Starting phenix.real_space_refine on Thu Feb 15 19:02:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oik_20079/02_2024/6oik_20079_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oik_20079/02_2024/6oik_20079.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oik_20079/02_2024/6oik_20079.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oik_20079/02_2024/6oik_20079.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oik_20079/02_2024/6oik_20079_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oik_20079/02_2024/6oik_20079_updated.pdb" } resolution = 3.6 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= 0.003 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 4681 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 60 5.16 5 Cl 1 4.86 5 C 5427 2.51 5 N 1436 2.21 5 O 1572 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 121": "NH1" <-> "NH2" Residue "R ARG 211": "NH1" <-> "NH2" Residue "R ARG 381": "NH1" <-> "NH2" Residue "A ARG 198": "NH1" <-> "NH2" Residue "A ARG 209": "NH1" <-> "NH2" Residue "A ARG 243": "NH1" <-> "NH2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "A GLU 318": "OE1" <-> "OE2" Residue "A ARG 349": "NH1" <-> "NH2" Residue "B ARG 48": "NH1" <-> "NH2" Residue "B ARG 134": "NH1" <-> "NH2" Residue "H ARG 202": "NH1" <-> "NH2" Residue "H GLU 220": "OE1" <-> "OE2" Residue "H GLU 246": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8496 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2087 Classifications: {'peptide': 278} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 11, 'TRANS': 266} Chain breaks: 1 Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 158 Unresolved non-hydrogen dihedrals: 100 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 2, 'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 44 Chain: "A" Number of atoms: 1678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1678 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 4, 'TRANS': 212} Chain breaks: 2 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 2538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2538 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 49 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': 3} Unresolved non-hydrogen planarities: 50 Chain: "G" 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: "H" 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: "R" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 43 Unusual residues: {'2CU': 1, 'IXO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.10, per 1000 atoms: 0.60 Number of scatterers: 8496 At special positions: 0 Unit cell: (107.06, 115.54, 109.18, 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 60 16.00 O 1572 8.00 N 1436 7.00 C 5427 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS R 96 " - pdb=" SG CYS R 176 " distance=2.37 Simple disulfide: pdb=" SG CYS R 413 " - pdb=" SG CYS R 416 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS H 159 " - pdb=" SG CYS H 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: 3.35 Conformation dependent library (CDL) restraints added in 1.6 seconds 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2100 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 25 helices and 13 sheets defined 32.4% alpha, 20.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.58 Creating SS restraints... Processing helix chain 'R' and resid 21 through 49 Processing helix chain 'R' and resid 57 through 86 removed outlier: 4.020A pdb=" N ILE R 71 " --> pdb=" O CYS R 67 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ILE R 72 " --> pdb=" O ALA R 68 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE R 75 " --> pdb=" O ILE R 71 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N MET R 77 " --> pdb=" O GLY R 73 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N ASN R 78 " --> pdb=" O VAL R 74 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU R 79 " --> pdb=" O PHE R 75 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N TYR R 80 " --> pdb=" O SER R 76 " (cutoff:3.500A) Processing helix chain 'R' and resid 95 through 126 Processing helix chain 'R' and resid 128 through 131 No H-bonds generated for 'chain 'R' and resid 128 through 131' Processing helix chain 'R' and resid 137 through 160 Proline residue: R 157 - end of helix Processing helix chain 'R' and resid 162 through 166 Processing helix chain 'R' and resid 185 through 194 removed outlier: 3.882A pdb=" N ALA R 193 " --> pdb=" O GLY R 189 " (cutoff:3.500A) Processing helix chain 'R' and resid 196 through 212 Processing helix chain 'R' and resid 380 through 411 removed outlier: 4.657A pdb=" N VAL R 385 " --> pdb=" O ARG R 381 " (cutoff:3.500A) Proline residue: R 402 - end of helix removed outlier: 4.106A pdb=" N THR R 411 " --> pdb=" O VAL R 407 " (cutoff:3.500A) Processing helix chain 'R' and resid 419 through 435 removed outlier: 4.265A pdb=" N ASN R 432 " --> pdb=" O LEU R 428 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N