Starting phenix.real_space_refine on Thu Feb 22 11:08:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z19_14445/02_2024/7z19_14445.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z19_14445/02_2024/7z19_14445.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z19_14445/02_2024/7z19_14445.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z19_14445/02_2024/7z19_14445.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z19_14445/02_2024/7z19_14445.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z19_14445/02_2024/7z19_14445.pdb" } resolution = 2.57 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.047 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 4 6.06 5 P 2 5.49 5 S 81 5.16 5 C 10607 2.51 5 N 2989 2.21 5 O 3705 1.98 5 H 16717 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 34105 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 2178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 2178 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 2, 'TRANS': 139} Chain: "B" Number of atoms: 2950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 2950 Classifications: {'peptide': 192} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 177} Chain breaks: 1 Chain: "C" Number of atoms: 5408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 5408 Classifications: {'peptide': 353} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 332} Chain: "D" Number of atoms: 4331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 4331 Classifications: {'peptide': 276} Link IDs: {'PTRANS': 20, 'TRANS': 255} Chain: "E" Number of atoms: 2194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2194 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Chain: "F" Number of atoms: 2955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 2955 Classifications: {'peptide': 192} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 177} Chain: "G" Number of atoms: 5408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 5408 Classifications: {'peptide': 353} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 332} Chain: "H" Number of atoms: 4317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 4317 Classifications: {'peptide': 275} Link IDs: {'PTRANS': 20, 'TRANS': 254} Chain: "I" Number of atoms: 3873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 3873 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 11, 'TRANS': 236} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 6 Unusual residues: {' ZN': 1, 'PO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 6 Unusual residues: {' ZN': 1, 'PO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 35 Classifications: {'water': 35} Link IDs: {None: 34} Chain: "B" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "C" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 110 Classifications: {'water': 110} Link IDs: {None: 109} Chain: "D" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 71 Classifications: {'water': 71} Link IDs: {None: 70} Chain: "E" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "F" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} Chain: "G" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 114 Classifications: {'water': 114} Link IDs: {None: 113} Chain: "H" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 68 Classifications: {'water': 68} Link IDs: {None: 67} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14330 SG CYS D 241 89.302 39.075 41.502 1.00 80.25 S ATOM 14369 SG CYS D 244 88.990 38.847 38.062 1.00 82.43 S ATOM 14689 SG CYS D 266 86.972 41.042 39.840 1.00 79.72 S ATOM 14769 SG CYS D 272 86.753 36.919 40.189 1.00 81.84 S ATOM 29204 SG CYS H 241 27.503 65.764 101.278 1.00 79.62 S ATOM 29243 SG CYS H 244 28.037 66.742 104.649 1.00 83.62 S ATOM 29563 SG CYS H 266 30.491 66.907 102.398 1.00 79.59 S ATOM 29643 SG CYS H 272 28.987 63.217 103.464 1.00 81.82 S Residues with excluded nonbonded symmetry interactions: 115 residue: pdb="ZN ZN C 401 " occ=0.51 residue: pdb="ZN ZN G 401 " occ=0.54 residue: pdb=" O HOH A 202 " occ=0.95 residue: pdb=" O HOH A 205 " occ=0.92 residue: pdb=" O HOH A 212 " occ=0.86 residue: pdb=" O HOH A 215 " occ=0.96 residue: pdb=" O HOH A 216 " occ=0.99 residue: pdb=" O HOH A 217 " occ=0.99 residue: pdb=" O HOH A 218 " occ=0.88 residue: pdb=" O HOH A 222 " occ=0.75 residue: pdb=" O HOH A 227 " occ=0.86 residue: pdb=" O HOH A 233 " occ=0.89 ... (remaining 103 not shown) Time building chain proxies: 14.36, per 1000 atoms: 0.42 Number of scatterers: 34105 At special positions: 0 Unit cell: (109.56, 126.16, 138.61, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 S 81 16.00 P 2 15.00 O 3705 8.00 N 2989 7.00 C 10607 6.00 H 16717 1.00 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 28.75 Conformation dependent library (CDL) restraints added in 3.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" NE2 HIS C 328 " pdb="ZN ZN C 401 " - pdb=" NE2 HIS C 333 " pdb=" ZN D 301 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 266 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 272 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 241 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 244 " pdb=" ZN G 401 " pdb="ZN ZN G 401 " - pdb=" NE2 HIS G 328 " pdb="ZN ZN G 401 " - pdb=" NE2 HIS G 333 " pdb=" ZN H 301 " pdb="ZN ZN H 301 " - pdb=" SG CYS H 244 " pdb="ZN ZN H 301 " - pdb=" SG CYS H 272 " pdb="ZN ZN H 301 " - pdb=" SG CYS H 266 " pdb="ZN ZN H 301 " - pdb=" SG CYS H 241 " Number of angles added : 12 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4042 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 19 sheets defined 45.7% alpha, 16.