Starting phenix.real_space_refine on Mon Mar 11 07:00:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8frp_29404/03_2024/8frp_29404.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8frp_29404/03_2024/8frp_29404.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8frp_29404/03_2024/8frp_29404.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8frp_29404/03_2024/8frp_29404.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8frp_29404/03_2024/8frp_29404.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8frp_29404/03_2024/8frp_29404.pdb" } resolution = 3.8 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= 0.040 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 36 5.16 5 C 4861 2.51 5 N 1280 2.21 5 O 1311 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 7488 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1876 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 6, 'TRANS': 232} Chain: "B" Number of atoms: 1869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1869 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 6, 'TRANS': 231} Chain: "C" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 105 Classifications: {'peptide': 21} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'TRANS': 20} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'UNK:plan-1': 21} Unresolved non-hydrogen planarities: 21 Chain: "F" Number of atoms: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1769 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 212} Chain breaks: 2 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "G" Number of atoms: 1869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1869 Classifications: {'peptide': 234} Link IDs: {'PTRANS': 10, 'TRANS': 223} Chain breaks: 2 Time building chain proxies: 4.63, per 1000 atoms: 0.62 Number of scatterers: 7488 At special positions: 0 Unit cell: (68.475, 108.075, 92.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 36 16.00 O 1311 8.00 N 1280 7.00 C 4861 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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: 2.81 Conformation dependent library (CDL) restraints added in 1.4 seconds 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1772 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 4 sheets defined 68.1% alpha, 10.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'A' and resid 49 through 59 Processing helix chain 'A' and resid 79 through 85 Processing helix chain 'A' and resid 102 through 112 removed outlier: 3.782A pdb=" N ILE A 110 " --> pdb=" O ASN A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 133 removed outlier: 3.506A pdb=" N GLN A 123 " --> pdb=" O LYS A 119 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLN A 124 " --> pdb=" O GLN A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 162 removed outlier: 3.804A pdb=" N ALA A 162 " --> pdb=" O ARG A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 194 removed outlier: 4.268A pdb=" N GLY A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ASP A 183 " --> pdb=" O ILE A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 209 Processing helix chain 'A' and resid 228 through 235 Processing helix chain 'A' and resid 235 through 242 removed outlier: 3.537A pdb=" N VAL A 241 " --> pdb=" O GLN A 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 59 Processing helix chain 'B' and resid 79 through 85 Processing helix chain 'B' and resid 102 through 112 removed outlier: 3.574A pdb=" N ILE B 110 " --> pdb=" O ASN B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 133 removed outlier: 3.656A pdb=" N GLN B 123 " --> pdb=" O LYS B 119 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLN B 124 " --> pdb=" O GLN B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 139 Processing helix chain 'B' and resid 142 through 146 removed outlier: 4.199A pdb=" N VAL B 146 " --> pdb=" O GLY B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 161 Processing helix chain 'B' and resid 180 through 194 Processing helix chain 'B' and resid 204 through 209 removed outlier: 3.563A pdb=" N THR B 208 " --> pdb=" O ASN B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 234 Processing helix chain 'B' and resid 235 through 242 Processing helix chain 'C' and resid 2 through 21 removed outlier: 3.523A pdb=" N UNK C 9 " --> pdb=" O UNK C 5 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N UNK C 17 " --> pdb=" O UNK C 13 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 36 removed outlier: 3.722A pdb=" N ARG F 30 " --> pdb=" O MET F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 50 through 55 Processing helix chain 'F' and resid 55 through 82 removed outlier: 4.040A pdb=" N LEU F 62 " --> pdb=" O GLU F 58 " (cutoff:3.500A) Proline residue: F 65 - end of helix Processing helix chain 'F' and resid 85 through 90 Processing helix chain 'F' and resid 94 through 101 Processing helix chain 'F' and resid 102 through 119 Processing helix chain 'F' and resid 119 through 132 Processing helix chain 'F' and resid 247 through 251 removed outlier: 3.515A pdb=" N LEU F 251 " --> pdb=" O VAL F 248 " (cutoff:3.500A) Processing helix chain 'F' and resid 252 through 257 Processing helix chain 'F' and resid 262 through 274 Processing helix