Starting phenix.real_space_refine on Fri Dec 27 12:53:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bzo_16344/12_2024/8bzo_16344.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bzo_16344/12_2024/8bzo_16344.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8bzo_16344/12_2024/8bzo_16344.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bzo_16344/12_2024/8bzo_16344.map" model { file = "/net/cci-nas-00/data/ceres_data/8bzo_16344/12_2024/8bzo_16344.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bzo_16344/12_2024/8bzo_16344.cif" } resolution = 3.5 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= 0.029 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 17 5.16 5 C 3134 2.51 5 N 821 2.21 5 O 861 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 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: 4834 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2212 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 19, 'TRANS': 264} Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'HIS:plan': 1, 'GLU:plan': 4, 'TPO:plan-1': 1, 'ARG:plan': 3, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 46 Chain: "B" Number of atoms: 2029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2029 Classifications: {'peptide': 258} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 243} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 34 Chain: "C" Number of atoms: 593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 593 Classifications: {'peptide': 72} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 7, 'TRANS': 64} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Time building chain proxies: 3.69, per 1000 atoms: 0.76 Number of scatterers: 4834 At special positions: 0 Unit cell: (81.32, 93.09, 80.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 17 16.00 P 1 15.00 O 861 8.00 N 821 7.00 C 3134 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: 1.15 Conformation dependent library (CDL) restraints added in 584.4 milliseconds 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1176 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 3 sheets defined 48.9% alpha, 4.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 45 through 55 removed outlier: 3.913A pdb=" N GLU A 51 " --> pdb=" O THR A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 94 Processing helix chain 'A' and resid 100 through 121 removed outlier: 3.701A pdb=" N LEU A 111 " --> pdb=" O TYR A 107 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLN A 113 " --> pdb=" O PHE A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 169 Processing helix chain 'A' and resid 170 through 176 removed outlier: 3.710A pdb=" N LEU A 175 " --> pdb=" O PRO A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 199 removed outlier: 3.917A pdb=" N ILE A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL A 197 " --> pdb=" O PHE A 193 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N THR A 198 " --> pdb=" O ALA A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 220 removed outlier: 3.716A pdb=" N ARG A 217 " --> pdb=" O PHE A 213 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N THR A 218 " --> pdb=" O ARG A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 252 removed outlier: 3.629A pdb=" N VAL A 251 " --> pdb=" O ASP A 247 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL A 252 " --> pdb=" O PHE A 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 247 through 252' Processing helix chain 'A' and resid 258 through 267 removed outlier: 4.154A pdb=" N LEU A 262 " --> pdb=" O ASP A 258 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU A 263 " --> pdb=" O GLY A 259 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER A 264 " --> pdb=" O ARG A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 281 removed outlier: 3.586A pdb=" N LEU A 281 " --> pdb=" O ALA A 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 190 Processing helix chain 'B' and resid 207 through 224 removed outlier: 3.730A pdb=" N ILE B 213 " --> pdb=" O SER B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 243 removed outlier: 4.159A pdb=" N LEU B 232 " --> pdb=" O GLN B 228 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N HIS B 233 " --> pdb=" O ASN B 229 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASN B 237 " --> pdb=" O HIS B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 269 removed outlier: 4.033A pdb=" N PHE B 267 " --> pdb=" O LEU B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 282 Processing helix chain 'B' and resid 287 through 292 removed outlier: 3.655A pdb=" N LEU B 292 " --> pdb=" O LYS