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.12 Creating SS restraints... Processing helix chain 'A' and resid 4 through 18 Processing helix chain 'A' and resid 19 through 31 Processing helix chain 'A' and resid 54 through 56 No H-bonds generated for 'chain 'A' and resid 54 through 56' Processing helix chain 'A' and resid 88 through 103 removed outlier: 3.653A pdb=" N GLN A 103 " --> pdb=" O ASP A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 115 removed outlier: 4.288A pdb=" N GLN A 109 " --> pdb=" O SER A 105 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N ASN A 110 " --> pdb=" O ARG A 106 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU A 113 " --> pdb=" O GLN A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 136 removed outlier: 3.763A pdb=" N ALA A 136 " --> pdb=" O ALA A 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 27 Processing helix chain 'B' and resid 46 through 56 Processing helix chain 'B' and resid 66 through 69 Processing helix chain 'B' and resid 70 through 80 Processing helix chain 'B' and resid 88 through 92 Processing helix chain 'B' and resid 102 through 109 removed outlier: 3.556A pdb=" N LEU B 109 " --> pdb=" O GLN B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 120 Processing helix chain 'B' and resid 154 through 164 Processing helix chain 'C' and resid 7 through 25 Processing helix chain 'C' and resid 33 through 41 Processing helix chain 'C' and resid 41 through 53 Processing helix chain 'C' and resid 56 through 67 Processing helix chain 'C' and resid 70 through 85 removed outlier: 3.579A pdb=" N THR C 83 " --> pdb=" O ARG C 79 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N THR C 84 " --> pdb=" O ALA C 80 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU C 85 " --> pdb=" O TYR C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 99 Processing helix chain 'C' and resid 130 through 135 Processing helix chain 'C' and resid 154 through 162 Processing helix chain 'C' and resid 188 through 198 Processing helix chain 'C' and resid 200 through 213 Processing helix chain 'C' and resid 280 through 295 removed outlier: 4.245A pdb=" N ALA C 284 " --> pdb=" O SER C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 300 removed outlier: 3.650A pdb=" N TYR C 299 " --> pdb=" O GLN C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 308 Processing helix chain 'C' and resid 309 through 316 removed outlier: 3.617A pdb=" N HIS C 316 " --> pdb=" O PHE C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 328 Processing helix chain 'C' and resid 329 through 331 No H-bonds generated for 'chain 'C' and resid 329 through 331' Processing helix chain 'C' and resid 333 through 352 Processing helix chain 'D' and resid 13 through 30 Processing helix chain 'D' and resid 49 through 60 Processing helix chain 'D' and resid 76 through 91 Processing helix chain 'D' and resid 137 through 147 removed outlier: 4.080A pdb=" N THR D 143 " --> pdb=" O THR D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 165 removed outlier: 3.758A pdb=" N GLN D 154 " --> pdb=" O TYR D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 197 Processing helix chain 'D' and resid 268 through 277 Processing helix chain 'E' and resid 4 through 18 Processing helix chain 'E' and resid 19 through 31 Processing helix chain 'E' and resid 54 through 56 No H-bonds generated for 'chain 'E' and resid 54 through 56' Processing helix chain 'E' and resid 88 through 103 removed outlier: 3.556A pdb=" N ALA E 92 " --> pdb=" O ASP E 88 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLN E 103 " --> pdb=" O ASP E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 115 removed outlier: 4.541A pdb=" N GLN E 109 " --> pdb=" O SER E 105 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N ASN E 110 " --> pdb=" O ARG E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 115 through 136 removed outlier: 3.713A pdb=" N ALA E 136 " --> pdb=" O ALA E 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 27 Processing helix chain 'F' and resid 45 through 56 Processing helix chain 'F' and resid 66 through 69 Processing helix chain 'F' and resid 70 through 80 Processing helix chain 'F' and resid 88 through 92 Processing helix chain 'F' and resid 102 through 109 Processing helix chain 'F' and resid 116 through 120 removed outlier: 3.814A pdb=" N GLY F 120 " --> pdb=" O PRO F 117 " (cutoff:3.500A) Processing helix chain 'F' and resid 154 through 164 Processing helix chain 'G' and resid 8 through 25 Processing helix chain 'G' and resid 33 through 41 Processing helix chain 'G' and resid 41 through 53 Processing helix chain 'G' and resid 56 through 67 Processing helix chain 'G' and resid 70 through 85 removed outlier: 3.605A pdb=" N THR G 83 " --> pdb=" O ARG G 79 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N THR G 84 " --> pdb=" O ALA G 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 99 Processing helix chain 'G' and resid 130 through 135 removed outlier: 3.590A pdb=" N ALA G 135 " --> pdb=" O THR G 132 " (cutoff:3.500A) Processing helix chain 'G' and resid 154 through 162 Processing helix chain 'G' and resid 188 through 199 Processing helix chain 'G' and resid 200 through 213 Processing helix chain 'G' and resid 280 through 295 removed outlier: 3.896A pdb=" N ALA G 284 " --> pdb=" O SER G 280 " (cutoff:3.500A) Processing helix chain 'G' and resid 295 through 300 Processing helix chain 'G' and resid 305 through 308 Processing helix chain 'G' and resid 309 through 316 removed outlier: 3.662A pdb=" N HIS G 316 " --> pdb=" O PHE G 312 " (cutoff:3.500A) Processing helix chain 'G' and resid 318 through 328 Processing helix chain 'G' and resid 329 through 331 No H-bonds generated for 'chain 'G' and resid 329 through 331' Processing helix chain 'G' and resid 333 through 351 removed outlier: 3.520A pdb=" N GLN G 351 " --> pdb=" O LEU G 347 " (cutoff:3.500A) Processing helix chain 'H' and resid 8 through 12 removed outlier: 4.047A pdb=" N LEU H 12 " --> pdb=" O PHE H 9 " (cutoff:3.500A) Processing helix chain 'H' and resid 13 through 30 Processing helix chain 'H' and resid 49 through 60 Processing helix chain 'H' and resid 76 through 91 Processing helix chain 'H' and resid 97 through 101 Processing helix chain 'H' and resid 137 through 148 removed outlier: 3.947A pdb=" N THR H 143 " --> pdb=" O THR H 139 " (cutoff:3.500A) Processing helix chain 'H' and resid 150 through 165 removed outlier: 3.571A pdb=" N GLN H 154 " --> pdb=" O TYR H 150 " (cutoff:3.500A) Processing helix chain 'H' and resid 189 through 197 Proline residue: H 194 - end of helix Processing helix chain 'H' and resid 268 through 278 Processing helix chain 'I' and resid 40 through 42 No H-bonds generated for 'chain 'I' and resid 40 through 42' Processing helix