Starting phenix.real_space_refine on Fri Mar 15 23:39:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t96_25752/03_2024/7t96_25752_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t96_25752/03_2024/7t96_25752.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t96_25752/03_2024/7t96_25752.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t96_25752/03_2024/7t96_25752.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t96_25752/03_2024/7t96_25752_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t96_25752/03_2024/7t96_25752_updated.pdb" } resolution = 3.22 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= 0.001 sd= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4680 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians S 59 5.16 5 Cl 1 4.86 5 C 5382 2.51 5 N 1431 2.21 5 O 1577 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 52": "NH1" <-> "NH2" Residue "A TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 121": "NH1" <-> "NH2" Residue "A ARG 135": "NH1" <-> "NH2" Residue "A TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 187": "OE1" <-> "OE2" Residue "B ARG 198": "NH1" <-> "NH2" Residue "B GLU 208": "OE1" <-> "OE2" Residue "B ARG 209": "NH1" <-> "NH2" Residue "B ARG 243": "NH1" <-> "NH2" Residue "B GLU 290": "OE1" <-> "OE2" Residue "B ARG 349": "NH1" <-> "NH2" Residue "C ARG 48": "NH1" <-> "NH2" Residue "C ARG 134": "NH1" <-> "NH2" Residue "C PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 202": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8450 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2015 Classifications: {'peptide': 274} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 12, 'TRANS': 261} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 174 Unresolved non-hydrogen angles: 219 Unresolved non-hydrogen dihedrals: 152 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 4, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 81 Chain: "B" Number of atoms: 1705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1705 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 4, 'TRANS': 213} Chain breaks: 2 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "C" Number of atoms: 2541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2541 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 4, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 47 Chain: "D" Number of atoms: 403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 403 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "E" Number of atoms: 1747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1747 Classifications: {'peptide': 236} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 225} Chain breaks: 1 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 52 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'2CU': 1, 'ACH': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.86, per 1000 atoms: 0.58 Number of scatterers: 8450 At special positions: 0 Unit cell: (91.8, 121.55, 124.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 1 17.00 S 59 16.00 O 1577 8.00 N 1431 7.00 C 5382 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 96 " - pdb=" SG CYS A 176 " distance=2.02 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.03 Conformation dependent library (CDL) restraints added in 1.6 seconds 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2094 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 27 helices and 13 sheets defined 32.6% alpha, 20.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.45 Creating SS restraints... Processing helix chain 'A' and resid 23 through 49 Processing helix chain 'A' and resid 57 through 59 No H-bonds generated for 'chain 'A' and resid 57 through 59' Processing helix chain 'A' and resid 61 through 72 removed outlier: 3.545A pdb=" N LEU A 65 " --> pdb=" O PHE A 61 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N CYS A 67 " --> pdb=" O PHE A 63 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N LEU A 70 " --> pdb=" O ALA A 66 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE A 72 " --> pdb=" O ALA A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 84 Processing helix chain 'A' and resid 92 through 94 No H-bonds generated for 'chain 'A' and resid 92 through 94' Processing helix chain 'A' and resid 96 through 126 Processing helix chain 'A' and resid 131 through 134 No H-bonds generated for 'chain 'A' and resid 131 through 134' Processing helix chain 'A' and resid 137 through 166 removed outlier: 3.589A pdb=" N SER A 151 " --> pdb=" O ALA A 147 " (cutoff:3.500A) Proline residue: A 157 - end of helix removed outlier: 5.354A pdb=" N GLN A 163 " --> pdb=" O ILE A 159 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N PHE A 164 " --> pdb=" O LEU A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 213 Proline residue: A 198 - end of helix Processing helix chain 'A' and resid 381 through 410 Proline residue: A 402 - end of helix