: 0.7914 (mm) cc_final: 0.7571 (pp) REVERT: i 85 MET cc_start: 0.8077 (tpt) cc_final: 0.6702 (tpt) REVERT: i 86 VAL cc_start: 0.9053 (t) cc_final: 0.8753 (p) REVERT: i 106 TRP cc_start: 0.7385 (t-100) cc_final: 0.7142 (t-100) REVERT: i 111 PHE cc_start: 0.9069 (p90) cc_final: 0.8300 (p90) REVERT: i 115 THR cc_start: 0.9444 (p) cc_final: 0.9223 (p) REVERT: i 119 LYS cc_start: 0.9067 (tptp) cc_final: 0.8813 (tptt) REVERT: p 99 ILE cc_start: 0.9260 (tp) cc_final: 0.9000 (tp) REVERT: p 116 ASP cc_start: 0.6556 (m-30) cc_final: 0.6127 (p0) REVERT: v 70 ARG cc_start: 0.7669 (mtt180) cc_final: 0.7196 (mpp80) REVERT: v 73 MET cc_start: 0.8461 (ppp) cc_final: 0.8161 (ppp) REVERT: v 77 GLU cc_start: 0.9175 (mt-10) cc_final: 0.8432 (mt-10) REVERT: AB 124 ASP cc_start: 0.7921 (t0) cc_final: 0.7603 (t0) REVERT: AB 125 ILE cc_start: 0.8956 (mt) cc_final: 0.8687 (pt) REVERT: U 156 ARG cc_start: 0.9045 (mmp-170) cc_final: 0.8797 (mmm160) REVERT: j 8 PHE cc_start: 0.8344 (m-80) cc_final: 0.7046 (m-80) REVERT: j 12 ASP cc_start: 0.7088 (t0) cc_final: 0.6660 (t70) REVERT: j 30 PHE cc_start: 0.8018 (m-80) cc_final: 0.7308 (m-80) REVERT: j 37 GLU cc_start: 0.7658 (pp20) cc_final: 0.6929 (tp30) REVERT: j 51 PHE cc_start: 0.5487 (m-80) cc_final: 0.4403 (m-10) REVERT: j 64 ASP cc_start: 0.7761 (p0) cc_final: 0.7094 (p0) REVERT: j 78 MET cc_start: 0.7435 (mtm) cc_final: 0.7210 (mpp) REVERT: j 85 MET cc_start: 0.6322 (tpp) cc_final: 0.6120 (tpp) REVERT: j 93 GLU cc_start: 0.9118 (mp0) cc_final: 0.8636 (pm20) REVERT: j 111 PHE cc_start: 0.8872 (p90) cc_final: 0.8638 (p90) REVERT: j 117 GLU cc_start: 0.8797 (pp20) cc_final: 0.8519 (tt0) REVERT: j 118 GLU cc_start: 0.8784 (OUTLIER) cc_final: 0.8160 (pm20) REVERT: j 129 MET cc_start: 0.7599 (tpt) cc_final: 0.7276 (tpt) REVERT: w 77 GLU cc_start: 0.8331 (tp30) cc_final: 0.7886 (tp30) outliers start: 4 outliers final: 0 residues processed: 472 average time/residue: 0.2005 time to fit residues: 140.1254 Evaluate side-chains 329 residues out of total 2685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 328 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 168 optimal weight: 9.9990 chunk 130 optimal weight: 20.0000 chunk 240 optimal weight: 2.9990 chunk 231 optimal weight: 1.9990 chunk 125 optimal weight: 5.9990 chunk 243 optimal weight: 8.9990 chunk 241 optimal weight: 7.9990 chunk 120 optimal weight: 4.9990 chunk 102 optimal weight: 9.9990 chunk 209 optimal weight: 0.8980 chunk 146 optimal weight: 9.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 238 ASN ** u 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 245 ASN ** T 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 238 ASN U 295 HIS ** b 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.082151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.060936 restraints weight = 166914.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.063128 restraints weight = 106261.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.062959 restraints weight = 67557.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.063594 restraints weight = 59750.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.063588 restraints weight = 53252.454| |-----------------------------------------------------------------------------| r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.7067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 24588 Z= 0.261 Angle : 0.763 7.931 33234 Z= 0.397 Chirality : 0.045 0.294 3978 Planarity : 0.006 0.057 4308 Dihedral : 4.954 21.718 3336 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 19.44 Ramachandran Plot: Outliers : 0.63 % Allowed : 4.09 % Favored : 95.28 % Rotamer: Outliers : 0.19 % Allowed : 4.51 % Favored : 95.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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 aren not related in a simple way. whole: 0.31 (0.15), residues: 3030 helix: 0.74 (0.12), residues: 1623 sheet: 0.65 (0.29), residues: 333 loop : -0.65 (0.19), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARGAB 137 TYR 0.021 0.003 TYR v 104 PHE 0.024 0.002 PHE j 124 TRP 0.025 0.002 TRP T 246 HIS 0.007 0.001 HIS T 295 Details of bonding type rmsd covalent geometry : bond 0.00552 (24588) covalent geometry : angle 0.76337 (33234) hydrogen bonds : bond 0.04858 ( 1388) hydrogen bonds : angle 5.51377 ( 4089) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 2685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 421 time to evaluate : 1.069 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 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 revert: symmetry clash REVERT: 0 106 ILE cc_start: 0.8794 (pt) cc_final: 0.8232 (mm) REVERT: S 54 LEU cc_start: 0.9378 (tp) cc_final: 0.9030 (tp) REVERT: S 165 TYR cc_start: 0.9535 (t80) cc_final: 0.8897 (t80) REVERT: Z 26 PHE cc_start: 0.2697 (m-10) cc_final: 0.2459 (m-10) REVERT: Z 132 THR cc_start: 0.9269 (m) cc_final: 0.8937 (p) REVERT: h 1 MET cc_start: 0.7117 (ppp) cc_final: 0.6741 (ppp) REVERT: h 12 ASP cc_start: 0.7819 (t0) cc_final: 0.7608 (t0) REVERT: h 19 ARG cc_start: 0.8645 (tpp80) cc_final: 0.8350 (mmm-85) REVERT: h 41 ASP cc_start: 0.8791 (t0) cc_final: 0.8558 (m-30) REVERT: h 57 ASP cc_start: 0.7400 (t70) cc_final: 0.6461 (t0) REVERT: h 78 MET cc_start: 0.6232 (mtt) cc_final: 0.5975 (mtt) REVERT: h 85 MET cc_start: 0.8848 (tpt) cc_final: 0.8566 (tpp) REVERT: o 117 LYS cc_start: 0.8347 (mttt) cc_final: 0.8062 (mmtt) REVERT: u 98 ASP cc_start: 0.8408 (m-30) cc_final: 0.8076 (m-30) REVERT: AA 71 THR cc_start: 0.6195 (t) cc_final: 0.5239 (m) REVERT: AA 76 LYS cc_start: 0.9051 (tttt) cc_final: 0.8842 (tttm) REVERT: AA 98 ASP cc_start: 0.7469 (m-30) cc_final: 0.7268 (m-30) REVERT: a 188 LEU cc_start: 0.8121 (mm) cc_final: 0.7820 (pp) REVERT: i 63 MET cc_start: 0.7433 (ttp) cc_final: 0.6683 (pmm) REVERT: i 68 LEU cc_start: 0.8616 (tp) cc_final: 0.8239 (mt) REVERT: i 85 MET cc_start: 0.7899 (tpt) cc_final: 0.6259 (tpt) REVERT: i 86 VAL cc_start: 0.9019 (t) cc_final: 0.8748 (p) REVERT: i 111 PHE cc_start: 0.9079 (p90) cc_final: 0.8215 (p90) REVERT: p 51 MET cc_start: 0.7329 (mmp) cc_final: 0.7057 (mmp) REVERT: p 116 ASP cc_start: 0.7764 (m-30) cc_final: 0.7064 (p0) REVERT: p 133 ARG cc_start: 0.9398 (tmm160) cc_final: 0.9185 (tmm-80) REVERT: v 60 ILE cc_start: 0.7226 (pt) cc_final: 0.6979 (pt) REVERT: v 66 VAL cc_start: 0.8383 (t) cc_final: 0.7690 (p) REVERT: v 70 ARG cc_start: 0.7850 (mtt180) cc_final: 0.7472 (mpp80) REVERT: v 73 MET cc_start: 0.8142 (ppp) cc_final: 0.7844 (ppp) REVERT: v 75 ILE cc_start: 0.9698 (mt) cc_final: 0.9484 (mt) REVERT: v 77 GLU cc_start: 0.9015 (mt-10) cc_final: 0.8413 (mp0) REVERT: AB 55 ASP cc_start: 0.8980 (t70) cc_final: 0.8560 (t70) REVERT: AB 124 ASP cc_start: 0.8291 (t0) cc_final: 0.8048 (t0) REVERT: AB 125 ILE cc_start: 0.8941 (OUTLIER) cc_final: 0.8688 (pt) REVERT: U 155 ASN cc_start: 0.9093 (t0) cc_final: 0.8884 (t0) REVERT: U 156 ARG cc_start: 0.8966 (mmp-170) cc_final: 0.8547 (mmm160) REVERT: U 270 LEU cc_start: 0.9377 (mt) cc_final: 0.9152 (mt) REVERT: U 295 HIS cc_start: 0.6358 (m-70) cc_final: 0.6067 (m-70) REVERT: j 8 PHE cc_start: 0.8321 (m-80) cc_final: 0.7738 (m-80) REVERT: j 12 ASP cc_start: 0.8317 (t0) cc_final: 0.8014 (t0) REVERT: j 27 GLU cc_start: 0.9357 (tm-30) cc_final: 0.9062 (tm-30) REVERT: j 34 GLU cc_start: 0.8905 (tt0) cc_final: 0.8513 (tp30) REVERT: j 78 MET cc_start: 0.7715 (mtm) cc_final: 0.7183 (ptt) REVERT: j 111 PHE cc_start: 0.9028 (p90) cc_final: 0.8725 (p90) REVERT: j 118 GLU cc_start: 0.8844 (OUTLIER) cc_final: 0.8282 (pm20) REVERT: w 77 GLU cc_start: 0.8631 (tp30) cc_final: 0.7783 (tp30) REVERT: w 80 ARG cc_start: 0.8294 (mmp80) cc_final: 0.8049 (ttm110) outliers start: 5 outliers final: 1 residues processed: 424 average time/residue: 0.1962 time to fit residues: 123.9445 Evaluate side-chains 310 residues out of total 2685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 307 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 264 optimal weight: 0.7980 chunk 263 optimal weight: 8.9990 chunk 59 optimal weight: 2.9990 chunk 155 optimal weight: 5.9990 chunk 65 optimal weight: 6.9990 chunk 28 optimal weight: 7.9990 chunk 89 optimal weight: 0.0870 chunk 118 optimal weight: 1.9990 chunk 258 optimal weight: 7.9990 chunk 58 optimal weight: 2.9990 chunk 187 optimal weight: 0.9980 overall best weight: 1.3762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 83 GLN ** 0 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 305 GLN T 71 ASN T 295 HIS a 46 GLN ** a 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 141 GLN U 90 HIS b 51 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.083865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.061667 restraints weight = 164172.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 72)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.063084 restraints weight = 101517.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.064017 restraints weight = 73270.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.064624 restraints weight = 58983.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.064994 restraints weight = 51243.167| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.7374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 24588 Z= 0.146 Angle : 0.630 9.294 33234 Z= 0.327 Chirality : 0.043 0.195 3978 Planarity : 0.004 0.059 4308 Dihedral : 4.539 20.949 3336 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.56 % Allowed : 3.86 % Favored : 95.58 % Rotamer: Outliers : 0.04 % Allowed : 2.72 % Favored : 97.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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 aren not related in a simple way. whole: 0.68 (0.15), residues: 3030 helix: 1.14 (0.13), residues: 1629 sheet: 0.76 (0.30), residues: 309 loop : -0.60 (0.19), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG Z 314 TYR 0.019 0.002 TYR T 165 PHE 0.028 0.002 PHE h 124 TRP 0.012 0.002 TRP T 246 HIS 0.003 0.001 HIS T 148 Details of bonding type rmsd covalent geometry : bond 0.00311 (24588) covalent geometry : angle 0.62975 (33234) hydrogen bonds : bond 0.03986 ( 1388) hydrogen bonds : angle 5.07039 ( 4089) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 2685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 421 time to evaluate : 0.924 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 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: 0 106 ILE cc_start: 0.8653 (pt) cc_final: 0.8032 (mm) REVERT: C 532 MET cc_start: 0.4088 (mmt) cc_final: 0.0942 (ptt) REVERT: S 54 LEU cc_start: 0.9396 (tp) cc_final: 0.9025 (tp) REVERT: S 165 TYR cc_start: 0.9437 (t80) cc_final: 0.8816 (t80) REVERT: Z 132 THR cc_start: 0.9401 (m) cc_final: 0.9037 (p) REVERT: h 19 ARG cc_start: 0.8752 (tpp80) cc_final: 0.8287 (mmm-85) REVERT: h 57 ASP cc_start: 0.7385 (t70) cc_final: 0.6425 (t70) REVERT: h 78 MET cc_start: 0.6538 (mtt) cc_final: 0.6089 (mtt) REVERT: u 67 GLU cc_start: 0.8244 (pp20) cc_final: 0.7981 (pp20) REVERT: AA 76 LYS cc_start: 0.9050 (tttt) cc_final: 0.8806 (tttp) REVERT: T 278 LEU cc_start: 0.9173 (mt) cc_final: 0.8967 (mt) REVERT: a 206 MET cc_start: 0.7857 (tpt) cc_final: 0.7569 (tpt) REVERT: i 8 PHE cc_start: 0.7624 (m-80) cc_final: 0.7291 (m-80) REVERT: i 24 LEU cc_start: 0.9129 (mt) cc_final: 0.8876 (pp) REVERT: i 45 LYS cc_start: 0.7403 (mmtm) cc_final: 0.6916 (pttt) REVERT: i 63 MET cc_start: 0.7686 (ttp) cc_final: 0.6977 (pmm) REVERT: i 68 LEU cc_start: 0.8526 (tp) cc_final: 0.8174 (mt) REVERT: i 85 MET cc_start: 0.8469 (tpt) cc_final: 0.8119 (tpp) REVERT: i 86 VAL cc_start: 0.9115 (t) cc_final: 0.8901 (p) REVERT: i 111 PHE cc_start: 0.9030 (p90) cc_final: 0.8207 (p90) REVERT: i 120 LEU cc_start: 0.9820 (mt) cc_final: 0.9596 (pp) REVERT: i 129 MET cc_start: 0.8555 (tmm) cc_final: 0.8271 (tmm) REVERT: p 51 MET cc_start: 0.7024 (mmp) cc_final: 0.6657 (mmp) REVERT: p 116 ASP cc_start: 0.7747 (m-30) cc_final: 0.6905 (p0) REVERT: v 60 ILE cc_start: 0.7002 (pt) cc_final: 0.6795 (pt) REVERT: v 66 VAL cc_start: 0.8333 (t) cc_final: 0.7731 (p) REVERT: v 70 ARG cc_start: 0.7657 (mtt180) cc_final: 0.7288 (mpp80) REVERT: v 73 MET cc_start: 0.8272 (ppp) cc_final: 0.8040 (ppp) REVERT: v 77 GLU cc_start: 0.9000 (mt-10) cc_final: 0.8422 (mp0) REVERT: v 101 ILE cc_start: 0.7928 (mm) cc_final: 0.7576 (tp) REVERT: v 130 GLU cc_start: 0.9157 (mm-30) cc_final: 0.8952 (mm-30) REVERT: v 133 ARG cc_start: 0.9236 (tpm170) cc_final: 0.8608 (tpp-160) REVERT: AB 55 ASP cc_start: 0.8866 (t70) cc_final: 0.8662 (t70) REVERT: AB 124 ASP cc_start: 0.8071 (t0) cc_final: 0.7810 (t0) REVERT: AB 125 ILE cc_start: 0.8641 (mt) cc_final: 0.8325 (pt) REVERT: U 54 LEU cc_start: 0.9655 (tp) cc_final: 0.9381 (tp) REVERT: U 58 ASN cc_start: 0.8725 (m110) cc_final: 0.8438 (m-40) REVERT: U 156 ARG cc_start: 0.9006 (mmp-170) cc_final: 0.8772 (mmm160) REVERT: U 255 GLN cc_start: 0.9474 (OUTLIER) cc_final: 0.9176 (pm20) REVERT: j 8 PHE cc_start: 0.8257 (m-80) cc_final: 0.7639 (m-80) REVERT: j 12 ASP cc_start: 0.8506 (t0) cc_final: 0.7533 (t70) REVERT: j 27 GLU cc_start: 0.9308 (tm-30) cc_final: 0.9044 (tm-30) REVERT: j 34 GLU cc_start: 0.9022 (tt0) cc_final: 0.8470 (tp30) REVERT: j 37 GLU cc_start: 0.8307 (pp20) cc_final: 0.8101 (tp30) REVERT: j 56 SER cc_start: 0.9143 (t) cc_final: 0.8857 (t) REVERT: j 78 MET cc_start: 0.7725 (mtm) cc_final: 0.7077 (ptt) REVERT: j 85 MET cc_start: 0.8483 (tpt) cc_final: 0.7924 (tpt) REVERT: j 106 TRP cc_start: 0.6324 (t-100) cc_final: 0.6067 (t-100) REVERT: j 111 PHE cc_start: 0.9031 (p90) cc_final: 0.8703 (p90) REVERT: w 58 MET cc_start: 0.7868 (tpp) cc_final: 0.7552 (tpt) REVERT: w 77 GLU cc_start: 0.8293 (tp30) cc_final: 0.7579 (tp30) REVERT: w 132 MET cc_start: 0.9218 (tpt) cc_final: 0.8933 (ppp) outliers start: 1 outliers final: 0 residues processed: 422 average time/residue: 0.1922 time to fit residues: 122.6633 Evaluate side-chains 321 residues out of total 2685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 320 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 5 optimal weight: 3.9990 chunk 92 optimal weight: 9.9990 chunk 222 optimal weight: 5.9990 chunk 154 optimal weight: 2.9990 chunk 227 optimal weight: 0.5980 chunk 63 optimal weight: 2.9990 chunk 78 optimal weight: 8.9990 chunk 173 optimal weight: 3.9990 chunk 165 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 169 optimal weight: 4.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 300 GLN T 295 HIS ** a 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 52 GLN U 155 ASN ** b 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.082965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.060814 restraints weight = 165396.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.062226 restraints weight = 102717.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 68)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.063135 restraints weight = 74508.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.063730 restraints weight = 60085.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.064032 restraints weight = 52319.388| |-----------------------------------------------------------------------------| r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.7802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 24588 Z= 0.156 Angle : 0.646 9.238 33234 Z= 0.335 Chirality : 0.043 0.220 3978 Planarity : 0.004 0.062 4308 Dihedral : 4.475 21.216 3336 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 0.59 % Allowed : 3.83 % Favored : 95.58 % Rotamer: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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 aren not related in a simple way. whole: 0.75 (0.15), residues: 3030 helix: 1.24 (0.13), residues: 1623 sheet: 0.52 (0.28), residues: 345 loop : -0.59 (0.20), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG Z 314 TYR 0.017 0.002 TYR T 165 PHE 0.041 0.002 PHE j 124 TRP 0.016 0.002 TRP T 246 HIS 0.004 0.001 HIS b 155 Details of bonding type rmsd covalent geometry : bond 0.00333 (24588) covalent geometry : angle 0.64589 (33234) hydrogen bonds : bond 0.03931 ( 1388) hydrogen bonds : angle 5.03182 ( 4089) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 2685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 399 time to evaluate : 1.157 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 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 106 ILE cc_start: 0.8668 (pt) cc_final: 0.8278 (mm) REVERT: C 532 MET cc_start: 0.4513 (mmt) cc_final: 0.1385 (ptt) REVERT: S 54 LEU cc_start: 0.9374 (tp) cc_final: 0.8993 (tp) REVERT: S 165 TYR cc_start: 0.9419 (t80) cc_final: 0.8807 (t80) REVERT: Z 132 THR cc_start: 0.9419 (m) cc_final: 0.9086 (p) REVERT: Z 233 MET cc_start: 0.6214 (ptp) cc_final: 0.5944 (ptp) REVERT: h 19 ARG cc_start: 0.8766 (tpp80) cc_final: 0.8457 (mmm-85) REVERT: h 41 ASP cc_start: 0.8727 (t0) cc_final: 0.8481 (m-30) REVERT: h 57 ASP cc_start: 0.7424 (t70) cc_final: 0.6572 (t70) REVERT: h 78 MET cc_start: 0.6562 (mtt) cc_final: 0.6325 (mtp) REVERT: h 85 MET cc_start: 0.8642 (tpt) cc_final: 0.8320 (tpp) REVERT: u 57 ILE cc_start: 0.8958 (mm) cc_final: 0.8582 (tp) REVERT: u 67 GLU cc_start: 0.8282 (pp20) cc_final: 0.8008 (pp20) REVERT: u 130 GLU cc_start: 0.9168 (pm20) cc_final: 0.8953 (pm20) REVERT: T 278 LEU cc_start: 0.9170 (mt) cc_final: 0.8958 (mt) REVERT: i 8 PHE cc_start: 0.7423 (m-80) cc_final: 0.7139 (m-80) REVERT: i 11 VAL cc_start: 0.9211 (t) cc_final: 0.9004 (t) REVERT: i 45 LYS cc_start: 0.7364 (mmtm) cc_final: 0.6877 (pttt) REVERT: i 63 MET cc_start: 0.7397 (ttp) cc_final: 0.6808 (pmm) REVERT: i 68 LEU cc_start: 0.8117 (tp) cc_final: 0.7748 (mt) REVERT: i 85 MET cc_start: 0.8544 (tpt) cc_final: 0.8048 (tpt) REVERT: i 86 VAL cc_start: 0.9146 (t) cc_final: 0.8895 (p) REVERT: i 111 PHE cc_start: 0.9012 (p90) cc_final: 0.8325 (p90) REVERT: p 51 MET cc_start: 0.7275 (mmp) cc_final: 0.6888 (mmp) REVERT: p 70 ARG cc_start: 0.8510 (mtp85) cc_final: 0.8188 (mmm-85) REVERT: p 117 LYS cc_start: 0.8334 (tttm) cc_final: 0.8103 (tttp) REVERT: v 66 VAL cc_start: 0.8388 (t) cc_final: 0.8113 (t) REVERT: v 70 ARG cc_start: 0.7704 (mtt180) cc_final: 0.7184 (mpp80) REVERT: v 77 GLU cc_start: 0.9006 (mt-10) cc_final: 0.8374 (mp0) REVERT: v 101 ILE cc_start: 0.7791 (mm) cc_final: 0.7447 (tp) REVERT: v 130 GLU cc_start: 0.9074 (mm-30) cc_final: 0.8822 (mm-30) REVERT: AB 55 ASP cc_start: 0.8869 (t70) cc_final: 0.8666 (t70) REVERT: AB 125 ILE cc_start: 0.8718 (mt) cc_final: 0.8477 (pt) REVERT: U 54 LEU cc_start: 0.9695 (tp) cc_final: 0.9440 (tp) REVERT: U 58 ASN cc_start: 0.8788 (m110) cc_final: 0.8472 (m-40) REVERT: U 156 ARG cc_start: 0.8971 (mmp-170) cc_final: 0.8739 (mmm160) REVERT: j 8 PHE cc_start: 0.8266 (m-80) cc_final: 0.7842 (m-80) REVERT: j 12 ASP cc_start: 0.8523 (t0) cc_final: 0.8092 (t70) REVERT: j 34 GLU cc_start: 0.8987 (tt0) cc_final: 0.8521 (tp30) REVERT: j 56 SER cc_start: 0.9156 (t) cc_final: 0.8843 (t) REVERT: j 78 MET cc_start: 0.7657 (mtm) cc_final: 0.6934 (ptt) REVERT: j 85 MET cc_start: 0.8435 (tpt) cc_final: 0.7762 (tpt) REVERT: j 106 TRP cc_start: 0.6404 (t-100) cc_final: 0.6055 (t-100) REVERT: j 111 PHE cc_start: 0.9098 (p90) cc_final: 0.8888 (p90) REVERT: w 77 GLU cc_start: 0.8248 (tp30) cc_final: 0.7972 (mm-30) outliers start: 0 outliers final: 0 residues processed: 399 average time/residue: 0.1906 time to fit residues: 116.1218 Evaluate side-chains 305 residues out of total 2685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 305 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 45 optimal weight: 20.0000 chunk 251 optimal weight: 6.9990 chunk 42 optimal weight: 2.9990 chunk 135 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 129 optimal weight: 0.0170 chunk 4 optimal weight: 0.9990 chunk 69 optimal weight: 8.9990 chunk 170 optimal weight: 9.9990 chunk 200 optimal weight: 3.9990 chunk 287 optimal weight: 4.9990 overall best weight: 2.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 295 HIS ** a 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 129 ASN U 155 ASN b 51 GLN b 74 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.081190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.060025 restraints weight = 167701.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.062144 restraints weight = 103719.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.062323 restraints weight = 65671.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.062725 restraints weight = 55079.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.062814 restraints weight = 52181.420| |-----------------------------------------------------------------------------| r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.8522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 24588 Z= 0.198 Angle : 0.695 11.336 33234 Z= 0.358 Chirality : 0.044 0.356 3978 Planarity : 0.005 0.069 4308 Dihedral : 4.701 21.648 3336 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 17.44 Ramachandran Plot: Outliers : 0.66 % Allowed : 3.99 % Favored : 95.35 % Rotamer: Outliers : 0.04 % Allowed : 3.05 % Favored : 96.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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 aren not related in a simple way. whole: 0.49 (0.15), residues: 3030 helix: 1.04 (0.13), residues: 1623 sheet: 0.61 (0.30), residues: 321 loop : -0.77 (0.19), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG T 63 TYR 0.024 0.002 TYR v 104 PHE 0.024 0.002 PHE i 124 TRP 0.022 0.002 TRP T 246 HIS 0.005 0.001 HIS S 241 Details of bonding type rmsd covalent geometry : bond 0.00419 (24588) covalent geometry : angle 0.69528 (33234) hydrogen bonds : bond 0.04093 ( 1388) hydrogen bonds : angle 5.23014 ( 4089) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 373 time to evaluate : 1.031 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 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: 0 106 ILE cc_start: 0.8704 (pt) cc_final: 0.8296 (mm) REVERT: S 54 LEU cc_start: 0.9403 (tp) cc_final: 0.9044 (tp) REVERT: S 131 PHE cc_start: 0.8822 (m-10) cc_final: 0.8620 (m-10) REVERT: S 165 TYR cc_start: 0.9434 (t80) cc_final: 0.8811 (t80) REVERT: h 19 ARG cc_start: 0.8956 (tpp80) cc_final: 0.8528 (tpp80) REVERT: h 41 ASP cc_start: 0.8802 (t0) cc_final: 0.8481 (m-30) REVERT: h 57 ASP cc_start: 0.7398 (t70) cc_final: 0.6292 (t70) REVERT: h 78 MET cc_start: 0.6605 (mtt) cc_final: 0.6365 (mtp) REVERT: h 85 MET cc_start: 0.8686 (tpt) cc_final: 0.8392 (tmm) REVERT: u 57 ILE cc_start: 0.8882 (mm) cc_final: 0.8622 (tp) REVERT: u 58 MET cc_start: 0.5475 (tpt) cc_final: 0.5197 (tpt) REVERT: u 98 ASP cc_start: 0.8449 (m-30) cc_final: 0.8166 (m-30) REVERT: u 121 ARG