chain 'I' and resid 43 through 52 Processing helix chain 'I' and resid 73 through 84 removed outlier: 3.572A pdb=" N ARG I 82 " --> pdb=" O ARG I 78 " (cutoff:3.500A) Processing helix chain 'I' and resid 91 through 96 removed outlier: 3.822A pdb=" N GLY I 95 " --> pdb=" O HIS I 91 " (cutoff:3.500A) Processing helix chain 'I' and resid 101 through 114 removed outlier: 4.811A pdb=" N ARG I 109 " --> pdb=" O ASN I 105 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N LEU I 110 " --> pdb=" O ILE I 106 " (cutoff:3.500A) Processing helix chain 'I' and resid 117 through 132 Processing helix chain 'I' and resid 135 through 139 removed outlier: 3.732A pdb=" N ARG I 138 " --> pdb=" O PRO I 135 " (cutoff:3.500A) Processing helix chain 'I' and resid 142 through 146 Processing helix chain 'I' and resid 147 through 161 Processing helix chain 'I' and resid 177 through 195 Processing helix chain 'I' and resid 205 through 213 removed outlier: 3.923A pdb=" N ALA I 209 " --> pdb=" O ASP I 205 " (cutoff:3.500A) Processing helix chain 'I' and resid 239 through 250 Processing sheet with id=AA1, first strand: chain 'A' and resid 79 through 85 removed outlier: 5.320A pdb=" N ILE A 49 " --> pdb=" O ALA A 62 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ASP A 64 " --> pdb=" O VAL A 47 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N VAL A 47 " --> pdb=" O ASP A 64 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N THR A 66 " --> pdb=" O GLY A 45 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N GLY A 45 " --> pdb=" O THR A 66 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N THR A 68 " --> pdb=" O GLU A 43 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N GLU A 43 " --> pdb=" O THR A 68 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N ALA A 70 " --> pdb=" O ALA A 41 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N ALA A 41 " --> pdb=" O ALA A 70 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N VAL A 72 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N ILE A 39 " --> pdb=" O VAL A 72 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N LEU A 74 " --> pdb=" O GLU A 37 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N GLU A 37 " --> pdb=" O LEU A 74 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N LEU C 88 " --> pdb=" O THR A 44 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N LEU A 46 " --> pdb=" O LEU C 88 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N VAL C 90 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N GLN A 48 " --> pdb=" O VAL C 90 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 116 through 117 removed outlier: 4.399A pdb=" N GLN C 116 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N VAL A 139 " --> pdb=" O GLY G 7 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N GLY G 7 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N PHE A 141 " --> pdb=" O VAL G 5 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL G 3 " --> pdb=" O THR A 143 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 32 through 33 removed outlier: 6.843A pdb=" N LEU B 123 " --> pdb=" O ILE B 175 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N THR B 177 " --> pdb=" O LEU B 123 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N LEU B 125 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ALA B 95 " --> pdb=" O ILE B 124 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N GLN B 126 " --> pdb=" O ALA B 95 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N THR B 97 " --> pdb=" O GLN B 126 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N TRP B 63 " --> pdb=" O VAL B 96 " (cutoff:3.500A) removed outlier: 8.443A pdb=" N ASP B 98 " --> pdb=" O TRP B 63 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 147 through 149 Processing sheet with id=AA5, first strand: chain 'C' and resid 2 through 4 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.444A pdb=" N SER C 227 " --> pdb=" O GLU C 102 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ARG C 104 " --> pdb=" O ILE C 225 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ILE C 225 " --> pdb=" O ARG C 104 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N ALA C 222 " --> pdb=" O VAL C 256 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N VAL C 256 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY C 246 " --> pdb=" O VAL C 232 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ILE C 234 " --> pdb=" O ASN C 244 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N ASN C 244 " --> pdb=" O ILE C 234 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N THR C 270 " --> pdb=" O ASN C 257 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N PHE C 259 " --> pdb=" O HIS C 268 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N HIS C 268 " --> pdb=" O PHE C 259 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 35 through 36 removed outlier: 6.457A pdb=" N ILE D 104 " --> pdb=" O ILE D 122 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N GLN D 124 " --> pdb=" O ILE D 104 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N THR D 106 " --> pdb=" O GLN D 124 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N VAL D 65 " --> pdb=" O VAL D 103 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N GLN D 105 " --> pdb=" O VAL D 65 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N LYS D 67 " --> pdb=" O GLN D 105 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N ARG D 107 " --> pdb=" O LYS D 67 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ILE D 69 " --> pdb=" O ARG D 107 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 181 through 183 removed outlier: 3.556A pdb=" N TYR D 181 " --> pdb=" O VAL D 177 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 251 through 255 Processing sheet with id=AB1, first strand: chain 'E' and resid 79 through 84 removed outlier: 5.311A pdb=" N PHE E 61 " --> pdb=" O ALA E 51 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ALA E 51 " --> pdb=" O PHE E 61 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N GLY E 63 " --> pdb=" O ILE E 49 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N ALA E 71 " --> pdb=" O ALA E 41 