Starting phenix.real_space_refine on Sat Dec 28 01:07:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8efd_28080/12_2024/8efd_28080.cif Found real_map, /net/cci-nas-00/data/ceres_data/8efd_28080/12_2024/8efd_28080.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8efd_28080/12_2024/8efd_28080.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8efd_28080/12_2024/8efd_28080.map" model { file = "/net/cci-nas-00/data/ceres_data/8efd_28080/12_2024/8efd_28080.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8efd_28080/12_2024/8efd_28080.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 40 5.16 5 C 4524 2.51 5 N 1210 2.21 5 O 1333 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 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: 7107 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 740, 5967 Classifications: {'peptide': 740} Link IDs: {'PTRANS': 28, 'TRANS': 711} Chain breaks: 3 Chain: "B" Number of atoms: 1140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1140 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 142} Time building chain proxies: 5.37, per 1000 atoms: 0.76 Number of scatterers: 7107 At special positions: 0 Unit cell: (86.24, 127.204, 117.502, 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 40 16.00 O 1333 8.00 N 1210 7.00 C 4524 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: 1.76 Conformation dependent library (CDL) restraints added in 987.3 milliseconds 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1658 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 9 sheets defined 57.2% alpha, 8.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 6 through 11 removed outlier: 6.202A pdb=" N ALA A 11 " --> pdb=" O VAL A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 12 through 17 removed outlier: 3.524A pdb=" N LEU A 16 " --> pdb=" O ALA A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 28 removed outlier: 3.759A pdb=" N THR A 28 " --> pdb=" O LEU A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 93 Processing helix chain 'A' and resid 97 through 111 removed outlier: 3.675A pdb=" N LEU A 102 " --> pdb=" O GLU A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 134 removed outlier: 4.436A pdb=" N TYR A 134 " --> pdb=" O LEU A 131 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 131 through 134' Processing helix chain 'A' and resid 135 through 143 Processing helix chain 'A' and resid 153 through 169 Processing helix chain 'A' and resid 183 through 197 Processing helix chain 'A' and resid 217 through 231 Proline residue: A 225 - end of helix Processing helix chain 'A' and resid 270 through 275 Processing helix chain 'A' and resid 283 through 290 removed outlier: 4.434A pdb=" N TYR A 287 " --> pdb=" O TYR A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 302 Processing helix chain 'A' and resid 306 through 309 Processing helix chain 'A' and resid 310 through 315 Processing helix chain 'A' and resid 324 through 338 Processing helix chain 'A' and resid 343 through 359 removed outlier: 3.577A pdb=" N ASN A 347 " --> pdb=" O SER A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 389 Processing helix chain 'A' and resid 391 through 401 Processing helix chain 'A' and resid 416 through 448 Processing helix chain 'A' and resid 472 through 504 Processing helix chain 'A' and resid 513 through 526 removed outlier: 3.709A pdb=" N LEU A 517 " --> pdb=" O PHE A 513 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ALA A 519 " --> pdb=" O MET A 515 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N CYS A 520 " --> pdb=" O ASP A 516 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ILE A 521 " --> pdb=" O LEU A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 540 removed outlier: 3.551A pdb=" N CYS A 538 " --> pdb=" O LEU A 534 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N MET