Starting phenix.real_space_refine on Fri Dec 27 12:11:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vu5_21387/12_2024/6vu5_21387.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vu5_21387/12_2024/6vu5_21387.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/6vu5_21387/12_2024/6vu5_21387.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vu5_21387/12_2024/6vu5_21387.map" model { file = "/net/cci-nas-00/data/ceres_data/6vu5_21387/12_2024/6vu5_21387.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vu5_21387/12_2024/6vu5_21387.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= -0.000 sd= 0.006 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 2 5.49 5 S 25 5.16 5 C 2961 2.51 5 N 815 2.21 5 O 854 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 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: 4657 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3454 Classifications: {'peptide': 441} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 14, 'TRANS': 426} Chain breaks: 3 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 43 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'TPO:plan-1': 1, 'ARG:plan': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 53 Chain: "A" Number of atoms: 135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 135 Classifications: {'peptide': 27} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'TRANS': 26} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'UNK:plan-1': 27} Unresolved non-hydrogen planarities: 27 Chain: "B" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1068 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 4, 'TRANS': 130} Chain breaks: 2 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 42 Time building chain proxies: 3.46, per 1000 atoms: 0.74 Number of scatterers: 4657 At special positions: 0 Unit cell: (109.06, 58.22, 83.64, 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 25 16.00 P 2 15.00 O 854 8.00 N 815 7.00 C 2961 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: 1.04 Conformation dependent library (CDL) restraints added in 593.7 milliseconds 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1168 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 2 sheets defined 58.3% alpha, 1.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 2 through 12 removed outlier: 3.771A pdb=" N ASP A 8 " --> pdb=" O ARG A 4 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N THR A 12 " --> pdb=" O ASP A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 29 removed outlier: 4.285A pdb=" N ARG A 27 " --> pdb=" O ARG A 23 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU A 28 " --> pdb=" O SER A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 38 No H-bonds generated for 'chain 'A' and resid 36 through 38' Processing helix chain 'A' and resid 39 through 57 removed outlier: 3.740A pdb=" N GLN A 56 " --> pdb=" O SER A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 74 Processing helix chain 'A' and resid 75 through 80 removed outlier: 6.287A pdb=" N SER A 78 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N CYS A 79 " --> pdb=" O ASP A 76 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU A 80 " --> pdb=" O ARG A 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 75 through 80' Processing helix chain 'A' and resid 85 through 96 removed outlier: 3.759A pdb=" N LEU A 89 " --> pdb=" O SER A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 127 Processing helix chain 'A' and resid 128 through 138 removed outlier: 3.727A pdb=" N MET A 133 " --> pdb=" O PRO A 129 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N LEU A 134 " --> pdb=" O THR A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 150 removed outlier: 4.474A pdb=" N GLU A 146 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG A 147 " --> pdb=" O ARG A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 174 removed outlier: 3.643A pdb=" N GLN A 161 " --> pdb=" O PRO A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 200 removed outlier: 3.592A pdb=" N LEU A 191 " --> pdb=" O HIS A 187 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU A 198 " --> pdb=" O ASP A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 232 