cc_start: 0.8062 (ttp80) cc_final: 0.7827 (ttp80) REVERT: T 38 TYR cc_start: 0.8177 (t80) cc_final: 0.7927 (t80) REVERT: i 35 GLU cc_start: 0.7954 (mt-10) cc_final: 0.6777 (mt-10) REVERT: i 85 MET cc_start: 0.8449 (tpt) cc_final: 0.8015 (tpt) REVERT: i 86 VAL cc_start: 0.8978 (t) cc_final: 0.8743 (t) REVERT: i 93 GLU cc_start: 0.8614 (pm20) cc_final: 0.8390 (pm20) REVERT: i 111 PHE cc_start: 0.9121 (p90) cc_final: 0.8603 (p90) REVERT: i 125 GLU cc_start: 0.9186 (tm-30) cc_final: 0.8986 (tm-30) REVERT: i 129 MET cc_start: 0.8617 (ppp) cc_final: 0.8085 (tmm) REVERT: p 70 ARG cc_start: 0.8444 (mtp85) cc_final: 0.8106 (mmm-85) REVERT: p 72 ARG cc_start: 0.8573 (mpp-170) cc_final: 0.8335 (mpp-170) REVERT: p 117 LYS cc_start: 0.8480 (tttm) cc_final: 0.8239 (tttp) REVERT: v 66 VAL cc_start: 0.8365 (t) cc_final: 0.8087 (t) REVERT: v 70 ARG cc_start: 0.7842 (mtt180) cc_final: 0.7173 (mpp80) REVERT: v 77 GLU cc_start: 0.8890 (mt-10) cc_final: 0.8080 (mt-10) REVERT: v 99 ILE cc_start: 0.9156 (pt) cc_final: 0.8650 (mp) REVERT: v 101 ILE cc_start: 0.7747 (mm) cc_final: 0.7456 (tp) REVERT: v 133 ARG cc_start: 0.9086 (tpm170) cc_final: 0.8689 (tpp-160) REVERT: AB 55 ASP cc_start: 0.8925 (t70) cc_final: 0.8705 (t70) REVERT: AB 125 ILE cc_start: 0.9100 (mt) cc_final: 0.8801 (pt) REVERT: j 3 ASP cc_start: 0.9127 (p0) cc_final: 0.8898 (p0) REVERT: j 8 PHE cc_start: 0.8150 (m-80) cc_final: 0.7934 (m-80) REVERT: j 56 SER cc_start: 0.9106 (t) cc_final: 0.8645 (t) REVERT: j 78 MET cc_start: 0.7824 (mtm) cc_final: 0.7174 (ptt) REVERT: j 106 TRP cc_start: 0.6877 (t-100) cc_final: 0.6512 (t-100) REVERT: j 129 MET cc_start: 0.8296 (tpt) cc_final: 0.8000 (ppp) REVERT: w 77 GLU cc_start: 0.8224 (tp30) cc_final: 0.7604 (tp30) outliers start: 1 outliers final: 0 residues processed: 374 average time/residue: 0.1886 time to fit residues: 107.7949 Evaluate side-chains 284 residues out of total 2685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 284 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 280 optimal weight: 0.9980 chunk 273 optimal weight: 0.9980 chunk 278 optimal weight: 5.9990 chunk 46 optimal weight: 5.9990 chunk 148 optimal weight: 0.8980 chunk 154 optimal weight: 5.9990 chunk 172 optimal weight: 0.9990 chunk 99 optimal weight: 0.3980 chunk 116 optimal weight: 3.9990 chunk 233 optimal weight: 0.9990 chunk 41 optimal weight: 10.0000 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 295 HIS Z 28 HIS h 100 GLN T 295 HIS ** a 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 155 ASN ** b 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 108 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.083413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.061406 restraints weight = 164649.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.063360 restraints weight = 104709.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.063666 restraints weight = 69545.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.064232 restraints weight = 57312.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.064309 restraints weight = 51685.052| |-----------------------------------------------------------------------------| r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.8652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24588 Z= 0.122 Angle : 0.632 9.420 33234 Z= 0.326 Chirality : 0.043 0.271 3978 Planarity : 0.004 0.074 4308 Dihedral : 4.398 22.463 3336 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.66 % Allowed : 3.63 % Favored : 95.71 % Rotamer: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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 aren not related in a simple way. whole: 0.85 (0.15), residues: 3030 helix: 1.43 (0.13), residues: 1605 sheet: 0.54 (0.29), residues: 321 loop : -0.68 (0.19), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG p 133 TYR 0.023 0.001 TYR S 165 PHE 0.020 0.001 PHE j 53 TRP 0.040 0.002 TRP U 246 HIS 0.004 0.001 HIS U 295 Details of bonding type rmsd covalent geometry : bond 0.00258 (24588) covalent geometry : angle 0.63217 (33234) hydrogen bonds : bond 0.03700 ( 1388) hydrogen bonds : angle 4.87741 ( 4089) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 380 time to evaluate : 1.182 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 106 ILE cc_start: 0.8650 (pt) cc_final: 0.8372 (mm) REVERT: S 54 LEU cc_start: 0.9430 (tp) cc_final: 0.9087 (tp) REVERT: Z 233 MET cc_start: 0.6309 (ptp) cc_final: 0.6065 (ptp) REVERT: h 19 ARG cc_start: 0.8916 (tpp80) cc_final: 0.8468 (tpp80) REVERT: h 41 ASP cc_start: 0.8752 (t0) cc_final: 0.8500 (m-30) REVERT: h 57 ASP cc_start: 0.7395 (t70) cc_final: 0.6941 (t0) REVERT: h 78 MET cc_start: 0.6672 (mtt) cc_final: 0.6455 (mtp) REVERT: h 85 MET cc_start: 0.8698 (tpt) cc_final: 0.8358 (tpp) REVERT: o 132 MET cc_start: 0.9000 (mmm) cc_final: 0.8663 (mmt) REVERT: u 57 ILE cc_start: 0.8825 (mm) cc_final: 0.8617 (tp) REVERT: u 58 MET cc_start: 0.5656 (tpt) cc_final: 0.5239 (tpt) REVERT: u 67 GLU cc_start: 0.8224 (pp20) cc_final: 0.7899 (pp20) REVERT: u 76 LYS cc_start: 0.9227 (tppt) cc_final: 0.8783 (mmtt) REVERT: D 539 MET cc_start: 0.6498 (mmp) cc_final: 0.6060 (mpp) REVERT: a 59 PHE cc_start: 0.8201 (t80) cc_final: 0.7715 (t80) REVERT: i 60 MET cc_start: 0.4234 (tmm) cc_final: 0.3953 (ttp) REVERT: i 68 LEU cc_start: 0.8547 (tp) cc_final: 0.8336 (mt) REVERT: i 85 MET cc_start: 0.8747 (tpt) cc_final: 0.8316 (tpt) REVERT: i 86 VAL cc_start: 0.9047 (t) cc_final: 0.8787 (t) REVERT: i 111 PHE cc_start: 0.8930 (p90) cc_final: 0.8662 (p90) REVERT: i 129 MET cc_start: 0.8566 (ppp) cc_final: 0.8144 (tmm) REVERT: p 99 ILE cc_start: 0.9314 (tp) cc_final: 0.9102 (tp) REVERT: v 66 VAL cc_start: 0.8349 (t) cc_final: 0.8003 (p) REVERT: v 70 ARG cc_start: 0.7909 (mtt180) cc_final: 0.7250 (mpp80) REVERT: v 77 GLU cc_start: 0.9056 (mt-10) cc_final: 0.8609 (mp0) REVERT: v 99 ILE cc_start: 0.9203 (pt) cc_final: 0.8796 (mp) REVERT: v 101 ILE cc_start: 0.7294 (mm) cc_final: 0.6996 (tp) REVERT: AB 55 ASP cc_start: 0.8908 (t70) cc_final: 0.8624 (t70) REVERT: U 156 ARG cc_start: 0.8995 (mmp-170) cc_final: 0.8736 (mmm160) REVERT: U 278 LEU cc_start: 0.8379 (mt) cc_final: 0.8175 (mt) REVERT: j 26 LYS cc_start: 0.9219 (tptp) cc_final: 0.9008 (tttt) REVERT: j 34 GLU cc_start: 0.9088 (tt0) cc_final: 0.8794 (tp30) REVERT: j 44 ASN cc_start: 0.8427 (t0) cc_final: 0.8192 (m-40) REVERT: j 64 ASP cc_start: 0.8257 (p0) cc_final: 0.8041 (p0) REVERT: j 78 MET cc_start: 0.7664 (mtm) cc_final: 0.7279 (ptt) REVERT: j 129 MET cc_start: 0.8103 (tpt) cc_final: 0.7503 (tmm) REVERT: w 77 GLU cc_start: 0.8097 (tp30) cc_final: 0.7797 (mm-30) REVERT: w 80 ARG cc_start: 0.8890 (ttm110) cc_final: 0.8592 (ttm110) outliers start: 0 outliers final: 0 residues processed: 380 average time/residue: 0.1904 time to fit residues: 109.9444 Evaluate side-chains 293 residues out of total 2685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 293 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 41 optimal weight: 20.0000 chunk 0 optimal weight: 6.9990 chunk 63 optimal weight: 6.9990 chunk 133 optimal weight: 3.9990 chunk 258 optimal weight: 4.9990 chunk 78 optimal weight: 9.9990 chunk 134 optimal weight: 0.5980 chunk 25 optimal weight: 0.0970 chunk 274 optimal weight: 9.9990 chunk 233 optimal weight: 6.9990 chunk 277 optimal weight: 4.9990 overall best weight: 2.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 103 ASN Z 28 HIS h 100 GLN T 295 HIS U 155 ASN b 51 GLN b 74 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.080249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.058595 restraints weight = 169346.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.060167 restraints weight = 113127.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.060369 restraints weight = 77188.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.060792 restraints weight = 65628.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.060912 restraints weight = 58928.581| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.9279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 24588 Z= 0.232 Angle : 0.752 10.224 33234 Z= 0.390 Chirality : 0.045 0.296 3978 Planarity : 0.005 0.069 4308 Dihedral : 4.914 28.494 3336 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 19.52 Ramachandran Plot: Outliers : 0.59 % Allowed : 4.75 % Favored : 94.65 % Rotamer: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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 aren not related in a simple way. whole: 0.32 (0.15), residues: 3030 helix: 1.01 (0.13), residues: 1602 sheet: 0.21 (0.29), residues: 321 loop : -0.89 (0.19), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG Z 314 TYR 0.028 0.002 TYR v 104 PHE 0.043 0.002 PHE i 124 TRP 0.025 0.003 TRP U 246 HIS 0.006 0.001 HIS S 241 Details of bonding type rmsd covalent geometry : bond 0.00497 (24588) covalent geometry : angle 0.75154 (33234) hydrogen bonds : bond 0.04299 ( 1388) hydrogen bonds : angle 5.42647 ( 4089) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 342 time to evaluate : 1.130 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 106 ILE cc_start: 0.8432 (pt) cc_final: 0.7936 (mm) REVERT: S 54 LEU cc_start: 0.9518 (tp) cc_final: 0.9102 (tp) REVERT: S 231 LEU cc_start: 0.9537 (mt) cc_final: 0.9177 (mt) REVERT: h 19 ARG cc_start: 0.8889 (tpp80) cc_final: 0.8451 (tpp80) REVERT: h 78 MET cc_start: 0.6740 (mtt) cc_final: 0.6530 (mtp) REVERT: h 85 MET cc_start: 0.8820 (tpt) cc_final: 0.8357 (tmm) REVERT: o 99 ILE cc_start: 0.9388 (mm) cc_final: 0.9185 (mm) REVERT: u 57 ILE cc_start: 0.8769 (mm) cc_final: 0.8501 (tp) REVERT: u 58 MET cc_start: 0.6214 (tpt) cc_final: 0.5736 (tpt) REVERT: u 98 ASP cc_start: 0.8413 (m-30) cc_final: 0.8158 (m-30) REVERT: AA 59 ASP cc_start: 0.8483 (p0) cc_final: 0.8260 (p0) REVERT: a 321 MET cc_start: 0.0414 (ppp) cc_final: -0.1597 (ptt) REVERT: i 60 MET cc_start: 0.4131 (tmm) cc_final: 0.3612 (tpp) REVERT: i 85 MET cc_start: 0.8626 (tpt) cc_final: 0.8162 (tpt) REVERT: i 86 VAL cc_start: 0.8792 (t) cc_final: 0.8538 (t) REVERT: i 111 PHE cc_start: 0.8924 (p90) cc_final: 0.8527 (p90) REVERT: i 129 MET cc_start: 0.8300 (ppp) cc_final: 0.7873 (tmm) REVERT: p 51 MET cc_start: 0.6394 (mmp) cc_final: 0.6107 (mpp) REVERT: p 99 ILE cc_start: 0.9222 (tp) cc_final: 0.9014 (tp) REVERT: p 117 LYS cc_start: 0.8599 (tttm) cc_final: 0.8366 (tttp) REVERT: p 132 MET cc_start: 0.9459 (tpt) cc_final: 0.9256 (tpt) REVERT: p 133 ARG cc_start: 0.9458 (tmm160) cc_final: 0.9197 (tmm-80) REVERT: v 70 ARG cc_start: 0.7757 (mtt180) cc_final: 0.6987 (mpp80) REVERT: v 77 GLU cc_start: 0.9032 (mt-10) cc_final: 0.8691 (mp0) REVERT: v 133 ARG cc_start: 0.9581 (mmm160) cc_final: 0.9289 (mmm160) REVERT: AB 55 ASP cc_start: 0.8999 (t70) cc_final: 0.8661 (t70) REVERT: U 278 LEU cc_start: 0.8568 (mt) cc_final: 0.8275 (mt) REVERT: j 8 PHE cc_start: 0.8832 (m-80) cc_final: 0.8397 (m-80) REVERT: j 26 LYS cc_start: 0.9250 (tptp) cc_final: 0.9036 (tttt) REVERT: j 34 GLU cc_start: 0.9041 (tt0) cc_final: 0.8694 (tp30) REVERT: j 56 SER cc_start: 0.8842 (t) cc_final: 0.8456 (t) REVERT: j 78 MET cc_start: 0.7942 (mtm) cc_final: 0.7422 (ptp) REVERT: j 85 MET cc_start: 0.8462 (tpt) cc_final: 0.7545 (tpp) REVERT: j 106 TRP cc_start: 0.6267 (t-100) cc_final: 0.5912 (t-100) REVERT: w 77 GLU cc_start: 0.8214 (tp30) cc_final: 0.7523 (tp30) outliers start: 0 outliers final: 0 residues processed: 342 average time/residue: 0.1763 time to fit residues: 94.3412 Evaluate side-chains 275 residues out of total 2685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 275 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 187 optimal weight: 0.4980 chunk 226 optimal weight: 0.7980 chunk 154 optimal weight: 2.9990 chunk 165 optimal weight: 6.9990 chunk 203 optimal weight: 0.8980 chunk 78 optimal weight: 6.9990 chunk 289 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 chunk 212 optimal weight: 4.9990 chunk 90 optimal weight: 4.9990 chunk 174 optimal weight: 2.