Starting phenix.real_space_refine on Fri Dec 27 13:41:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x1b_37989/12_2024/8x1b_37989.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x1b_37989/12_2024/8x1b_37989.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8x1b_37989/12_2024/8x1b_37989.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x1b_37989/12_2024/8x1b_37989.map" model { file = "/net/cci-nas-00/data/ceres_data/8x1b_37989/12_2024/8x1b_37989.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x1b_37989/12_2024/8x1b_37989.cif" } resolution = 2.59 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= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 24 5.16 5 C 3224 2.51 5 N 837 2.21 5 O 1021 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 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: 5106 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 5106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 658, 5106 Classifications: {'peptide': 658} Link IDs: {'PTRANS': 34, 'TRANS': 623} Time building chain proxies: 6.28, per 1000 atoms: 1.23 Number of scatterers: 5106 At special positions: 0 Unit cell: (62.9, 82.45, 94.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 24 16.00 O 1021 8.00 N 837 7.00 C 3224 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 511 " - pdb=" SG CYS A 513 " distance=2.04 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: 1.25 Conformation dependent library (CDL) restraints added in 723.3 milliseconds 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1182 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 9 sheets defined 23.9% alpha, 29.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'A' and resid 280 through 293 removed outlier: 3.723A pdb=" N GLY A 284 " --> pdb=" O ASP A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 296 No H-bonds generated for 'chain 'A' and resid 294 through 296' Processing helix chain 'A' and resid 301 through 305 removed outlier: 4.006A pdb=" N ILE A 305 " --> pdb=" O PRO A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 Processing helix chain 'A' and resid 331 through 339 removed outlier: 3.735A pdb=" N LEU A 335 " --> pdb=" O LYS A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 380 removed outlier: 3.725A pdb=" N ALA A 370 " --> pdb=" O GLY A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 403 Processing helix chain 'A' and resid 404 through 407 removed outlier: 3.507A pdb=" N PHE A 407 " --> pdb=" O PRO A 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 404 through 407' Processing helix chain 'A' and resid 437 through 454 removed outlier: 3.801A pdb=" N ILE A 441 " --> pdb=" O ALA A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 485 removed outlier: 4.011A pdb=" N SER A 484 " --> pdb=" O PRO A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 503 removed outlier: 4.126A pdb=" N ILE A 491 " --> pdb=" O LYS A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 525 removed outlier: 3.535A pdb=" N SER A 521 " --> pdb=" O ASP A 518 " (cutoff:3.500A) Proline residue: A 523 - end of helix Processing helix chain 'A' and resid 535 through 551 Processing helix chain 'A' and resid 564 through 571 Processing helix chain 'A' and resid 583 through 600 Processing sheet with id=AA1, first strand: chain 'A' and resid 45 through 46 removed outlier: 3.588A pdb=" N ARG A 52 " --> pdb=" O TYR A 65 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR A 61 " --> pdb=" O ASP A 56 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 46 removed outlier: 3.588A pdb=" N ARG A 52 " --> pdb=" O TYR A 65 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR A 61 " --> pdb=" O ASP A 56 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 76 through 77 removed outlier: 4.830A pdb=" N GLU A 166 " --> pdb=" O LYS A 77 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N TRP A 159 " --> pdb=" O VAL A 85 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 76 through 77 removed outlier: 4.830A pdb=" N GLU A 166 " --> pdb=" O LYS A 77 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N VAL A 164 " --> pdb=" O VAL A 252 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N VAL A 252 " --> pdb=" O VAL A 164 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N GLU A 166 " --> pdb=" O ALA A 250 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ALA A 250 " --> pdb=" O GLU A 166 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 94 through 107 removed outlier: 5.648A pdb=" N HIS A 96 " --> pdb=" O GLN A 120 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N GLN A 120 " --> pdb=" O HIS A 96 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER A 98 " --> pdb=" O THR A 118 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N SER A 104 " --> pdb=" O GLY A 112 