Processing helix chain 'A' and resid 242 through 260 removed outlier: 4.121A pdb=" N MET A 259 " --> pdb=" O ARG A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 280 Processing helix chain 'A' and resid 282 through 287 removed outlier: 3.676A pdb=" N LEU A 286 " --> pdb=" O LEU A 283 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASP A 287 " --> pdb=" O LYS A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 320 Processing helix chain 'A' and resid 332 through 341 removed outlier: 4.586A pdb=" N THR A 338 " --> pdb=" O LEU A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 356 Processing helix chain 'A' and resid 371 through 380 Processing helix chain 'A' and resid 384 through 389 Processing helix chain 'A' and resid 389 through 398 removed outlier: 4.516A pdb=" N LEU A 395 " --> pdb=" O ALA A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 411 Processing helix chain 'A' and resid 413 through 417 removed outlier: 3.672A pdb=" N ALA A 416 " --> pdb=" O GLY A 413 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY A 417 " --> pdb=" O ASN A 414 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 413 through 417' Processing helix chain 'A' and resid 474 through 483 Processing helix chain 'B' and resid 246 through 255 Processing helix chain 'B' and resid 255 through 260 removed outlier: 3.817A pdb=" N ILE B 259 " --> pdb=" O PHE B 255 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N THR B 260 " --> pdb=" O ARG B 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 255 through 260' Processing helix chain 'B' and resid 275 through 279 Processing helix chain 'B' and resid 287 through 291 removed outlier: 4.149A pdb=" N TYR B 291 " --> pdb=" O LEU B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 315 Processing helix chain 'B' and resid 338 through 354 Processing sheet with id=AA1, first strand: chain 'A' and resid 211 through 212 Processing sheet with id=AA2, first strand: chain 'B' and resid 268 through 272 removed outlier: 6.660A pdb=" N VAL B 269 " --> pdb=" O TYR B 325 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N HIS B 327 " --> pdb=" O VAL B 269 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LEU B 271 " --> pdb=" O HIS B 327 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 193 hydrogen bonds defined for protein. 567 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: 1.07 Time building geometry restraints manager: 1.24 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: 1329 1.33 - 1.45: 735 1.45 - 1.57: 2621 1.57 - 1.69: 7 1.69 - 1.81: 39 Bond restraints: 4731 Sorted by residual: bond pdb=" OG1 TPO A 440 " pdb=" P TPO A 440 " ideal model delta sigma weight residual 1.717 1.608 0.109 2.00e-02 2.50e+03 2.97e+01 bond pdb=" O3P TPO A 440 " pdb=" P TPO A 440 " ideal model delta sigma weight residual 1.528 1.608 -0.080 2.00e-02 2.50e+03 1.61e+01 bond pdb=" O2P TPO A 440 " pdb=" P TPO A 440 " ideal model delta sigma weight residual 1.528 1.608 -0.080 2.00e-02 2.50e+03 1.59e+01 bond pdb=" O1P TPO A 440 " pdb=" P TPO A 440 " ideal model delta sigma weight residual 1.525 1.476 0.049 2.00e-02 2.50e+03 6.08e+00 bond pdb=" CB VAL A 275 " pdb=" CG1 VAL A 275 " ideal model delta sigma weight residual 1.521 1.460 0.061 3.30e-02 9.18e+02 3.41e+00 ... (remaining 4726 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.50: 6213 2.50 - 4.99: 166 4.99 - 7.49: 21 7.49 - 9.99: 9 9.99 - 12.49: 1 Bond angle restraints: 6410 Sorted by residual: angle pdb=" CB TPO A 440 " pdb=" OG1 TPO A 440 " pdb=" P TPO A 440 " ideal model delta sigma weight residual 119.31 106.82 12.49 3.00e+00 1.11e-01 1.73e+01 angle pdb=" C VAL B 223 " pdb=" N THR B 224 " pdb=" CA THR B 224 " ideal model delta sigma weight residual 121.54 128.71 -7.17 1.91e+00 2.74e-01 1.41e+01 angle pdb=" OG1 TPO A 440 " pdb=" P TPO A 440 " pdb=" O1P TPO A 440 " ideal model delta sigma weight residual 100.43 109.19 -8.76 3.00e+00 1.11e-01 8.52e+00 angle pdb=" CA LEU A 278 " pdb=" CB LEU A 278 " pdb=" CG LEU A 278 " ideal model delta sigma weight residual 116.30 126.28 -9.98 3.50e+00 8.16e-02 8.14e+00 angle pdb=" C ILE B 337 " pdb=" N ARG B 338 " pdb=" CA ARG B 338 " ideal model delta sigma weight residual 122.61 126.88 -4.27 1.56e+00 4.11e-01 