chain 'F' and resid 277 through 289 removed outlier: 3.566A pdb=" N ALA F 286 " --> pdb=" O ALA F 282 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA F 288 " --> pdb=" O MET F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 301 through 325 removed outlier: 3.508A pdb=" N ALA F 305 " --> pdb=" O ARG F 301 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE F 308 " --> pdb=" O PRO F 304 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU F 312 " --> pdb=" O ILE F 308 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG F 322 " --> pdb=" O ALA F 318 " (cutoff:3.500A) Processing helix chain 'F' and resid 331 through 348 removed outlier: 3.726A pdb=" N ALA F 335 " --> pdb=" O TRP F 331 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 35 Processing helix chain 'G' and resid 50 through 58 Processing helix chain 'G' and resid 58 through 85 Proline residue: G 68 - end of helix removed outlier: 3.565A pdb=" N LEU G 72 " --> pdb=" O PRO G 68 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU G 82 " --> pdb=" O GLY G 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 86 through 93 removed outlier: 4.023A pdb=" N VAL G 90 " --> pdb=" O SER G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 97 through 123 removed outlier: 3.519A pdb=" N SER G 108 " --> pdb=" O TRP G 104 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL G 111 " --> pdb=" O ARG G 107 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU G 112 " --> pdb=" O SER G 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 123 through 135 removed outlier: 3.753A pdb=" N GLU G 129 " --> pdb=" O PRO G 125 " (cutoff:3.500A) Processing helix chain 'G' and resid 246 through 261 removed outlier: 3.662A pdb=" N TYR G 260 " --> pdb=" O TYR G 256 " (cutoff:3.500A) Processing helix chain 'G' and resid 264 through 276 removed outlier: 3.556A pdb=" N ALA G 270 " --> pdb=" O THR G 266 " (cutoff:3.500A) Processing helix chain 'G' and resid 276 through 294 Processing helix chain 'G' and resid 300 through 327 removed outlier: 3.720A pdb=" N LEU G 327 " --> pdb=" O GLY G 323 " (cutoff:3.500A) Processing helix chain 'G' and resid 332 through 354 removed outlier: 4.030A pdb=" N PHE G 336 " --> pdb=" O SER G 332 " (cutoff:3.500A) Proline residue: G 340 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 24 through 35 removed outlier: 6.505A pdb=" N LYS A 19 " --> pdb=" O VAL A 26 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N LYS A 28 " --> pdb=" O LEU A 17 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LEU A 17 " --> pdb=" O LYS A 28 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N VAL A 30 " --> pdb=" O LYS A 15 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N LYS A 15 " --> pdb=" O VAL A 30 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N PHE A 32 " --> pdb=" O CYS A 13 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N CYS A 13 " --> pdb=" O PHE A 32 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N MET A 34 " --> pdb=" O THR A 11 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N THR A 11 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N LEU A 17 " --> pdb=" O LYS A 65 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LYS A 65 " --> pdb=" O LEU A 17 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 88 through 91 removed outlier: 6.662A pdb=" N ILE A 39 " --> pdb=" O HIS A 214 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N TYR A 216 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N GLY A 41 " --> pdb=" O TYR A 216 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N VAL A 218 " --> pdb=" O GLY A 41 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N LEU A 43 " --> pdb=" O VAL A 218 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ALA A 215 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLU A 226 " --> pdb=" O ALA A 215 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ILE A 217 " --> pdb=" O ILE A 224 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 24 through 35 removed outlier: 5.998A pdb=" N VAL B 26 " --> pdb=" O ASN B 20 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N ASN B 20 " --> pdb=" O VAL B 26 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N LYS B 28 " --> pdb=" O ALA B 18 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ALA B 18 " --> pdb=" O LYS B 28 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N VAL B 30 " --> pdb=" O HIS B 16 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N HIS B 16 " --> pdb=" O VAL B 30 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N LEU B 17 " --> pdb=" O LYS B 65 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N LYS B 65 " --> pdb=" O LEU B 17 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 88 through 91 removed outlier: 6.747A pdb=" N ILE B 39 " --> pdb=" O HIS B 214 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N TYR B 216 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N GLY B 41 " --> pdb=" O TYR B 216 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N VAL B 218 " --> pdb=" O GLY B 41 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LEU B 43 " --> pdb=" O VAL B 218 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ALA B 215 " --> pdb=" O GLU B 226 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N GLU B 226 " --> pdb=" O ALA B 215 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ILE B 217 " --> pdb=" O ILE B 224 " (cutoff:3.500A) 458 hydrogen bonds defined for protein. 