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N GLY A 112 " --> pdb=" O SER A 104 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N SER A 106 " --> pdb=" O GLY A 110 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N GLY A 110 " --> pdb=" O SER A 106 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU A 126 " --> pdb=" O SER A 121 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N SER A 135 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N VAL A 141 " --> pdb=" O SER A 135 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N THR A 146 " --> pdb=" O GLY A 270 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N GLY A 270 " --> pdb=" O THR A 146 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N TYR A 148 " --> pdb=" O GLU A 268 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N GLU A 268 " --> pdb=" O TYR A 148 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N ALA A 150 " --> pdb=" O VAL A 266 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N VAL A 266 " --> pdb=" O ALA A 150 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 313 through 314 removed outlier: 6.689A pdb=" N ARG A 313 " --> pdb=" O GLU A 577 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 342 through 345 removed outlier: 7.051A pdb=" N ALA A 384 " --> pdb=" O GLY A 459 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N LYS A 461 " --> pdb=" O ALA A 384 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU A 386 " --> pdb=" O LYS A 461 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N ASP A 463 " --> pdb=" O LEU A 386 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N TRP A 388 " --> pdb=" O ASP A 463 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 605 through 607 removed outlier: 3.660A pdb=" N VAL A 622 " --> pdb=" O ILE A 607 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU A 619 " --> pdb=" O TYR A 634 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N MET A 629 " --> pdb=" O ALA A 693 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N MET A 658 " --> pdb=" O ILE A 696 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N TYR A 659 " --> pdb=" O THR A 672 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N THR A 672 " --> pdb=" O TYR A 659 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N ILE A 661 " --> pdb=" O VAL A 670 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 648 through 649 205 hydrogen bonds defined for protein. 576 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.90 Time building geometry restraints manager: 1.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1687 1.35 - 1.47: 1331 1.47 - 1.59: 2179 1.59 - 1.70: 1 1.70 - 1.82: 42 Bond restraints: 5240 Sorted by residual: bond pdb=" CB PRO A 642 " pdb=" CG PRO A 642 " ideal model delta sigma weight residual 1.492 1.605 -0.113 5.00e-02 4.00e+02 5.10e+00 bond pdb=" CG PRO A 642 " pdb=" CD PRO A 642 " ideal model delta sigma weight residual 1.503 1.565 -0.062 3.40e-02 8.65e+02 3.30e+00 bond pdb=" CB ASP A 248 " pdb=" CG ASP A 248 " ideal model delta sigma weight residual 1.516 1.544 -0.028 2.50e-02 1.60e+03 1.28e+00 bond pdb=" CB PRO A 701 " pdb=" CG PRO A 701 " ideal model delta sigma weight residual 1.492 1.539 -0.047 5.00e-02 4.00e+02 8.97e-01 bond pdb=" CA LYS A 625 " pdb=" CB LYS A 625 " ideal model delta sigma weight residual 1.529 1.515 0.014 1.54e-02 4.22e+03 8.38e-01 ... (remaining 5235 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.57: 7008 1.57 - 3.13: 116 3.13 - 4.70: 15 4.70 - 6.27: 0 6.27 - 7.84: 2 Bond angle restraints: 7141 Sorted by residual: angle pdb=" CA PRO A 642 " pdb=" N PRO A 642 " pdb=" CD PRO A 642 " ideal model delta sigma weight residual 112.00 104.16 7.84 1.40e+00 5.10e-01 3.13e+01 angle pdb=" C ASP A 346 " pdb=" N ASP A 347 " pdb=" CA ASP A 347 " ideal model delta sigma weight residual 120.82 125.02 -4.20 1.47e+00 4.63e-01 8.15e+00 angle pdb=" N ASP A 347 " pdb=" CA ASP A 347 " pdb=" C ASP A 347 " ideal model delta sigma weight residual 110.24 113.82 -3.58 1.30e+00 5.92e-01 7.60e+00 angle pdb=" N PRO A 642 " pdb=" CA PRO A 642 " pdb=" CB PRO A 642 " ideal model delta sigma weight residual 103.25 100.40 2.85 1.05e+00 9.07e-01 7.39e+00 angle pdb=" N GLY A 107 " pdb=" CA GLY A 107 " pdb=" C GLY A 107 " ideal model delta sigma weight residual 111.20 114.26 -3.06 1.39e+00 5.18e-01 4.84e+00 ... (remaining 7136 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 2653 17.93 - 35.86: 303 35.86 - 53.80: 77 53.80 - 71.73: 16 71.73 - 89.66: 6 Dihedral angle restraints: 3055 sinusoidal: 1173 harmonic: 1882 Sorted by residual: dihedral pdb=" CB CYS A 511 " pdb=" SG CYS A 511 " pdb=" SG CYS A 513 " pdb=" CB CYS A 513 " ideal model delta sinusoidal sigma weight residual 93.00 147.50 -54.50 1 1.00e+01 1.00e-02 4.02e+01 dihedral pdb=" CA ASN A 512 " pdb=" C ASN A 512 " pdb=" N CYS A 513 " pdb=" CA CYS A 513 " ideal model delta harmonic sigma weight residual -180.00 -162.33 -17.67 0 5.00e+00 4.00e-02 1.25e+01 dihedral pdb=" CA LYS A 578 " pdb=" C LYS A 578 " pdb=" N ARG A 579 " pdb=" CA ARG A 579 " ideal model delta harmonic sigma weight residual 180.00 -163.51 -16.49 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 3052 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 454 0.029 - 0.058: 173 0.058 - 0.087: 62 0.087 - 0.116: 55 0.116 - 0.146: 10 Chirality restraints: 754 Sorted by residual: chirality pdb=" CA ASP A 248 " pdb=" N ASP A 248 " pdb=" C ASP A 248 " pdb=" CB ASP A 248 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.29e-01 chirality pdb=" CA PRO A 390 " pdb=" N PRO A 390 " pdb=" C PRO A 390 " pdb=" CB PRO A 390 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.13 2.00e-01 2.50e+01 4.45e-01 chirality pdb=" CA PRO A 642 " pdb=" N PRO A 642 " pdb=" C PRO A 642 " pdb=" CB PRO A 642 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.21e-01 ... (remaining 751 not shown) Planarity restraints: 940 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS A 403 " -0.046 5.00e-02 4.00e+02 7.03e-02 7.90e+00 pdb=" N PRO A 404 " 0.122 5.00e-02 4.00e+02 pdb=" CA PRO A 404 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 404 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 641 " 0.044 5.00e-02 4.00e+02 6.32e-02 6.39e+00 pdb=" N PRO A 642 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO A 642 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 642 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 426 " 0.022 5.00e-02 4.00e+02 3.36e-02 1.81e+00 pdb=" N PRO A 427 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 427 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 427 " 0.019 5.00e-02 4.00e+02 ... (remaining 937 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 895 2.77 - 3.30: 4378 3.30 - 3.83: 8474 3.83 - 4.37: 9810 4.37 - 4.90: 17834 Nonbonded interactions: 41391 Sorted by model distance: nonbonded pdb=" O LEU A 510 " pdb=" NE2 GLN A 517 " model vdw 2.236 3.120 nonbonded pdb=" O PRO A 469 " pdb=" OG SER A 484 " model vdw 2.306 3.040 nonbonded pdb=" NH1 ARG A 286 " pdb=" O ALA A 548 " model vdw 2.332 3.120 nonbonded pdb=" O ALA A 262 " pdb=" OG SER A 265 " model vdw 2.354 3.040 nonbonded pdb=" OG SER A 233 " pdb=" O THR A 235 " model vdw 2.359 3.040 ... (remaining 41386 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 21.800 Find NCS groups from input model: 0.050 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:17.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 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 : 0.003 0.113 5240 Z= 0.178 Angle : 0.496 7.835 7141 Z= 0.274 Chirality : 0.044 0.146 754 Planarity : 0.005 0.070 940 Dihedral : 16.586 89.660 1870 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.48 % Allowed : 24.35 % Favored : 74.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.33), residues: 656 helix: 1.47 (0.46), residues: 135 sheet: 0.96 (0.38), residues: 195 loop : -0.50 (0.32), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 323 HIS 0.003 0.001 HIS A 96 PHE 0.006 0.001 PHE A 202 TYR 0.018 0.001 TYR A 406 ARG 0.001 0.000 ARG A 52 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 140 time to evaluate : 0.581 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 144 average time/residue: 1.0724 time to fit residues: 162.4714 Evaluate side-chains 143 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 138 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 464 TYR Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 672 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 54 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 59 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 GLN A 352 ASN A 477 ASN A 600 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.0852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 5240 Z= 0.299 Angle : 0.537 5.945 7141 Z= 0.293 Chirality : 0.047 0.158 754 Planarity : 0.005 0.049 940 Dihedral : 4.941 44.884 730 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 4.80 % Allowed : 18.82 % Favored : 76.