SER R 433 " --> pdb=" O CYS R 429 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N THR R 434 " --> pdb=" O TYR R 430 " (cutoff:3.500A) Processing helix chain 'R' and resid 437 through 440 No H-bonds generated for 'chain 'R' and resid 437 through 440' Processing helix chain 'R' and resid 445 through 453 Processing helix chain 'A' and resid 10 through 31 Processing helix chain 'A' and resid 46 through 51 Processing helix chain 'A' and resid 209 through 211 No H-bonds generated for 'chain 'A' and resid 209 through 211' Processing helix chain 'A' and resid 243 through 254 Processing helix chain 'A' and resid 272 through 281 Processing helix chain 'A' and resid 297 through 311 removed outlier: 4.189A pdb=" N LYS A 311 " --> pdb=" O GLN A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 351 Processing helix chain 'B' and resid 4 through 24 Processing helix chain 'G' and resid 8 through 22 Processing helix chain 'G' and resid 30 through 47 removed outlier: 4.682A pdb=" N LYS G 46 " --> pdb=" O GLU G 42 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N GLU G 47 " --> pdb=" O ALA G 43 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 31 No H-bonds generated for 'chain 'H' and resid 29 through 31' Processing helix chain 'H' and resid 53 through 55 No H-bonds generated for 'chain 'H' and resid 53 through 55' Processing helix chain 'H' and resid 221 through 223 No H-bonds generated for 'chain 'H' and resid 221 through 223' Processing sheet with id= A, first strand: chain 'A' and resid 319 through 323 removed outlier: 6.874A pdb=" N ILE A 265 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.450A pdb=" N HIS A 322 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N LEU A 267 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N ILE A 222 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N PHE A 268 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N PHE A 224 " --> pdb=" O PHE A 268 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ASN A 270 " --> pdb=" O PHE A 224 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N VAL A 226 " --> pdb=" O ASN A 270 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA A 221 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N CYS A 225 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.645A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.916A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.814A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 198 through 201 removed outlier: 6.706A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.666A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 276 through 278 removed outlier: 3.954A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 47 through 52 removed outlier: 6.814A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'H' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.803A pdb=" N THR H 118 " --> pdb=" O GLY H 10 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL H 12 " --> pdb=" O THR H 118 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ALA H 40 " --> pdb=" O LEU H 45 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N LEU H 45 " --> pdb=" O ALA H 40 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'H' and resid 146 through 149 removed outlier: 6.469A pdb=" N LYS H 244 " --> pdb=" O VAL H 147 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N VAL H 149 " --> pdb=" O LYS H 244 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N GLU H 246 " --> pdb=" O VAL H 149 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'H' and resid 155 through 160 Processing sheet with id= M, first strand: chain 'H' and resid 226 through 231 removed outlier: 6.202A pdb=" N LEU H 178 " --> pdb=" O LEU H 187 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N LEU H 187 " --> pdb=" O LEU H 178 " (cutoff:3.500A) 379 hydrogen bonds defined for protein. 1083 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: 2.23 Time building geometry restraints manager: 3.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1367 1.31 - 1.44: 2433 1.44 - 1.56: 4794 1.56 - 1.69: 1 1.69 - 1.81: 88 Bond restraints: 8683 Sorted by residual: bond pdb=" C10 IXO R 501 " pdb=" N11 IXO R 501 " ideal model delta sigma weight residual 1.270 1.473 -0.203 2.00e-02 2.50e+03 1.03e+02 bond pdb=" C10 IXO R 501 " pdb=" C14 IXO R 501 " ideal model delta sigma weight residual 1.492 1.331 0.161 2.00e-02 2.50e+03 6.52e+01 bond pdb=" C13 IXO R 501 " pdb=" O12 IXO R 501 " ideal model delta sigma weight residual 1.439 1.543 -0.104 2.00e-02 2.50e+03 2.71e+01 bond pdb=" C05 IXO R 501 " pdb=" C06 IXO R 501 " ideal model delta sigma weight residual 1.450 1.534 -0.084 2.00e-02 2.50e+03 1.78e+01 bond pdb=" C TRP B 99 " pdb=" N VAL B 100 " ideal model delta sigma weight residual 1.331 1.283 0.047 1.32e-02 5.74e+03 1.29e+01 ... (remaining 8678 not shown) Histogram of bond angle deviations from ideal: 59.77 - 83.43: 3 83.43 - 107.09: 237 107.09 - 130.75: 11533 130.75 - 154.40: 48 154.40 - 178.06: 2 Bond angle restraints: 11823 Sorted by residual: angle pdb=" C VAL H 12 " pdb=" N GLN H 13 " pdb=" CA GLN H 13 " ideal model delta sigma weight residual 120.39 133.39 -13.00 1.39e+00 5.18e-01 8.74e+01 angle pdb=" N VAL R 94 " pdb=" CA VAL R 94 " pdb=" C VAL R 94 " ideal model delta sigma weight residual 111.90 106.72 5.18 8.10e-01 1.52e+00 4.09e+01 angle pdb=" C ARG H 191 " pdb=" N MET H 192 " pdb=" CA MET H 192 " ideal model delta sigma weight residual 121.54 130.41 -8.87 1.91e+00 2.74e-01 2.16e+01 angle pdb=" N ILE R 159 " pdb=" CA ILE R 159 " pdb=" C ILE R 159 " ideal model delta sigma weight residual 113.53 109.43 4.10 9.80e-01 1.04e+00 1.75e+01 angle pdb=" C THR B 86 " pdb=" N THR B 87 " pdb=" CA THR B 87 " ideal model delta sigma weight residual 121.54 129.50 -7.96 1.91e+00 2.74e-01 1.74e+01 ... (remaining 11818 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.80: 4896 28.80 - 57.60: 169 57.60 - 86.41: 10 86.41 - 115.21: 2 115.21 - 144.01: 3 Dihedral angle restraints: 5080 sinusoidal: 1821 harmonic: 3259 Sorted by residual: dihedral pdb=" CB CYS R 413 " pdb=" SG CYS R 413 " pdb=" SG CYS R 416 " pdb=" CB CYS R 416 " ideal model delta sinusoidal sigma weight residual 93.00 151.61 -58.61 1 1.00e+01 1.00e-02 4.60e+01 dihedral pdb=" CA ILE B 81 " pdb=" C ILE B 81 " pdb=" N TRP B 82 " pdb=" CA TRP B 82 " ideal model delta harmonic sigma weight residual -180.00 -154.03 -25.97 0 5.00e+00 4.00e-02 2.70e+01 dihedral pdb=" CA TRP B 82 " pdb=" C TRP B 82 " pdb=" N ASP B 83 " pdb=" CA ASP B 83 " ideal model delta harmonic sigma weight residual 180.00 154.64 25.36 0 5.00e+00 4.00e-02 2.57e+01 ... (remaining 5077 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1068 0.073 - 0.147: 265 0.147 - 0.220: 28 0.220 - 0.294: 2 0.294 - 0.367: 3 Chirality restraints: 1366 Sorted by residual: chirality pdb=" CB THR H 172 " pdb=" CA THR H 172 " pdb=" OG1 THR H 172 " pdb=" CG2 THR H 172 " both_signs ideal model delta sigma weight residual False 2.55 2.18 0.37 2.00e-01 2.50e+01 3.37e+00 chirality pdb=" CA ASP H 74 " pdb=" N ASP H 74 " pdb=" C ASP H 74 " pdb=" CB ASP H 74 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.46e+00 chirality pdb=" CB VAL A 202 " pdb=" CA VAL A 202 " pdb=" CG1 VAL A 202 " pdb=" CG2 VAL A 202 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.28e+00 ... (remaining 1363 not shown) Planarity restraints: 1488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C12 2CU R 502 " 0.001 2.00e-02 2.50e+03 2.14e-02 1.60e+01 pdb=" C13 2CU R 502 " 0.006 2.00e-02 2.50e+03 pdb=" C15 2CU R 502 " 0.002 2.00e-02 2.50e+03 pdb=" C16 2CU R 502 " 0.007 2.00e-02 2.50e+03 pdb=" C17 2CU R 502 " -0.009 2.00e-02 2.50e+03 pdb=" C18 2CU R 502 " -0.015 2.00e-02 2.50e+03 pdb=" C20 2CU R 502 " 0.009 2.00e-02 2.50e+03 pdb=" C22 2CU R 502 " -0.013 2.00e-02 2.50e+03 pdb=" C24 2CU R 502 " 0.057 2.00e-02 2.50e+03 pdb=" N19 2CU R 502 " -0.037 2.00e-02 2.50e+03 pdb=" N23 2CU R 502 " -0.008 2.00e-02 2.50e+03 pdb=" O11 2CU R 502 " 0.006 2.00e-02 2.50e+03 pdb=" S21 2CU R 502 " -0.025 2.00e-02 2.50e+03 pdb="CL1 2CU R 502 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C04 2CU R 502 " -0.017 2.00e-02 2.50e+03 2.41e-02 8.68e+00 pdb=" C06 2CU R 502 " 0.035 2.00e-02 2.50e+03 pdb=" C08 2CU R 502 " -0.007 2.00e-02 2.50e+03 pdb=" C10 2CU R 502 " 0.031 2.00e-02 2.50e+03 pdb=" N05 2CU R 502 " -0.023 2.00e-02 2.50e+03 pdb=" O09 2CU R 502 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP G 48 " 0.044 5.00e-02 4.00e+02 6.59e-02 6.95e+00 pdb=" N PRO G 49 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO G 49 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO G 49 " 0.036 5.00e-02 4.00e+02 ... (remaining 1485 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 83 2.57 - 3.15: 6629 3.15 - 3.73: 13607 3.73 - 4.32: 18304 4.32 - 4.90: 30684 Nonbonded interactions: 69307 Sorted by model distance: nonbonded pdb=" OH TYR R 104 " pdb=" OH TYR R 426 " model vdw 1.986 2.440 nonbonded pdb=" OH TYR A 291 " pdb=" OD2 ASP A 299 " model vdw 2.238 2.440 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.239 2.440 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.242 2.440 nonbonded pdb=" OG1 THR B 321 " pdb=" OD1 ASP B 323 " model vdw 2.257 2.440 ... (remaining 69302 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.610 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: 2.730 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 25.960 Find NCS groups from input model: 0.220 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: 0.010 Load rotamer database and sin/cos tables:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 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 : 0.009 0.203 8683 Z= 0.615 Angle : 1.060 12.997 11823 Z= 0.614 Chirality : 0.063 0.367 1366 Planarity : 0.007 0.066 1488 Dihedral : 14.958 144.009 2968 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 1.04 % Allowed : 13.26 % Favored : 