1353 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: 2.26 Time building geometry restraints manager: 3.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2398 1.34 - 1.46: 1039 1.46 - 1.57: 4126 1.57 - 1.69: 0 1.69 - 1.81: 66 Bond restraints: 7629 Sorted by residual: bond pdb=" CA ASN B 20 " pdb=" CB ASN B 20 " ideal model delta sigma weight residual 1.534 1.556 -0.022 2.33e-02 1.84e+03 8.96e-01 bond pdb=" CA ASN B 72 " pdb=" CB ASN B 72 " ideal model delta sigma weight residual 1.530 1.546 -0.016 1.69e-02 3.50e+03 8.70e-01 bond pdb=" CA GLU A 220 " pdb=" CB GLU A 220 " ideal model delta sigma weight residual 1.530 1.545 -0.015 1.69e-02 3.50e+03 8.05e-01 bond pdb=" CB ASN B 20 " pdb=" CG ASN B 20 " ideal model delta sigma weight residual 1.516 1.536 -0.020 2.50e-02 1.60e+03 6.19e-01 bond pdb=" CB GLU A 220 " pdb=" CG GLU A 220 " ideal model delta sigma weight residual 1.520 1.542 -0.022 3.00e-02 1.11e+03 5.42e-01 ... (remaining 7624 not shown) Histogram of bond angle deviations from ideal: 100.21 - 106.96: 185 106.96 - 113.71: 4277 113.71 - 120.46: 3056 120.46 - 127.22: 2727 127.22 - 133.97: 76 Bond angle restraints: 10321 Sorted by residual: angle pdb=" C ASP B 71 " pdb=" N ASN B 72 " pdb=" CA ASN B 72 " ideal model delta sigma weight residual 121.54 127.83 -6.29 1.91e+00 2.74e-01 1.08e+01 angle pdb=" CA GLU A 220 " pdb=" CB GLU A 220 " pdb=" CG GLU A 220 " ideal model delta sigma weight residual 114.10 118.59 -4.49 2.00e+00 2.50e-01 5.04e+00 angle pdb=" CA ASN B 72 " pdb=" CB ASN B 72 " pdb=" CG ASN B 72 " ideal model delta sigma weight residual 112.60 114.61 -2.01 1.00e+00 1.00e+00 4.02e+00 angle pdb=" C SER A 219 " pdb=" N GLU A 220 " pdb=" CA GLU A 220 " ideal model delta sigma weight residual 121.54 125.34 -3.80 1.91e+00 2.74e-01 3.96e+00 angle pdb=" C ASP A 71 " pdb=" N ASN A 72 " pdb=" CA ASN A 72 " ideal model delta sigma weight residual 122.07 124.40 -2.33 1.43e+00 4.89e-01 2.65e+00 ... (remaining 10316 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.52: 4089 17.52 - 35.05: 403 35.05 - 52.57: 61 52.57 - 70.09: 9 70.09 - 87.62: 5 Dihedral angle restraints: 4567 sinusoidal: 1817 harmonic: 2750 Sorted by residual: dihedral pdb=" CA ASP B 246 " pdb=" CB ASP B 246 " pdb=" CG ASP B 246 " pdb=" OD1 ASP B 246 " ideal model delta sinusoidal sigma weight residual -30.00 -88.98 58.98 1 2.00e+01 2.50e-03 1.16e+01 dihedral pdb=" CA PHE A 98 " pdb=" C PHE A 98 " pdb=" N ARG A 99 " pdb=" CA ARG A 99 " ideal model delta harmonic sigma weight residual -180.00 -163.58 -16.42 0 5.00e+00 4.00e-02 1.08e+01 dihedral pdb=" CB GLU A 82 " pdb=" CG GLU A 82 " pdb=" CD GLU A 82 " pdb=" OE1 GLU A 82 " ideal model delta sinusoidal sigma weight residual 0.00 -87.62 87.62 1 3.00e+01 1.11e-03 1.02e+01 ... (remaining 4564 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 691 0.026 - 0.053: 310 0.053 - 0.079: 127 0.079 - 0.105: 55 0.105 - 0.131: 17 Chirality restraints: 1200 Sorted by residual: chirality pdb=" CA ASN B 72 " pdb=" N ASN B 72 " pdb=" C ASN B 72 " pdb=" CB ASN B 72 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.31e-01 chirality pdb=" CA ILE A 14 " pdb=" N ILE A 14 " pdb=" C ILE A 14 " pdb=" CB ILE A 14 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.38e-01 chirality pdb=" CA ILE A 68 " pdb=" N ILE A 68 " pdb=" C ILE A 68 " pdb=" CB ILE A 68 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.33e-01 ... (remaining 1197 not shown) Planarity restraints: 1289 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER F 293 " -0.030 5.00e-02 4.00e+02 4.63e-02 3.43e+00 pdb=" N PRO F 294 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO F 294 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO F 294 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE F 303 " -0.025 5.00e-02 4.00e+02 3.86e-02 2.38e+00 pdb=" N PRO F 304 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO F 304 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO F 304 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY F 275 " -0.024 5.00e-02 4.00e+02 3.62e-02 2.09e+00 pdb=" N PRO F 276 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO F 276 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO F 276 " -0.020 5.00e-02 4.00e+02 ... (remaining 1286 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2016 2.81 - 3.33: 7160 3.33 - 3.86: 11934 3.86 - 4.38: 14690 4.38 - 4.90: 25187 Nonbonded interactions: 60987 Sorted by model distance: nonbonded pdb=" NZ LYS G 265 " pdb=" O TYR G 329 " model vdw 2.290 2.520 nonbonded pdb=" OE2 GLU F 268 " pdb=" NE ARG F 272 " model vdw 2.321 2.520 nonbonded pdb=" O VAL F 87 " pdb=" OG SER F 91 " model vdw 2.397 2.440 nonbonded pdb=" O ILE F 63 " pdb=" N GLY F 67 " model vdw 2.436 2.520 nonbonded pdb=" OD1 ASN A 190 " pdb=" NH2 ARG A 194 " model vdw 2.451 2.520 ... (remaining 60982 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 10 through 247) selection = chain 'B' } 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: 1.