Starting phenix.real_space_refine on Sat Dec 28 13:09:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vb8_43116/12_2024/8vb8_43116.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vb8_43116/12_2024/8vb8_43116.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vb8_43116/12_2024/8vb8_43116.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vb8_43116/12_2024/8vb8_43116.map" model { file = "/net/cci-nas-00/data/ceres_data/8vb8_43116/12_2024/8vb8_43116.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vb8_43116/12_2024/8vb8_43116.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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: 6 Type Number sf(0) Gaussians P 40 5.49 5 Mg 2 5.21 5 S 13 5.16 5 C 5380 2.51 5 N 1416 2.21 5 O 1660 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 8511 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4480 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 553, 4473 Classifications: {'peptide': 553} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 515} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Conformer: "B" Number of residues, atoms: 553, 4473 Classifications: {'peptide': 553} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 515} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 bond proxies already assigned to first conformer: 4582 Chain: "B" Number of atoms: 3238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3238 Classifications: {'peptide': 398} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 29, 'TRANS': 368} Chain breaks: 2 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 52 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 3, 'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "F" Number of atoms: 761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 761 Classifications: {'DNA': 35, 'RNA': 2} Modifications used: {'rna3p': 2} Link IDs: {'rna3p': 36} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 6 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 2, 'DTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 6.40, per 1000 atoms: 0.75 Number of scatterers: 8511 At special positions: 0 Unit cell: (79.2, 96.525, 124.575, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 13 16.00 P 40 15.00 Mg 2 11.99 O 1660 8.00 N 1416 7.00 C 5380 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.23 Conformation dependent library (CDL) restraints added in 1.4 seconds 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1796 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 14 sheets defined 36.8% alpha, 14.1% beta 13 base pairs and 26 stacking pairs defined. Time for finding SS restraints: 3.16 Creating SS restraints... Processing helix chain 'A' and resid 27 through 44 removed outlier: 3.699A pdb=" N GLU A 40 " --> pdb=" O GLU A 36 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU A 42 " --> pdb=" O CYS A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 84 removed outlier: 3.585A pdb=" N ARG A 83 " --> pdb=" O GLU A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 100 Processing helix chain 'A' and resid 114 through 118 Processing helix chain 'A' and resid 121 through 125 Processing helix chain 'A' and resid 155 through 175 Proline residue: A 170 - end of helix Processing helix chain 'A' and resid 194 through 211 Processing helix chain 'A' and resid 217 through 221 removed outlier: 3.615A pdb=" N HIS A 221 " --> pdb=" O ASP A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 268 removed outlier: 3.512A pdb=" N GLN A 258 " --> pdb=" O VAL A 254 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N LYS A 263 " --> pdb=" O LYS A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 282 removed outlier: 3.647A pdb=" N LEU A 282 " --> pdb=" O GLN A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 310 Processing helix chain 'A' and resid 363 through 384 removed outlier: 3.640A pdb=" N VAL A 381 " --> pdb=" O THR A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 403 Processing helix chain 'A' and resid 475 through 488 Processing helix chain 'A' and resid 499 through 508 removed outlier: 4.130A pdb=" N LEU A 503 " --> pdb=" O SER A 499 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ALA A 508 " --> pdb=" O GLY A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 528 removed outlier: 3.637A pdb=" N LYS A 527 " --> pdb=" O GLU A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 552 Processing helix chain 'B' and resid 27 through 33 Processing helix chain 'B' and resid 34 through 44 Processing helix chain 'B' and resid 77 through 85 removed outlier: 