removed outlier: 4.132A pdb=" N LEU A 408 " --> pdb=" O ASN A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 441 removed outlier: 4.062A pdb=" N GLY A 425 " --> pdb=" O VAL A 421 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N TYR A 426 " --> pdb=" O TRP A 422 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ASN A 432 " --> pdb=" O LEU A 428 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N SER A 433 " --> pdb=" O CYS A 429 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR A 434 " --> pdb=" O TYR A 430 " (cutoff:3.500A) Proline residue: A 437 - end of helix Processing helix chain 'A' and resid 447 through 456 Processing helix chain 'B' and resid 9 through 31 Processing helix chain 'B' and resid 46 through 51 removed outlier: 3.539A pdb=" N VAL B 50 " --> pdb=" O LYS B 46 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LYS B 51 " --> pdb=" O SER B 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 46 through 51' Processing helix chain 'B' and resid 209 through 211 No H-bonds generated for 'chain 'B' and resid 209 through 211' Processing helix chain 'B' and resid 214 through 216 No H-bonds generated for 'chain 'B' and resid 214 through 216' Processing helix chain 'B' and resid 243 through 255 Processing helix chain 'B' and resid 274 through 279 Processing helix chain 'B' and resid 284 through 286 No H-bonds generated for 'chain 'B' and resid 284 through 286' Processing helix chain 'B' and resid 297 through 311 removed outlier: 4.076A pdb=" N ALA B 302 " --> pdb=" O GLU B 298 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N LYS B 311 " --> pdb=" O GLN B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 350 Processing helix chain 'C' and resid 4 through 25 Processing helix chain 'C' and resid 30 through 35 Processing helix chain 'D' and resid 8 through 23 Processing helix chain 'D' and resid 30 through 43 Processing helix chain 'E' and resid 29 through 31 No H-bonds generated for 'chain 'E' and resid 29 through 31' Processing helix chain 'E' and resid 88 through 90 No H-bonds generated for 'chain 'E' and resid 88 through 90' Processing sheet with id= A, first strand: chain 'B' and resid 319 through 322 removed outlier: 6.663A pdb=" N ILE B 265 " --> pdb=" O TYR B 320 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N HIS B 322 " --> pdb=" O ILE B 265 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N LEU B 267 " --> pdb=" O HIS B 322 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA B 221 " --> pdb=" O LYS B 35 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N CYS B 225 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N HIS B 196 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N LEU B 36 " --> pdb=" O HIS B 196 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ARG B 198 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N LEU B 38 " --> pdb=" O ARG B 198 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N PHE B 200 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 9.078A pdb=" N GLY B 40 " --> pdb=" O PHE B 200 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE B 190 " --> pdb=" O PHE B 197 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 58 through 63 removed outlier: 7.090A pdb=" N ALA C 73 " --> pdb=" O TYR C 59 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N MET C 61 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL C 71 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N TRP C 63 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N LEU C 69 " --> pdb=" O TRP C 63 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU C 70 " --> pdb=" O TRP C 82 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N HIS C 91 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.844A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG C 137 " --> pdb=" O ILE C 123 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N VAL C 135 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 178 through 181 removed outlier: 3.531A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ILE C 157 " --> pdb=" O TRP C 169 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N CYS C 148 " --> pdb=" O SER C 160 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 200 through 203 removed outlier: 4.394A pdb=" N SER C 207 " --> pdb=" O ALA C 203 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.530A pdb=" N GLY C 244 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ILE C 232 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ALA C 242 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N PHE C 234 " --> pdb=" O ALA C 240 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N ALA C 240 " --> pdb=" O PHE C 234 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 307 through 309 removed outlier: 4.148A pdb=" N ASN C 293 " --> pdb=" O TYR C 289 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 336 through 339 Processing sheet with id= I, first strand: chain 