7.51e+00 ... (remaining 6405 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.08: 2527 17.08 - 34.16: 277 34.16 - 51.24: 61 51.24 - 68.32: 10 68.32 - 85.40: 3 Dihedral angle restraints: 2878 sinusoidal: 1100 harmonic: 1778 Sorted by residual: dihedral pdb=" CA PRO A 358 " pdb=" C PRO A 358 " pdb=" N LEU A 359 " pdb=" CA LEU A 359 " ideal model delta harmonic sigma weight residual 180.00 -150.71 -29.29 0 5.00e+00 4.00e-02 3.43e+01 dihedral pdb=" CA LEU A 395 " pdb=" C LEU A 395 " pdb=" N PHE A 396 " pdb=" CA PHE A 396 " ideal model delta harmonic sigma weight residual 180.00 154.40 25.60 0 5.00e+00 4.00e-02 2.62e+01 dihedral pdb=" CA LEU A 334 " pdb=" C LEU A 334 " pdb=" N SER A 335 " pdb=" CA SER A 335 " ideal model delta harmonic sigma weight residual 180.00 155.04 24.96 0 5.00e+00 4.00e-02 2.49e+01 ... (remaining 2875 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 712 0.100 - 0.199: 47 0.199 - 0.299: 2 0.299 - 0.399: 0 0.399 - 0.499: 1 Chirality restraints: 762 Sorted by residual: chirality pdb=" CB ILE B 337 " pdb=" CA ILE B 337 " pdb=" CG1 ILE B 337 " pdb=" CG2 ILE B 337 " both_signs ideal model delta sigma weight residual False 2.64 2.15 0.50 2.00e-01 2.50e+01 6.22e+00 chirality pdb=" CB VAL A 288 " pdb=" CA VAL A 288 " pdb=" CG1 VAL A 288 " pdb=" CG2 VAL A 288 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CB VAL A 355 " pdb=" CA VAL A 355 " pdb=" CG1 VAL A 355 " pdb=" CG2 VAL A 355 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.11e+00 ... (remaining 759 not shown) Planarity restraints: 818 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR B 261 " 0.048 5.00e-02 4.00e+02 7.33e-02 8.59e+00 pdb=" N PRO B 262 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO B 262 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 262 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 156 " 0.038 5.00e-02 4.00e+02 5.78e-02 5.34e+00 pdb=" N PRO A 157 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO A 157 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 157 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 331 " -0.037 5.00e-02 4.00e+02 5.48e-02 4.81e+00 pdb=" N PRO A 332 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 332 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 332 " -0.031 5.00e-02 4.00e+02 ... (remaining 815 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 839 2.76 - 3.30: 4361 3.30 - 3.83: 7693 3.83 - 4.37: 8746 4.37 - 4.90: 14932 Nonbonded interactions: 36571 Sorted by model distance: nonbonded pdb=" O LEU A 168 " pdb=" OG1 THR A 172 " model vdw 2.230 3.040 nonbonded pdb=" O LEU A 227 " pdb=" OG1 THR A 231 " model vdw 2.241 3.040 nonbonded pdb=" O PRO A 213 " pdb=" OG1 THR A 217 " model vdw 2.328 3.040 nonbonded pdb=" O LEU A 281 " pdb=" NH2 ARG B 338 " model vdw 2.363 3.120 nonbonded pdb=" ND2 ASN B 266 " pdb=" O SER B 268 " model vdw 2.372 3.120 ... (remaining 36566 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: 0.510 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: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 15.350 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 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 : 0.007 0.109 4731 Z= 0.437 Angle : 0.990 12.485 6410 Z= 0.505 Chirality : 0.056 0.499 762 Planarity : 0.007 0.073 818 Dihedral : 15.263 85.402 1710 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.99 % Favored : 91.01 % Rotamer: Outliers : 0.00 % Allowed : 10.08 % Favored : 89.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.94 (0.26), residues: 556 helix: -3.14 (0.20), residues: 331 sheet: -1.07 (1.45), residues: 12 loop : -3.43 (0.34), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 263 HIS 0.008 0.002 HIS A 158 PHE 0.029 0.002 PHE A 270 TYR 0.013 0.002 TYR B 235 ARG 0.004 0.001 ARG A 43 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.567 Fit side-chains revert: symmetry clash REVERT: A 67 LEU cc_start: 0.7825 (mt) cc_final: 0.7516 (mt) REVERT: A 150 LEU cc_start: 0.8718 (tp) cc_final: 0.8432 (tt) REVERT: A 180 GLN cc_start: 0.7267 (mm-40) cc_final: 0.6799 (mm110) REVERT: A 257 CYS cc_start: 0.7732 (t) cc_final: 0.7320 (t) REVERT: A 306 MET cc_start: 0.8405 (mmt) cc_final: 0.7749 (mmt) REVERT: B 249 GLU