4.058A pdb=" N GLN B 85 " --> pdb=" O ASN B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 125 removed outlier: 3.507A pdb=" N ARG B 125 " --> pdb=" O GLU B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 138 Processing helix chain 'B' and resid 154 through 160 removed outlier: 4.037A pdb=" N ALA B 158 " --> pdb=" O LYS B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 168 removed outlier: 6.029A pdb=" N LYS B 166 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ILE B 167 " --> pdb=" O SER B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 173 Processing helix chain 'B' and resid 194 through 213 removed outlier: 3.629A pdb=" N THR B 200 " --> pdb=" O GLY B 196 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU B 205 " --> pdb=" O LYS B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 239 removed outlier: 3.836A pdb=" N TRP B 239 " --> pdb=" O PRO B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 271 removed outlier: 4.123A pdb=" N GLN B 269 " --> pdb=" O ASN B 265 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE B 270 " --> pdb=" O TRP B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 312 removed outlier: 3.612A pdb=" N GLU B 312 " --> pdb=" O GLU B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 383 Processing helix chain 'B' and resid 394 through 406 removed outlier: 3.530A pdb=" N THR B 400 " --> pdb=" O GLU B 396 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TRP B 401 " --> pdb=" O THR B 397 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N THR B 403 " --> pdb=" O GLU B 399 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N GLU B 404 " --> pdb=" O THR B 400 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N TYR B 405 " --> pdb=" O TRP B 401 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 49 Processing sheet with id=AA2, first strand: chain 'A' and resid 60 through 64 Processing sheet with id=AA3, first strand: chain 'A' and resid 105 through 110 Processing sheet with id=AA4, first strand: chain 'A' and resid 227 through 229 Processing sheet with id=AA5, first strand: chain 'A' and resid 252 through 253 removed outlier: 4.175A pdb=" N TRP A 252 " --> pdb=" O ILE A 293 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 347 through 354 removed outlier: 8.611A pdb=" N ASN A 348 " --> pdb=" O GLN A 343 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N GLN A 343 " --> pdb=" O ASN A 348 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE A 329 " --> pdb=" O LYS A 390 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 361 through 362 Processing sheet with id=AA8, first strand: chain 'A' and resid 439 through 441 Processing sheet with id=AA9, first strand: chain 'A' and resid 443 through 446 Processing sheet with id=AB1, first strand: chain 'B' and resid 47 through 49 Processing sheet with id=AB2, first strand: chain 'B' and resid 60 through 64 Processing sheet with id=AB3, first strand: chain 'B' and resid 105 through 110 removed outlier: 3.861A pdb=" N SER B 105 " --> pdb=" O SER B 191 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 329 through 331 removed outlier: 7.204A pdb=" N GLN B 343 " --> pdb=" O ASN B 348 " (cutoff:3.500A) removed outlier: 8.694A pdb=" N ASN B 348 " --> pdb=" O GLN B 343 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 389 through 391 removed outlier: 6.218A pdb=" N PHE B 389 " --> pdb=" O GLU B 415 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 288 hydrogen bonds defined for protein. 798 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 36 hydrogen bonds 72 hydrogen bond angles 0 basepair planarities 13 basepair parallelities 26 stacking parallelities Total time for adding SS restraints: 2.94 Time building geometry restraints manager: 2.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2152 1.33 - 1.45: 1739 1.45 - 1.57: 4818 1.57 - 1.69: 79 1.69 - 1.80: 23 Bond restraints: 8811 Sorted by residual: bond pdb=" C1' DTP A 701 " pdb=" N9 DTP A 701 " ideal model delta sigma weight residual 1.457 1.408 0.049 1.20e-02 6.94e+03 1.64e+01 bond pdb=" O2B DTP A 701 " pdb=" PB DTP A 701 " ideal model delta sigma weight residual 1.529 1.460 0.069 2.20e-02 2.07e+03 9.98e+00 bond pdb=" N ILE B 94 " pdb=" CA ILE B 94 " ideal model delta sigma weight residual 1.461 1.499 -0.038 1.23e-02 6.61e+03 9.48e+00 bond pdb=" N ILE A 135 " pdb=" CA ILE A 135 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.25e-02 6.40e+03 9.30e+00 bond pdb=" CA SER A 134 " pdb=" CB SER A 134 " ideal model delta sigma weight residual 1.535 1.490 0.045 1.51e-02 4.39e+03 8.75e+00 ... (remaining 8806 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 11814 1.71 - 3.43: 266 3.43 - 5.14: 52 5.14 - 6.86: 14 6.86 - 8.57: 5 Bond angle restraints: 12151 Sorted by residual: angle pdb=" PB DTP A 701 " pdb=" O3B DTP A 701 " pdb=" PG DTP A 701 " ideal model delta sigma weight residual 139.87 134.07 5.80 1.00e+00 1.00e+00 3.36e+01 angle pdb=" CA GLU A 297 " pdb=" CB GLU A 297 " pdb=" CG GLU A 297 " ideal model delta sigma weight residual 114.10 122.45 -8.35 2.00e+00 2.50e-01 1.74e+01 angle pdb=" CA THR A 107 " pdb=" C THR A 107 " pdb=" O THR A 107 " ideal model delta sigma weight residual 120.60 116.06 4.54 1.20e+00 6.94e-01 1.43e+01 angle pdb=" CB ARG B 277 " pdb=" CG ARG B 277 " pdb=" CD ARG B 277 " ideal model delta sigma weight residual 111.30 119.87 -8.57 2.30e+00 1.89e-01 1.39e+01 angle pdb=" CA VAL A 108 " pdb=" C VAL A 108 " pdb=" O VAL A 108 " ideal model delta sigma weight residual 120.48 116.80 3.68 1.06e+00 8.90e-01 1.20e+01 ... (remaining 12146 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.61: 4683 30.61 - 61.22: 462 61.22 - 91.83: 30 91.83 - 122.44: 0 122.44 - 153.06: 1 Dihedral angle restraints: 5176 sinusoidal: 2393 harmonic: 2783 Sorted by residual: dihedral pdb=" CA PRO A 420 " pdb=" C PRO A 420 " pdb=" N PRO A 421 " pdb=" CA PRO A 421 " ideal model delta harmonic sigma weight residual -180.00 -156.77 -23.23 0 5.00e+00 4.00e-02 2.16e+01 dihedral pdb=" O1B DTP A 701 " pdb=" O3B DTP A 701 " pdb=" PB DTP A 701 " pdb=" PG DTP A 701 " ideal model delta sinusoidal sigma weight residual 299.93 146.87 153.06 1 3.00e+01 1.11e-03 2.02e+01 dihedral pdb=" C ILE B 94 " pdb=" N ILE B 94 " pdb=" CA ILE B 94 " pdb=" CB ILE B 94 " ideal model delta harmonic sigma weight residual -122.00 -131.06 9.06 0 2.50e+00 1.60e-01 1.31e+01 ... (remaining 5173 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 1291 0.103 - 0.207: 41 0.207 - 0.310: 1 0.310 - 0.414: 0 0.414 - 0.517: 1 Chirality restraints: 1334 Sorted by residual: chirality pdb=" P DT F 17 " pdb=" OP1 DT F 17 " pdb=" OP2 DT F 17 " pdb=" O5' DT F 17 " both_signs ideal model delta sigma weight residual True 2.35 -2.86 -0.52 2.00e-01 2.50e+01 6.69e+00 chirality pdb=" CB ILE B 94 " pdb=" CA ILE B 94 " pdb=" CG1 ILE B 94 " pdb=" CG2 ILE B 94 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" CA ILE A 135 " pdb=" N ILE A 135 " pdb=" C ILE A 135 " pdb=" CB ILE A 135 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.57e-01 ... (remaining 1331 not shown) Planarity restraints: 1399 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 419 " -0.064 5.00e-02 4.00e+02 9.58e-02 1.47e+01 pdb=" N PRO A 420 " 0.166 5.00e-02 4.00e+02 pdb=" CA PRO A 420 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO A 420 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 420 " -0.045 5.00e-02 4.00e+02 6.73e-02 7.24e+00 pdb=" N PRO A 421 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO A 421 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 421 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 414 " -0.018 2.00e-02 2.50e+03 1.52e-02 5.74e+00 pdb=" CG TRP A 414 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP A 414 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP A 414 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 414 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 414 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 414 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 414 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 414 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 414 " -0.003 2.00e-02 2.50e+03 ... (remaining 1396 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 91 2.60 - 3.17: 6694 3.17 - 3.75: 13546 3.75 - 4.32: 18910 4.32 - 4.90: 30801 Nonbonded interactions: 70042 Sorted by model distance: nonbonded pdb=" OD1 ASP A 110 " pdb="MG MG A 702 " model vdw 2.019 2.170 nonbonded pdb=" O VAL A 111 " pdb="MG MG A 702 " model vdw 2.119 2.170 nonbonded pdb=" O THR A 439 " pdb=" OG1 THR A 459 " model vdw 2.241 3.040 nonbonded pdb=" O VAL B 372 " pdb=" OG1 THR B 376 " model vdw 2.253 3.040 nonbonded pdb=" OG SER A 280 " pdb=" O3' DC F 7 " model vdw 2.254 3.040 ... (remaining 70037 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 14.330 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: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 29.200 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.050 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:12.