'E' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.530A pdb=" N THR E 118 " --> pdb=" O GLY E 10 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL E 37 " --> pdb=" O TYR E 95 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL E 97 " --> pdb=" O HIS E 35 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N ALA E 40 " --> pdb=" O LEU E 45 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N LEU E 45 " --> pdb=" O ALA E 40 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 146 through 149 removed outlier: 6.875A pdb=" N LYS E 244 " --> pdb=" O VAL E 147 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N VAL E 149 " --> pdb=" O LYS E 244 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N GLU E 246 " --> pdb=" O VAL E 149 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'E' and resid 154 through 160 Processing sheet with id= M, first strand: chain 'E' and resid 226 through 231 removed outlier: 3.741A pdb=" N ILE E 189 " --> pdb=" O TRP E 176 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N LEU E 178 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N LEU E 187 " --> pdb=" O LEU E 178 " (cutoff:3.500A) 363 hydrogen bonds defined for protein. 1041 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: 2.29 Time building geometry restraints manager: 3.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 1364 1.28 - 1.41: 2209 1.41 - 1.55: 4967 1.55 - 1.69: 2 1.69 - 1.83: 85 Bond restraints: 8627 Sorted by residual: bond pdb=" C01 2CU A 502 " pdb=" N02 2CU A 502 " ideal model delta sigma weight residual 1.445 1.257 0.188 2.00e-02 2.50e+03 8.81e+01 bond pdb=" C SER A 76 " pdb=" O SER A 76 " ideal model delta sigma weight residual 1.237 1.138 0.098 1.17e-02 7.31e+03 7.09e+01 bond pdb=" C TYR A 80 " pdb=" O TYR A 80 " ideal model delta sigma weight residual 1.236 1.152 0.084 1.26e-02 6.30e+03 4.44e+01 bond pdb=" C24 2CU A 502 " pdb=" N26 2CU A 502 " ideal model delta sigma weight residual 1.353 1.481 -0.128 2.00e-02 2.50e+03 4.10e+01 bond pdb=" C08 2CU A 502 " pdb=" N05 2CU A 502 " ideal model delta sigma weight residual 1.346 1.474 -0.128 2.00e-02 2.50e+03 4.08e+01 ... (remaining 8622 not shown) Histogram of bond angle deviations from ideal: 59.92 - 74.86: 3 74.86 - 89.80: 0 89.80 - 104.74: 126 104.74 - 119.68: 7326 119.68 - 134.62: 4291 Bond angle restraints: 11746 Sorted by residual: angle pdb=" N TYR A 80 " pdb=" CA TYR A 80 " pdb=" C TYR A 80 " ideal model delta sigma weight residual 111.82 99.80 12.02 1.16e+00 7.43e-01 1.07e+02 angle pdb=" N PRO A 418 " pdb=" CA PRO A 418 " pdb=" C PRO A 418 " ideal model delta sigma weight residual 113.53 101.66 11.87 1.39e+00 5.18e-01 7.29e+01 angle pdb=" N PHE A 61 " pdb=" CA PHE A 61 " pdb=" C PHE A 61 " ideal model delta sigma weight residual 112.54 102.43 10.11 1.22e+00 6.72e-01 6.87e+01 angle pdb=" N THR A 446 " pdb=" CA THR A 446 " pdb=" C THR A 446 " ideal model delta sigma weight residual 113.41 103.74 9.67 1.22e+00 6.72e-01 6.28e+01 angle pdb=" N THR A 420 " pdb=" CA THR A 420 " pdb=" C THR A 420 " ideal model delta sigma weight residual 114.62 106.97 7.65 1.14e+00 7.69e-01 4.51e+01 ... (remaining 11741 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.96: 4587 15.96 - 31.92: 358 31.92 - 47.88: 91 47.88 - 63.83: 14 63.83 - 79.79: 3 Dihedral angle restraints: 5053 sinusoidal: 1806 harmonic: 3247 Sorted by residual: dihedral pdb=" CB CYS A 96 " pdb=" SG CYS A 96 " pdb=" SG CYS A 176 " pdb=" CB CYS A 176 " ideal model delta sinusoidal sigma weight residual -86.00 -162.75 76.75 1 1.00e+01 1.00e-02 7.40e+01 dihedral pdb=" C ASP B 273 " pdb=" N ASP B 273 " pdb=" CA ASP B 273 " pdb=" CB ASP B 273 " ideal model delta harmonic sigma weight residual -122.60 -110.83 -11.77 0 2.50e+00 1.60e-01 2.22e+01 dihedral pdb=" CA GLN C 75 " pdb=" C GLN C 75 " pdb=" N ASP C 76 " pdb=" CA ASP C 76 " ideal model delta harmonic sigma weight residual 180.00 156.86 23.14 0 5.00e+00 4.00e-02 2.14e+01 ... (remaining 5050 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 1195 0.080 - 0.159: 145 0.159 - 0.239: 19 0.239 - 0.319: 6 0.319 - 0.398: 4 Chirality restraints: 1369 Sorted by residual: chirality pdb=" CA ASP B 273 " pdb=" N ASP B 273 " pdb=" C ASP B 273 " pdb=" CB ASP B 273 " both_signs ideal model delta sigma weight residual False 2.51 2.91 -0.40 2.00e-01 2.50e+01 3.97e+00 chirality pdb=" CB VAL A 50 " pdb=" CA VAL A 50 " pdb=" CG1 VAL A 50 " pdb=" CG2 VAL A 50 " both_signs ideal model delta sigma weight residual False -2.63 -2.25 -0.38 2.00e-01 2.50e+01 3.57e+00 chirality pdb=" CA THR A 420 " pdb=" N THR A 420 " pdb=" C THR A 420 " pdb=" CB THR A 420 " both_signs ideal model delta sigma weight residual False 2.53 2.86 -0.33 2.00e-01 2.50e+01 2.77e+00 ... (remaining 1366 not shown) Planarity restraints: 1479 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 409 " -0.017 2.00e-02 2.50e+03 3.37e-02 1.14e+01 pdb=" C ILE A 409 " 0.058 2.00e-02 2.50e+03 pdb=" O ILE A 409 " -0.022 2.00e-02 2.50e+03 pdb=" N ASN A 410 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 49 " 0.016 2.00e-02 2.50e+03 3.14e-02 9.88e+00 pdb=" C LYS A 49 " -0.054 2.00e-02 2.50e+03 pdb=" O LYS A 49 " 0.020 2.00e-02 2.50e+03 pdb=" N VAL A 50 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 58 " -0.015 2.00e-02 2.50e+03 2.93e-02 8.58e+00 pdb=" C ASN A 58 " 0.051 2.00e-02 2.50e+03 pdb=" O ASN A 58 " -0.019 2.00e-02 2.50e+03 pdb=" N ASN A 59 " -0.017 2.00e-02 2.50e+03 ... (remaining 1476 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 166 2.65 - 3.21: 7915 3.21 - 3.78: 12324 3.78 - 4.34: 16696 4.34 - 4.90: 28037 Nonbonded interactions: 65138 Sorted by model distance: nonbonded pdb=" O ILE A 431 " pdb=" OG1 THR A 434 " model vdw 2.091 2.440 nonbonded pdb=" OG SER C 161 " pdb=" OD1 ASP C 163 " model vdw 2.125 2.440 nonbonded pdb=" OG SER C 245 " pdb=" OD1 ASP C 247 " model vdw 2.144 2.440 nonbonded pdb=" OG SER C 74 " pdb=" OD1 ASP C 76 " model vdw 2.179 2.440 nonbonded pdb=" OE2 GLU C 215 " pdb=" NH2 ARG C 219 " model vdw 2.220 2.520 ... (remaining 65133 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 6.870 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 25.130 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 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 : 0.008 0.188 8627 Z= 0.501 Angle : 0.939 12.018 11746 Z= 0.573 Chirality : 0.059 0.398 1369 Planarity : 0.005 0.058 1479 Dihedral : 12.639 79.793 2950 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 0.35 % Allowed : 1.15 % Favored : 98.50 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.25), residues: 1102 helix: 0.82 (0.28), residues: 349 sheet: -0.57 (0.32), residues: 269 loop : -1.82 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP A 99 HIS 0.006 0.002 HIS B 189 PHE 0.018 0.002 PHE E 68 TYR 0.019 0.002 TYR E 94 ARG 0.004 0.001 ARG A 135 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 250 time to evaluate : 0.894 Fit side-chains revert: symmetry clash REVERT: A 33 LEU cc_start: 0.8979 (mt) cc_final: 0.8738 (mp) REVERT: A 177 TYR cc_start: 0.7169 (p90) cc_final: 0.6856 (p90) REVERT: A 397 ILE cc_start: 0.8301 (mm) cc_final: 0.8087 (tt) REVERT: A 404 ASN cc_start: 0.8666 (m-40) cc_final: 0.8289 (m-40) REVERT: B 218 ASP cc_start: 0.7088 (t0) cc_final: 0.6847 (t0) REVERT: B 247 SER cc_start: 0.7795 (m) cc_final: 0.7535 (t) REVERT: B 250 LEU cc_start: 0.8012 (tp) cc_final: 0.7789 (tt) REVERT: B 272 LYS cc_start: 0.8563 (pttt) cc_final: 0.8238 (ttpt) REVERT: B 351 CYS cc_start: 0.7712 (m) cc_final: 0.7507 (m) REVERT: C 49 ARG cc_start: 0.7909 (mmt-90) cc_final: 0.7558 (mpt180) REVERT: C 198 LEU cc_start: 0.8466 (pt) cc_final: 0.8185 (pp) REVERT: C 239 ASN cc_start: 0.7623 (m-40) cc_final: 0.6461 (t0) REVERT: C 290 ASP cc_start: 0.6860 (m-30) cc_final: 0.6627 (m-30) outliers start: 3 outliers final: 3 residues processed: 250 average time/residue: 0.2102 time to fit residues: 70.1311 Evaluate side-chains 221 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 218 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 420 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 0.0370 chunk 82 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 chunk 55 optimal weight: 0.7980 chunk 44 optimal weight: 0.1980 chunk 85 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 98 optimal weight: 0.6980 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN A 51 ASN B 194 ASN ** B 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 322 HIS C 75 GLN C 110 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.1303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8627 Z= 0.194 Angle : 0.626 11.563 11746 Z= 0.317 Chirality : 0.044 0.203 1369 Planarity : 0.004 0.060 1479 Dihedral : 5.596 59.157 1217 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 2.53 % Allowed : 13.36 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.26), residues: 1102 helix: 1.71 (0.30), residues: 339 sheet: -0.55 (0.32), residues: 278 loop : -1.67 (0.27), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 212 HIS 0.004 0.001 HIS E 35 PHE 0.027 0.001 PHE A 181 TYR 0.015 0.001 TYR E 190 ARG 0.003 0.000 ARG C 52 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 211 time to evaluate : 0.930 Fit side-chains REVERT: A 33 LEU cc_start: 0.8877 (mt) cc_final: 0.8500 (mp) REVERT: A 404 ASN cc_start: 0.8650 (m-40) cc_final: 0.8260 (m-40) REVERT: B 218 ASP cc_start: 0.6984 (t0) cc_final: 0.6770 (t0) REVERT: B 247 SER cc_start: 0.7762 (m) cc_final: 0.7547 (t) REVERT: B 272 LYS cc_start: 0.8645 (pttt) cc_final: 0.8278 (ttpt) REVERT: B 274 LEU cc_start: 0.8119 (tt) cc_final: 0.7881 (tt) REVERT: B 343 ILE cc_start: 0.8293 (mm) cc_final: 0.8030 (mt) REVERT: C 49 ARG cc_start: 0.7886 (mmt-90) cc_final: 0.7643 (mmt-90) REVERT: C 198 LEU cc_start: 0.8375 (pt) cc_final: 0.8160 (pp) REVERT: C 239 ASN cc_start: 0.7654 (m-40) cc_final: 0.6437 (t0) outliers start: 22 outliers final: 