A 539 " --> pdb=" O GLU A 535 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N PHE A 540 " --> pdb=" O GLU A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 557 Processing helix chain 'A' and resid 592 through 598 removed outlier: 3.971A pdb=" N LYS A 598 " --> pdb=" O LEU A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 611 Processing helix chain 'A' and resid 615 through 620 Processing helix chain 'A' and resid 647 through 664 removed outlier: 3.913A pdb=" N SER A 664 " --> pdb=" O THR A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 696 Processing helix chain 'A' and resid 697 through 707 Processing helix chain 'A' and resid 715 through 723 removed outlier: 3.506A pdb=" N ARG A 723 " --> pdb=" O ARG A 719 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 749 Processing helix chain 'A' and resid 752 through 754 No H-bonds generated for 'chain 'A' and resid 752 through 754' Processing helix chain 'A' and resid 766 through 796 removed outlier: 3.915A pdb=" N LEU A 770 " --> pdb=" O LYS A 766 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLY A 771 " --> pdb=" O ALA A 767 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 57 Processing helix chain 'B' and resid 65 through 75 removed outlier: 3.962A pdb=" N VAL B 69 " --> pdb=" O THR B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 89 Processing helix chain 'B' and resid 95 through 100 Processing helix chain 'B' and resid 103 through 116 Proline residue: B 109 - end of helix removed outlier: 3.655A pdb=" N ASN B 116 " --> pdb=" O GLN B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 132 removed outlier: 3.547A pdb=" N VAL B 132 " --> pdb=" O GLU B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 153 Processing helix chain 'B' and resid 158 through 166 Processing helix chain 'B' and resid 178 through 188 Processing sheet with id=AA1, first strand: chain 'A' and resid 49 through 51 Processing sheet with id=AA2, first strand: chain 'A' and resid 115 through 118 removed outlier: 4.053A pdb=" N PHE A 121 " --> pdb=" O SER A 118 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 258 through 266 removed outlier: 6.691A pdb=" N LYS A 246 " --> pdb=" O LEU A 460 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N LEU A 460 " --> pdb=" O LYS A 246 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ILE A 248 " --> pdb=" O GLY A 458 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N GLY A 458 " --> pdb=" O ILE A 248 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N ILE A 250 " --> pdb=" O PHE A 456 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N PHE A 456 " --> pdb=" O ILE A 250 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N GLN A 172 " --> pdb=" O PHE A 456 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 232 through 233 Processing sheet with id=AA5, first strand: chain 'A' and resid 365 through 366 Processing sheet with id=AA6, first strand: chain 'A' and resid 403 through 406 Processing sheet with id=AA7, first strand: chain 'A' and resid 577 through 581 removed outlier: 3.726A pdb=" N PHE A 577 " --> pdb=" O TYR A 588 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 711 through 714 Processing sheet with id=AA9, first strand: chain 'B' and resid 140 through 142 removed outlier: 3.630A pdb=" N VAL B 141 " --> pdb=" O ILE B 176 " (cutoff:3.500A) 356 hydrogen bonds defined for protein. 1032 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: 2.16 Time building geometry restraints manager: 2.