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N ALA E 41 " --> pdb=" O ALA E 71 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N ARG E 73 " --> pdb=" O ILE E 39 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ILE E 39 " --> pdb=" O ARG E 73 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N LEU G 88 " --> pdb=" O THR E 44 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N LEU E 46 " --> pdb=" O LEU G 88 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N VAL G 90 " --> pdb=" O LEU E 46 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N GLN E 48 " --> pdb=" O VAL G 90 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 138 through 139 removed outlier: 4.328A pdb=" N GLN G 116 " --> pdb=" O VAL E 139 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 32 through 33 removed outlier: 6.696A pdb=" N LEU F 123 " --> pdb=" O ILE F 175 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N THR F 177 " --> pdb=" O LEU F 123 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N LEU F 125 " --> pdb=" O THR F 177 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ALA F 95 " --> pdb=" O ILE F 124 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N GLN F 126 " --> pdb=" O ALA F 95 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N THR F 97 " --> pdb=" O GLN F 126 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N TRP F 63 " --> pdb=" O VAL F 96 " (cutoff:3.500A) removed outlier: 8.412A pdb=" N ASP F 98 " --> pdb=" O TRP F 63 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 147 through 149 Processing sheet with id=AB5, first strand: chain 'G' and resid 100 through 105 removed outlier: 6.465A pdb=" N SER G 227 " --> pdb=" O GLU G 102 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ARG G 104 " --> pdb=" O ILE G 225 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ILE G 225 " --> pdb=" O ARG G 104 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N ALA G 222 " --> pdb=" O VAL G 256 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N VAL G 256 " --> pdb=" O ALA G 222 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLY G 246 " --> pdb=" O VAL G 232 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ILE G 234 " --> pdb=" O ASN G 244 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N ASN G 244 " --> pdb=" O ILE G 234 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR G 270 " --> pdb=" O ASN G 257 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N PHE G 259 " --> pdb=" O HIS G 268 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N HIS G 268 " --> pdb=" O PHE G 259 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 35 through 36 removed outlier: 6.462A pdb=" N ILE H 104 " --> pdb=" O ILE H 122 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N GLN H 124 " --> pdb=" O ILE H 104 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N THR H 106 " --> pdb=" O GLN H 124 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 181 through 183 Processing sheet with id=AB8, first strand: chain 'H' and resid 251 through 255 Processing sheet with id=AB9, first strand: chain 'I' and resid 21 through 26 removed outlier: 5.615A pdb=" N LEU I 11 " --> pdb=" O ASP I 23 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N SER I 25 " --> pdb=" O ASN I 9 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ASN I 9 " --> pdb=" O SER I 25 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N VAL I 8 " --> pdb=" O HIS I 63 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N HIS I 63 " --> pdb=" O VAL I 8 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N ASN I 10 " --> pdb=" O GLU I 61 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N GLU I 61 " --> pdb=" O ASN I 10 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 85 through 88 removed outlier: 6.249A pdb=" N GLY I 86 " --> pdb=" O PHE I 168 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N ASP I 170 " --> pdb=" O GLY I 86 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N VAL I 88 " --> pdb=" O ASP I 170 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N VAL I 167 " --> pdb=" O VAL I 200 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N VAL I 202 " --> pdb=" O VAL I 167 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N MET I 169 " --> pdb=" O VAL I 202 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLY I 38 " --> pdb=" O THR I 203 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N LEU I 216 " --> pdb=" O SER I 227 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N SER I 227 " --> pdb=" O LEU I 216 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL I 218 " --> pdb=" O VAL I 225 " (cutoff:3.500A) 782 hydrogen bonds defined for protein. 2181 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: 14.64 Time building geometry restraints manager: 29.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 16705 1.03 - 1.23: 83 1.23 - 1.42: 7024 1.42 - 1.62: 10003 1.62 - 1.81: 142 Bond restraints: 33957 Sorted by residual: bond pdb=" C ARG H 107 " pdb=" O ARG H 107 " ideal model delta sigma weight residual 1.234 1.141 0.093 1.17e-02 7.31e+03 6.38e+01 bond pdb=" C HIS G 333 " pdb=" O HIS G 333 " ideal model delta sigma weight residual 1.236 1.173 0.063 1.26e-02 6.30e+03 2.52e+01 bond pdb=" C GLU B 192 " pdb=" O GLU B 192 " ideal model delta sigma weight residual 1.235 1.188 0.047 1.18e-02 7.18e+03 1.58e+01 bond pdb=" C HIS C 333 " pdb=" O HIS C 333 " ideal model delta sigma weight residual 1.235 1.192 0.043 1.12e-02 7.97e+03 1.49e+01 bond pdb=" C ARG D 107 " pdb=" O ARG D 107 " ideal model delta sigma weight residual 1.236 1.194 0.042 1.14e-02 7.69e+03 1.38e+01 ... (remaining 33952 not shown) Histogram of bond angle deviations from ideal: 96.96 - 104.45: 335 104.45 - 111.94: 38915 111.94 - 119.44: 8560 119.44 - 126.93: 13340 126.93 - 134.42: 231 Bond angle restraints: 61381 Sorted by residual: angle pdb=" CA ARG H 107 " pdb=" C ARG H 107 " pdb=" N HIS H 108 " ideal model delta sigma weight residual 117.34 125.68 -8.34 1.22e+00 6.72e-01 4.67e+01 angle pdb=" CA ARG H 107 " pdb=" C ARG H 107 " pdb=" O ARG H 107 " ideal model delta sigma weight residual 120.42 110.65 9.77 1.48e+00 4.57e-01 4.36e+01 angle pdb=" CB GLN G 351 " pdb=" CG GLN G 351 " pdb=" CD