B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 302 removed outlier: 4.178A pdb=" N LYS B 300 " --> pdb=" O HIS B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 320 removed outlier: 3.900A pdb=" N LEU B 315 " --> pdb=" O VAL B 311 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLN B 317 " --> pdb=" O GLN B 313 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LEU B 320 " --> pdb=" O THR B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 343 removed outlier: 3.674A pdb=" N SER B 340 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N LEU B 341 " --> pdb=" O GLY B 337 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ILE B 342 " --> pdb=" O GLU B 338 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ASP B 343 " --> pdb=" O LEU B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 368 removed outlier: 3.599A pdb=" N GLY B 357 " --> pdb=" O SER B 353 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N TYR B 365 " --> pdb=" O HIS B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 378 removed outlier: 3.944A pdb=" N ARG B 378 " --> pdb=" O SER B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 401 removed outlier: 3.808A pdb=" N GLN B 396 " --> pdb=" O MET B 392 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N THR B 397 " --> pdb=" O ASP B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 404 No H-bonds generated for 'chain 'B' and resid 402 through 404' Processing helix chain 'B' and resid 408 through 415 removed outlier: 3.997A pdb=" N ASN B 415 " --> pdb=" O GLU B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 419 Processing helix chain 'B' and resid 420 through 424 removed outlier: 3.672A pdb=" N LEU B 423 " --> pdb=" O GLY B 420 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 52 removed outlier: 3.540A pdb=" N HIS C 48 " --> pdb=" O ASP C 44 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N MET C 52 " --> pdb=" O HIS C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 90 removed outlier: 3.506A pdb=" N TYR C 88 " --> pdb=" O PRO C 85 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ARG C 90 " --> pdb=" O PHE C 87 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 18 through 22 removed outlier: 4.549A pdb=" N VAL A 18 " --> pdb=" O VAL C 79 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 30 through 36 removed outlier: 7.022A pdb=" N GLU A 81 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N LEU A 66 " --> pdb=" O GLU A 81 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 85 through 86 173 hydrogen bonds defined for protein. 495 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: 1.20 Time building geometry restraints manager: 1.34 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: 982 1.33 - 1.45: 1144 1.45 - 1.57: 2811 1.57 - 1.69: 1 1.69 - 1.82: 27 Bond restraints: 4965 Sorted by residual: bond pdb=" OG1 TPO A 160 " pdb=" P TPO A 160 " ideal model delta sigma weight residual 1.717 1.627 0.090 2.00e-02 2.50e+03 2.01e+01 bond pdb=" N VAL B 311 " pdb=" CA VAL B 311 " ideal model delta sigma weight residual 1.462 1.513 -0.051 1.17e-02 7.31e+03 1.89e+01 bond pdb=" N ARG A 122 " pdb=" CA ARG A 122 " ideal model delta sigma weight residual 1.459 1.502 -0.043 1.15e-02 7.56e+03 1.39e+01 bond pdb=" CA SER B 386 " pdb=" CB SER B 386 " ideal model delta sigma weight residual 1.531 1.470 0.060 1.69e-02 3.50e+03 1.28e+01 bond pdb=" CB TPO A 160 " pdb=" OG1 TPO A 160 " ideal model delta sigma weight residual 1.406 1.472 -0.066 2.00e-02 2.50e+03 1.08e+01 ... (remaining 4960 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 6493 1.72 - 3.44: 224 3.44 - 5.15: 35 5.15 - 6.87: 10 6.87 - 8.59: 3 Bond angle restraints: 6765 Sorted by residual: angle pdb=" N HIS C 23 " pdb=" CA HIS C 23 " pdb=" C HIS C 23 " ideal model delta sigma weight residual 109.64 101.51 8.13 1.27e+00 6.20e-01 4.09e+01 angle pdb=" N ILE B 377 " pdb=" CA ILE B 377 " pdb=" C ILE B 377 " ideal model delta sigma weight residual 112.90 107.27 5.63 9.60e-01 1.09e+00 3.44e+01 angle pdb=" N LEU B 384 " pdb=" CA LEU B 384 " pdb=" C LEU B 384 " ideal model delta sigma weight residual 113.18 107.93 5.25 1.21e+00 6.83e-01 1.88e+01 angle pdb=" C GLU A 195 " pdb=" CA GLU A 195 " pdb=" CB GLU A 195 " ideal model delta sigma weight residual 109.67 101.08 8.59 2.01e+00 2.48e-01 1.83e+01 angle pdb=" C LEU A 78 " pdb=" N VAL A 79 " pdb=" CA VAL A 79 " ideal model delta sigma weight residual 122.43 127.45 -5.02 1.26e+00 6.30e-01 1.59e+01 ... (remaining 6760 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.13: 2520 16.13 - 32.26: 319 32.26 - 48.38: 111 48.38 - 64.51: 15 64.51 - 80.64: 7 Dihedral