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2344 1.34 - 1.46: 1365 1.46 - 1.58: 3466 1.58 - 1.69: 0 1.69 - 1.81: 70 Bond restraints: 7245 Sorted by residual: bond pdb=" CG GLU A 775 " pdb=" CD GLU A 775 " ideal model delta sigma weight residual 1.516 1.490 0.026 2.50e-02 1.60e+03 1.11e+00 bond pdb=" C GLU A 374 " pdb=" O GLU A 374 " ideal model delta sigma weight residual 1.245 1.229 0.016 1.53e-02 4.27e+03 1.08e+00 bond pdb=" CG1 ILE A 289 " pdb=" CD1 ILE A 289 " ideal model delta sigma weight residual 1.513 1.474 0.039 3.90e-02 6.57e+02 9.80e-01 bond pdb=" N LYS A 570 " pdb=" CA LYS A 570 " ideal model delta sigma weight residual 1.457 1.469 -0.011 1.29e-02 6.01e+03 7.48e-01 bond pdb=" C GLU A 374 " pdb=" N PRO A 375 " ideal model delta sigma weight residual 1.330 1.339 -0.009 1.22e-02 6.72e+03 5.83e-01 ... (remaining 7240 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.03: 9335 1.03 - 2.06: 330 2.06 - 3.09: 57 3.09 - 4.11: 27 4.11 - 5.14: 5 Bond angle restraints: 9754 Sorted by residual: angle pdb=" N GLU A 775 " pdb=" CA GLU A 775 " pdb=" CB GLU A 775 " ideal model delta sigma weight residual 110.28 115.42 -5.14 1.55e+00 4.16e-01 1.10e+01 angle pdb=" C GLU A 774 " pdb=" N GLU A 775 " pdb=" CA GLU A 775 " ideal model delta sigma weight residual 120.31 115.74 4.57 1.52e+00 4.33e-01 9.04e+00 angle pdb=" CA GLU A 775 " pdb=" CB GLU A 775 " pdb=" CG GLU A 775 " ideal model delta sigma weight residual 114.10 118.94 -4.84 2.00e+00 2.50e-01 5.85e+00 angle pdb=" CA PRO A 375 " pdb=" C PRO A 375 " pdb=" O PRO A 375 " ideal model delta sigma weight residual 122.08 119.30 2.78 1.28e+00 6.10e-01 4.73e+00 angle pdb=" N PHE A 364 " pdb=" CA PHE A 364 " pdb=" C PHE A 364 " ideal model delta sigma weight residual 110.91 113.33 -2.42 1.17e+00 7.31e-01 4.26e+00 ... (remaining 9749 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 3959 17.91 - 35.81: 365 35.81 - 53.72: 61 53.72 - 71.63: 6 71.63 - 89.53: 9 Dihedral angle restraints: 4400 sinusoidal: 1829 harmonic: 2571 Sorted by residual: dihedral pdb=" CB GLU A 328 " pdb=" CG GLU A 328 " pdb=" CD GLU A 328 " pdb=" OE1 GLU A 328 " ideal model delta sinusoidal sigma weight residual 0.00 -89.53 89.53 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLU A 98 " pdb=" CG GLU A 98 " pdb=" CD GLU A 98 " pdb=" OE1 GLU A 98 " ideal model delta sinusoidal sigma weight residual 0.00 -88.09 88.09 1 3.00e+01 1.11e-03 1.03e+01 dihedral pdb=" CA ARG A 706 " pdb=" CB ARG A 706 " pdb=" CG ARG A 706 " pdb=" CD ARG A 706 " ideal model delta sinusoidal sigma weight residual -60.00 -110.94 50.94 3 1.50e+01 4.44e-03 8.96e+00 ... (remaining 4397 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 682 0.027 - 0.055: 248 0.055 - 0.082: 75 0.082 - 0.109: 38 0.109 - 0.136: 17 Chirality restraints: 1060 Sorted by residual: chirality pdb=" CA VAL A 459 " pdb=" N VAL A 459 " pdb=" C VAL A 459 " pdb=" CB VAL A 459 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.64e-01 chirality pdb=" CA ILE A 674 " pdb=" N ILE A 674 " pdb=" C ILE A 674 " pdb=" CB ILE A 674 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.54e-01 chirality pdb=" CA PRO A 710 " pdb=" N PRO A 710 " pdb=" C PRO A 710 " pdb=" CB PRO A 710 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.22e-01 ... (remaining 1057 not shown) Planarity restraints: 1269 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 224 " -0.016 5.00e-02 4.00e+02 2.46e-02 9.65e-01 pdb=" N PRO A 225 " 0.042 5.00e-02 4.00e+02 pdb=" CA PRO A 225 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 225 " -0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 609 " 0.006 2.00e-02 2.50e+03 6.55e-03 8.57e-01 pdb=" CG TYR A 609 " -0.016 2.00e-02 2.50e+03 pdb=" CD1 TYR A 609 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR A 609 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR A 609 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 609 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 609 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 609 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 709 " 0.015 5.00e-02 4.00e+02 2.22e-02 7.85e-01 pdb=" N PRO A 710 " -0.038 5.00e-02 4.00e+02 pdb=" CA PRO A 710 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO A 710 " 0.012 5.00e-02 4.00e+02 ... (remaining 1266 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 117 2.62 - 3.19: 6966 3.19 - 3.76: 11311 3.76 - 4.33: 14687 4.33 - 4.90: 24028 Nonbonded interactions: 57109 Sorted by model distance: nonbonded pdb=" OG1 THR A 235 " pdb=" O ASN A 238 " model vdw 2.048 3.040 nonbonded pdb=" O THR A 449 " pdb=" NH2 ARG A 453 " model vdw 2.086 3.120 nonbonded pdb=" O ALA A 141 " pdb=" NZ LYS A 145 " model vdw 2.092 3.120 nonbonded pdb=" OG1 THR A 94 " pdb=" O ALA A 767 " model vdw 2.098 3.040 nonbonded pdb=" O LEU A 166 " pdb=" NH1 ARG A 169 " model vdw 2.119 3.120 ... (remaining 57104 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: 15.420 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: 21.110 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 7245 Z= 0.144 Angle : 0.492 5.144 9754 Z= 0.272 Chirality : 0.037 0.136 1060 Planarity : 0.002 0.025 1269 Dihedral : 14.097 89.535 2742 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 0.13 % Allowed : 0.39 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.29), residues: 876 helix: 1.91 (0.25), residues: 446 sheet: -1.37 (0.62), residues: 82 loop : -0.78 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 130 HIS 0.006 0.001 HIS B 148 PHE 0.013 0.001 PHE A 510 TYR 0.016 0.001 TYR A 609 ARG 0.002 0.000 ARG A 108 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 58 time to evaluate : 0.856 Fit side-chains REVERT: A 165 MET cc_start: 0.8946 (tmm) cc_final: 0.8712 (tmm) REVERT: A 388 MET cc_start: 0.8990 (mpp) cc_final: 0.8761 (mpp) REVERT: A 439 MET cc_start: 0.9109 (mpp) cc_final: 0.8881 (mpp) REVERT: A 546 MET cc_start: 0.8837 (tpt) cc_final: 0.8613 (tpp) REVERT: A 776 MET cc_start: 0.9460 (mmp) cc_final: 0.9223 (mmm) outliers start: 1 outliers final: 0 residues processed: 59 average time/residue: 0.1645 time to fit residues: 14.2737 Evaluate side-chains 45 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 0.7980 chunk 66 optimal weight: 0.0870 chunk 37 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 44 optimal weight: 0.4980 chunk 35 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 chunk 41 optimal weight: 0.5980 chunk 51 optimal weight: 0.7980 chunk 79 optimal weight: 20.0000 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 ASN A 691 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7245 Z= 0.181 Angle : 0.552 5.754 9754 Z= 0.290 Chirality : 0.040 0.143 1060 Planarity : 0.004 0.039 1269 Dihedral : 3.838 16.530 954 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.04 % Allowed : 7.15 % Favored : 91.81 % 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: 0.74 (0.29), residues: 876 helix: 1.81 (0.25), residues: 452 sheet: -1.29 (0.61), residues: 82 loop : -0.82 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 593 HIS 0.002 0.001 HIS A 401 PHE 0.027 0.001 PHE B 181 TYR 0.017 0.001 TYR A 609 ARG 0.004 0.001 ARG A 453 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 50 time to evaluate : 0.809 Fit side-chains REVERT: A 6 MET cc_start: 0.7822 (tmm) cc_final: 0.7571 (tmm) REVERT: A 388 MET cc_start: 0.8995 (mpp) cc_final: 0.8421 (mpp) REVERT: A 546 MET cc_start: 0.8820 (tpt) cc_final: 0.8553 (tpp) REVERT: A 609 TYR cc_start: 0.8871 (m-80) cc_final: 0.8601 (m-80) REVERT: B 97 MET cc_start: 0.4965 (ptt) cc_final: 0.3738 (tpt) outliers start: 8 outliers final: 4 residues processed: 53 average time/residue: 0.1907 time to fit residues: 14.5843 Evaluate side-chains 48 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 44 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain B residue 148 HIS Chi-restraints excluded: chain B residue 184 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 44 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 54 optimal weight: 0.4980 chunk 22 optimal weight: 0.9990 chunk 80 