GLN G 351 " ideal model delta sigma weight residual 112.60 103.81 8.79 1.70e+00 3.46e-01 2.67e+01 angle pdb=" N HIS G 333 " pdb=" CA HIS G 333 " pdb=" C HIS G 333 " ideal model delta sigma weight residual 111.71 104.87 6.84 1.34e+00 5.57e-01 2.61e+01 angle pdb=" CA ARG D 107 " pdb=" C ARG D 107 " pdb=" O ARG D 107 " ideal model delta sigma weight residual 120.40 115.39 5.01 1.05e+00 9.07e-01 2.28e+01 ... (remaining 61376 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 14620 17.82 - 35.64: 963 35.64 - 53.45: 274 53.45 - 71.27: 87 71.27 - 89.09: 52 Dihedral angle restraints: 15996 sinusoidal: 8858 harmonic: 7138 Sorted by residual: dihedral pdb=" CA LEU G 101 " pdb=" C LEU G 101 " pdb=" N GLU G 102 " pdb=" CA GLU G 102 " ideal model delta harmonic sigma weight residual 180.00 158.65 21.35 0 5.00e+00 4.00e-02 1.82e+01 dihedral pdb=" CA MET C 255 " pdb=" C MET C 255 " pdb=" N VAL C 256 " pdb=" CA VAL C 256 " ideal model delta harmonic sigma weight residual 180.00 163.70 16.30 0 5.00e+00 4.00e-02 1.06e+01 dihedral pdb=" CA HIS I 239 " pdb=" C HIS I 239 " pdb=" N PRO I 240 " pdb=" CA PRO I 240 " ideal model delta harmonic sigma weight residual 180.00 -164.09 -15.91 0 5.00e+00 4.00e-02 1.01e+01 ... (remaining 15993 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 2174 0.048 - 0.097: 334 0.097 - 0.145: 138 0.145 - 0.194: 8 0.194 - 0.242: 2 Chirality restraints: 2656 Sorted by residual: chirality pdb=" CA VAL B 191 " pdb=" N VAL B 191 " pdb=" C VAL B 191 " pdb=" CB VAL B 191 " both_signs ideal model delta sigma weight residual False 2.44 2.68 -0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CA ARG I 67 " pdb=" N ARG I 67 " pdb=" C ARG I 67 " pdb=" CB ARG I 67 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.94e-01 chirality pdb=" CB VAL B 191 " pdb=" CA VAL B 191 " pdb=" CG1 VAL B 191 " pdb=" CG2 VAL B 191 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 9.00e-01 ... (remaining 2653 not shown) Planarity restraints: 5143 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN G 352 " 0.019 2.00e-02 2.50e+03 4.42e-01 2.93e+03 pdb=" CG ASN G 352 " -0.003 2.00e-02 2.50e+03 pdb=" OD1 ASN G 352 " -0.019 2.00e-02 2.50e+03 pdb=" ND2 ASN G 352 " -0.000 2.00e-02 2.50e+03 pdb="HD21 ASN G 352 " -0.763 2.00e-02 2.50e+03 pdb="HD22 ASN G 352 " 0.766 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN G 349 " -0.072 2.00e-02 2.50e+03 4.39e-01 2.89e+03 pdb=" CD GLN G 349 " 0.001 2.00e-02 2.50e+03 pdb=" OE1 GLN G 349 " 0.071 2.00e-02 2.50e+03 pdb=" NE2 GLN G 349 " -0.000 2.00e-02 2.50e+03 pdb="HE21 GLN G 349 " -0.757 2.00e-02 2.50e+03 pdb="HE22 GLN G 349 " 0.757 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN G 348 " -0.233 2.00e-02 2.50e+03 3.92e-01 2.31e+03 pdb=" CD GLN G 348 " 0.022 2.00e-02 2.50e+03 pdb=" OE1 GLN G 348 " 0.223 2.00e-02 2.50e+03 pdb=" NE2 GLN G 348 " 0.003 2.00e-02 2.50e+03 pdb="HE21 GLN G 348 " 0.633 2.00e-02 2.50e+03 pdb="HE22 GLN G 348 " -0.647 2.00e-02 2.50e+03 ... (remaining 5140 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.21: 2630 2.21 - 2.81: 72793 2.81 - 3.40: 99282 3.40 - 4.00: 136687 4.00 - 4.60: 209848 Nonbonded interactions: 521240 Sorted by model distance: nonbonded pdb=" O PHE H 86 " pdb=" HG1 THR H 90 " model vdw 1.609 1.850 nonbonded pdb=" O ASN A 31 " pdb="HD21 ASN A 31 " model vdw 1.612 1.850 nonbonded pdb=" OD1 ASP C 177 " pdb=" HG1 THR C 179 " model vdw 1.618 1.850 nonbonded pdb=" H CYS C 187 " pdb=" OE2 GLU C 310 " model vdw 1.621 1.850 nonbonded pdb="HH11 ARG F 137 " pdb=" OE1 GLU F 146 " model vdw 1.622 1.850 ... (remaining 521235 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'E' and resid 3 through 144) } ncs_group { reference = (chain 'B' and resid 3 through 194) selection = (chain 'F' and (resid 3 through 43 or resid 45 through 194)) } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = (chain 'D' and (resid 4 through 278 or resid 301 through 302)) selection = chain 'H' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.780 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: 0.570 Extract box with map and model: 14.950 Check model and map are aligned: 0.500 Set scattering table: 0.290 Process input model: 118.040 Find NCS groups from input model: 1.410 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 154.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 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 : 0.005 0.093 17240 Z= 0.339 Angle : 0.617 9.772 23426 Z= 0.371 Chirality : 0.043 0.242 2656 Planarity : 0.004 0.050 3102 Dihedral : 13.359 89.040 6412 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.28 % Allowed : 0.55 % Favored : 99.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.19), residues: 2154 helix: 1.95 (0.19), residues: 842 sheet: -0.09 (0.28), residues: 360 loop : 0.11 (0.20), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.003 TRP A 11 HIS 0.019 0.002 HIS H 108 PHE 0.040 0.002 PHE C 156 TYR 0.021 0.001 TYR H 181 ARG 0.008 0.000 ARG G 180 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 200 time to evaluate : 2.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 MET cc_start: 0.8066 (ptt) cc_final: 0.7833 (ptm) REVERT: E 122 ASP cc_start: 0.8187 (m-30) cc_final: 0.7948 (m-30) REVERT: I 127 LYS cc_start: 0.8867 (tmmt) cc_final: 0.8427 (tttm) REVERT: I 216 LEU cc_start: 0.8334 (tp) cc_final: 0.8109 (tm) outliers start: 5 outliers final: 0 residues processed: 203 average time/residue: 2.9275 time to fit residues: 664.6460 Evaluate side-chains 149 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 3.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 180 optimal weight: 1.9990 chunk 162 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 109 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 167 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 chunk 101 optimal weight: 3.9990 chunk 124 optimal weight: 0.7980 chunk 194 optimal weight: 5.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 ASN B 58 ASN ** C 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 319 ASN H 15 GLN ** I 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.0652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 17240 Z= 0.239 Angle : 0.508 7.037 23426 Z= 0.263 Chirality : 0.040 0.146 2656 Planarity : 0.004 0.045 3102 Dihedral : 4.080 57.990 2378 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.44 % Allowed : 5.66 % Favored : 93.