85.70 % 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: -3.68 (0.21), residues: 1107 helix: -2.35 (0.21), residues: 373 sheet: -1.87 (0.28), residues: 275 loop : -2.73 (0.24), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP B 211 HIS 0.005 0.002 HIS B 91 PHE 0.028 0.003 PHE R 25 TYR 0.034 0.003 TYR R 104 ARG 0.003 0.001 ARG H 18 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 204 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 120 ASP cc_start: 0.8752 (t70) cc_final: 0.8405 (t0) REVERT: R 134 LYS cc_start: 0.7363 (mmtt) cc_final: 0.6686 (tttm) REVERT: A 217 GLU cc_start: 0.7473 (pt0) cc_final: 0.7027 (pt0) REVERT: A 246 GLU cc_start: 0.8341 (tm-30) cc_final: 0.7820 (tp30) outliers start: 9 outliers final: 5 residues processed: 211 average time/residue: 0.2400 time to fit residues: 66.2788 Evaluate side-chains 142 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 137 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 316 ASN Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain H residue 216 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 85 optimal weight: 0.0670 chunk 33 optimal weight: 0.4980 chunk 51 optimal weight: 6.9990 chunk 63 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 41 ASN R 59 ASN ** R 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 22 ASN A 214 HIS A 270 ASN A 347 ASN B 88 ASN B 259 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8683 Z= 0.184 Angle : 0.594 7.806 11823 Z= 0.314 Chirality : 0.043 0.159 1366 Planarity : 0.005 0.060 1488 Dihedral : 7.272 140.909 1234 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.92 % Allowed : 18.45 % Favored : 77.62 % 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: -2.22 (0.24), residues: 1107 helix: -0.48 (0.26), residues: 374 sheet: -1.49 (0.28), residues: 283 loop : -2.22 (0.26), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 211 HIS 0.004 0.001 HIS A 322 PHE 0.023 0.001 PHE R 447 TYR 0.012 0.001 TYR B 105 ARG 0.003 0.000 ARG A 209 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 179 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 134 LYS cc_start: 0.7210 (mmtt) cc_final: 0.6565 (tttm) REVERT: R 150 LEU cc_start: 0.7778 (OUTLIER) cc_final: 0.7495 (tt) REVERT: A 205 GLN cc_start: 0.7997 (tp40) cc_final: 0.7710 (tp40) REVERT: A 244 MET cc_start: 0.8203 (OUTLIER) cc_final: 0.7778 (mpp) REVERT: A 246 GLU cc_start: 0.8010 (tm-30) cc_final: 0.7686 (tp30) REVERT: A 254 ILE cc_start: 0.9454 (tp) cc_final: 0.9227 (tp) REVERT: H 223 ASP cc_start: 0.6656 (m-30) cc_final: 0.6085 (m-30) outliers start: 34 outliers final: 15 residues processed: 200 average time/residue: 0.2125 time to fit residues: 57.2135 Evaluate side-chains 170 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 153 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 143 MET Chi-restraints excluded: chain R residue 150 LEU Chi-restraints excluded: chain R residue 426 TYR Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain A residue 316 ASN Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 74 ASP Chi-restraints excluded: chain H residue 216 ILE Chi-restraints excluded: chain H residue 238 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 82 optimal weight: 8.9990 chunk 67 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 99 optimal weight: 40.0000 chunk 107 optimal weight: 0.8980 chunk 88 optimal weight: 4.9990 chunk 98 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 453 HIS A 270 ASN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN H 186 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8683 Z= 0.267 Angle : 0.608 8.680 11823 Z= 0.322 Chirality : 0.045 0.200 1366 Planarity : 0.004 0.054 1488 Dihedral : 6.869 140.616 1232 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 5.19 % Allowed : 20.76 % Favored : 74.05 % 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: -1.74 (0.24), residues: 1107 helix: 0.02 (0.27), residues: 374 sheet: -1.38 (0.29), residues: 283 loop : -1.93 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 82 HIS 0.003 0.001 HIS A 322 PHE 0.021 0.001 PHE R 447 TYR 0.023 0.001 TYR R 177 ARG 0.009 0.000 ARG H 180 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 154 time to evaluate : 1.