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.32), residues: 656 helix: 1.31 (0.45), residues: 137 sheet: 0.84 (0.38), residues: 189 loop : -0.66 (0.32), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 323 HIS 0.004 0.001 HIS A 96 PHE 0.008 0.001 PHE A 606 TYR 0.017 0.002 TYR A 406 ARG 0.004 0.000 ARG A 128 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 148 time to evaluate : 0.606 Fit side-chains REVERT: A 248 ASP cc_start: 0.7303 (p0) cc_final: 0.7096 (p0) outliers start: 26 outliers final: 14 residues processed: 154 average time/residue: 0.9326 time to fit residues: 151.2775 Evaluate side-chains 157 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 143 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 185 MET Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 317 TRP Chi-restraints excluded: chain A residue 322 ASN Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 559 ASP Chi-restraints excluded: chain A residue 658 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 32 optimal weight: 0.0050 chunk 18 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 59 optimal weight: 0.0670 chunk 63 optimal weight: 0.5980 chunk 52 optimal weight: 0.6980 chunk 58 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 overall best weight: 0.4332 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 ASN A 477 ASN A 600 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.0998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5240 Z= 0.186 Angle : 0.503 5.659 7141 Z= 0.274 Chirality : 0.046 0.139 754 Planarity : 0.004 0.046 940 Dihedral : 4.699 50.385 725 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 4.43 % Allowed : 20.11 % Favored : 75.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.32), residues: 656 helix: 1.69 (0.46), residues: 131 sheet: 0.88 (0.38), residues: 189 loop : -0.62 (0.32), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 323 HIS 0.003 0.001 HIS A 96 PHE 0.009 0.001 PHE A 681 TYR 0.017 0.001 TYR A 406 ARG 0.004 0.000 ARG A 128 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 143 time to evaluate : 0.618 Fit side-chains REVERT: A 239 VAL cc_start: 0.8076 (OUTLIER) cc_final: 0.7718 (p) REVERT: A 248 ASP cc_start: 0.7312 (p0) cc_final: 0.7096 (p0) REVERT: A 600 GLN cc_start: 0.8224 (mm110) cc_final: 0.8006 (mm-40) REVERT: A 611 TYR cc_start: 0.7535 (OUTLIER) cc_final: 0.7307 (m-10) outliers start: 24 outliers final: 11 residues processed: 150 average time/residue: 0.9667 time to fit residues: 153.0959 Evaluate side-chains 156 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 143 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 317 TRP Chi-restraints excluded: chain A residue 322 ASN Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 611 TYR Chi-restraints excluded: chain A residue 656 ASN Chi-restraints excluded: chain A residue 677 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 58 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 30 optimal weight: 0.0570 chunk 6 optimal weight: 4.9990 chunk 28 optimal weight: 0.6980 chunk 39 optimal weight: 0.0070 chunk 59 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 31 optimal weight: 0.0770 chunk 56 optimal weight: 0.8980 chunk 16 optimal weight: 0.0170 overall best weight: 0.1712 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 ASN A 477 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.1142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 5240 Z= 0.126 Angle : 0.476 4.879 7141 Z= 0.259 Chirality : 0.045 0.130 754 Planarity : 0.004 0.045 940 Dihedral : 4.478 45.678 725 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.69 % Allowed : 21.03 % Favored : 75.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.32), residues: 656 helix: 1.92 (0.47), residues: 131 sheet: 0.92 (0.39), residues: 189 loop : -0.60 (0.31), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 323 HIS 0.003 0.001 HIS A 403 PHE 0.008 0.001 PHE A 681 TYR 0.018 0.001 TYR A 406 ARG 0.004 0.000 ARG A 128 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 149 time to evaluate : 0.600 Fit side-chains REVERT: A 138 GLU cc_start: 0.7509 (mm-30) cc_final: 0.7302 (mm-30) REVERT: A 239 VAL cc_start: 0.7980 (OUTLIER) cc_final: 0.7633 (p) REVERT: A 248 ASP cc_start: 0.7336 (p0) cc_final: 0.7090 (p0) REVERT: A 468 MET cc_start: 0.8469 (tpp) cc_final: 0.8069 (tpp) REVERT: A 611 TYR cc_start: 0.7422 (OUTLIER) cc_final: 0.7211 (m-10) outliers start: 20 outliers final: 10 residues processed: 154 average time/residue: 0.8853 time to fit residues: 144.2841 Evaluate side-chains 155 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 143 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 317 TRP Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 464 TYR Chi-restraints excluded: chain A residue 611 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 52 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 32 optimal weight: 0.3980 chunk 56 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 21 optimal weight: 0.0570 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 352 ASN A 477 ASN A 517 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.1239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5240 Z= 0.204 Angle : 0.496 5.521 7141 Z= 0.269 Chirality : 0.046 0.146 754 Planarity : 0.004 0.044 940 Dihedral : 4.482 39.758 725 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 4.80 % Allowed : 21.03 % Favored : 74.