12 residues processed: 220 average time/residue: 0.2123 time to fit residues: 63.3222 Evaluate side-chains 214 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 202 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ASN Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain C residue 267 ASP Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 174 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 82 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 99 optimal weight: 10.0000 chunk 107 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 98 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 79 optimal weight: 0.6980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 176 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.1427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8627 Z= 0.263 Angle : 0.634 10.971 11746 Z= 0.322 Chirality : 0.045 0.203 1369 Planarity : 0.004 0.065 1479 Dihedral : 5.313 57.172 1214 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 3.11 % Allowed : 16.82 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.26), residues: 1102 helix: 1.88 (0.30), residues: 339 sheet: -0.34 (0.32), residues: 273 loop : -1.66 (0.27), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 339 HIS 0.004 0.001 HIS B 189 PHE 0.015 0.001 PHE C 241 TYR 0.017 0.001 TYR E 190 ARG 0.006 0.000 ARG E 202 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 217 time to evaluate : 0.875 Fit side-chains REVERT: A 45 MET cc_start: 0.6204 (mtm) cc_final: 0.5935 (mtm) REVERT: B 218 ASP cc_start: 0.7030 (t0) cc_final: 0.6784 (t0) REVERT: B 247 SER cc_start: 0.7777 (m) cc_final: 0.7557 (t) REVERT: B 250 LEU cc_start: 0.8029 (tp) cc_final: 0.7818 (tt) REVERT: B 272 LYS cc_start: 0.8671 (pttt) cc_final: 0.8342 (ttpt) REVERT: B 274 LEU cc_start: 0.8149 (tt) cc_final: 0.7883 (tt) REVERT: B 343 ILE cc_start: 0.8301 (mm) cc_final: 0.8059 (mt) REVERT: C 49 ARG cc_start: 0.7879 (mmt-90) cc_final: 0.7666 (mmt-90) REVERT: C 198 LEU cc_start: 0.8389 (pt) cc_final: 0.8160 (pp) REVERT: C 235 PHE cc_start: 0.8181 (t80) cc_final: 0.7962 (t80) REVERT: C 239 ASN cc_start: 0.7712 (m-40) cc_final: 0.6455 (t0) REVERT: E 178 LEU cc_start: 0.8365 (tp) cc_final: 0.8115 (tp) outliers start: 27 outliers final: 19 residues processed: 230 average time/residue: 0.2071 time to fit residues: 64.0677 Evaluate side-chains 234 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 215 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ASN Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 410 ASN Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 267 ASP Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 230 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 0.4980 chunk 74 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 chunk 10 optimal weight: 0.0570 chunk 47 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 99 optimal weight: 7.9990 chunk 105 optimal weight: 0.8980 chunk 94 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 87 optimal weight: 0.5980 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8627 Z= 0.193 Angle : 0.594 10.986 11746 Z= 0.301 Chirality : 0.043 0.211 1369 Planarity : 0.004 0.064 1479 Dihedral : 5.100 54.739 1214 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 3.00 % Allowed : 17.74 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.26), residues: 1102 helix: 2.01 (0.30), residues: 338 sheet: -0.27 (0.32), residues: 273 loop : -1.48 (0.27), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 155 HIS 0.004 0.001 HIS B 189 PHE 0.021 0.001 PHE A 195 TYR 0.014 0.001 TYR E 190 ARG 0.002 0.000 ARG C 52 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 202 time to evaluate : 0.907 Fit side-chains REVERT: A 114 LEU cc_start: 0.7670 (mt) cc_final: 0.7393 (mp) REVERT: A 389 ILE cc_start: 0.7843 (OUTLIER) cc_final: 0.7605 (mt) REVERT: A 404 ASN cc_start: 0.8729 (m110) cc_final: 0.8348 (m-40) REVERT: B 218 ASP cc_start: 0.7004 (t0) cc_final: 0.6754 (t0) REVERT: B 247 SER cc_start: 0.7744 (m) cc_final: 0.7516 (t) REVERT: B 272 LYS cc_start: 0.8620 (pttt) cc_final: 0.8301 (ttpt) REVERT: B 278 LYS cc_start: 0.8544 (ttmm) cc_final: 0.8332 (ttmt) REVERT: B 343 ILE cc_start: 0.8290 (mm) cc_final: 0.8043 (mt) REVERT: C 49 ARG cc_start: 0.7835 (mmt-90) cc_final: 0.7631 (mmt-90) REVERT: C 198 LEU cc_start: 0.8376 (pt) cc_final: 0.8137 (pp) REVERT: C 239 ASN cc_start: 0.7696 (m-40) cc_final: 0.6438 (t0) REVERT: E 97 VAL cc_start: 0.7404 (OUTLIER) cc_final: 0.7004 (t) REVERT: E 140 MET cc_start: 0.8228 (mtm) cc_final: 0.7988 (mtm) REVERT: E 178 LEU cc_start: 0.8334 (tp) cc_final: 0.8085 (tp) outliers start: 26 outliers final: 17 residues processed: 215 average time/residue: 0.2097 time to fit residues: 60.6076 Evaluate side-chains 220 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 201 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ASN Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 267 