cc_start: 0.7349 (tm-30) cc_final: 0.6754 (tm-30) outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.1617 time to fit residues: 25.3310 Evaluate side-chains 79 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 49 optimal weight: 0.9980 chunk 44 optimal weight: 10.0000 chunk 24 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 46 optimal weight: 0.0270 chunk 17 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 34 optimal weight: 0.3980 chunk 53 optimal weight: 0.9990 overall best weight: 0.6842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 HIS A 180 GLN A 184 GLN A 414 ASN ** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 4731 Z= 0.208 Angle : 0.641 8.876 6410 Z= 0.320 Chirality : 0.040 0.157 762 Planarity : 0.005 0.045 818 Dihedral : 5.843 26.445 655 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.09 % Favored : 91.91 % Rotamer: Outliers : 3.78 % Allowed : 15.34 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.52 (0.31), residues: 556 helix: -1.94 (0.25), residues: 331 sheet: None (None), residues: 0 loop : -2.83 (0.36), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 263 HIS 0.019 0.002 HIS A 62 PHE 0.020 0.001 PHE A 270 TYR 0.008 0.001 TYR A 445 ARG 0.008 0.000 ARG A 345 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 90 time to evaluate : 0.522 Fit side-chains REVERT: A 150 LEU cc_start: 0.8652 (tp) cc_final: 0.8207 (tt) REVERT: A 151 TYR cc_start: 0.6426 (m-10) cc_final: 0.5924 (m-10) REVERT: A 306 MET cc_start: 0.8287 (mmt) cc_final: 0.7824 (mmt) REVERT: B 249 GLU cc_start: 0.7252 (tm-30) cc_final: 0.6722 (tm-30) REVERT: B 294 GLU cc_start: 0.7867 (mp0) cc_final: 0.7663 (mp0) outliers start: 18 outliers final: 9 residues processed: 103 average time/residue: 0.1619 time to fit residues: 22.6098 Evaluate side-chains 88 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 79 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 90 HIS Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 359 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 29 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 44 optimal weight: 10.0000 chunk 36 optimal weight: 1.9990 chunk 14 optimal weight: 0.0270 chunk 53 optimal weight: 10.0000 chunk 57 optimal weight: 7.9990 chunk 47 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 43 optimal weight: 10.0000 chunk 40 optimal weight: 1.9990 overall best weight: 1.1042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 352 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 4731 Z= 0.245 Angle : 0.632 9.874 6410 Z= 0.315 Chirality : 0.041 0.169 762 Planarity : 0.004 0.033 818 Dihedral : 5.572 28.118 655 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 4.41 % Allowed : 16.81 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.05 (0.33), residues: 556 helix: -1.52 (0.27), residues: 337 sheet: 0.06 (1.61), residues: 14 loop : -2.92 (0.38), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 263 HIS 0.004 0.001 HIS A 158 PHE 0.019 0.001 PHE A 270 TYR 0.015 0.001 TYR A 445 ARG 0.004 0.000 ARG A 345 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 85 time to evaluate : 0.610 Fit side-chains REVERT: A 150 LEU cc_start: 0.8646 (tp) cc_final: 0.8240 (tt) REVERT: A 151 TYR cc_start: 0.6400 (m-10) cc_final: 0.5889 (m-10) REVERT: B 249 GLU cc_start: 0.7290 (tm-30) cc_final: 0.6760 (tm-30) outliers start: 21 outliers final: 13 residues processed: 95 average time/residue: 0.1627 time to fit residues: 19.9982 Evaluate side-chains 89 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 76 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 90 HIS Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 359 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 27 optimal weight: 0.9990 chunk 5 optimal weight: 4.9990 chunk 25 optimal weight: 0.5980 chunk 36 optimal weight: 0.5980 chunk 53 optimal weight: 10.0000 chunk 57 optimal weight: 0.4980 chunk 28 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7204 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4731 Z= 0.198 Angle : 0.667 9.963 6410 Z= 0.316 Chirality : 0.041 0.217 762 Planarity : 0.004 0.032 818 Dihedral : 5.272 27.603 655 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 3.15 % Allowed : 19.12 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.81 (0.33), residues: 556 helix: -1.26 (0.27), residues: 339 sheet: -0.26 (1.51), residues: 14 loop : -2.92 (0.37), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 263 HIS 0.004 0.001 HIS A 158 PHE 0.009 0.001 PHE A 315 TYR 0.034 0.002 TYR A 95 ARG 0.002 0.000 ARG A 345 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 83 time to evaluate : 0.492 Fit side-chains REVERT: A 150 LEU cc_start: 0.8627 (tp) cc_final: 0.8222 (tt) REVERT: A 151 TYR cc_start: 0.6349 (m-10) cc_final: 0.5736 (m-10) REVERT: A 302 MET cc_start: 0.7801 (ptt) cc_final: 0.7503 (ptt) REVERT: B 227 MET cc_start: 0.3558 (ppp) cc_final: 0.2005 (mtm) REVERT: B 249 GLU cc_start: 0.7230 (tm-30) cc_final: 0.6681 (tm-30) outliers start: 15 outliers final: 11 residues processed: 91 average time/residue: 0.1626 time to fit residues: 19.0620 Evaluate side-chains 83 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 72 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 359 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 0 optimal weight: 10.0000 chunk 42 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 chunk 48 optimal weight: 7.9990 chunk 39 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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: 0.7216 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4731 Z= 0.221 Angle : 0.650 10.403 6410 Z= 0.313 Chirality : 0.041 0.172 762 Planarity : 0.004 0.031 818 Dihedral : 5.182 28.095 655 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 3.99 % Allowed : 19.96 % Favored : 76.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.60 (0.33), residues: 556 helix: -1.07 (0.28), residues: 335 sheet: -0.41 (1.46), residues: 14 loop : -2.85 (0.38), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP B 263 HIS 0.004 0.001 HIS A 158 PHE 0.010 0.001 PHE A 163 TYR 0.014 0.002 TYR A 95 ARG 0.002 0.000 ARG A 345 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 83 time to evaluate : 0.503 Fit side-chains REVERT: A 150 LEU cc_start: 0.8635 (tp) cc_final: 0.8220 (tt) REVERT: A 151 TYR cc_start: 0.6375 (m-10) cc_final: 0.5754 (m-10) REVERT: B 227 MET cc_start: 0.3684 (ppp) cc_final: 0.1418 (mtm) outliers start: 19 outliers final: 15 residues processed: 91 average time/residue: 0.1668 time to fit residues: 19.6046 Evaluate side-chains 90 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 75 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain B residue 218 HIS Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 359 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 14 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 26 optimal weight: 0.5980 chunk 4 optimal weight: 2.9990 chunk 18 optimal weight: 0.4980 chunk 29 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 32 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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: 0.7227 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4731 Z= 0.231 Angle : 0.657 12.578 6410 Z= 0.314 Chirality : 0.040 0.144 762 Planarity : 0.004 0.032 818 Dihedral : 5.136 28.727 655 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 3.78 % Allowed : 21.64 % Favored : 74.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.52 (0.33), residues: 556 helix: -0.97 (0.28), residues: 334 sheet: -0.63 (1.45), residues: 14 loop : -2.84 (0.37), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP B 263 HIS 0.004 0.001 HIS A 158 PHE 0.010 0.001 PHE A 163 TYR 0.011 0.002 TYR A 95 ARG 0.002 0.000 ARG A 345 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 78 time to evaluate : 0.591 Fit side-chains REVERT: A 150 LEU cc_start: 0.8670 (tp) cc_final: 0.8238 (tt) REVERT: A 151 TYR cc_start: 0.6414 (m-10) cc_final: 0.5777 (m-10) outliers start: 18 outliers final: 15 residues processed: 87 average time/residue: 0.1608 time to fit residues: 18.4420 Evaluate side-chains 88 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 73 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 449 LYS Chi-restraints excluded: chain B residue 218 HIS Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 359 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 32 optimal