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.32), residues: 656 helix: 1.78 (0.46), residues: 131 sheet: 0.92 (0.39), residues: 189 loop : -0.60 (0.32), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 323 HIS 0.003 0.001 HIS A 96 PHE 0.022 0.001 PHE A 160 TYR 0.021 0.001 TYR A 406 ARG 0.006 0.000 ARG A 414 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 143 time to evaluate : 0.579 Fit side-chains REVERT: A 239 VAL cc_start: 0.8105 (OUTLIER) cc_final: 0.7777 (p) REVERT: A 248 ASP cc_start: 0.7377 (p0) cc_final: 0.7158 (p0) REVERT: A 611 TYR cc_start: 0.7516 (OUTLIER) cc_final: 0.7282 (m-10) outliers start: 26 outliers final: 10 residues processed: 148 average time/residue: 0.9273 time to fit residues: 144.4557 Evaluate side-chains 149 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 137 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 317 TRP Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 611 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 56 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 15 optimal weight: 0.5980 chunk 62 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 60 optimal weight: 0.1980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 ASN A 477 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.1344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 5240 Z= 0.241 Angle : 0.526 5.794 7141 Z= 0.284 Chirality : 0.046 0.151 754 Planarity : 0.004 0.044 940 Dihedral : 4.836 58.443 725 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.69 % Allowed : 22.51 % Favored : 73.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.32), residues: 656 helix: 1.63 (0.45), residues: 131 sheet: 0.90 (0.39), residues: 189 loop : -0.61 (0.32), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 323 HIS 0.003 0.001 HIS A 96 PHE 0.018 0.002 PHE A 160 TYR 0.024 0.002 TYR A 406 ARG 0.005 0.000 ARG A 414 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 141 time to evaluate : 0.599 Fit side-chains REVERT: A 248 ASP cc_start: 0.7395 (p0) cc_final: 0.7193 (p0) outliers start: 20 outliers final: 13 residues processed: 149 average time/residue: 1.2913 time to fit residues: 201.8793 Evaluate side-chains 153 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 140 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 317 TRP Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 379 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 7 optimal weight: 3.9990 chunk 35 optimal weight: 0.2980 chunk 45 optimal weight: 0.7980 chunk 52 optimal weight: 0.0980 chunk 62 optimal weight: 0.0270 chunk 39 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 overall best weight: 0.4038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 ASN A 477 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.1390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5240 Z= 0.177 Angle : 0.493 5.325 7141 Z= 0.266 Chirality : 0.045 0.137 754 Planarity : 0.004 0.043 940 Dihedral : 4.596 48.446 725 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.77 % Allowed : 24.17 % Favored : 73.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.32), residues: 656 helix: 1.76 (0.46), residues: 131 sheet: 0.89 (0.39), residues: 188 loop : -0.56 (0.32), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 323 HIS 0.003 0.001 HIS A 96 PHE 0.015 0.001 PHE A 160 TYR 0.020 0.001 TYR A 406 ARG 0.005 0.000 ARG A 414 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 143 time to evaluate : 0.738 Fit side-chains REVERT: A 239 VAL cc_start: 0.8059 (OUTLIER) cc_final: 0.7730 (p) outliers start: 15 outliers final: 12 residues processed: 147 average time/residue: 0.9296 time to fit residues: 144.3882 Evaluate side-chains 154 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 141 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 317 TRP Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 464 TYR Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain A residue 654 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 12 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 chunk 54 optimal weight: 0.6980 chunk 58 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 ASN A 477 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 5240 Z= 0.260 Angle : 0.531 5.922 7141 Z= 0.287 Chirality : 0.047 0.154 754 Planarity : 0.004 0.043 940 Dihedral : 4.524 31.769 725 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.32 % Allowed : 23.99 % Favored : 72.