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 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 : 0.004 0.086 8811 Z= 0.255 Angle : 0.663 8.573 12151 Z= 0.374 Chirality : 0.045 0.517 1334 Planarity : 0.006 0.096 1399 Dihedral : 21.076 153.056 3380 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.20 % Favored : 94.59 % Rotamer: Outliers : 4.88 % Allowed : 32.02 % Favored : 63.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % 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: -1.07 (0.28), residues: 944 helix: 0.26 (0.31), residues: 317 sheet: -0.95 (0.38), residues: 188 loop : -1.26 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP A 414 HIS 0.003 0.001 HIS A 221 PHE 0.010 0.001 PHE B 87 TYR 0.020 0.001 TYR B 354 ARG 0.011 0.001 ARG B 277 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 62 time to evaluate : 0.981 Fit side-chains outliers start: 41 outliers final: 36 residues processed: 102 average time/residue: 1.0784 time to fit residues: 118.6989 Evaluate side-chains 97 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 61 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 TRP Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 223 LYS Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 258 GLN Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 489 SER Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 182 GLN Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 287 LYS Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 418 ASN Chi-restraints excluded: chain B residue 422 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 81 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 39 optimal weight: 0.0870 chunk 76 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 overall best weight: 1.1562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 GLN ** A 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 269 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.0905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 8811 Z= 0.329 Angle : 0.589 8.065 12151 Z= 0.308 Chirality : 0.043 0.165 1334 Planarity : 0.005 0.090 1399 Dihedral : 17.069 152.822 1472 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.15 % Favored : 93.64 % Rotamer: Outliers : 3.81 % Allowed : 31.19 % Favored : 65.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % 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: -0.88 (0.28), residues: 944 helix: 0.61 (0.31), residues: 323 sheet: -0.92 (0.38), residues: 188 loop : -1.30 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 414 HIS 0.003 0.001 HIS A 221 PHE 0.012 0.001 PHE B 61 TYR 0.029 0.001 TYR A 457 ARG 0.007 0.001 ARG A 358 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 63 time to evaluate : 1.021 Fit side-chains REVERT: A 358 ARG cc_start: 0.8310 (mtp85) cc_final: 0.7853 (mtp85) REVERT: A 530 LYS cc_start: 0.8150 (mttp) cc_final: 0.7908 (mmmm) REVERT: A 535 TRP cc_start: 0.8337 (t60) cc_final: 0.7661 (t60) REVERT: B 186 ASP cc_start: 0.7301 (m-30) cc_final: 0.7094 (m-30) REVERT: B 353 LYS cc_start: 0.9028 (tttp) cc_final: 0.8399 (ttpp) outliers start: 32 outliers final: 19 residues processed: 94 average time/residue: 1.0746 time to fit residues: 109.8131 Evaluate side-chains 75 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 56 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 TRP Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 425 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 48 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 59 optimal weight: 0.0870 chunk 24 optimal weight: 0.6980 chunk 88 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 87 optimal weight: 0.0070 chunk 30 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 ASN ** B 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 418 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.1060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 8811 Z= 0.234 Angle : 0.551 7.169 12151 Z= 0.288 Chirality : 0.041 0.163 1334 Planarity : 0.005 0.083 1399 Dihedral : 16.715 145.451 1438 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.30 % Favored : 94.49 % Rotamer: Outliers : 4.17 % Allowed : 30.71 % Favored : 65.