weight: 0.9980 chunk 48 optimal weight: 0.1980 chunk 31 optimal weight: 0.5980 chunk 56 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 chunk 34 optimal weight: 0.5980 chunk 26 optimal weight: 0.0870 chunk 22 optimal weight: 0.2980 chunk 33 optimal weight: 0.5980 chunk 17 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 overall best weight: 0.3558 ------------------------------------------------------------------------------- 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: 0.7121 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4731 Z= 0.172 Angle : 0.668 12.877 6410 Z= 0.312 Chirality : 0.040 0.175 762 Planarity : 0.003 0.033 818 Dihedral : 4.808 27.173 655 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 4.20 % Allowed : 21.01 % Favored : 74.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.34), residues: 556 helix: -0.78 (0.28), residues: 333 sheet: None (None), residues: 0 loop : -2.65 (0.38), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP B 263 HIS 0.004 0.001 HIS A 158 PHE 0.011 0.001 PHE A 163 TYR 0.011 0.001 TYR A 95 ARG 0.002 0.000 ARG A 345 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 85 time to evaluate : 0.841 Fit side-chains REVERT: A 77 ARG cc_start: 0.8340 (tpt90) cc_final: 0.8122 (tpt90) REVERT: A 150 LEU cc_start: 0.8621 (tp) cc_final: 0.8332 (tt) REVERT: A 151 TYR cc_start: 0.6446 (m-10) cc_final: 0.5759 (m-10) outliers start: 20 outliers final: 17 residues processed: 97 average time/residue: 0.1695 time to fit residues: 21.2367 Evaluate side-chains 93 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 76 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 449 LYS Chi-restraints excluded: chain B residue 218 HIS Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 359 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 11 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 44 optimal weight: 10.0000 chunk 51 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 52 optimal weight: 0.0570 chunk 31 optimal weight: 1.9990 overall best weight: 1.1502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 352 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4731 Z= 0.252 Angle : 0.684 13.324 6410 Z= 0.324 Chirality : 0.042 0.184 762 Planarity : 0.004 0.032 818 Dihedral : 4.975 29.482 655 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 4.83 % Allowed : 21.01 % Favored : 74.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.34), residues: 556 helix: -0.83 (0.28), residues: 331 sheet: None (None), residues: 0 loop : -2.60 (0.38), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 263 HIS 0.004 0.001 HIS A 158 PHE 0.013 0.001 PHE A 163 TYR 0.014 0.002 TYR A 445 ARG 0.002 0.000 ARG A 255 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 74 time to evaluate : 0.600 Fit side-chains REVERT: A 77 ARG cc_start: 0.8434 (tpt90) cc_final: 0.8152 (tpt90) REVERT: A 150 LEU cc_start: 0.8654 (tp) cc_final: 0.8385 (tt) REVERT: A 151 TYR cc_start: 0.6443 (m-10) cc_final: 0.5748 (m-10) REVERT: A 306 MET cc_start: 0.8288 (mmt) cc_final: 0.8024 (mmt) REVERT: A 343 MET cc_start: 0.7410 (ptp) cc_final: 0.7092 (ptp) outliers start: 23 outliers final: 17 residues processed: 87 average time/residue: 0.1685 time to fit residues: 18.7934 Evaluate side-chains 88 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 71 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 449 LYS Chi-restraints excluded: chain B residue 218 HIS Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 359 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 23 optimal weight: 0.8980 chunk 41 optimal weight: 0.0470 chunk 16 optimal weight: 0.8980 chunk 47 optimal weight: 0.5980 chunk 50 optimal weight: 4.9990 chunk 52 optimal weight: 10.0000 chunk 34 optimal weight: 0.1980 chunk 56 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 overall best weight: 0.4678 ------------------------------------------------------------------------------- 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: 0.7143 moved from start: 0.3051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4731 Z= 0.180 Angle : 0.654 12.270 6410 Z= 0.311 Chirality : 0.040 0.160 762 Planarity : 0.003 0.033 818 Dihedral : 4.795 28.715 655 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 3.36 % Allowed : 23.32 % Favored : 73.