optimal weight: 0.9990 chunk 86 optimal weight: 8.9990 chunk 71 optimal weight: 0.5980 chunk 79 optimal weight: 0.3980 chunk 27 optimal weight: 0.6980 chunk 64 optimal weight: 0.0980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7245 Z= 0.155 Angle : 0.508 5.415 9754 Z= 0.266 Chirality : 0.039 0.132 1060 Planarity : 0.003 0.031 1269 Dihedral : 3.789 16.501 954 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.30 % Allowed : 9.36 % Favored : 89.34 % 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: 0.64 (0.29), residues: 876 helix: 1.61 (0.25), residues: 461 sheet: -1.23 (0.61), residues: 82 loop : -0.78 (0.34), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 508 HIS 0.002 0.001 HIS A 491 PHE 0.010 0.001 PHE A 669 TYR 0.012 0.001 TYR A 609 ARG 0.002 0.000 ARG A 442 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.855 Fit side-chains revert: symmetry clash REVERT: A 6 MET cc_start: 0.7712 (tmm) cc_final: 0.7427 (tmm) REVERT: A 113 MET cc_start: 0.6538 (ttm) cc_final: 0.6190 (ttm) REVERT: A 546 MET cc_start: 0.8839 (tpt) cc_final: 0.8574 (tpp) REVERT: A 609 TYR cc_start: 0.8857 (m-80) cc_final: 0.8563 (m-80) REVERT: B 97 MET cc_start: 0.5208 (ptt) cc_final: 0.4304 (tpt) outliers start: 10 outliers final: 4 residues processed: 53 average time/residue: 0.1577 time to fit residues: 12.6863 Evaluate side-chains 47 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 43 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain B residue 148 HIS Chi-restraints excluded: chain B residue 184 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 8 optimal weight: 0.4980 chunk 38 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 ASN A 163 GLN A 171 ASN A 437 ASN A 711 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7245 Z= 0.284 Angle : 0.599 6.184 9754 Z= 0.313 Chirality : 0.041 0.163 1060 Planarity : 0.004 0.042 1269 Dihedral : 4.202 20.032 954 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 1.69 % Allowed : 12.61 % Favored : 85.70 % 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 (0.29), residues: 876 helix: 1.44 (0.25), residues: 458 sheet: -1.42 (0.60), residues: 82 loop : -0.83 (0.34), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 508 HIS 0.004 0.001 HIS A 651 PHE 0.025 0.002 PHE B 104 TYR 0.011 0.001 TYR A 287 ARG 0.003 0.001 ARG B 58 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 44 time to evaluate : 0.876 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.6705 (ttm) cc_final: 0.6228 (ttm) REVERT: A 195 PHE cc_start: 0.8398 (OUTLIER) cc_final: 0.8068 (m-80) REVERT: A 609 TYR cc_start: 0.8863 (m-80) cc_final: 0.8587 (m-80) REVERT: B 97 MET cc_start: 0.5058 (ptt) cc_final: 0.4166 (tpt) outliers start: 13 outliers final: 7 residues processed: 52 average time/residue: 0.1696 time to fit residues: 13.5545 Evaluate side-chains 52 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 195 PHE Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain B residue 123 TYR Chi-restraints excluded: chain B residue 148 HIS Chi-restraints excluded: chain B residue 184 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 48 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 0 optimal weight: 0.6980 chunk 43 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 21 optimal weight: 0.4980 chunk 28 optimal weight: 0.0570 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 104 ASN A 163 GLN B 120 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7245 Z= 0.183 Angle : 0.552 8.159 9754 Z= 0.283 Chirality : 0.040 0.151 1060 Planarity : 0.003 0.034 1269 Dihedral : 4.083 18.752 954 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.69 % Allowed : 13.65 % Favored : 84.66 % 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: 0.47 (0.29), residues: 876 helix: 1.50 (0.25), residues: 457 sheet: -1.41 (0.60), residues: 82 loop : -0.84 (0.33), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 508 HIS 0.002 0.001 HIS A 401 PHE 0.012 0.001 PHE B 104 TYR 0.009 0.001 TYR B 123 ARG 0.002 0.000 ARG A 453 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 46 time to evaluate : 0.893 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.6601 (ttm) cc_final: 0.6125 (ttm) REVERT: A 163 GLN cc_start: 0.9171 (OUTLIER) cc_final: 0.8919 (pm20) REVERT: A 195 PHE cc_start: 0.8511 (OUTLIER) cc_final: 0.8144 (m-80) REVERT: A 609 TYR cc_start: 0.8864 (m-80) cc_final: 0.8595 (m-80) REVERT: B 97 MET cc_start: 0.5204 (ptt) cc_final: 0.4476 (tpt) outliers start: 13 outliers final: 7 residues processed: 54 average time/residue: 0.1516 time to fit residues: 12.6125 Evaluate side-chains 55 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 46 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 195 PHE Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain B residue 148 HIS Chi-restraints excluded: chain B residue 184 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 76 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 49 optimal weight: 0.0370 chunk 20 optimal weight: 0.6980 chunk 85 optimal weight: 0.5980 chunk 70 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 7 optimal weight: 5.9990 chunk 28 optimal weight: 0.3980 chunk 44 optimal weight: 0.8980 chunk 82 optimal weight: 4.9990 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 ASN A 163 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7245 Z= 0.163 Angle : 0.560 10.965 9754 Z= 0.279 Chirality : 0.039 0.145 1060 Planarity : 0.003 0.032 1269 Dihedral : 3.965 18.159 954 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.95 % Allowed : 14.69 % Favored : 83.36 % 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: 0.47 (0.29), residues: 876 helix: 1.50 (0.25), residues: 457 sheet: -1.38 (0.61), residues: 82 loop : -0.86 (0.33), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 508 HIS 0.002 0.001 HIS A 491 PHE 0.013 0.001 PHE A 230 TYR 0.009 0.001 TYR B 123 ARG 0.002 0.000 ARG A 453 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 49 time to evaluate : 0.883 Fit side-chains revert: symmetry clash REVERT: A 113 MET cc_start: 0.6545 (ttm) cc_final: 0.6319 (ttm) REVERT: A 163 GLN cc_start: 0.9054 (OUTLIER) cc_final: 0.8854 (pm20) REVERT: A 195 PHE cc_start: 0.8577 (OUTLIER) cc_final: 0.8077 (m-80) REVERT: A 546 MET cc_start: 0.8908 (tpt) cc_final: 0.8620 (tpp) REVERT: A 609 TYR cc_start: 0.8857 (m-80) cc_final: 0.8610 (m-80) REVERT: B 97 MET cc_start: 0.5487 (ptt) cc_final: 0.4896 (tpt) outliers start: 15 outliers final: 7 residues processed: 59 average time/residue: 0.1792 time to fit residues: 15.6908 Evaluate side-chains 54 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 45 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 195 PHE Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain B residue 123 TYR Chi-restraints excluded: chain B residue 148 HIS Chi-restraints excluded: chain B residue 184 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 9 optimal weight: 0.9990 chunk 48 optimal weight: 4.9990 chunk 62 optimal weight: 0.4980 chunk 71 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 84 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 33 optimal weight: 0.0980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 ASN A 163 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7245 Z= 0.186 Angle : 0.585 10.730 9754 Z= 0.291 Chirality : 0.039 0.144 1060 Planarity : 0.003 0.033 1269 Dihedral : 4.017 19.198 954 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.95 % Allowed : 15.73 % Favored : 82.31 % 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: 0.41 (0.29), residues: 876 helix: 1.45 (0.25), residues: 461 sheet: -1.42 (0.61), residues: 82 loop : -0.90 (0.33), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 