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % 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: -0.58 (0.28), residues: 944 helix: 0.95 (0.31), residues: 318 sheet: -0.83 (0.38), residues: 183 loop : -1.15 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 414 HIS 0.003 0.001 HIS A 221 PHE 0.009 0.001 PHE A 160 TYR 0.030 0.001 TYR A 457 ARG 0.009 0.001 ARG B 83 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 63 time to evaluate : 0.948 Fit side-chains revert: symmetry clash REVERT: A 358 ARG cc_start: 0.8292 (mtp85) cc_final: 0.7850 (mtp85) REVERT: A 530 LYS cc_start: 0.8040 (mttp) cc_final: 0.7830 (mmmm) REVERT: A 535 TRP cc_start: 0.8356 (t60) cc_final: 0.7886 (t60) REVERT: B 270 ILE cc_start: 0.8562 (tt) cc_final: 0.8191 (pt) REVERT: B 353 LYS cc_start: 0.9007 (tttp) cc_final: 0.8375 (ttpp) outliers start: 35 outliers final: 20 residues processed: 96 average time/residue: 1.0447 time to fit residues: 109.0179 Evaluate side-chains 76 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 56 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 TRP Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 258 GLN Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 523 GLU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 418 ASN Chi-restraints excluded: chain B residue 425 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 87 optimal weight: 6.9990 chunk 66 optimal weight: 0.9980 chunk 45 optimal weight: 6.9990 chunk 9 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 chunk 59 optimal weight: 0.6980 chunk 88 optimal weight: 0.0670 chunk 93 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 83 optimal weight: 0.3980 chunk 25 optimal weight: 0.8980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 HIS ** B 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 269 GLN B 418 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.1175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 8811 Z= 0.212 Angle : 0.539 7.047 12151 Z= 0.281 Chirality : 0.041 0.160 1334 Planarity : 0.005 0.075 1399 Dihedral : 16.401 138.212 1431 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.09 % Favored : 94.70 % Rotamer: Outliers : 3.57 % Allowed : 30.95 % Favored : 65.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % 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: -0.52 (0.28), residues: 944 helix: 1.12 (0.31), residues: 317 sheet: -0.85 (0.37), residues: 192 loop : -1.19 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 414 HIS 0.003 0.001 HIS A 221 PHE 0.012 0.001 PHE B 87 TYR 0.034 0.001 TYR A 457 ARG 0.008 0.001 ARG B 83 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 61 time to evaluate : 0.960 Fit side-chains revert: symmetry clash REVERT: A 358 ARG cc_start: 0.8366 (mtp85) cc_final: 0.7940 (mtp85) REVERT: A 373 GLN cc_start: 0.8097 (OUTLIER) cc_final: 0.6946 (mp10) REVERT: A 535 TRP cc_start: 0.8394 (t60) cc_final: 0.7827 (t60) REVERT: B 193 LEU cc_start: 0.9267 (OUTLIER) cc_final: 0.8508 (pp) REVERT: B 270 ILE cc_start: 0.8592 (tt) cc_final: 0.8270 (pt) REVERT: B 353 LYS cc_start: 0.8982 (tttp) cc_final: 0.8453 (ttmm) outliers start: 30 outliers final: 16 residues processed: 89 average time/residue: 1.0969 time to fit residues: 105.4845 Evaluate side-chains 74 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 56 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 TRP Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 258 GLN Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 373 GLN Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 523 GLU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 425 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 78 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 69 optimal weight: 0.9990 chunk 38 optimal weight: 0.4980 chunk 80 optimal weight: 4.9990 chunk 64 optimal weight: 0.8980 chunk 0 optimal weight: 0.5980 chunk 47 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 23 optimal weight: 0.0030 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 GLN ** A 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 418 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.1299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 8811 Z= 0.206 Angle : 0.536 6.980 12151 Z= 0.280 Chirality : 0.041 0.154 1334 Planarity : 0.004 0.066 1399 Dihedral : 16.191 130.795 1430 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.20 % Favored : 94.59 % Rotamer: Outliers : 3.81 % Allowed : 30.12 % Favored : 66.