ASP Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 174 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 89 optimal weight: 0.9980 chunk 72 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8627 Z= 0.273 Angle : 0.628 10.351 11746 Z= 0.320 Chirality : 0.045 0.216 1369 Planarity : 0.004 0.069 1479 Dihedral : 5.298 59.346 1214 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 3.57 % Allowed : 19.01 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.26), residues: 1102 helix: 1.99 (0.30), residues: 338 sheet: -0.31 (0.32), residues: 274 loop : -1.43 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 155 HIS 0.004 0.001 HIS B 189 PHE 0.018 0.002 PHE A 195 TYR 0.017 0.001 TYR E 190 ARG 0.003 0.000 ARG C 52 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 209 time to evaluate : 0.941 Fit side-chains revert: symmetry clash REVERT: A 389 ILE cc_start: 0.7909 (OUTLIER) cc_final: 0.7682 (tp) REVERT: A 393 LEU cc_start: 0.7169 (tp) cc_final: 0.6951 (tt) REVERT: B 218 ASP cc_start: 0.7036 (t0) cc_final: 0.6774 (t0) REVERT: B 247 SER cc_start: 0.7767 (m) cc_final: 0.7552 (t) REVERT: B 272 LYS cc_start: 0.8655 (pttt) cc_final: 0.8342 (ttpt) REVERT: B 343 ILE cc_start: 0.8301 (mm) cc_final: 0.8060 (mt) REVERT: C 49 ARG cc_start: 0.7864 (mmt-90) cc_final: 0.7649 (mmt-90) REVERT: C 198 LEU cc_start: 0.8399 (pt) cc_final: 0.8145 (pp) REVERT: C 239 ASN cc_start: 0.7738 (m-40) cc_final: 0.6500 (t0) REVERT: E 97 VAL cc_start: 0.7492 (OUTLIER) cc_final: 0.7114 (t) REVERT: E 140 MET cc_start: 0.8213 (OUTLIER) cc_final: 0.7573 (mtm) REVERT: E 178 LEU cc_start: 0.8356 (tp) cc_final: 0.8110 (tp) REVERT: E 213 THR cc_start: 0.8527 (OUTLIER) cc_final: 0.8146 (p) REVERT: E 237 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8239 (mp) outliers start: 31 outliers final: 19 residues processed: 224 average time/residue: 0.2241 time to fit residues: 67.9294 Evaluate side-chains 227 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 203 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 58 ASN Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 267 ASP Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 237 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 105 optimal weight: 0.8980 chunk 87 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 101 optimal weight: 0.0870 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 333 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8627 Z= 0.240 Angle : 0.605 9.352 11746 Z= 0.310 Chirality : 0.044 0.225 1369 Planarity : 0.004 0.069 1479 Dihedral : 5.197 54.582 1214 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 4.72 % Allowed : 18.43 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.27), residues: 1102 helix: 2.05 (0.30), residues: 337 sheet: -0.31 (0.32), residues: 274 loop : -1.41 (0.28), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 155 HIS 0.004 0.001 HIS B 189 PHE 0.017 0.001 PHE A 195 TYR 0.017 0.001 TYR E 50 ARG 0.003 0.000 ARG C 52 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 210 time to evaluate : 0.865 Fit side-chains revert: symmetry clash REVERT: A 389 ILE cc_start: 0.7906 (OUTLIER) cc_final: 0.7688 (tp) REVERT: A 404 ASN cc_start: 0.8775 (m110) cc_final: 0.8367 (m-40) REVERT: B 218 ASP cc_start: 0.7031 (t0) cc_final: 0.6771 (t0) REVERT: B 247 SER cc_start: 0.7778 (m) cc_final: 0.7572 (t) REVERT: B 272 LYS cc_start: 0.8642 (pttt) cc_final: 0.8339 (ttpt) REVERT: B 343 ILE cc_start: 0.8298 (mm) cc_final: 0.8051 (mt) REVERT: C 49 ARG cc_start: 0.7880 (mmt-90) cc_final: 0.7644 (mmt-90) REVERT: C 198 LEU cc_start: 0.8382 (pt) cc_final: 0.8137 (pp) REVERT: C 239 ASN cc_start: 0.7742 (m-40) cc_final: 0.6458 (t0) REVERT: C 262 MET cc_start: 0.7433 (ttm) cc_final: 0.7200 (mtm) REVERT: E 97 VAL cc_start: 0.7443 (OUTLIER) cc_final: 0.7048 (t) REVERT: E 140 MET cc_start: 0.8223 (OUTLIER) cc_final: 0.7576 (mtm) REVERT: E 178 LEU cc_start: 0.8349 (tp) cc_final: 0.8103 (tp) REVERT: E 213 THR cc_start: 0.8515 (OUTLIER) cc_final: 0.8152 (p) REVERT: E 237 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8243 (mp) outliers start: 41 outliers final: 26 residues processed: 235 average time/residue: 0.2022 time to fit residues: 64.3144 Evaluate side-chains 237 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 206 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ASN Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 267 ASP Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 94 TYR Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 237 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 chunk 77 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 88 optimal weight: 0.0570 chunk 58 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 64 optimal weight: 0.7980 chunk 48 optimal weight: 0.0060 chunk 41 optimal weight: 4.9990 overall best weight: 0.4514 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8627 Z= 0.176 Angle : 0.580 8.775 11746 Z= 0.296 Chirality : 0.043 0.240 1369 Planarity : 0.004 0.070 1479 Dihedral : 5.076 62.758 1214 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 3.23 % Allowed : 20.16 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.27), residues: 1102 helix: 2.05 (0.30), residues: 338 sheet: -0.23 (0.32), residues: 274 loop : -1.30 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 148 HIS 0.004 0.001 HIS B 196 PHE 0.014 0.001 PHE A 195 TYR 0.016 0.001 TYR E 50 ARG 0.002 0.000 ARG C 52 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 197 time to evaluate : 0.854 Fit side-chains REVERT: A 389 ILE cc_start: 0.7860 (OUTLIER) cc_final: 0.7638 (tp) REVERT: A 450 THR cc_start: 0.8290 (OUTLIER) cc_final: 0.8087 (p) REVERT: B 218 ASP cc_start: 0.6985 (t0) cc_final: 0.6730 (t0) REVERT: B 272 LYS cc_start: 0.8591 (pttt) cc_final: 0.8306 (ttpt) REVERT: B 343 ILE cc_start: 0.8290 (mm) cc_final: 0.8034 (mt) REVERT: C 49 ARG cc_start: 0.7868 (mmt-90) cc_final: 0.7623 (mmt-90) REVERT: C 52 ARG cc_start: 0.7412 (ptp90) cc_final: 0.7209 (ptp-170) REVERT: C 198 LEU cc_start: 0.8326 (pt) cc_final: 0.8103 (pp) REVERT: C 239 ASN cc_start: 0.7659 (m110) cc_final: 0.6427 (t0) REVERT: E 97 VAL cc_start: 0.7383 (OUTLIER) cc_final: 0.6961 (t) REVERT: E 140 MET cc_start: 0.8222 (mtm) cc_final: 0.7614 (mtm) REVERT: E 178 LEU cc_start: 0.8327 (tp) cc_final: 0.8102 (tt) REVERT: E 213 THR cc_start: 0.8469 (OUTLIER) cc_final: 0.8127 (p) outliers start: 28 outliers final: 19 residues processed: 216 average time/residue: 0.2057 time to fit residues: 60.2148 Evaluate side-chains 213 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 190 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ASN Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 267 ASP Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 213 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 0.0770 chunk 31 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 66 optimal weight: 0.7980 chunk 71 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 chunk 82 optimal weight: 3.9990 chunk 95 optimal weight: 0.6980 chunk 100 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 ASN ** B 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8627 Z= 0.197 Angle : 0.581 8.536 11746 Z= 0.300 Chirality : 0.043 0.232 1369 Planarity : 0.004 0.073 1479 Dihedral : 5.229 78.050 1214 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 4.26 % Allowed : 19.47 % Favored : 76.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.26), residues: 1102 helix: 2.04 (0.30), residues: 343 sheet: -0.22 (0.32), residues: 275 loop : -1.29 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 148 HIS 0.004 0.001 HIS B 196 PHE 0.013 0.001 PHE A 195 TYR 0.014 0.001 TYR E 190 ARG 0.002 0.000 ARG C 52 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 192 time to evaluate : 0.822 Fit side-chains REVERT: A 72 ILE cc_start: 0.8350 (OUTLIER) cc_final: 0.7964 (tt) REVERT: A 389 ILE cc_start: 0.7870 (OUTLIER) cc_final: 0.7647 (tp) REVERT: B 218 ASP cc_start: 0.6990 (t0) cc_final: 0.6770 (t0) REVERT: B 272 LYS cc_start: 0.8587 (pttt) cc_final: 0.8308 (ttpt) REVERT: B 343 ILE cc_start: 0.8284 (mm) cc_final: 0.8034 (mt) REVERT: C 49 ARG cc_start: 0.7896 (mmt-90) cc_final: 0.7656 (mmt-90) REVERT: C 198 LEU cc_start: 0.8331 (pt) cc_final: 0.8113 (pp) REVERT: C 239 ASN cc_start: 0.7657 (m110) cc_final: 0.6662 (t0) REVERT: E 97 VAL cc_start: 0.7392 (OUTLIER) cc_final: 0.6976 (t) REVERT: E 140 MET cc_start: 0.8227 (OUTLIER) cc_final: 0.7618 (mtm) REVERT: E 213 THR cc_start: 0.8482 (OUTLIER) cc_final: 0.8140 (p) outliers start: 37 outliers final: 23 residues processed: 215 average time/residue: 0.2212 time to fit residues: 63.7114 Evaluate side-chains 219 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 191 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ASN Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 267 ASP Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 94 TYR Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 213 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 0.7980 chunk 100 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 42 optimal weight: 0.0470 chunk 76 optimal weight: 0.6980 chunk 30 optimal weight: 0.2980 chunk 88 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 chunk 103 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 205 GLN ** B 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8627 Z= 0.185 Angle : 0.588 9.796 11746 Z= 0.301 Chirality : 0.043 0.239 1369 Planarity : 0.004 0.074 1479 Dihedral : 5.327 87.452 1214 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 3.69 % Allowed : 21.08 % Favored : 75.