508 HIS 0.002 0.001 HIS A 401 PHE 0.022 0.001 PHE B 181 TYR 0.009 0.001 TYR A 164 ARG 0.002 0.000 ARG A 453 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 45 time to evaluate : 0.773 Fit side-chains revert: symmetry clash REVERT: A 77 MET cc_start: 0.7786 (pmm) cc_final: 0.6885 (ptm) REVERT: A 113 MET cc_start: 0.6562 (ttm) cc_final: 0.6348 (ttm) REVERT: A 163 GLN cc_start: 0.9052 (OUTLIER) cc_final: 0.8848 (pm20) REVERT: A 195 PHE cc_start: 0.8627 (OUTLIER) cc_final: 0.8106 (m-80) REVERT: A 546 MET cc_start: 0.8924 (tpt) cc_final: 0.8636 (tpp) REVERT: A 609 TYR cc_start: 0.8876 (m-80) cc_final: 0.8634 (m-80) REVERT: B 97 MET cc_start: 0.5291 (ptt) cc_final: 0.4741 (tpt) outliers start: 15 outliers final: 6 residues processed: 56 average time/residue: 0.1527 time to fit residues: 13.1382 Evaluate side-chains 54 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 195 PHE Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain B residue 123 TYR Chi-restraints excluded: chain B residue 148 HIS Chi-restraints excluded: chain B residue 184 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 50 optimal weight: 0.6980 chunk 25 optimal weight: 0.5980 chunk 16 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 7 optimal weight: 0.0170 chunk 66 optimal weight: 0.6980 chunk 77 optimal weight: 0.0770 chunk 81 optimal weight: 2.9990 chunk 74 optimal weight: 0.4980 overall best weight: 0.3576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 ASN A 163 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 7245 Z= 0.150 Angle : 0.594 11.694 9754 Z= 0.291 Chirality : 0.039 0.171 1060 Planarity : 0.003 0.032 1269 Dihedral : 3.935 18.574 954 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.56 % Allowed : 16.25 % Favored : 82.18 % 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 (0.29), residues: 876 helix: 1.52 (0.25), residues: 457 sheet: -1.37 (0.62), residues: 82 loop : -0.84 (0.33), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 508 HIS 0.001 0.000 HIS A 153 PHE 0.009 0.001 PHE A 669 TYR 0.008 0.001 TYR A 164 ARG 0.002 0.000 ARG A 777 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 46 time to evaluate : 0.862 Fit side-chains revert: symmetry clash REVERT: A 77 MET cc_start: 0.7783 (pmm) cc_final: 0.6776 (ptm) REVERT: A 163 GLN cc_start: 0.9104 (OUTLIER) cc_final: 0.8825 (pm20) REVERT: A 195 PHE cc_start: 0.8604 (OUTLIER) cc_final: 0.7975 (m-80) REVERT: A 546 MET cc_start: 0.8888 (tpt) cc_final: 0.8604 (tpp) REVERT: A 609 TYR cc_start: 0.8859 (m-80) cc_final: 0.8621 (m-80) REVERT: B 97 MET cc_start: 0.5455 (ptt) cc_final: 0.4974 (tpt) outliers start: 12 outliers final: 4 residues processed: 53 average time/residue: 0.1500 time to fit residues: 12.2427 Evaluate side-chains 51 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 195 PHE Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain B residue 148 HIS Chi-restraints excluded: chain B residue 184 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 0.3980 chunk 81 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7245 Z= 0.200 Angle : 0.611 12.011 9754 Z= 0.301 Chirality : 0.040 0.176 1060 Planarity : 0.003 0.034 1269 Dihedral : 4.003 18.213 954 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.56 % Allowed : 16.38 % Favored : 82.05 % 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: 0.51 (0.29), residues: 876 helix: 1.60 (0.25), residues: 446 sheet: -1.44 (0.61), residues: 82 loop : -0.85 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 508 HIS 0.002 0.001 HIS A 401 PHE 0.024 0.001 PHE B 181 TYR 0.015 0.001 TYR A 164 ARG 0.002 0.000 ARG A 780 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 45 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 MET cc_start: 0.7760 (pmm) cc_final: 0.6858 (ptm) REVERT: A 195 PHE cc_start: 0.8610 (OUTLIER) cc_final: 0.8060 (m-80) REVERT: A 546 MET cc_start: 0.8897 (tpt) cc_final: 0.8603 (tpp) REVERT: A 609 TYR cc_start: 0.8874 (m-80) cc_final: 0.8634 (m-80) REVERT: B 97 MET cc_start: 0.5230 (ptt) cc_final: 0.4751 (tpt) outliers start: 12 outliers final: 6 residues processed: 53 average time/residue: 0.1691 time to fit residues: 13.5546 Evaluate side-chains 50 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 142 TYR Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 195 PHE Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain B residue 148 HIS Chi-restraints excluded: chain B residue 184 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 51 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 58 optimal weight: 0.7980 chunk 87 optimal weight: 0.3980 chunk 80 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 7 optimal weight: 0.5980 chunk 53 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 55 optimal weight: 0.3980 chunk 74 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7245 Z= 0.172 Angle : 0.612 12.782 9754 Z= 0.302 Chirality : 0.040 0.176 1060 Planarity : 0.003 0.033 1269 Dihedral : 4.054 19.447 954 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.30 % Allowed : 16.91 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.29), residues: 876 helix: 1.58 (0.25), residues: 444 sheet: -1.40 (0.62), residues: 82 loop : -0.76 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 508 HIS 0.002 0.001 HIS A 401 PHE 0.010 0.001 PHE B 107 TYR 0.010 0.001 TYR B 123 ARG 0.002 0.000 ARG A 453 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 44 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 MET cc_start: 0.7875 (pmm) cc_final: 0.7052 (ptm) REVERT: A 195 PHE cc_start: 0.8625 (OUTLIER) cc_final: 0.7981 (m-80) REVERT: A 546 MET cc_start: 0.8876 (tpt) cc_final: 0.8578 (tpp) REVERT: A 609 TYR cc_start: 0.8863 (m-80) cc_final: 0.8625 (m-80) REVERT: B 97 MET cc_start: 0.5554 (ptt) cc_final: 0.5113 (tpt) outliers start: 10 outliers final: 8 residues processed: 52 average time/residue: 0.1685 time to fit residues: 13.2626 Evaluate side-chains 52 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 43 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 142 TYR Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 195 PHE Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain B residue 148 HIS Chi-restraints excluded: chain B residue 184 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 21 optimal weight: 0.3980 chunk 64 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 19 optimal weight: 0.4980 chunk 69 optimal weight: 0.9990 chunk 29 optimal weight: 0.1980 chunk 71 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 3 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.049045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.039260 restraints weight = 61027.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.040235 restraints weight = 33734.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.040858 restraints weight = 21751.467| |-----------------------------------------------------------------------------| r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.3105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7245 Z= 0.171 Angle : 0.608 12.460 9754 Z= 0.299 Chirality : 0.040 0.175 1060 Planarity : 0.003 0.036 1269 Dihedral : 4.025 18.956 954 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.17 % Allowed : 17.04 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.29), residues: 876 helix: 1.64 (0.25), residues: 442 sheet: -1.39 (0.62), residues: 82 loop : -0.73 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 508 HIS 0.002 0.001 HIS B 184 PHE 0.022 0.001 PHE B 181 TYR 0.010 0.001 TYR B 123 ARG 0.002 0.000 ARG A 108 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1724.70 seconds wall clock time: 36 minutes 0.80 seconds (2160.80 seconds total)