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 7.420 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 24.310 Find NCS groups from input model: 0.330 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 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 : 0.002 0.024 7629 Z= 0.104 Angle : 0.429 6.290 10321 Z= 0.219 Chirality : 0.038 0.131 1200 Planarity : 0.004 0.046 1289 Dihedral : 13.741 87.618 2795 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.26), residues: 918 helix: -0.66 (0.20), residues: 561 sheet: 1.17 (0.69), residues: 68 loop : -1.06 (0.36), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 331 HIS 0.002 0.000 HIS A 214 PHE 0.005 0.001 PHE F 109 TYR 0.005 0.001 TYR F 333 ARG 0.003 0.000 ARG F 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 372 time to evaluate : 0.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 TYR cc_start: 0.8811 (m-80) cc_final: 0.8591 (m-10) REVERT: A 108 MET cc_start: 0.8311 (tpt) cc_final: 0.7866 (tpp) REVERT: A 202 ASP cc_start: 0.7998 (t0) cc_final: 0.7514 (t70) REVERT: B 202 ASP cc_start: 0.8171 (t0) cc_final: 0.7906 (t0) REVERT: B 243 LEU cc_start: 0.7814 (mt) cc_final: 0.7502 (mt) REVERT: F 300 TYR cc_start: 0.6933 (t80) cc_final: 0.5911 (t80) REVERT: G 255 ASN cc_start: 0.6596 (m-40) cc_final: 0.6034 (m-40) outliers start: 0 outliers final: 0 residues processed: 372 average time/residue: 0.2215 time to fit residues: 106.3419 Evaluate side-chains 219 residues out of total 793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 219 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 chunk 39 optimal weight: 0.0000 chunk 24 optimal weight: 0.0970 chunk 47 optimal weight: 9.9990 chunk 37 optimal weight: 4.9990 chunk 72 optimal weight: 6.9990 chunk 28 optimal weight: 0.9990 chunk 44 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 overall best weight: 0.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN A 121 GLN A 214 HIS B 81 HIS B 214 HIS G 85 ASN G 249 GLN G 268 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.3788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 7629 Z= 0.244 Angle : 0.691 10.464 10321 Z= 0.352 Chirality : 0.046 0.184 1200 Planarity : 0.005 0.047 1289 Dihedral : 3.910 15.007 1037 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 4.55 % Allowed : 15.80 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.26), residues: 918 helix: 0.73 (0.21), residues: 570 sheet: 1.88 (0.71), residues: 60 loop : -1.30 (0.33), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 57 HIS 0.005 0.001 HIS A 69 PHE 0.022 0.002 PHE A 32 TYR 0.018 0.002 TYR G 64 ARG 0.008 0.001 ARG B 206 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 233 time to evaluate : 0.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 TYR cc_start: 0.8670 (m-80) cc_final: 0.8463 (m-10) REVERT: A 217 ILE cc_start: 0.9125 (mm) cc_final: 0.8843 (tp) REVERT: B 111 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8378 (mm) REVERT: B 243 LEU cc_start: 0.7863 (mt) cc_final: 0.7489 (mt) outliers start: 36 outliers final: 23 residues processed: 252 average time/residue: 0.1830 time to fit residues: 62.4103 Evaluate side-chains 231 residues out of total 793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 207 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain F residue 31 LEU Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 93 ILE Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 115 ILE Chi-restraints excluded: chain F residue 121 THR Chi-restraints excluded: chain F residue 280 VAL Chi-restraints excluded: chain F residue 287 VAL Chi-restraints excluded: chain F residue 303 ILE Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 316 LEU Chi-restraints excluded: chain F residue 340 TYR Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 86 SER Chi-restraints excluded: chain G residue 91 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 46 optimal weight: 7.9990 chunk 26 optimal weight: 0.0970 chunk 70 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 chunk 23 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 75 optimal weight: 0.9990 chunk 83 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 67 optimal weight: 6.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 128 ASN G 249 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.4342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7629 Z= 0.209 Angle : 0.615 9.349 10321 Z= 0.312 Chirality : 0.044 0.168 1200 Planarity : 0.004 0.049 1289 Dihedral : 3.827 14.816 1037 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 4.42 % Allowed : 19.47 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.27), residues: 918 helix: 1.21 (0.21), residues: 574 sheet: 2.01 (0.61), residues: 64 loop : -1.20 (0.35), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 123 HIS 0.005 0.001 HIS A 203 PHE 0.022 0.002 PHE G 321 TYR 0.020 0.001 TYR G 126 ARG 0.004 0.000 ARG G 61 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 228 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 MET cc_start: 0.7014 (OUTLIER) cc_final: 0.6476 (ttp) REVERT: B 34 MET cc_start: 0.7622 (tmm) cc_final: 0.7393 (tmm) REVERT: G 257 MET cc_start: 0.7549 (mtm) cc_final: 0.6498 (mtm) outliers start: 35 outliers final: 28 residues processed: 244 average time/residue: 0.1674 time to fit residues: 