angle restraints: 2972 sinusoidal: 1156 harmonic: 1816 Sorted by residual: dihedral pdb=" C GLU A 195 " pdb=" N GLU A 195 " pdb=" CA GLU A 195 " pdb=" CB GLU A 195 " ideal model delta harmonic sigma weight residual -122.60 -111.61 -10.99 0 2.50e+00 1.60e-01 1.93e+01 dihedral pdb=" CA HIS C 23 " pdb=" C HIS C 23 " pdb=" N PRO C 24 " pdb=" CA PRO C 24 " ideal model delta harmonic sigma weight residual -180.00 -158.68 -21.32 0 5.00e+00 4.00e-02 1.82e+01 dihedral pdb=" CA LEU A 83 " pdb=" C LEU A 83 " pdb=" N HIS A 84 " pdb=" CA HIS A 84 " ideal model delta harmonic sigma weight residual -180.00 -162.19 -17.81 0 5.00e+00 4.00e-02 1.27e+01 ... (remaining 2969 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 559 0.046 - 0.093: 165 0.093 - 0.139: 30 0.139 - 0.185: 4 0.185 - 0.231: 3 Chirality restraints: 761 Sorted by residual: chirality pdb=" CA GLU A 195 " pdb=" N GLU A 195 " pdb=" C GLU A 195 " pdb=" CB GLU A 195 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CA LYS C 47 " pdb=" N LYS C 47 " pdb=" C LYS C 47 " pdb=" CB LYS C 47 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA ARG B 378 " pdb=" N ARG B 378 " pdb=" C ARG B 378 " pdb=" CB ARG B 378 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.08e+00 ... (remaining 758 not shown) Planarity restraints: 860 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR B 199 " 0.014 2.00e-02 2.50e+03 2.84e-02 8.09e+00 pdb=" C TYR B 199 " -0.049 2.00e-02 2.50e+03 pdb=" O TYR B 199 " 0.018 2.00e-02 2.50e+03 pdb=" N MET B 200 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 353 " -0.012 2.00e-02 2.50e+03 2.46e-02 6.05e+00 pdb=" C SER B 353 " 0.043 2.00e-02 2.50e+03 pdb=" O SER B 353 " -0.016 2.00e-02 2.50e+03 pdb=" N VAL B 354 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS A 60 " -0.032 5.00e-02 4.00e+02 4.77e-02 3.64e+00 pdb=" N PRO A 61 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO A 61 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 61 " -0.027 5.00e-02 4.00e+02 ... (remaining 857 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 942 2.77 - 3.30: 4554 3.30 - 3.83: 7541 3.83 - 4.37: 8874 4.37 - 4.90: 15177 Nonbonded interactions: 37088 Sorted by model distance: nonbonded pdb=" OD2 ASP A 68 " pdb=" NE1 TRP C 60 " model vdw 2.231 3.120 nonbonded pdb=" OG1 THR A 137 " pdb=" OE2 GLU A 138 " model vdw 2.232 3.040 nonbonded pdb=" O GLU A 42 " pdb=" NZ LYS B 266 " model vdw 2.251 3.120 nonbonded pdb=" OG SER B 331 " pdb=" O TYR B 418 " model vdw 2.258 3.040 nonbonded pdb=" NZ LYS A 278 " pdb=" O ASP B 177 " model vdw 2.267 3.120 ... (remaining 37083 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=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: 2.590 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: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 15.030 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 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:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 4965 Z= 0.345 Angle : 0.733 8.588 6765 Z= 0.428 Chirality : 0.046 0.231 761 Planarity : 0.005 0.048 860 Dihedral : 16.406 80.641 1796 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.62 % Favored : 94.21 % Rotamer: Outliers : 0.99 % Allowed : 24.21 % Favored : 74.80 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 2.50 % 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: -1.51 (0.34), residues: 605 helix: -0.73 (0.33), residues: 270 sheet: -0.06 (1.14), residues: 25 loop : -1.27 (0.35), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 167 HIS 0.010 0.001 HIS B 361 PHE 0.012 0.002 PHE A 80 TYR 0.015 0.001 TYR B 199 ARG 0.007 0.001 ARG A 150 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 95 time to evaluate : 0.535 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 97 average time/residue: 0.2122 time to fit residues: 25.4580 Evaluate side-chains 87 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 85 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 395 HIS Chi-restraints excluded: chain C residue 66 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 chunk 35 optimal weight: 0.0270 chunk 54 optimal weight: 3.9990 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 179 HIS B 296 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.1050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4965 Z= 0.217 Angle : 0.597 7.219 6765 Z= 0.306 Chirality : 0.042 0.134 761 Planarity : 0.005 0.048 860 Dihedral : 5.067 42.992 672 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.46 % Favored : 95.37 % Rotamer: Outliers : 2.58 % Allowed : 23.02 % Favored : 74.