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.19), residues: 2154 helix: 2.03 (0.19), residues: 848 sheet: -0.06 (0.28), residues: 358 loop : 0.08 (0.20), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP A 11 HIS 0.005 0.001 HIS C 333 PHE 0.014 0.001 PHE D 86 TYR 0.015 0.001 TYR D 214 ARG 0.007 0.000 ARG H 142 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 156 time to evaluate : 2.785 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: A 144 MET cc_start: 0.8045 (ptt) cc_final: 0.7810 (ptm) REVERT: E 122 ASP cc_start: 0.8174 (m-30) cc_final: 0.7934 (m-30) outliers start: 8 outliers final: 3 residues processed: 159 average time/residue: 2.5118 time to fit residues: 456.5623 Evaluate side-chains 149 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 146 time to evaluate : 2.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 42 ASN Chi-restraints excluded: chain E residue 93 GLU Chi-restraints excluded: chain I residue 204 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 108 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 161 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 194 optimal weight: 5.9990 chunk 210 optimal weight: 2.9990 chunk 173 optimal weight: 0.9980 chunk 193 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 156 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 ASN B 107 ASN ** D 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 261 ASN G 319 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.0818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 17240 Z= 0.267 Angle : 0.497 5.991 23426 Z= 0.254 Chirality : 0.040 0.144 2656 Planarity : 0.004 0.046 3102 Dihedral : 4.009 46.124 2378 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.61 % Allowed : 6.10 % Favored : 93.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.19), residues: 2154 helix: 2.09 (0.18), residues: 854 sheet: -0.09 (0.28), residues: 356 loop : 0.11 (0.20), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 11 HIS 0.005 0.001 HIS C 333 PHE 0.014 0.001 PHE D 86 TYR 0.016 0.001 TYR D 214 ARG 0.005 0.000 ARG B 137 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 151 time to evaluate : 2.903 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: A 144 MET cc_start: 0.8071 (ptt) cc_final: 0.7821 (ptm) REVERT: E 122 ASP cc_start: 0.8175 (m-30) cc_final: 0.7957 (m-30) REVERT: I 196 ASN cc_start: 0.8350 (t0) cc_final: 0.8136 (t0) outliers start: 11 outliers final: 3 residues processed: 157 average time/residue: 2.4561 time to fit residues: 441.7207 Evaluate side-chains 145 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 142 time to evaluate : 2.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 42 ASN Chi-restraints excluded: chain I residue 50 SER Chi-restraints excluded: chain I residue 156 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 192 optimal weight: 5.9990 chunk 146 optimal weight: 1.9990 chunk 101 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 130 optimal weight: 0.8980 chunk 195 optimal weight: 4.9990 chunk 206 optimal weight: 0.6980 chunk 102 optimal weight: 2.9990 chunk 185 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 ASN ** D 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 319 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.0927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 17240 Z= 0.255 Angle : 0.486 5.640 23426 Z= 0.249 Chirality : 0.040 0.145 2656 Planarity : 0.004 0.042 3102 Dihedral : 3.935 34.195 2378 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.50 % Allowed : 6.82 % Favored : 92.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.19), residues: 2154 helix: 2.13 (0.18), residues: 854 sheet: 0.02 (0.29), residues: 332 loop : 0.16 (0.20), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 11 HIS 0.004 0.001 HIS C 333 PHE 0.013 0.001 PHE D 86 TYR 0.015 0.001 TYR D 214 ARG 0.007 0.000 ARG G 180 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 155 time to evaluate : 2.932 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: A 144 MET cc_start: 0.8028 (ptt) cc_final: 0.7789 (ptm) REVERT: C 328 HIS cc_start: 0.9121 (OUTLIER) cc_final: 0.8905 (p-80) REVERT: E 122 ASP cc_start: 0.8139 (m-30) cc_final: 0.7922 (m-30) REVERT: G 51 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.8194 (mt-10) REVERT: I 196 ASN cc_start: 0.8330 (t0) cc_final: 0.8059 (t0) outliers start: 9 outliers final: 3 residues processed: 160 average time/residue: 2.5212 time to fit residues: 459.3901 Evaluate side-chains 147 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 142 time to evaluate : 2.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 42 ASN Chi-restraints excluded: chain C residue 328 HIS Chi-restraints excluded: chain G residue 51 GLU Chi-restraints excluded: chain I residue 156 ILE Chi-restraints excluded: chain I residue 204 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 172 optimal weight: 4.9990 chunk 117 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 154 optimal weight: 0.9990 chunk 85 optimal weight: 0.6980 chunk 176 optimal weight: 2.9990 chunk 142 optimal weight: 6.9990 chunk 0 optimal weight: 2.9990 chunk 105 optimal weight: 0.6980 chunk 185 optimal weight: 0.1980 chunk 52 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 ASN ** D 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 319 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.1006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 17240 Z= 0.177 Angle : 0.470 5.799 23426 Z= 0.240 Chirality : 0.040 0.147 2656 Planarity : 0.004 0.072 3102 Dihedral : 3.827 30.719 2378 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.44 % Allowed : 7.04 % Favored : 92.