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 134 LYS cc_start: 0.7172 (mmtt) cc_final: 0.6558 (tttm) REVERT: R 150 LEU cc_start: 0.7776 (OUTLIER) cc_final: 0.7500 (tt) REVERT: R 423 THR cc_start: 0.8141 (m) cc_final: 0.7904 (p) REVERT: A 244 MET cc_start: 0.8223 (OUTLIER) cc_final: 0.7678 (mpp) REVERT: A 325 CYS cc_start: 0.5562 (p) cc_final: 0.5308 (p) REVERT: H 140 MET cc_start: 0.7713 (mtp) cc_final: 0.7497 (mtp) REVERT: H 223 ASP cc_start: 0.6645 (m-30) cc_final: 0.6428 (m-30) outliers start: 45 outliers final: 28 residues processed: 183 average time/residue: 0.2142 time to fit residues: 53.8047 Evaluate side-chains 183 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 153 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 96 CYS Chi-restraints excluded: chain R residue 117 ILE Chi-restraints excluded: chain R residue 143 MET Chi-restraints excluded: chain R residue 150 LEU Chi-restraints excluded: chain R residue 392 ILE Chi-restraints excluded: chain R residue 426 TYR Chi-restraints excluded: chain R residue 453 HIS Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain A residue 316 ASN Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 74 ASP Chi-restraints excluded: chain H residue 216 ILE Chi-restraints excluded: chain H residue 230 MET Chi-restraints excluded: chain H residue 238 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 51 optimal weight: 7.9990 chunk 10 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 99 optimal weight: 40.0000 chunk 105 optimal weight: 10.0000 chunk 94 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 87 optimal weight: 4.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 11 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8683 Z= 0.268 Angle : 0.609 8.673 11823 Z= 0.322 Chirality : 0.045 0.199 1366 Planarity : 0.005 0.071 1488 Dihedral : 6.908 140.615 1232 Min Nonbonded Distance : 1.565 Molprobity Statistics. All-atom Clashscore : 18.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.46 % Allowed : 23.18 % Favored : 73.36 % 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: -1.74 (0.24), residues: 1107 helix: 0.02 (0.27), residues: 374 sheet: -1.38 (0.29), residues: 283 loop : -1.93 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 82 HIS 0.003 0.001 HIS R 453 PHE 0.021 0.001 PHE R 447 TYR 0.023 0.001 TYR R 177 ARG 0.009 0.000 ARG H 180 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 153 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 69 ASP cc_start: 0.8080 (m-30) cc_final: 0.7798 (t0) REVERT: R 134 LYS cc_start: 0.7170 (mmtt) cc_final: 0.6563 (tttm) REVERT: R 150 LEU cc_start: 0.7789 (OUTLIER) cc_final: 0.7501 (tt) REVERT: A 244 MET cc_start: 0.8225 (OUTLIER) cc_final: 0.7670 (mpp) REVERT: A 246 GLU cc_start: 0.8107 (tm-30) cc_final: 0.7773 (tp30) REVERT: A 325 CYS cc_start: 0.5567 (p) cc_final: 0.5311 (p) REVERT: H 140 MET cc_start: 0.7709 (mtp) cc_final: 0.7494 (mtp) outliers start: 30 outliers final: 28 residues processed: 172 average time/residue: 0.1979 time to fit residues: 46.9140 Evaluate side-chains 178 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 148 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 96 CYS Chi-restraints excluded: chain R residue 117 ILE Chi-restraints excluded: chain R residue 143 MET Chi-restraints excluded: chain R residue 150 LEU Chi-restraints excluded: chain R residue 392 ILE Chi-restraints excluded: chain R residue 426 TYR Chi-restraints excluded: chain R residue 453 HIS Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain A residue 316 ASN Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 74 ASP Chi-restraints excluded: chain H residue 216 ILE Chi-restraints excluded: chain H residue 230 MET Chi-restraints excluded: chain H residue 238 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 78 optimal weight: 10.0000 chunk 43 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 53 optimal weight: 4.9990 chunk 94 optimal weight: 0.8980 chunk 26 optimal weight: 8.9990 chunk 35 optimal weight: 0.2980 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 453 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8683 Z= 0.194 Angle : 0.580 7.552 11823 Z= 0.308 Chirality : 0.044 0.196 1366 Planarity : 0.004 0.050 1488 Dihedral : 6.585 140.605 1232 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 4.38 % Allowed : 22.84 % Favored : 72.78 % 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: -1.28 (0.25), residues: 1107 helix: 0.47 (0.27), residues: 374 sheet: -1.19 (0.28), residues: 281 loop : -1.68 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 82 HIS 0.006 0.001 HIS R 453 PHE 0.016 0.001 PHE R 447 TYR 0.021 0.001 TYR R 177 ARG 0.015 0.001 ARG R 169 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 174 time to evaluate : 0.994 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: R 69 ASP cc_start: 0.7989 (m-30) cc_final: 0.7788 (t0) REVERT: R 83 TYR cc_start: 0.8439 (t80) cc_final: 0.8232 (t80) REVERT: R 134 LYS cc_start: 0.7240 (mmtt) cc_final: 0.6641 (tttm) REVERT: R 150 LEU cc_start: 0.7778 (OUTLIER) cc_final: 0.7503 (tt) REVERT: R 439 CYS cc_start: 0.8011 (OUTLIER) cc_final: 0.7616 (p) REVERT: A 244 MET cc_start: 0.8136 (OUTLIER) cc_final: 0.7463 (mpp) REVERT: A 246 GLU cc_start: 0.8096 (tm-30) cc_final: 0.7761 (tp30) REVERT: A 333 GLN cc_start: 0.8130 (tp40) cc_final: 0.7912 (tp40) REVERT: B 111 TYR cc_start: 0.8625 (m-80) cc_final: 0.8377 (m-10) outliers start: 38 outliers final: 26 residues processed: 197 average time/residue: 0.1994 time to fit residues: 54.1253 Evaluate side-chains 179 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 150 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 96 