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -0.95 (0.35), residues: 605 helix: -0.15 (0.33), residues: 277 sheet: 1.14 (1.41), residues: 15 loop : -1.12 (0.35), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 372 HIS 0.006 0.001 HIS B 361 PHE 0.010 0.001 PHE A 80 TYR 0.010 0.001 TYR C 88 ARG 0.006 0.001 ARG C 58 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 0.562 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 8 residues processed: 106 average time/residue: 0.1756 time to fit residues: 23.6637 Evaluate side-chains 94 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 86 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 395 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 30 optimal weight: 3.9990 chunk 16 optimal weight: 0.3980 chunk 45 optimal weight: 0.9980 chunk 37 optimal weight: 0.5980 chunk 15 optimal weight: 0.5980 chunk 54 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 18 optimal weight: 0.3980 chunk 43 optimal weight: 0.0670 chunk 53 optimal weight: 0.7980 overall best weight: 0.4118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.1340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4965 Z= 0.185 Angle : 0.561 7.361 6765 Z= 0.285 Chirality : 0.040 0.132 761 Planarity : 0.005 0.044 860 Dihedral : 4.691 38.854 670 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.13 % Favored : 95.70 % Rotamer: Outliers : 3.17 % Allowed : 23.61 % Favored : 73.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -0.66 (0.35), residues: 605 helix: 0.08 (0.34), residues: 279 sheet: 1.13 (1.42), residues: 15 loop : -0.96 (0.36), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 372 HIS 0.005 0.001 HIS B 296 PHE 0.011 0.001 PHE A 80 TYR 0.011 0.001 TYR C 88 ARG 0.005 0.000 ARG C 58 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 96 time to evaluate : 0.548 Fit side-chains revert: symmetry clash REVERT: A 71 HIS cc_start: 0.7641 (t70) cc_final: 0.7042 (t70) outliers start: 16 outliers final: 8 residues processed: 109 average time/residue: 0.1542 time to fit residues: 21.9338 Evaluate side-chains 100 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 92 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 377 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 41 optimal weight: 0.6980 chunk 28 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 54 optimal weight: 0.0970 chunk 57 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 HIS ** B 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 4965 Z= 0.331 Angle : 0.638 6.839 6765 Z= 0.321 Chirality : 0.043 0.130 761 Planarity : 0.005 0.045 860 Dihedral : 4.735 29.216 668 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.12 % Favored : 94.71 % Rotamer: Outliers : 3.97 % Allowed : 23.81 % Favored : 72.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -0.92 (0.35), residues: 605 helix: -0.05 (0.33), residues: 277 sheet: -0.17 (1.12), residues: 25 loop : -1.14 (0.36), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 372 HIS 0.012 0.001 HIS B 296 PHE 0.013 0.002 PHE C 62 TYR 0.015 0.002 TYR B 199 ARG 0.006 0.001 ARG C 58 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 93 time to evaluate : 0.565 Fit side-chains revert: symmetry clash REVERT: A 195 GLU cc_start: 0.8526 (tm-30) cc_final: 0.8235 (tm-30) REVERT: C 77 GLN cc_start: 0.7290 (mt0) cc_final: 0.7053 (mt0) outliers start: 20 outliers final: 13 residues processed: 109 average time/residue: 0.1578 time to fit residues: 22.5552 Evaluate side-chains 104 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 91 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 243 TRP Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 316 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 0 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 23 optimal weight: 0.3980 chunk 49 optimal weight: 0.0070 chunk 40 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 14 optimal weight: 0.2980 chunk 19 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 overall best weight: 0.4398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4965 Z= 0.181 Angle : 0.556 6.627 6765 Z= 0.281 Chirality : 0.040 0.129 761 Planarity : 0.005 0.046 860 Dihedral : 4.398 28.416 668 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 4.17 % Allowed : 23.41 % Favored : 72.