57.2707 Evaluate side-chains 226 residues out of total 793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 197 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 80 MET Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain B residue 20 ASN Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 115 ILE Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 121 THR Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 281 ILE Chi-restraints excluded: chain F residue 303 ILE Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 340 TYR Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 91 MET Chi-restraints excluded: chain G residue 266 THR Chi-restraints excluded: chain G residue 290 SER Chi-restraints excluded: chain G residue 292 ILE Chi-restraints excluded: chain G residue 330 ASN Chi-restraints excluded: chain G residue 343 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 83 optimal weight: 10.0000 chunk 63 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 chunk 9 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 89 optimal weight: 6.9990 chunk 44 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 HIS ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 249 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.4932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 7629 Z= 0.395 Angle : 0.731 11.427 10321 Z= 0.368 Chirality : 0.048 0.279 1200 Planarity : 0.005 0.053 1289 Dihedral : 4.114 18.283 1037 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 16.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 7.08 % Allowed : 20.48 % Favored : 72.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.27), residues: 918 helix: 1.18 (0.21), residues: 575 sheet: 1.12 (0.56), residues: 75 loop : -1.26 (0.36), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP G 57 HIS 0.005 0.001 HIS A 203 PHE 0.023 0.002 PHE G 253 TYR 0.016 0.002 TYR F 333 ARG 0.006 0.001 ARG G 61 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 201 time to evaluate : 1.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 MET cc_start: 0.7207 (OUTLIER) cc_final: 0.6772 (ttp) REVERT: B 33 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7526 (pp20) REVERT: B 34 MET cc_start: 0.7613 (tmm) cc_final: 0.7341 (tmm) REVERT: B 80 MET cc_start: 0.8377 (OUTLIER) cc_final: 0.7695 (tpp) REVERT: B 107 ILE cc_start: 0.8808 (OUTLIER) cc_final: 0.8575 (mp) REVERT: B 212 CYS cc_start: 0.8509 (t) cc_final: 0.8191 (t) outliers start: 56 outliers final: 39 residues processed: 230 average time/residue: 0.1697 time to fit residues: 54.6179 Evaluate side-chains 233 residues out of total 793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 190 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 80 MET Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain B residue 20 ASN Chi-restraints excluded: chain B residue 33 GLU Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 27 MET Chi-restraints excluded: chain F residue 60 LEU Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 115 ILE Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 121 THR Chi-restraints excluded: chain F residue 127 GLN Chi-restraints excluded: chain F residue 258 ASN Chi-restraints excluded: chain F residue 281 ILE Chi-restraints excluded: chain F residue 287 VAL Chi-restraints excluded: chain F residue 303 ILE Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 316 LEU Chi-restraints excluded: chain F residue 340 TYR Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 86 SER Chi-restraints excluded: chain G residue 91 MET Chi-restraints excluded: chain G residue 132 ASN Chi-restraints excluded: chain G residue 284 LEU Chi-restraints excluded: chain G residue 330 ASN Chi-restraints excluded: chain G residue 343 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 74 optimal weight: 4.9990 chunk 51 optimal weight: 9.9990 chunk 1 optimal weight: 0.0470 chunk 66 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 overall best weight: 0.9080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 249 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.5176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7629 Z= 0.227 Angle : 0.641 10.914 10321 Z= 0.318 Chirality : 0.045 0.304 1200 Planarity : 0.004 0.053 1289 Dihedral : 3.970 16.884 1037 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 5.31 % Allowed : 24.91 % Favored : 69.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.28), residues: 918 helix: 1.44 (0.22), residues: 570 sheet: 1.11 (0.56), residues: 70 loop : -1.14 (0.36), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 271 HIS 0.006 0.001 HIS A 203 PHE 0.016 0.001 PHE G 321 TYR 0.015 0.001 TYR F 80 ARG 0.005 0.000 ARG G 130 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 200 time to evaluate : 0.