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.19), residues: 2154 helix: 2.23 (0.18), residues: 854 sheet: 0.13 (0.30), residues: 321 loop : 0.19 (0.20), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 11 HIS 0.003 0.001 HIS I 239 PHE 0.011 0.001 PHE D 86 TYR 0.014 0.001 TYR D 214 ARG 0.009 0.000 ARG G 180 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 153 time to evaluate : 2.659 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: A 144 MET cc_start: 0.8008 (ptt) cc_final: 0.7786 (ptm) REVERT: E 122 ASP cc_start: 0.8128 (m-30) cc_final: 0.7901 (m-30) REVERT: G 180 ARG cc_start: 0.8470 (mmm-85) cc_final: 0.8252 (mtp85) REVERT: I 196 ASN cc_start: 0.8345 (t0) cc_final: 0.8054 (t0) outliers start: 8 outliers final: 3 residues processed: 156 average time/residue: 2.4053 time to fit residues: 433.0406 Evaluate side-chains 147 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 144 time to evaluate : 2.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 328 HIS Chi-restraints excluded: chain E residue 93 GLU Chi-restraints excluded: chain I residue 156 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 69 optimal weight: 1.9990 chunk 186 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 51 optimal weight: 0.0010 chunk 207 optimal weight: 5.9990 chunk 171 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 overall best weight: 1.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 ASN ** D 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 319 ASN I 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.1055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 17240 Z= 0.276 Angle : 0.483 5.434 23426 Z= 0.247 Chirality : 0.040 0.143 2656 Planarity : 0.004 0.056 3102 Dihedral : 3.854 25.872 2378 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.72 % Allowed : 7.10 % Favored : 92.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.19), residues: 2154 helix: 2.25 (0.18), residues: 853 sheet: 0.11 (0.30), residues: 322 loop : 0.16 (0.20), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 11 HIS 0.004 0.001 HIS C 333 PHE 0.013 0.001 PHE D 86 TYR 0.015 0.001 TYR D 214 ARG 0.009 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 147 time to evaluate : 2.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 MET cc_start: 0.8042 (ptt) cc_final: 0.7818 (ptm) REVERT: C 311 GLU cc_start: 0.8742 (OUTLIER) cc_final: 0.7557 (tm-30) REVERT: E 122 ASP cc_start: 0.8127 (m-30) cc_final: 0.7901 (m-30) REVERT: I 50 SER cc_start: 0.9355 (m) cc_final: 0.8717 (p) REVERT: I 196 ASN cc_start: 0.8325 (t0) cc_final: 0.8012 (t0) outliers start: 13 outliers final: 3 residues processed: 156 average time/residue: 2.3565 time to fit residues: 423.1821 Evaluate side-chains 147 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 143 time to evaluate : 2.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain C residue 311 GLU Chi-restraints excluded: chain C residue 328 HIS Chi-restraints excluded: chain I residue 204 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 199 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 chunk 151 optimal weight: 0.2980 chunk 174 optimal weight: 0.9990 chunk 115 optimal weight: 0.7980 chunk 206 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 127 optimal weight: 0.6980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 ASN ** D 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 319 ASN H 15 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.1109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17240 Z= 0.180 Angle : 0.467 5.667 23426 Z= 0.238 Chirality : 0.039 0.147 2656 Planarity : 0.004 0.051 3102 Dihedral : 3.788 25.077 2378 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.44 % Allowed : 7.54 % Favored : 92.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.19), residues: 2154 helix: 2.27 (0.18), residues: 852 sheet: 0.13 (0.30), residues: 322 loop : 0.21 (0.20), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 11 HIS 0.003 0.001 HIS E 107 PHE 0.011 0.001 PHE D 86 TYR 0.014 0.001 TYR D 214 ARG 0.008 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 148 time to evaluate : 2.693 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: A 144 MET cc_start: 0.8009 (ptt) cc_final: 0.7787 (ptm) REVERT: E 32 ILE cc_start: 0.9213 (tp) cc_final: 0.8987 (tt) REVERT: E 122 ASP cc_start: 0.8116 (m-30) cc_final: 0.7896 (m-30) REVERT: I 50 SER cc_start: 0.9354 (OUTLIER) cc_final: 0.8737 (p) REVERT: I 196 ASN cc_start: 0.8342 (t0) cc_final: 0.8023 (t0) outliers start: 8 outliers final: 2 residues processed: 151 average time/residue: 2.4385 time to fit residues: 421.7946 Evaluate side-chains 145 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 142 time to evaluate : 2.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 328 HIS Chi-restraints excluded: chain E residue 93 GLU Chi-restraints excluded: chain I residue 50 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 82 optimal weight: 2.9990 chunk 123 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 140 optimal weight: 0.6980 chunk 101 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 162 optimal weight: 2.9990 chunk 187 optimal weight: 1.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 ASN ** D 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 319 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.1145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 17240 Z= 0.262 Angle : 0.480 6.095 23426 Z= 0.246 Chirality : 0.040 0.144 2656 Planarity : 0.004 0.073 3102 Dihedral : 3.818 21.618 2378 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.67 % Allowed : 7.27 % Favored : 92.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.19), residues: 2154 helix: 2.28 (0.18), residues: 852 sheet: 0.12 (0.30), residues: 322 loop : 0.20 (0.20), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 11 HIS 0.003 0.001 HIS C 333 PHE 0.012 0.001 PHE D 86 TYR 0.015 0.001 TYR D 214 ARG 0.014 0.000 ARG G 180 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 146 time to evaluate : 2.693 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: A 144 MET cc_start: 0.8027 (OUTLIER) cc_final: 0.7784 (ptm) REVERT: C 311 GLU cc_start: 0.8685 (OUTLIER) cc_final: 0.7378 (tm-30) REVERT: E 122 ASP cc_start: 0.8122 (m-30) cc_final: 0.7899 (m-30) REVERT: I 50 SER cc_start: 0.9337 (OUTLIER) cc_final: 0.8700 (p) REVERT: I 196 ASN cc_start: 0.8332 (t0) cc_final: 0.8016 (t0) outliers start: 12 outliers final: 4 residues processed: 152 average time/residue: 2.3636 time to fit residues: 412.6995 Evaluate side-chains 151 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 144 time to evaluate : 2.