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % 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: -0.28 (0.28), residues: 944 helix: 1.43 (0.32), residues: 307 sheet: -0.77 (0.37), residues: 192 loop : -1.05 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 414 HIS 0.003 0.001 HIS A 221 PHE 0.008 0.001 PHE A 160 TYR 0.037 0.001 TYR A 457 ARG 0.008 0.000 ARG B 83 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 64 time to evaluate : 0.875 Fit side-chains revert: symmetry clash REVERT: A 308 GLU cc_start: 0.8911 (tp30) cc_final: 0.8682 (tp30) REVERT: A 373 GLN cc_start: 0.8104 (OUTLIER) cc_final: 0.6954 (mp10) REVERT: A 535 TRP cc_start: 0.8445 (t60) cc_final: 0.7937 (t60) REVERT: B 193 LEU cc_start: 0.9264 (OUTLIER) cc_final: 0.8531 (pp) REVERT: B 270 ILE cc_start: 0.8583 (tt) cc_final: 0.8292 (pt) REVERT: B 353 LYS cc_start: 0.8976 (tttp) cc_final: 0.8439 (ttmm) REVERT: B 354 TYR cc_start: 0.7694 (t80) cc_final: 0.7490 (t80) outliers start: 32 outliers final: 20 residues processed: 93 average time/residue: 1.0391 time to fit residues: 104.4842 Evaluate side-chains 81 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 59 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 TRP Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 258 GLN Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 373 GLN Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 523 GLU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 418 ASN Chi-restraints excluded: chain B residue 425 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 31 optimal weight: 1.9990 chunk 84 optimal weight: 0.4980 chunk 18 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 23 optimal weight: 0.4980 chunk 93 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 90 optimal weight: 0.1980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 269 GLN B 336 GLN B 418 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.1412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8811 Z= 0.200 Angle : 0.533 7.150 12151 Z= 0.275 Chirality : 0.041 0.141 1334 Planarity : 0.004 0.051 1399 Dihedral : 16.122 127.908 1430 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.09 % Favored : 94.80 % Rotamer: Outliers : 3.33 % Allowed : 30.48 % Favored : 66.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % 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 (0.28), residues: 944 helix: 1.47 (0.32), residues: 305 sheet: -0.77 (0.37), residues: 194 loop : -1.00 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 414 HIS 0.003 0.001 HIS B 208 PHE 0.016 0.001 PHE B 87 TYR 0.036 0.001 TYR A 457 ARG 0.008 0.001 ARG B 83 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 61 time to evaluate : 0.891 Fit side-chains revert: symmetry clash REVERT: A 373 GLN cc_start: 0.8100 (OUTLIER) cc_final: 0.6949 (mp10) REVERT: A 535 TRP cc_start: 0.8446 (t60) cc_final: 0.7909 (t60) REVERT: B 192 ASP cc_start: 0.8855 (t0) cc_final: 0.8455 (m-30) REVERT: B 193 LEU cc_start: 0.9269 (OUTLIER) cc_final: 0.8887 (pp) REVERT: B 270 ILE cc_start: 0.8598 (tt) cc_final: 0.8367 (pt) REVERT: B 336 GLN cc_start: 0.8467 (OUTLIER) cc_final: 0.8229 (mp10) REVERT: B 353 LYS cc_start: 0.8976 (tttp) cc_final: 0.8418 (ttmm) REVERT: B 354 TYR cc_start: 0.7670 (t80) cc_final: 0.7433 (t80) REVERT: B 356 ARG cc_start: 0.8259 (OUTLIER) cc_final: 0.7722 (ptp90) outliers start: 28 outliers final: 16 residues processed: 86 average time/residue: 1.1038 time to fit residues: 102.4671 Evaluate side-chains 78 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 58 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 TRP Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 373 GLN Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 523 GLU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 336 GLN Chi-restraints excluded: chain B residue 356 ARG Chi-restraints excluded: chain B residue 425 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 10 optimal weight: 0.7980 chunk 53 optimal weight: 0.0870 chunk 68 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 93 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 43 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.7162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 418 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8811 Z= 0.227 Angle : 0.537 7.720 12151 Z= 0.277 Chirality : 0.041 0.144 1334 Planarity : 0.004 0.050 1399 Dihedral : 16.096 127.534 1429 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.77 % Favored : 95.12 % Rotamer: Outliers : 3.45 % Allowed : 31.07 % Favored : 65.