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -0.54 (0.36), residues: 605 helix: 0.25 (0.34), residues: 277 sheet: 1.07 (1.42), residues: 15 loop : -0.96 (0.36), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 217 HIS 0.008 0.001 HIS B 296 PHE 0.008 0.001 PHE A 80 TYR 0.011 0.001 TYR B 199 ARG 0.007 0.000 ARG C 58 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 91 time to evaluate : 0.607 Fit side-chains revert: symmetry clash REVERT: A 195 GLU cc_start: 0.8393 (tm-30) cc_final: 0.8146 (tm-30) REVERT: A 265 GLN cc_start: 0.8079 (mp10) cc_final: 0.7031 (mp10) outliers start: 21 outliers final: 9 residues processed: 107 average time/residue: 0.1451 time to fit residues: 20.9177 Evaluate side-chains 95 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 86 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 377 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 14 optimal weight: 0.0570 chunk 58 optimal weight: 0.5980 chunk 48 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 19 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 55 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 HIS B 296 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4965 Z= 0.196 Angle : 0.556 7.662 6765 Z= 0.278 Chirality : 0.041 0.146 761 Planarity : 0.005 0.044 860 Dihedral : 4.310 26.610 668 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 3.77 % Allowed : 25.40 % Favored : 70.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -0.46 (0.36), residues: 605 helix: 0.32 (0.34), residues: 279 sheet: 0.95 (1.40), residues: 15 loop : -0.92 (0.37), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 372 HIS 0.007 0.001 HIS B 296 PHE 0.009 0.001 PHE A 80 TYR 0.012 0.001 TYR B 199 ARG 0.007 0.000 ARG C 58 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 91 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 14 residues processed: 106 average time/residue: 0.1444 time to fit residues: 20.5731 Evaluate side-chains 103 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 243 TRP Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 377 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 32 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 23 optimal weight: 0.0020 chunk 34 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 11 optimal weight: 0.2980 chunk 39 optimal weight: 1.9990 overall best weight: 0.8190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4965 Z= 0.245 Angle : 0.582 6.669 6765 Z= 0.292 Chirality : 0.042 0.157 761 Planarity : 0.005 0.045 860 Dihedral : 4.419 24.923 668 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 4.17 % Allowed : 25.00 % Favored : 70.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -0.53 (0.36), residues: 605 helix: 0.24 (0.33), residues: 280 sheet: 0.80 (1.38), residues: 15 loop : -0.93 (0.37), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 372 HIS 0.005 0.001 HIS B 296 PHE 0.011 0.001 PHE C 62 TYR 0.014 0.001 TYR B 199 ARG 0.007 0.000 ARG C 58 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 95 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 77 GLN cc_start: 0.7377 (mt0) cc_final: 0.7164 (mt0) outliers start: 21 outliers final: 16 residues processed: 110 average time/residue: 0.1553 time to fit residues: 22.4705 Evaluate side-chains 107 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 91 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 243 TRP Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 377 ILE Chi-restraints excluded: chain B residue 392 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 28 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 chunk 32 optimal weight: 0.5980 chunk 23 optimal weight: 0.0970 chunk 42 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 229 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4965 Z= 0.208 Angle : 0.564 6.547 6765 Z= 0.286 Chirality : 0.041 0.151 761 Planarity : 0.005 0.044 860 Dihedral : 4.357 24.051 668 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 3.97 % Allowed : 25.60 % Favored : 70.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -0.42 (0.36), residues: 605 helix: 0.35 (0.34), residues: 279 sheet: 1.03 (1.42), residues: 15 loop : -0.90 (0.37), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 167 HIS 0.006 0.001 HIS A 71 PHE 0.009 0.001 PHE C 62 TYR 0.012 0.001 TYR B 199 ARG 0.007 0.000 ARG A 150 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 90 time to evaluate : 0.552 Fit side-chains revert: symmetry clash REVERT: C 77 GLN cc_start: 0.7400 (mt0) cc_final: 0.7184 (mt0) outliers start: 20 outliers final: 19 residues processed: 103 average time/residue: 0.1526 time to fit residues: 20.8921 Evaluate side-chains 107 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 88 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 243 TRP Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 377 ILE Chi-restraints excluded: chain B residue 392 MET Chi-restraints excluded: chain C residue 70 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 53 optimal weight: 0.4980 chunk 35 optimal weight: 1.9990 chunk 56 optimal weight: 0.1980 chunk 34 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 59 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 229 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4965 Z= 0.222 Angle : 0.580 6.571 6765 Z= 0.294 Chirality : 0.041 0.150 761 Planarity : 0.005 0.044 860 Dihedral : 4.373 22.931 668 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 3.97 % Allowed : 25.60 % Favored : 70.