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 MET cc_start: 0.7140 (OUTLIER) cc_final: 0.6698 (ttp) REVERT: B 34 MET cc_start: 0.7544 (tmm) cc_final: 0.7295 (tmm) REVERT: B 80 MET cc_start: 0.8066 (tpp) cc_final: 0.7740 (ttt) REVERT: B 107 ILE cc_start: 0.8770 (OUTLIER) cc_final: 0.8504 (mp) REVERT: B 204 ASN cc_start: 0.7497 (t0) cc_final: 0.6838 (t0) REVERT: B 207 GLU cc_start: 0.7283 (mp0) cc_final: 0.7082 (mp0) REVERT: G 67 LEU cc_start: 0.8727 (mt) cc_final: 0.8518 (mt) outliers start: 42 outliers final: 29 residues processed: 222 average time/residue: 0.1664 time to fit residues: 51.4917 Evaluate side-chains 215 residues out of total 793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 184 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 80 MET Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain B residue 20 ASN Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 115 ILE Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 121 THR Chi-restraints excluded: chain F residue 127 GLN Chi-restraints excluded: chain F residue 257 TRP Chi-restraints excluded: chain F residue 281 ILE Chi-restraints excluded: chain F residue 303 ILE Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 340 TYR Chi-restraints excluded: chain G residue 86 SER Chi-restraints excluded: chain G residue 91 MET Chi-restraints excluded: chain G residue 249 GLN Chi-restraints excluded: chain G residue 330 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 30 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 89 optimal weight: 6.9990 chunk 74 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 7 optimal weight: 4.9990 chunk 29 optimal weight: 0.0970 chunk 47 optimal weight: 10.0000 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 85 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.5364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 7629 Z= 0.247 Angle : 0.657 9.875 10321 Z= 0.324 Chirality : 0.046 0.375 1200 Planarity : 0.004 0.054 1289 Dihedral : 3.957 16.291 1037 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 15.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 6.19 % Allowed : 24.27 % Favored : 69.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.28), residues: 918 helix: 1.41 (0.22), residues: 578 sheet: 1.04 (0.56), residues: 70 loop : -1.16 (0.36), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 271 HIS 0.008 0.001 HIS F 83 PHE 0.011 0.001 PHE B 133 TYR 0.014 0.001 TYR G 64 ARG 0.004 0.000 ARG G 61 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 204 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 MET cc_start: 0.7142 (OUTLIER) cc_final: 0.6776 (ttp) REVERT: B 34 MET cc_start: 0.7532 (tmm) cc_final: 0.7283 (tmm) REVERT: B 62 ARG cc_start: 0.8174 (mmm160) cc_final: 0.7931 (mmp80) REVERT: B 80 MET cc_start: 0.8125 (tpp) cc_final: 0.7781 (ttt) REVERT: B 94 GLU cc_start: 0.7787 (pm20) cc_final: 0.7482 (pm20) REVERT: B 107 ILE cc_start: 0.8735 (OUTLIER) cc_final: 0.8460 (mp) REVERT: B 204 ASN cc_start: 0.7521 (t0) cc_final: 0.6983 (t0) REVERT: B 207 GLU cc_start: 0.7346 (mp0) cc_final: 0.7121 (mp0) REVERT: G 67 LEU cc_start: 0.8641 (mt) cc_final: 0.8378 (mt) REVERT: G 85 ASN cc_start: 0.8052 (OUTLIER) cc_final: 0.7597 (t0) outliers start: 49 outliers final: 33 residues processed: 229 average time/residue: 0.1694 time to fit residues: 54.3366 Evaluate side-chains 226 residues out of total 793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 190 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 80 MET Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain B residue 20 ASN Chi-restraints excluded: chain B residue 63 MET Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 115 ILE Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 121 THR Chi-restraints excluded: chain F residue 127 GLN Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 257 TRP Chi-restraints excluded: chain F residue 258 ASN Chi-restraints excluded: chain F residue 281 ILE Chi-restraints excluded: chain F residue 287 VAL Chi-restraints excluded: chain F residue 303 ILE Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain F residue 340 TYR Chi-restraints excluded: chain G residue 85 ASN Chi-restraints excluded: chain G residue 86 SER Chi-restraints excluded: chain G residue 91 MET Chi-restraints excluded: chain G residue 330 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 86 optimal weight: 0.6980 chunk 10 optimal weight: 3.9990 chunk 51 optimal weight: 8.9990 chunk 65 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 75 optimal weight: 4.9990 chunk 89 optimal weight: 0.9990 chunk 56 optimal weight: 0.0970 chunk 54 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 85 ASN ** G 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.5485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 7629 Z= 0.221 Angle : 0.655 9.979 10321 Z= 0.322 Chirality : 0.046 0.385 1200 Planarity : 0.004 0.054 1289 Dihedral : 3.939 16.949 1037 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 5.31 % Allowed : 26.42 % Favored : 68.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.28), residues: 918 helix: 1.58 (0.22), residues: 564 sheet: 1.03 (0.56), residues: 70 loop : -1.05 (0.36), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 331 HIS 0.005 0.001 HIS A 203 PHE 0.016 0.001 PHE G 321 TYR 0.016 0.001 TYR F 340 ARG 0.004 0.000 ARG G 61 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 195 time to evaluate : 0.