CYS Chi-restraints excluded: chain R residue 103 ASP Chi-restraints excluded: chain R residue 150 LEU Chi-restraints excluded: chain R residue 426 TYR Chi-restraints excluded: chain R residue 434 THR Chi-restraints excluded: chain R residue 439 CYS Chi-restraints excluded: chain R residue 453 HIS Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain A residue 316 ASN Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 74 ASP Chi-restraints excluded: chain H residue 192 MET Chi-restraints excluded: chain H residue 216 ILE Chi-restraints excluded: chain H residue 230 MET Chi-restraints excluded: chain H residue 238 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 7.9990 chunk 20 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 chunk 26 optimal weight: 7.9990 chunk 105 optimal weight: 9.9990 chunk 87 optimal weight: 4.9990 chunk 48 optimal weight: 10.0000 chunk 8 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 8683 Z= 0.372 Angle : 0.659 7.673 11823 Z= 0.349 Chirality : 0.047 0.204 1366 Planarity : 0.005 0.057 1488 Dihedral : 6.673 139.476 1232 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 5.31 % Allowed : 24.11 % Favored : 70.59 % 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: -1.28 (0.25), residues: 1107 helix: 0.48 (0.27), residues: 374 sheet: -1.31 (0.28), residues: 288 loop : -1.58 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 211 HIS 0.019 0.002 HIS R 453 PHE 0.019 0.002 PHE R 447 TYR 0.025 0.002 TYR R 177 ARG 0.007 0.001 ARG R 169 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 142 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 83 TYR cc_start: 0.8478 (t80) cc_final: 0.8245 (t80) REVERT: R 134 LYS cc_start: 0.7248 (mmtt) cc_final: 0.6632 (tttm) REVERT: R 150 LEU cc_start: 0.7866 (OUTLIER) cc_final: 0.7592 (tt) REVERT: R 439 CYS cc_start: 0.8026 (OUTLIER) cc_final: 0.7583 (p) REVERT: A 244 MET cc_start: 0.8180 (OUTLIER) cc_final: 0.7354 (mpp) REVERT: A 333 GLN cc_start: 0.8234 (tp40) cc_final: 0.7994 (tp40) REVERT: H 140 MET cc_start: 0.7825 (mtp) cc_final: 0.7587 (mtp) outliers start: 46 outliers final: 37 residues processed: 173 average time/residue: 0.1947 time to fit residues: 46.8039 Evaluate side-chains 174 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 134 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 25 PHE Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 96 CYS Chi-restraints excluded: chain R residue 103 ASP Chi-restraints excluded: chain R residue 117 ILE Chi-restraints excluded: chain R residue 150 LEU Chi-restraints excluded: chain R residue 199 VAL Chi-restraints excluded: chain R residue 426 TYR Chi-restraints excluded: chain R residue 434 THR Chi-restraints excluded: chain R residue 439 CYS Chi-restraints excluded: chain R residue 453 HIS Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain A residue 316 ASN Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 74 ASP Chi-restraints excluded: chain H residue 141 THR Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain H residue 192 MET Chi-restraints excluded: chain H residue 216 ILE Chi-restraints excluded: chain H residue 230 MET Chi-restraints excluded: chain H residue 237 LEU Chi-restraints excluded: chain H residue 238 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 6.9990 chunk 60 optimal weight: 0.7980 chunk 77 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 105 optimal weight: 7.9990 chunk 65 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 48 optimal weight: 7.9990 chunk 41 optimal weight: 0.0770 overall best weight: 1.1744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 179 GLN ** R 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8683 Z= 0.205 Angle : 0.600 8.335 11823 Z= 0.313 Chirality : 0.044 0.207 1366 Planarity : 0.004 0.053 1488 Dihedral : 6.620 140.380 1232 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 5.31 % Allowed : 25.14 % Favored : 69.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.03 (0.25), residues: 1107 helix: 0.69 (0.27), residues: 374 sheet: -1.15 (0.28), residues: 286 loop : -1.45 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 82 HIS 0.007 0.001 HIS R 453 PHE 0.014 0.001 PHE H 68 TYR 0.018 0.001 TYR R 177 ARG 0.006 0.000 ARG A 209 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 147 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 83 TYR cc_start: 0.8452 (t80) cc_final: 0.8200 (t80) REVERT: R 134 LYS cc_start: 0.7206 (mmtt) cc_final: 0.6639 (tttm) REVERT: R 150 LEU cc_start: 0.7836 (OUTLIER) cc_final: 0.7558 (tt) REVERT: R 439 CYS cc_start: 0.7971 (OUTLIER) cc_final: 0.7610 (p) REVERT: A 244 MET cc_start: 0.8166 (OUTLIER) cc_final: 0.7441 (mpp) REVERT: A 333 GLN cc_start: 0.8258 (tp40) cc_final: 0.8005 (tp40) REVERT: B 105 TYR cc_start: 0.9039 (t80) cc_final: 0.8838 (t80) outliers start: 46 outliers final: 32 residues processed: 181 average time/residue: 0.1971 time to fit residues: 49.2479 Evaluate side-chains 184 