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -0.42 (0.36), residues: 605 helix: 0.34 (0.33), residues: 280 sheet: 0.95 (1.41), residues: 15 loop : -0.88 (0.37), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 167 HIS 0.008 0.001 HIS C 48 PHE 0.010 0.001 PHE C 62 TYR 0.012 0.001 TYR B 199 ARG 0.007 0.000 ARG C 58 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 88 time to evaluate : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 265 GLN cc_start: 0.8098 (mp10) cc_final: 0.7872 (mp10) REVERT: C 77 GLN cc_start: 0.7412 (mt0) cc_final: 0.7202 (mt0) outliers start: 20 outliers final: 19 residues processed: 101 average time/residue: 0.1540 time to fit residues: 20.6910 Evaluate side-chains 105 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 86 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 243 TRP Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 377 ILE Chi-restraints excluded: chain B residue 392 MET Chi-restraints excluded: chain C residue 70 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 4 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 50 optimal weight: 0.5980 chunk 14 optimal weight: 0.0370 chunk 43 optimal weight: 0.6980 chunk 7 optimal weight: 0.6980 chunk 13 optimal weight: 0.5980 chunk 47 optimal weight: 0.6980 chunk 19 optimal weight: 0.3980 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 229 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4965 Z= 0.188 Angle : 0.556 6.547 6765 Z= 0.283 Chirality : 0.041 0.145 761 Planarity : 0.005 0.044 860 Dihedral : 4.219 22.013 668 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 3.37 % Allowed : 25.99 % Favored : 70.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -0.35 (0.36), residues: 605 helix: 0.43 (0.34), residues: 280 sheet: 1.10 (1.45), residues: 15 loop : -0.89 (0.37), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 372 HIS 0.008 0.001 HIS C 48 PHE 0.008 0.001 PHE A 152 TYR 0.010 0.001 TYR B 199 ARG 0.007 0.000 ARG C 58 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 91 time to evaluate : 0.565 Fit side-chains revert: symmetry clash REVERT: A 265 GLN cc_start: 0.8090 (mp10) cc_final: 0.7866 (mp10) outliers start: 17 outliers final: 17 residues processed: 101 average time/residue: 0.1667 time to fit residues: 22.4993 Evaluate side-chains 104 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 87 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 243 TRP Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 377 ILE Chi-restraints excluded: chain B residue 392 MET Chi-restraints excluded: chain C residue 70 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 41 optimal weight: 0.5980 chunk 2 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 54 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 chunk 40 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 229 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.178678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.152031 restraints weight = 6555.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.156205 restraints weight = 4367.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.159127 restraints weight = 3263.652| |-----------------------------------------------------------------------------| r_work (final): 0.3762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7235 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4965 Z= 0.232 Angle : 0.583 6.557 6765 Z= 0.296 Chirality : 0.042 0.148 761 Planarity : 0.005 0.044 860 Dihedral : 4.332 21.728 668 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 3.57 % Allowed : 25.60 % Favored : 70.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -0.41 (0.36), residues: 605 helix: 0.37 (0.33), residues: 281 sheet: 0.94 (1.43), residues: 15 loop : -0.90 (0.37), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 167 HIS 0.008 0.001 HIS C 48 PHE 0.011 0.001 PHE C 62 TYR 0.013 0.001 TYR B 199 ARG 0.007 0.000 ARG C 58 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1398.99 seconds wall clock time: 26 minutes 13.94 seconds (1573.94 seconds total)