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 103 ASN h 100 GLN T 295 HIS U 155 ASN b 51 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.082014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.060651 restraints weight = 168442.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.062020 restraints weight = 112471.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.062142 restraints weight = 79051.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.062496 restraints weight = 65414.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.062678 restraints weight = 62501.476| |-----------------------------------------------------------------------------| r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.9331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 24588 Z= 0.138 Angle : 0.675 12.922 33234 Z= 0.345 Chirality : 0.044 0.268 3978 Planarity : 0.004 0.049 4308 Dihedral : 4.592 23.766 3336 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.63 % Allowed : 4.13 % Favored : 95.25 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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 aren not related in a simple way. whole: 0.62 (0.15), residues: 3030 helix: 1.30 (0.13), residues: 1603 sheet: 0.21 (0.28), residues: 329 loop : -0.80 (0.19), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG Z 314 TYR 0.018 0.002 TYR v 104 PHE 0.027 0.002 PHE a 274 TRP 0.019 0.002 TRP T 246 HIS 0.004 0.001 HIS Z 126 Details of bonding type rmsd covalent geometry : bond 0.00303 (24588) covalent geometry : angle 0.67454 (33234) hydrogen bonds : bond 0.03811 ( 1388) hydrogen bonds : angle 5.06539 ( 4089) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 369 time to evaluate : 1.119 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 106 ILE cc_start: 0.8594 (pt) cc_final: 0.8245 (mm) REVERT: 0 127 THR cc_start: 0.8539 (m) cc_final: 0.8255 (p) REVERT: S 54 LEU cc_start: 0.9515 (tp) cc_final: 0.9128 (tp) REVERT: S 231 LEU cc_start: 0.9476 (mt) cc_final: 0.9205 (mp) REVERT: h 12 ASP cc_start: 0.8014 (t0) cc_final: 0.7791 (t0) REVERT: h 19 ARG cc_start: 0.8938 (tpp80) cc_final: 0.8481 (tpp80) REVERT: h 38 ASP cc_start: 0.7130 (p0) cc_final: 0.6705 (p0) REVERT: h 85 MET cc_start: 0.8593 (tpt) cc_final: 0.8273 (tpp) REVERT: u 57 ILE cc_start: 0.8765 (mm) cc_final: 0.8561 (tp) REVERT: u 58 MET cc_start: 0.5945 (tpt) cc_final: 0.5532 (tpt) REVERT: u 67 GLU cc_start: 0.8073 (pp20) cc_final: 0.7798 (pp20) REVERT: u 76 LYS cc_start: 0.9065 (mptt) cc_final: 0.8856 (mptt) REVERT: AA 59 ASP cc_start: 0.8280 (p0) cc_final: 0.8078 (p0) REVERT: a 193 MET cc_start: 0.7444 (ttt) cc_final: 0.6983 (tmm) REVERT: a 206 MET cc_start: 0.8251 (tpt) cc_final: 0.7583 (tpt) REVERT: a 321 MET cc_start: -0.0008 (ppp) cc_final: -0.2065 (ptt) REVERT: i 85 MET cc_start: 0.8688 (tpt) cc_final: 0.8304 (tpt) REVERT: i 86 VAL cc_start: 0.8993 (t) cc_final: 0.8726 (t) REVERT: i 111 PHE cc_start: 0.8828 (p90) cc_final: 0.8563 (p90) REVERT: i 129 MET cc_start: 0.8064 (ppp) cc_final: 0.7725 (tmm) REVERT: v 67 GLU cc_start: 0.8124 (pp20) cc_final: 0.7615 (mp0) REVERT: v 70 ARG cc_start: 0.7571 (mtt180) cc_final: 0.7069 (mpp80) REVERT: v 80 ARG cc_start: 0.9288 (ttm110) cc_final: 0.8500 (ptp-110) REVERT: v 99 ILE cc_start: 0.9364 (pt) cc_final: 0.8737 (mp) REVERT: v 101 ILE cc_start: 0.8140 (mm) cc_final: 0.7337 (tp) REVERT: v 133 ARG cc_start: 0.9572 (mmm160) cc_final: 0.9322 (mmm160) REVERT: AB 55 ASP cc_start: 0.8992 (t70) cc_final: 0.8646 (t70) REVERT: U 156 ARG cc_start: 0.9022 (mmp-170) cc_final: 0.8742 (mmm160) REVERT: b 146 LEU cc_start: 0.9063 (mt) cc_final: 0.8797 (pp) REVERT: j 6 LEU cc_start: 0.8632 (tp) cc_final: 0.8264 (tt) REVERT: j 8 PHE cc_start: 0.8689 (m-80) cc_final: 0.8233 (m-80) REVERT: j 34 GLU cc_start: 0.9026 (tt0) cc_final: 0.8776 (tp30) REVERT: j 85 MET cc_start: 0.8424 (tpt) cc_final: 0.7463 (tpp) REVERT: j 106 TRP cc_start: 0.6418 (t-100) cc_final: 0.5837 (t-100) REVERT: j 129 MET cc_start: 0.8912 (tpt) cc_final: 0.8176 (tmm) REVERT: w 77 GLU cc_start: 0.8083 (tp30) cc_final: 0.7128 (tp30) REVERT: w 80 ARG cc_start: 0.8890 (ttm110) cc_final: 0.8342 (ttm170) outliers start: 0 outliers final: 0 residues processed: 369 average time/residue: 0.1773 time to fit residues: 102.0707 Evaluate side-chains 293 residues out of total 2685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 293 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 266 optimal weight: 5.9990 chunk 23 optimal weight: 0.9990 chunk 208 optimal weight: 2.9990 chunk 188 optimal weight: 0.6980 chunk 142 optimal weight: 20.0000 chunk 290 optimal weight: 0.9980 chunk 65 optimal weight: 10.0000 chunk 270 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 chunk 152 optimal weight: 9.9990 chunk 117 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: h 100 GLN T 295 HIS U 155 ASN b 51 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.081457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.060223 restraints weight = 167435.