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.35), residues: 556 helix: -0.69 (0.28), residues: 329 sheet: -0.16 (1.89), residues: 10 loop : -2.38 (0.40), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 263 HIS 0.004 0.001 HIS A 256 PHE 0.010 0.001 PHE A 162 TYR 0.013 0.001 TYR A 445 ARG 0.002 0.000 ARG A 255 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 71 time to evaluate : 0.538 Fit side-chains REVERT: A 77 ARG cc_start: 0.8424 (tpt90) cc_final: 0.8202 (tpt90) REVERT: A 150 LEU cc_start: 0.8614 (tp) cc_final: 0.8348 (tt) REVERT: A 151 TYR cc_start: 0.6491 (m-10) cc_final: 0.5767 (m-10) outliers start: 16 outliers final: 15 residues processed: 79 average time/residue: 0.1673 time to fit residues: 17.1393 Evaluate side-chains 85 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 70 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 449 LYS Chi-restraints excluded: chain B residue 218 HIS Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 359 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 54 optimal weight: 1.9990 chunk 46 optimal weight: 0.1980 chunk 4 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 43 optimal weight: 0.2980 chunk 6 optimal weight: 0.9980 chunk 13 optimal weight: 4.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- 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: 0.7152 moved from start: 0.3142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4731 Z= 0.196 Angle : 0.666 12.731 6410 Z= 0.316 Chirality : 0.040 0.154 762 Planarity : 0.004 0.036 818 Dihedral : 4.758 29.510 655 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 3.15 % Allowed : 23.74 % Favored : 73.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.35), residues: 556 helix: -0.69 (0.28), residues: 330 sheet: 0.01 (1.92), residues: 10 loop : -2.39 (0.40), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 263 HIS 0.023 0.001 HIS A 62 PHE 0.009 0.001 PHE A 163 TYR 0.012 0.001 TYR A 445 ARG 0.001 0.000 ARG A 345 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 0.557 Fit side-chains REVERT: A 150 LEU cc_start: 0.8611 (tp) cc_final: 0.8340 (tt) REVERT: A 151 TYR cc_start: 0.6493 (m-10) cc_final: 0.5764 (m-10) REVERT: A 221 MET cc_start: 0.7400 (mmm) cc_final: 0.6982 (mmm) outliers start: 15 outliers final: 14 residues processed: 79 average time/residue: 0.1686 time to fit residues: 17.3923 Evaluate side-chains 85 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 71 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 449 LYS Chi-restraints excluded: chain B residue 218 HIS Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 359 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 46 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 chunk 48 optimal weight: 0.0470 chunk 5 optimal weight: 0.9980 chunk 8 optimal weight: 4.9990 chunk 41 optimal weight: 0.7980 chunk 2 optimal weight: 5.9990 chunk 33 optimal weight: 0.7980 chunk 53 optimal weight: 8.9990 chunk 31 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.179041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.149190 restraints weight = 6510.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.153211 restraints weight = 3887.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.155962 restraints weight = 2774.812| |-----------------------------------------------------------------------------| r_work (final): 0.3958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4731 Z= 0.196 Angle : 0.664 13.018 6410 Z= 0.315 Chirality : 0.040 0.144 762 Planarity : 0.004 0.035 818 Dihedral : 4.755 29.797 655 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 3.36 % Allowed : 23.11 % Favored : 73.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.35), residues: 556 helix: -0.69 (0.28), residues: 331 sheet: 0.01 (1.91), residues: 10 loop : -2.39 (0.40), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 263 HIS 0.021 0.002 HIS A 62 PHE 0.009 0.001 PHE A 162 TYR 0.020 0.002 TYR B 261 ARG 0.002 0.000 ARG A 77 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1312.63 seconds wall clock time: 24 minutes 27.58 seconds (1467.58 seconds total)