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 149 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 96 CYS Chi-restraints excluded: chain R residue 103 ASP Chi-restraints excluded: chain R residue 150 LEU Chi-restraints excluded: chain R residue 199 VAL Chi-restraints excluded: chain R residue 433 SER Chi-restraints excluded: chain R residue 434 THR Chi-restraints excluded: chain R residue 439 CYS Chi-restraints excluded: chain R residue 453 HIS Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain A residue 316 ASN Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 74 ASP Chi-restraints excluded: chain H residue 149 VAL Chi-restraints excluded: chain H residue 192 MET Chi-restraints excluded: chain H residue 216 ILE Chi-restraints excluded: chain H residue 230 MET Chi-restraints excluded: chain H residue 237 LEU Chi-restraints excluded: chain H residue 238 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 4.9990 chunk 31 optimal weight: 0.4980 chunk 20 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 82 optimal weight: 0.0970 chunk 95 optimal weight: 1.9990 chunk 100 optimal weight: 9.9990 chunk 91 optimal weight: 0.4980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8683 Z= 0.205 Angle : 0.600 8.335 11823 Z= 0.313 Chirality : 0.044 0.207 1366 Planarity : 0.004 0.053 1488 Dihedral : 6.620 140.380 1232 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 16.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 4.04 % Allowed : 25.84 % Favored : 70.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.03 (0.25), residues: 1107 helix: 0.69 (0.27), residues: 374 sheet: -1.15 (0.28), residues: 286 loop : -1.45 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 82 HIS 0.007 0.001 HIS R 453 PHE 0.014 0.001 PHE H 68 TYR 0.018 0.001 TYR R 177 ARG 0.006 0.000 ARG A 209 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 149 time to evaluate : 1.035 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: R 83 TYR cc_start: 0.8443 (t80) cc_final: 0.8201 (t80) REVERT: R 134 LYS cc_start: 0.7212 (mmtt) cc_final: 0.6639 (tttm) REVERT: R 150 LEU cc_start: 0.7822 (OUTLIER) cc_final: 0.7560 (tt) REVERT: R 439 CYS cc_start: 0.7963 (OUTLIER) cc_final: 0.7608 (p) REVERT: A 244 MET cc_start: 0.8170 (OUTLIER) cc_final: 0.7437 (mpp) REVERT: A 246 GLU cc_start: 0.8113 (tm-30) cc_final: 0.7772 (tp30) REVERT: A 333 GLN cc_start: 0.8259 (tp40) cc_final: 0.8005 (tp40) REVERT: B 105 TYR cc_start: 0.9040 (t80) cc_final: 0.8838 (t80) outliers start: 35 outliers final: 32 residues processed: 171 average time/residue: 0.2000 time to fit residues: 47.5333 Evaluate side-chains 181 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 146 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 96 CYS Chi-restraints excluded: chain R residue 103 ASP Chi-restraints excluded: chain R residue 150 LEU Chi-restraints excluded: chain R residue 199 VAL Chi-restraints excluded: chain R residue 433 SER Chi-restraints excluded: chain R residue 434 THR Chi-restraints excluded: chain R residue 439 CYS Chi-restraints excluded: chain R residue 453 HIS Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain A residue 316 ASN Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 74 ASP Chi-restraints excluded: chain H residue 149 VAL Chi-restraints excluded: chain H residue 192 MET Chi-restraints excluded: chain H residue 216 ILE Chi-restraints excluded: chain H residue 230 MET Chi-restraints excluded: chain H residue 237 LEU Chi-restraints excluded: chain H residue 238 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 4.9990 chunk 100 optimal weight: 10.0000 chunk 58 optimal weight: 3.9990 chunk 42 optimal weight: 8.9990 chunk 76 optimal weight: 0.7980 chunk 30 optimal weight: 4.9990 chunk 88 optimal weight: 0.7980 chunk 92 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 103 optimal weight: 6.9990 chunk 63 optimal weight: 1.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 453 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8683 Z= 0.291 Angle : 0.650 10.134 11823 Z= 0.338 Chirality : 0.046 0.297 1366 Planarity : 0.004 0.057 1488 Dihedral : 6.663 143.055 1232 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 5.31 % Allowed : 24.45 % Favored : 70.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.97 (0.26), residues: 1107 helix: 0.74 (0.28), residues: 373 sheet: -1.10 (0.29), residues: 282 loop : -1.43 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP R 422 HIS 0.002 0.001 HIS B 142 PHE 0.026 0.001 PHE H 68 TYR 0.014 0.001 TYR H 190 ARG 0.007 0.001 ARG A 209 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 152 time to evaluate : 1.