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.061717 restraints weight = 112294.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.062324 restraints weight = 72672.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.062328 restraints weight = 67268.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.062323 restraints weight = 59552.514| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.9568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 24588 Z= 0.159 Angle : 0.689 13.794 33234 Z= 0.353 Chirality : 0.044 0.268 3978 Planarity : 0.004 0.049 4308 Dihedral : 4.642 23.847 3336 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 15.46 Ramachandran Plot: Outliers : 0.63 % Allowed : 4.55 % Favored : 94.82 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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 aren not related in a simple way. whole: 0.57 (0.15), residues: 3030 helix: 1.26 (0.13), residues: 1604 sheet: 0.21 (0.29), residues: 319 loop : -0.82 (0.19), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG Z 314 TYR 0.017 0.002 TYR o 104 PHE 0.021 0.002 PHE a 26 TRP 0.021 0.002 TRP T 246 HIS 0.004 0.001 HIS S 241 Details of bonding type rmsd covalent geometry : bond 0.00347 (24588) covalent geometry : angle 0.68885 (33234) hydrogen bonds : bond 0.03815 ( 1388) hydrogen bonds : angle 5.09188 ( 4089) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 357 time to evaluate : 1.072 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 106 ILE cc_start: 0.8448 (pt) cc_final: 0.8075 (mm) REVERT: 0 127 THR cc_start: 0.8465 (m) cc_final: 0.8167 (p) REVERT: S 54 LEU cc_start: 0.9485 (tp) cc_final: 0.9061 (tp) REVERT: S 231 LEU cc_start: 0.9495 (mt) cc_final: 0.9244 (mp) REVERT: h 19 ARG cc_start: 0.8933 (tpp80) cc_final: 0.8504 (tpp80) REVERT: h 41 ASP cc_start: 0.8655 (t0) cc_final: 0.8449 (p0) REVERT: h 61 PRO cc_start: 0.4803 (Cg_endo) cc_final: 0.4032 (Cg_exo) REVERT: h 63 MET cc_start: 0.6111 (pmm) cc_final: 0.5899 (pmm) REVERT: h 78 MET cc_start: 0.6575 (mtt) cc_final: 0.6349 (mtp) REVERT: h 85 MET cc_start: 0.8908 (tpt) cc_final: 0.8391 (tpp) REVERT: u 58 MET cc_start: 0.6024 (tpt) cc_final: 0.5602 (tpt) REVERT: u 67 GLU cc_start: 0.8157 (pp20) cc_final: 0.7879 (pp20) REVERT: a 206 MET cc_start: 0.8292 (tpt) cc_final: 0.7602 (tpt) REVERT: a 321 MET cc_start: 0.0176 (ppp) cc_final: -0.2030 (ptt) REVERT: i 63 MET cc_start: 0.7271 (tmm) cc_final: 0.7011 (tmm) REVERT: i 86 VAL cc_start: 0.8810 (t) cc_final: 0.8591 (t) REVERT: i 93 GLU cc_start: 0.8592 (pm20) cc_final: 0.8382 (pm20) REVERT: i 129 MET cc_start: 0.7880 (ppp) cc_final: 0.7316 (tmm) REVERT: v 70 ARG cc_start: 0.7553 (mtt180) cc_final: 0.7036 (mpp80) REVERT: AB 55 ASP cc_start: 0.8955 (t70) cc_final: 0.8593 (t70) REVERT: U 156 ARG cc_start: 0.9010 (mmp-170) cc_final: 0.8529 (mmm160) REVERT: U 278 LEU cc_start: 0.8447 (mt) cc_final: 0.8148 (mt) REVERT: b 146 LEU cc_start: 0.9096 (mt) cc_final: 0.8806 (pp) REVERT: j 8 PHE cc_start: 0.8773 (m-80) cc_final: 0.8334 (m-80) REVERT: j 34 GLU cc_start: 0.9086 (tt0) cc_final: 0.8785 (tp30) REVERT: j 85 MET cc_start: 0.8314 (tpt) cc_final: 0.7187 (tpp) REVERT: j 106 TRP cc_start: 0.6553 (t-100) cc_final: 0.6084 (t-100) REVERT: j 129 MET cc_start: 0.8977 (tpt) cc_final: 0.8677 (tpt) REVERT: w 77 GLU cc_start: 0.8086 (tp30) cc_final: 0.7387 (tp30) outliers start: 0 outliers final: 0 residues processed: 357 average time/residue: 0.1740 time to fit residues: 96.4571 Evaluate side-chains 280 residues out of total 2685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 280 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 109 optimal weight: 8.9990 chunk 204 optimal weight: 1.9990 chunk 226 optimal weight: 0.9980 chunk 18 optimal weight: 3.9990 chunk 12 optimal weight: 0.5980 chunk 36 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 148 optimal weight: 0.3980 chunk 129 optimal weight: 0.0570 chunk 101 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 52 GLN T 295 HIS U 155 ASN b 51 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.083271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.061919 restraints weight = 165846.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.064190 restraints weight = 107163.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.064273 restraints weight = 70536.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.064593 restraints weight = 55751.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.064680 restraints weight = 54979.834| |-----------------------------------------------------------------------------| r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.9627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 24588 Z= 0.122 Angle : 0.656 9.549 33234 Z= 0.337 Chirality : 0.044 0.246 3978 Planarity : 0.004 0.047 4308 Dihedral : 4.410 24.976 3336 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.59 % Allowed : 3.99 % Favored : 95.41 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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 aren not related in a simple way. whole: 0.81 (0.16), residues: 3030 helix: 1.47 (0.13), residues: 1604 sheet: 0.19 (0.29), residues: 319 loop : -0.70 (0.19), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG 0 131 TYR 0.018 0.001 TYR q 118 PHE 0.043 0.002 PHE i 124 TRP 0.014 0.001 TRP T 246 HIS 0.004 0.001 HIS U 295 Details of bonding type rmsd covalent geometry : bond 0.00259 (24588) covalent geometry : angle 0.65630 (33234) hydrogen bonds : bond 0.03519 ( 1388) hydrogen bonds : angle 4.86662 ( 4089) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5604.90 seconds wall clock time: 97 minutes 12.33 seconds (5832.33 seconds total)