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.32), residues: 656 helix: 1.57 (0.45), residues: 131 sheet: 0.89 (0.39), residues: 188 loop : -0.58 (0.32), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 323 HIS 0.003 0.001 HIS A 96 PHE 0.017 0.002 PHE A 160 TYR 0.021 0.002 TYR A 406 ARG 0.005 0.000 ARG A 414 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 139 time to evaluate : 0.578 Fit side-chains outliers start: 18 outliers final: 12 residues processed: 144 average time/residue: 1.0043 time to fit residues: 152.8198 Evaluate side-chains 152 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 140 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 317 TRP Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 480 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 25 optimal weight: 0.0170 chunk 45 optimal weight: 0.5980 chunk 17 optimal weight: 0.9990 chunk 52 optimal weight: 0.5980 chunk 55 optimal weight: 0.4980 chunk 58 optimal weight: 0.3980 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 37 optimal weight: 0.1980 chunk 29 optimal weight: 1.9990 chunk 42 optimal weight: 0.1980 overall best weight: 0.2618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 ASN A 477 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 5240 Z= 0.146 Angle : 0.495 5.112 7141 Z= 0.267 Chirality : 0.045 0.158 754 Planarity : 0.004 0.044 940 Dihedral : 4.226 18.209 725 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.48 % Allowed : 26.20 % Favored : 72.32 % 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: 0.50 (0.32), residues: 656 helix: 1.77 (0.46), residues: 131 sheet: 0.82 (0.39), residues: 188 loop : -0.52 (0.32), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 323 HIS 0.003 0.001 HIS A 96 PHE 0.013 0.001 PHE A 160 TYR 0.016 0.001 TYR A 406 ARG 0.005 0.000 ARG A 414 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 140 time to evaluate : 0.460 Fit side-chains REVERT: A 468 MET cc_start: 0.8451 (tpp) cc_final: 0.8023 (tpp) outliers start: 8 outliers final: 6 residues processed: 142 average time/residue: 1.0166 time to fit residues: 151.9856 Evaluate side-chains 145 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 139 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 317 TRP Chi-restraints excluded: chain A residue 464 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 64 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 51 optimal weight: 0.0970 chunk 5 optimal weight: 2.9990 chunk 39 optimal weight: 0.3980 chunk 31 optimal weight: 0.9980 chunk 40 optimal weight: 0.2980 chunk 54 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 ASN A 477 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5240 Z= 0.190 Angle : 0.512 5.157 7141 Z= 0.276 Chirality : 0.046 0.164 754 Planarity : 0.004 0.042 940 Dihedral : 4.194 18.558 724 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.48 % Allowed : 26.57 % Favored : 71.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.32), residues: 656 helix: 1.77 (0.46), residues: 131 sheet: 0.85 (0.39), residues: 188 loop : -0.52 (0.32), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP A 323 HIS 0.003 0.001 HIS A 96 PHE 0.014 0.001 PHE A 160 TYR 0.018 0.001 TYR A 406 ARG 0.005 0.000 ARG A 414 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 140 time to evaluate : 0.604 Fit side-chains outliers start: 8 outliers final: 7 residues processed: 143 average time/residue: 0.9190 time to fit residues: 138.8037 Evaluate side-chains 145 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 138 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 317 TRP Chi-restraints excluded: chain A residue 464 TYR Chi-restraints excluded: chain A residue 480 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 14 optimal weight: 0.9980 chunk 51 optimal weight: 0.0980 chunk 21 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 6 optimal weight: 0.0980 chunk 9 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 59 optimal weight: 0.5980 chunk 34 optimal weight: 0.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 ASN A 477 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.120831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.113429 restraints weight = 7131.659| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 1.66 r_work: 0.3448 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3323 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5240 Z= 0.211 Angle : 0.528 5.560 7141 Z= 0.285 Chirality : 0.046 0.166 754 Planarity : 0.004 0.043 940 Dihedral : 4.271 18.891 724 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.48 % Allowed : 26.38 % Favored : 72.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.32), residues: 656 helix: 1.65 (0.46), residues: 131 sheet: 0.81 (0.38), residues: 188 loop : -0.53 (0.32), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP A 323 HIS 0.003 0.001 HIS A 96 PHE 0.015 0.001 PHE A 160 TYR 0.018 0.001 TYR A 406 ARG 0.005 0.000 ARG A 414 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2882.63 seconds wall clock time: 54 minutes 59.78 seconds (3299.78 seconds total)