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.26), residues: 1102 helix: 2.00 (0.30), residues: 346 sheet: -0.21 (0.32), residues: 275 loop : -1.28 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 148 HIS 0.004 0.001 HIS B 196 PHE 0.014 0.001 PHE A 195 TYR 0.013 0.001 TYR A 177 ARG 0.005 0.000 ARG C 52 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 190 time to evaluate : 0.821 Fit side-chains REVERT: A 62 LEU cc_start: 0.7466 (tp) cc_final: 0.7214 (tp) REVERT: A 389 ILE cc_start: 0.7871 (OUTLIER) cc_final: 0.7645 (tp) REVERT: A 404 ASN cc_start: 0.8685 (m-40) cc_final: 0.8456 (m-40) REVERT: B 218 ASP cc_start: 0.6988 (t0) cc_final: 0.6761 (t0) REVERT: B 272 LYS cc_start: 0.8576 (pttt) cc_final: 0.8304 (ttpt) REVERT: B 343 ILE cc_start: 0.8282 (mm) cc_final: 0.8028 (mt) REVERT: C 49 ARG cc_start: 0.7713 (mmt-90) cc_final: 0.7511 (mmt-90) REVERT: C 198 LEU cc_start: 0.8278 (pt) cc_final: 0.8061 (pp) REVERT: C 239 ASN cc_start: 0.7648 (m110) cc_final: 0.6637 (t0) REVERT: E 97 VAL cc_start: 0.7370 (OUTLIER) cc_final: 0.6949 (t) REVERT: E 140 MET cc_start: 0.8215 (OUTLIER) cc_final: 0.7615 (mtm) REVERT: E 213 THR cc_start: 0.8464 (OUTLIER) cc_final: 0.8167 (p) outliers start: 32 outliers final: 24 residues processed: 211 average time/residue: 0.2140 time to fit residues: 60.7484 Evaluate side-chains 216 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 188 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ASN Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 267 ASP Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 94 TYR Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 213 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 3.9990 chunk 71 optimal weight: 0.6980 chunk 108 optimal weight: 0.0770 chunk 99 optimal weight: 0.2980 chunk 86 optimal weight: 0.5980 chunk 8 optimal weight: 0.5980 chunk 66 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 68 optimal weight: 0.9980 chunk 92 optimal weight: 0.2980 chunk 26 optimal weight: 0.6980 overall best weight: 0.3738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8627 Z= 0.163 Angle : 0.573 9.981 11746 Z= 0.294 Chirality : 0.043 0.246 1369 Planarity : 0.004 0.069 1479 Dihedral : 5.270 87.259 1214 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 3.23 % Allowed : 21.54 % Favored : 75.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.26), residues: 1102 helix: 2.11 (0.30), residues: 343 sheet: -0.26 (0.32), residues: 277 loop : -1.23 (0.28), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 148 HIS 0.004 0.001 HIS B 196 PHE 0.014 0.001 PHE A 195 TYR 0.014 0.001 TYR E 190 ARG 0.003 0.000 ARG C 52 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 193 time to evaluate : 0.852 Fit side-chains REVERT: A 62 LEU cc_start: 0.7430 (tp) cc_final: 0.7189 (tp) REVERT: A 72 ILE cc_start: 0.8318 (OUTLIER) cc_final: 0.7948 (tt) REVERT: A 389 ILE cc_start: 0.7848 (OUTLIER) cc_final: 0.7622 (tp) REVERT: A 404 ASN cc_start: 0.8683 (m-40) cc_final: 0.8416 (m-40) REVERT: B 218 ASP cc_start: 0.6961 (t0) cc_final: 0.6738 (t0) REVERT: B 272 LYS cc_start: 0.8566 (pttt) cc_final: 0.8303 (ttpt) REVERT: B 343 ILE cc_start: 0.8292 (mm) cc_final: 0.8031 (mt) REVERT: C 49 ARG cc_start: 0.7679 (mmt-90) cc_final: 0.7446 (mmt-90) REVERT: C 198 LEU cc_start: 0.8235 (pt) cc_final: 0.8032 (pp) REVERT: C 239 ASN cc_start: 0.7616 (m110) cc_final: 0.6602 (t0) REVERT: E 97 VAL cc_start: 0.7358 (OUTLIER) cc_final: 0.6931 (t) REVERT: E 140 MET cc_start: 0.8217 (OUTLIER) cc_final: 0.7632 (mtm) REVERT: E 213 THR cc_start: 0.8451 (OUTLIER) cc_final: 0.8148 (p) outliers start: 28 outliers final: 17 residues processed: 209 average time/residue: 0.2094 time to fit residues: 58.4708 Evaluate side-chains 212 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 190 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 58 ASN Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 267 ASP Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 213 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 24 optimal weight: 0.1980 chunk 86 optimal weight: 0.2980 chunk 36 optimal weight: 2.9990 chunk 88 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 76 optimal weight: 0.8980 chunk 4 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.126748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.112036 restraints weight = 13529.583| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 2.26 r_work: 0.3375 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3228 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8627 Z= 0.184 Angle : 0.595 10.316 11746 Z= 0.302 Chirality : 0.043 0.238 1369 Planarity : 0.004 0.067 1479 Dihedral : 5.259 85.927 1213 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 3.34 % Allowed : 21.89 % Favored : 74.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.26), residues: 1102 helix: 2.10 (0.30), residues: 344 sheet: -0.20 (0.32), residues: 275 loop : -1.21 (0.28), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 148 HIS 0.004 0.001 HIS B 196 PHE 0.015 0.001 PHE A 195 TYR 0.018 0.001 TYR E 50 ARG 0.003 0.000 ARG C 52 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2325.52 seconds wall clock time: 42 minutes 19.34 seconds (2539.34 seconds total)