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 134 LYS cc_start: 0.7210 (mmtt) cc_final: 0.6650 (tttm) REVERT: R 150 LEU cc_start: 0.7740 (OUTLIER) cc_final: 0.7458 (tt) REVERT: R 439 CYS cc_start: 0.7942 (OUTLIER) cc_final: 0.7619 (p) REVERT: A 244 MET cc_start: 0.8221 (OUTLIER) cc_final: 0.7439 (mpp) REVERT: A 246 GLU cc_start: 0.8152 (tm-30) cc_final: 0.7810 (tp30) REVERT: A 333 GLN cc_start: 0.8195 (tp40) cc_final: 0.7959 (tp40) outliers start: 46 outliers final: 37 residues processed: 187 average time/residue: 0.1917 time to fit residues: 49.8974 Evaluate side-chains 181 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 141 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 25 PHE Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 96 CYS Chi-restraints excluded: chain R residue 103 ASP Chi-restraints excluded: chain R residue 150 LEU Chi-restraints excluded: chain R residue 199 VAL Chi-restraints excluded: chain R residue 433 SER Chi-restraints excluded: chain R residue 434 THR Chi-restraints excluded: chain R residue 439 CYS Chi-restraints excluded: chain R residue 453 HIS Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 232 ASP Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain A residue 316 ASN Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 74 ASP Chi-restraints excluded: chain H residue 149 VAL Chi-restraints excluded: chain H residue 192 MET Chi-restraints excluded: chain H residue 216 ILE Chi-restraints excluded: chain H residue 230 MET Chi-restraints excluded: chain H residue 237 LEU Chi-restraints excluded: chain H residue 238 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 0.9990 chunk 71 optimal weight: 0.9990 chunk 108 optimal weight: 0.9990 chunk 99 optimal weight: 9.9990 chunk 86 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 68 optimal weight: 6.9990 chunk 92 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 179 GLN A 307 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 8683 Z= 0.202 Angle : 0.652 12.630 11823 Z= 0.336 Chirality : 0.045 0.259 1366 Planarity : 0.004 0.062 1488 Dihedral : 6.526 140.705 1232 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 4.84 % Allowed : 26.07 % Favored : 69.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.82 (0.26), residues: 1107 helix: 0.81 (0.28), residues: 373 sheet: -1.02 (0.29), residues: 282 loop : -1.29 (0.31), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP R 422 HIS 0.003 0.000 HIS R 453 PHE 0.016 0.001 PHE R 25 TYR 0.015 0.001 TYR R 177 ARG 0.007 0.000 ARG A 209 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 153 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 134 LYS cc_start: 0.7184 (mmtt) cc_final: 0.6623 (tttm) REVERT: R 150 LEU cc_start: 0.7726 (OUTLIER) cc_final: 0.7457 (tt) REVERT: A 244 MET cc_start: 0.8127 (OUTLIER) cc_final: 0.7392 (mpp) REVERT: A 246 GLU cc_start: 0.8139 (tm-30) cc_final: 0.7794 (tp30) REVERT: B 111 TYR cc_start: 0.8618 (m-80) cc_final: 0.8382 (m-10) outliers start: 42 outliers final: 36 residues processed: 183 average time/residue: 0.2037 time to fit residues: 52.0436 Evaluate side-chains 180 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 142 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 25 PHE Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 96 CYS Chi-restraints excluded: chain R residue 103 ASP Chi-restraints excluded: chain R residue 150 LEU Chi-restraints excluded: chain R residue 199 VAL Chi-restraints excluded: chain R residue 417 ILE Chi-restraints excluded: chain R residue 433 SER Chi-restraints excluded: chain R residue 434 THR Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 232 ASP Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain A residue 316 ASN Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 74 ASP Chi-restraints excluded: chain H residue 149 VAL Chi-restraints excluded: chain H residue 192 MET Chi-restraints excluded: chain H residue 216 ILE Chi-restraints excluded: chain H residue 230 MET Chi-restraints excluded: chain H residue 237 LEU Chi-restraints excluded: chain H residue 238 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 36 optimal weight: 5.9990 chunk 88 optimal weight: 0.8980 chunk 10 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.118370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.088445 restraints weight = 15585.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.091592 restraints weight = 8347.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.093649 restraints weight = 5707.430| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8683 Z= 0.215 Angle : 0.682 24.184 11823 Z= 0.345 Chirality : 0.046 0.272 1366 Planarity : 0.004 0.064 1488 Dihedral : 6.538 140.598 1232 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 4.50 % Allowed : 26.53 % Favored : 68.97 % 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: -0.75 (0.26), residues: 1107 helix: 0.82 (0.28), residues: 374 sheet: -0.87 (0.29), residues: 278 loop : -1.30 (0.31), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 82 HIS 0.002 0.000 HIS R 453 PHE 0.020 0.001 PHE R 451 TYR 0.016 0.001 TYR R 177 ARG 0.007 0.000 ARG A 209 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2027.17 seconds wall clock time: 37 minutes 32.89 seconds (2252.89 seconds total)