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 MET cc_start: 0.7190 (OUTLIER) cc_final: 0.6792 (ttp) REVERT: A 206 ARG cc_start: 0.7758 (OUTLIER) cc_final: 0.7520 (ttt180) REVERT: B 62 ARG cc_start: 0.8165 (mmm160) cc_final: 0.7915 (mmp80) REVERT: B 80 MET cc_start: 0.8153 (tpp) cc_final: 0.7814 (ttt) REVERT: B 94 GLU cc_start: 0.7695 (pm20) cc_final: 0.7357 (pm20) REVERT: B 204 ASN cc_start: 0.7719 (t0) cc_final: 0.6942 (t0) REVERT: B 207 GLU cc_start: 0.7339 (mp0) cc_final: 0.7050 (mp0) REVERT: G 85 ASN cc_start: 0.8122 (OUTLIER) cc_final: 0.7760 (t0) REVERT: G 352 LEU cc_start: 0.8684 (mt) cc_final: 0.8304 (mt) outliers start: 42 outliers final: 27 residues processed: 216 average time/residue: 0.1735 time to fit residues: 51.6340 Evaluate side-chains 220 residues out of total 793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 190 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 80 MET Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 206 ARG Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain B residue 20 ASN Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 109 PHE Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 115 ILE Chi-restraints excluded: chain F residue 121 THR Chi-restraints excluded: chain F residue 127 GLN Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 257 TRP Chi-restraints excluded: chain F residue 258 ASN Chi-restraints excluded: chain F residue 281 ILE Chi-restraints excluded: chain F residue 303 ILE Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain G residue 85 ASN Chi-restraints excluded: chain G residue 330 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 35 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 61 optimal weight: 4.9990 chunk 44 optimal weight: 5.9990 chunk 8 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 81 optimal weight: 7.9990 chunk 85 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 85 ASN G 249 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.5600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 7629 Z= 0.235 Angle : 0.668 9.737 10321 Z= 0.327 Chirality : 0.045 0.393 1200 Planarity : 0.004 0.054 1289 Dihedral : 3.922 17.996 1037 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 5.06 % Allowed : 27.43 % Favored : 67.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.28), residues: 918 helix: 1.56 (0.22), residues: 566 sheet: 1.14 (0.55), residues: 70 loop : -1.02 (0.37), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 123 HIS 0.005 0.001 HIS A 203 PHE 0.015 0.001 PHE A 32 TYR 0.019 0.001 TYR F 340 ARG 0.004 0.000 ARG G 61 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 192 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 MET cc_start: 0.7201 (OUTLIER) cc_final: 0.6790 (ttp) REVERT: B 62 ARG cc_start: 0.8153 (mmm160) cc_final: 0.7910 (mmp80) REVERT: B 80 MET cc_start: 0.8175 (tpp) cc_final: 0.7842 (ttt) REVERT: B 204 ASN cc_start: 0.7652 (t0) cc_final: 0.6824 (t0) REVERT: B 207 GLU cc_start: 0.7337 (mp0) cc_final: 0.7053 (mp0) REVERT: G 85 ASN cc_start: 0.8057 (OUTLIER) cc_final: 0.7757 (t0) REVERT: G 352 LEU cc_start: 0.8703 (mt) cc_final: 0.8314 (mt) outliers start: 40 outliers final: 28 residues processed: 209 average time/residue: 0.1710 time to fit residues: 49.9109 Evaluate side-chains 220 residues out of total 793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 190 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 80 MET Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain B residue 20 ASN Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 109 PHE Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 115 ILE Chi-restraints excluded: chain F residue 121 THR Chi-restraints excluded: chain F residue 127 GLN Chi-restraints excluded: chain F residue 257 TRP Chi-restraints excluded: chain F residue 258 ASN Chi-restraints excluded: chain F residue 281 ILE Chi-restraints excluded: chain F residue 287 VAL Chi-restraints excluded: chain F residue 303 ILE Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain G residue 85 ASN Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 249 GLN Chi-restraints excluded: chain G residue 330 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 0.6980 chunk 83 optimal weight: 9.9990 chunk 85 optimal weight: 0.5980 chunk 50 optimal weight: 5.9990 chunk 36 optimal weight: 0.0170 chunk 65 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 chunk 54 optimal weight: 0.1980 chunk 88 optimal weight: 3.9990 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 85 ASN G 249 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.5681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 7629 Z= 0.205 Angle : 0.666 9.588 10321 Z= 0.325 Chirality : 0.044 0.166 1200 Planarity : 0.004 0.053 1289 Dihedral : 3.868 18.126 1037 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 4.30 % Allowed : 27.56 % Favored : 68.