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain C residue 311 GLU Chi-restraints excluded: chain C residue 328 HIS Chi-restraints excluded: chain G residue 51 GLU Chi-restraints excluded: chain G residue 328 HIS Chi-restraints excluded: chain I residue 50 SER Chi-restraints excluded: chain I residue 204 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 197 optimal weight: 0.9990 chunk 180 optimal weight: 1.9990 chunk 192 optimal weight: 4.9990 chunk 115 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 150 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 173 optimal weight: 2.9990 chunk 181 optimal weight: 0.4980 chunk 191 optimal weight: 6.9990 chunk 126 optimal weight: 0.7980 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 ASN ** D 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 193 ASN G 319 ASN H 15 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.1180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17240 Z= 0.218 Angle : 0.472 5.801 23426 Z= 0.241 Chirality : 0.040 0.146 2656 Planarity : 0.004 0.061 3102 Dihedral : 3.791 21.172 2378 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.55 % Allowed : 7.54 % Favored : 91.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.19), residues: 2154 helix: 2.27 (0.18), residues: 858 sheet: 0.13 (0.30), residues: 322 loop : 0.21 (0.20), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 11 HIS 0.003 0.001 HIS D 108 PHE 0.012 0.001 PHE D 86 TYR 0.014 0.001 TYR D 214 ARG 0.011 0.000 ARG G 180 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 145 time to evaluate : 2.706 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: A 144 MET cc_start: 0.8026 (OUTLIER) cc_final: 0.7799 (ptm) REVERT: E 122 ASP cc_start: 0.8114 (m-30) cc_final: 0.7895 (m-30) REVERT: I 50 SER cc_start: 0.9324 (OUTLIER) cc_final: 0.8692 (p) REVERT: I 196 ASN cc_start: 0.8307 (t0) cc_final: 0.7985 (t0) outliers start: 10 outliers final: 3 residues processed: 151 average time/residue: 2.3603 time to fit residues: 409.0356 Evaluate side-chains 150 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 145 time to evaluate : 2.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain C residue 328 HIS Chi-restraints excluded: chain E residue 93 GLU Chi-restraints excluded: chain G residue 328 HIS Chi-restraints excluded: chain I residue 50 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 203 optimal weight: 0.3980 chunk 124 optimal weight: 3.9990 chunk 96 optimal weight: 0.6980 chunk 141 optimal weight: 2.9990 chunk 213 optimal weight: 4.9990 chunk 196 optimal weight: 2.9990 chunk 169 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 131 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 134 optimal weight: 0.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 319 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.1227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 17240 Z= 0.187 Angle : 0.464 6.309 23426 Z= 0.236 Chirality : 0.039 0.147 2656 Planarity : 0.003 0.065 3102 Dihedral : 3.727 20.183 2378 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.33 % Allowed : 7.82 % Favored : 91.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.19), residues: 2154 helix: 2.33 (0.18), residues: 858 sheet: 0.15 (0.30), residues: 322 loop : 0.24 (0.20), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 11 HIS 0.003 0.001 HIS D 108 PHE 0.011 0.001 PHE D 86 TYR 0.014 0.001 TYR D 214 ARG 0.013 0.000 ARG I 67 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 146 time to evaluate : 2.815 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: D 258 ASP cc_start: 0.8176 (p0) cc_final: 0.7938 (p0) REVERT: E 122 ASP cc_start: 0.8115 (m-30) cc_final: 0.7875 (m-30) REVERT: F 82 ASN cc_start: 0.8664 (t0) cc_final: 0.8157 (t0) REVERT: I 50 SER cc_start: 0.9310 (OUTLIER) cc_final: 0.8688 (p) REVERT: I 196 ASN cc_start: 0.8284 (t0) cc_final: 0.7962 (t0) outliers start: 6 outliers final: 2 residues processed: 150 average time/residue: 2.3546 time to fit residues: 406.5446 Evaluate side-chains 148 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 145 time to evaluate : 2.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 328 HIS Chi-restraints excluded: chain G residue 328 HIS Chi-restraints excluded: chain I residue 50 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 180 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 156 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 170 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 chunk 174 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 149 optimal weight: 3.9990 overall best weight: 0.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.077731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.061710 restraints weight = 95024.781| |-----------------------------------------------------------------------------| r_work (start): 0.2808 rms_B_bonded: 2.12 r_work: 0.2721 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2612 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2612 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2581 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2581 r_free = 0.2581 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2579 r_free = 0.2579 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.2579 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.1263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17240 Z= 0.178 Angle : 0.463 5.943 23426 Z= 0.235 Chirality : 0.039 0.146 2656 Planarity : 0.003 0.062 3102 Dihedral : 3.698 19.375 2378 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.28 % Allowed : 8.04 % Favored : 91.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.19), residues: 2154 helix: 2.36 (0.18), residues: 859 sheet: 0.19 (0.30), residues: 320 loop : 0.23 (0.20), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 11 HIS 0.003 0.001 HIS I 239 PHE 0.011 0.001 PHE D 86 TYR 0.016 0.001 TYR I 241 ARG 0.015 0.000 ARG I 67 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9799.56 seconds wall clock time: 173 minutes 12.63 seconds (10392.63 seconds total)