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % 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: -0.19 (0.28), residues: 944 helix: 1.52 (0.32), residues: 307 sheet: -0.77 (0.37), residues: 194 loop : -0.97 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 414 HIS 0.003 0.001 HIS B 208 PHE 0.009 0.001 PHE A 160 TYR 0.030 0.001 TYR A 457 ARG 0.008 0.000 ARG B 83 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 60 time to evaluate : 0.952 Fit side-chains revert: symmetry clash REVERT: A 373 GLN cc_start: 0.8100 (OUTLIER) cc_final: 0.6949 (mp10) REVERT: A 535 TRP cc_start: 0.8481 (t60) cc_final: 0.7928 (t60) REVERT: B 192 ASP cc_start: 0.8846 (t0) cc_final: 0.8459 (m-30) REVERT: B 193 LEU cc_start: 0.9247 (OUTLIER) cc_final: 0.8833 (pp) REVERT: B 270 ILE cc_start: 0.8661 (tt) cc_final: 0.8411 (pt) REVERT: B 353 LYS cc_start: 0.8999 (tttp) cc_final: 0.8429 (ttmm) REVERT: B 354 TYR cc_start: 0.7701 (t80) cc_final: 0.7480 (t80) REVERT: B 356 ARG cc_start: 0.8279 (OUTLIER) cc_final: 0.7759 (ptp90) outliers start: 29 outliers final: 18 residues processed: 86 average time/residue: 1.0187 time to fit residues: 95.5154 Evaluate side-chains 80 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 59 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 TRP Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 373 GLN Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 523 GLU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 356 ARG Chi-restraints excluded: chain B residue 418 ASN Chi-restraints excluded: chain B residue 425 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 55 optimal weight: 0.0980 chunk 28 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 73 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 81 optimal weight: 0.2980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 269 GLN B 418 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8811 Z= 0.245 Angle : 0.545 7.885 12151 Z= 0.280 Chirality : 0.041 0.148 1334 Planarity : 0.004 0.058 1399 Dihedral : 16.099 128.491 1429 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.30 % Favored : 94.59 % Rotamer: Outliers : 3.10 % Allowed : 30.71 % Favored : 66.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % 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: -0.16 (0.28), residues: 944 helix: 1.56 (0.32), residues: 307 sheet: -0.75 (0.37), residues: 194 loop : -0.96 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 414 HIS 0.003 0.001 HIS B 208 PHE 0.017 0.001 PHE B 87 TYR 0.030 0.001 TYR A 457 ARG 0.007 0.000 ARG B 83 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 58 time to evaluate : 0.964 Fit side-chains revert: symmetry clash REVERT: A 373 GLN cc_start: 0.8103 (OUTLIER) cc_final: 0.6955 (mp10) REVERT: A 535 TRP cc_start: 0.8496 (t60) cc_final: 0.7953 (t60) REVERT: B 192 ASP cc_start: 0.8837 (t0) cc_final: 0.8496 (m-30) REVERT: B 193 LEU cc_start: 0.9241 (OUTLIER) cc_final: 0.8780 (pp) REVERT: B 270 ILE cc_start: 0.8646 (tt) cc_final: 0.8408 (pt) REVERT: B 353 LYS cc_start: 0.8990 (tttp) cc_final: 0.8425 (ttmm) REVERT: B 354 TYR cc_start: 0.7683 (t80) cc_final: 0.7464 (t80) REVERT: B 356 ARG cc_start: 0.8266 (OUTLIER) cc_final: 0.7745 (ptp90) outliers start: 26 outliers final: 17 residues processed: 80 average time/residue: 1.0499 time to fit residues: 91.1369 Evaluate side-chains 77 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 57 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 340 GLN Chi-restraints excluded: chain A residue 373 GLN Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 523 GLU Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 356 ARG Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 418 ASN Chi-restraints excluded: chain B residue 425 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 87 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 68 optimal weight: 0.9990 chunk 26 optimal weight: 0.5980 chunk 78 optimal weight: 8.9990 chunk 82 optimal weight: 6.9990 chunk 86 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 269 GLN B 418 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8811 Z= 0.242 Angle : 0.546 8.490 12151 Z= 0.280 Chirality : 0.041 0.147 1334 Planarity : 0.004 0.061 1399 Dihedral : 15.991 128.791 1424 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.30 % Favored : 94.59 % Rotamer: Outliers : 2.50 % Allowed : 31.07 % Favored : 66.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.28), residues: 944 helix: 1.60 (0.32), residues: 307 sheet: -0.72 (0.37), residues: 194 loop : -0.95 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 414 HIS 0.003 0.001 HIS B 208 PHE 0.010 0.001 PHE A 160 TYR 0.035 0.001 TYR A 457 ARG 0.015 0.001 ARG A 358 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 58 time to evaluate : 0.896 Fit side-chains revert: symmetry clash REVERT: A 373 GLN cc_start: 0.8104 (OUTLIER) cc_final: 0.6955 (mp10) REVERT: A 535 TRP cc_start: 0.8469 (t60) cc_final: 0.7887 (t60) REVERT: B 192 ASP cc_start: 0.8804 (t0) cc_final: 0.8491 (m-30) REVERT: B 193 LEU cc_start: 0.9238 (OUTLIER) cc_final: 0.8784 (pp) REVERT: B 270 ILE cc_start: 0.8609 (tt) cc_final: 