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.28), residues: 918 helix: 1.54 (0.22), residues: 566 sheet: 1.29 (0.56), residues: 70 loop : -0.99 (0.37), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 271 HIS 0.005 0.001 HIS A 203 PHE 0.015 0.001 PHE A 32 TYR 0.022 0.001 TYR F 340 ARG 0.004 0.000 ARG G 61 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 192 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 MET cc_start: 0.7117 (OUTLIER) cc_final: 0.6830 (ttp) REVERT: B 62 ARG cc_start: 0.8148 (mmm160) cc_final: 0.7919 (mmp80) REVERT: B 80 MET cc_start: 0.8139 (tpp) cc_final: 0.7843 (ttt) REVERT: B 94 GLU cc_start: 0.7687 (pm20) cc_final: 0.7317 (pm20) REVERT: B 204 ASN cc_start: 0.7673 (t0) cc_final: 0.6805 (t0) REVERT: B 207 GLU cc_start: 0.7342 (mp0) cc_final: 0.7020 (mp0) REVERT: G 352 LEU cc_start: 0.8627 (mt) cc_final: 0.8272 (mt) outliers start: 34 outliers final: 27 residues processed: 209 average time/residue: 0.1657 time to fit residues: 48.2336 Evaluate side-chains 211 residues out of total 793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 183 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 80 MET Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain B residue 20 ASN Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 109 PHE Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 115 ILE Chi-restraints excluded: chain F residue 121 THR Chi-restraints excluded: chain F residue 127 GLN Chi-restraints excluded: chain F residue 257 TRP Chi-restraints excluded: chain F residue 258 ASN Chi-restraints excluded: chain F residue 281 ILE Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 249 GLN Chi-restraints excluded: chain G residue 290 SER Chi-restraints excluded: chain G residue 320 ASP Chi-restraints excluded: chain G residue 330 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 53 optimal weight: 0.7980 chunk 41 optimal weight: 0.5980 chunk 61 optimal weight: 6.9990 chunk 92 optimal weight: 3.9990 chunk 85 optimal weight: 0.4980 chunk 73 optimal weight: 9.9990 chunk 7 optimal weight: 6.9990 chunk 56 optimal weight: 0.6980 chunk 45 optimal weight: 0.5980 chunk 58 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.5779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 7629 Z= 0.216 Angle : 0.675 9.838 10321 Z= 0.328 Chirality : 0.044 0.163 1200 Planarity : 0.004 0.053 1289 Dihedral : 3.861 17.442 1037 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.92 % Allowed : 28.19 % Favored : 67.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.28), residues: 918 helix: 1.59 (0.22), residues: 565 sheet: 1.25 (0.56), residues: 70 loop : -0.91 (0.37), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 271 HIS 0.005 0.001 HIS A 203 PHE 0.014 0.001 PHE A 32 TYR 0.023 0.001 TYR F 340 ARG 0.006 0.000 ARG F 126 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 190 time to evaluate : 0.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 MET cc_start: 0.7141 (OUTLIER) cc_final: 0.6884 (ttp) REVERT: B 62 ARG cc_start: 0.8156 (mmm160) cc_final: 0.7917 (mmp80) REVERT: B 80 MET cc_start: 0.8154 (tpp) cc_final: 0.7860 (ttt) REVERT: B 94 GLU cc_start: 0.7674 (pm20) cc_final: 0.7396 (pm20) REVERT: F 316 LEU cc_start: 0.7262 (tp) cc_final: 0.7054 (tt) REVERT: G 352 LEU cc_start: 0.8613 (mt) cc_final: 0.8286 (mt) outliers start: 31 outliers final: 27 residues processed: 203 average time/residue: 0.1834 time to fit residues: 52.3296 Evaluate side-chains 212 residues out of total 793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 184 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 80 MET Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain B residue 20 ASN Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 109 PHE Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 115 ILE Chi-restraints excluded: chain F residue 121 THR Chi-restraints excluded: chain F residue 127 GLN Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 257 TRP Chi-restraints excluded: chain F residue 258 ASN Chi-restraints excluded: chain F residue 281 ILE Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 340 TYR Chi-restraints excluded: chain G residue 290 SER Chi-restraints excluded: chain G residue 320 ASP Chi-restraints excluded: chain G residue 330 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 22 optimal weight: 0.8980 chunk 68 optimal weight: 10.0000 chunk 10 optimal weight: 0.9980 chunk 20 optimal weight: 0.0570 chunk 73 optimal weight: 0.4980 chunk 30 optimal weight: 1.9990 chunk 75 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 7.9990 chunk 64 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 319 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 = 0.3831 r_free = 0.3831 target = 0.141432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.118528 restraints weight = 13684.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.122172 restraints weight = 7242.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.124606 restraints weight = 4736.939| |-----------------------------------------------------------------------------| r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.5884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 7629 Z= 0.204 Angle : 0.680 10.103 10321 Z= 0.327 Chirality : 0.043 0.161 1200 Planarity : 0.004 0.053 1289 Dihedral : 3.860 19.605 1037 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.54 % Allowed : 28.70 % Favored : 67.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.28), residues: 918 helix: 1.60 (0.22), residues: 568 sheet: 1.29 (0.56), residues: 70 loop : -0.86 (0.37), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP F 271 HIS 0.005 0.001 HIS A 203 PHE 0.015 0.001 PHE A 32 TYR 0.022 0.001 TYR F 340 ARG 0.004 0.000 ARG G 61 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1910.60 seconds wall clock time: 35 minutes 18.67 seconds (2118.67 seconds total)