0.8386 (pt) REVERT: B 353 LYS cc_start: 0.8978 (tttp) cc_final: 0.8413 (ttmm) REVERT: B 356 ARG cc_start: 0.8263 (OUTLIER) cc_final: 0.7746 (ptp90) outliers start: 21 outliers final: 15 residues processed: 76 average time/residue: 1.1339 time to fit residues: 93.0724 Evaluate side-chains 74 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 56 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 373 GLN Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 523 GLU Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 356 ARG Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 418 ASN Chi-restraints excluded: chain B residue 425 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 56 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 64 optimal weight: 0.1980 chunk 96 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 59 optimal weight: 0.1980 chunk 47 optimal weight: 0.8980 chunk 61 optimal weight: 0.7980 chunk 81 optimal weight: 5.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 269 GLN B 418 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8811 Z= 0.196 Angle : 0.540 8.502 12151 Z= 0.278 Chirality : 0.041 0.140 1334 Planarity : 0.004 0.065 1399 Dihedral : 15.952 125.750 1424 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.98 % Favored : 94.80 % Rotamer: Outliers : 2.14 % Allowed : 31.90 % Favored : 65.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.28), residues: 944 helix: 1.55 (0.31), residues: 313 sheet: -0.67 (0.38), residues: 188 loop : -0.95 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 414 HIS 0.003 0.001 HIS B 208 PHE 0.022 0.001 PHE B 87 TYR 0.035 0.001 TYR A 457 ARG 0.008 0.001 ARG B 83 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 58 time to evaluate : 0.985 Fit side-chains revert: symmetry clash REVERT: A 357 MET cc_start: 0.8694 (mmt) cc_final: 0.8390 (mmm) REVERT: A 358 ARG cc_start: 0.8188 (mtp85) cc_final: 0.7850 (mtp85) REVERT: A 373 GLN cc_start: 0.8079 (OUTLIER) cc_final: 0.6929 (mp10) REVERT: A 535 TRP cc_start: 0.8444 (t60) cc_final: 0.7881 (t60) REVERT: B 192 ASP cc_start: 0.8779 (t0) cc_final: 0.8486 (m-30) REVERT: B 193 LEU cc_start: 0.9203 (OUTLIER) cc_final: 0.8759 (pp) REVERT: B 270 ILE cc_start: 0.8600 (tt) cc_final: 0.8388 (pt) REVERT: B 353 LYS cc_start: 0.8978 (tttp) cc_final: 0.8402 (ttmm) REVERT: B 356 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.7575 (ptp90) outliers start: 18 outliers final: 12 residues processed: 73 average time/residue: 1.1752 time to fit residues: 92.3942 Evaluate side-chains 73 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 58 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 373 GLN Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 523 GLU Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 356 ARG Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 425 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 23 optimal weight: 0.5980 chunk 70 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 21 optimal weight: 0.7980 chunk 77 optimal weight: 0.0040 chunk 32 optimal weight: 0.5980 chunk 79 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 14 optimal weight: 0.5980 chunk 67 optimal weight: 0.4980 chunk 4 optimal weight: 0.9990 overall best weight: 0.4592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 418 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.115639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.078507 restraints weight = 18145.933| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 3.04 r_work: 0.2913 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2922 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2922 r_free = 0.2922 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2922 r_free = 0.2922 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2922 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8811 Z= 0.183 Angle : 0.532 9.002 12151 Z= 0.273 Chirality : 0.041 0.137 1334 Planarity : 0.004 0.069 1399 Dihedral : 15.785 120.529 1422 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.88 % Favored : 94.91 % Rotamer: Outliers : 2.26 % Allowed : 32.14 % Favored : 65.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.28), residues: 944 helix: 1.60 (0.31), residues: 313 sheet: -0.64 (0.37), residues: 188 loop : -0.95 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 414 HIS 0.003 0.001 HIS B 208 PHE 0.008 0.001 PHE A 160 TYR 0.037 0.001 TYR B 354 ARG 0.008 0.001 ARG B 83 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2869.25 seconds wall clock time: 52 minutes 53.34 seconds (3173.34 seconds total)