Starting phenix.real_space_refine on Wed Jun 11 23:55:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tt7_26113/06_2025/7tt7_26113.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tt7_26113/06_2025/7tt7_26113.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tt7_26113/06_2025/7tt7_26113.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tt7_26113/06_2025/7tt7_26113.map" model { file = "/net/cci-nas-00/data/ceres_data/7tt7_26113/06_2025/7tt7_26113.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tt7_26113/06_2025/7tt7_26113.cif" } resolution = 4.8 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= 0.006 sd= 0.048 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 26 5.16 5 C 4323 2.51 5 N 1158 2.21 5 O 1321 1.98 5 H 6468 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 13296 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 7625 Classifications: {'peptide': 496} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 477} Chain breaks: 7 Chain: "C" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 396 Classifications: {'peptide': 28} Link IDs: {'PTRANS': 4, 'TRANS': 23} Chain breaks: 1 Chain: "E" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 1381 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 5, 'TRANS': 83} Chain: "D" Number of atoms: 1599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 1599 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain breaks: 3 Chain: "P" Number of atoms: 2295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 2295 Classifications: {'peptide': 152} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 150} Chain breaks: 8 Time building chain proxies: 6.66, per 1000 atoms: 0.50 Number of scatterers: 13296 At special positions: 0 Unit cell: (92.3485, 94.4962, 128.858, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 26 16.00 O 1321 8.00 N 1158 7.00 C 4323 6.00 H 6468 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 425 " - pdb=" SG CYS P1299 " distance=2.04 Simple disulfide: pdb=" SG CYS A 690 " - pdb=" SG CYS A 700 " distance=2.03 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: 3.35 Conformation dependent library (CDL) restraints added in 1.1 seconds 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1568 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 6 sheets defined 21.0% alpha, 37.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.17 Creating SS restraints... Processing helix chain 'A' and resid 280 through 289 Processing helix chain 'A' and resid 300 through 313 Processing helix chain 'A' and resid 361 through 366 removed outlier: 4.076A pdb=" N LEU A 365 " --> pdb=" O LYS A 361 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG A 366 " --> pdb=" O ASP A 362 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 361 through 366' Processing helix chain 'A' and resid 367 through 369 No H-bonds generated for 'chain 'A' and resid 367 through 369' Processing helix chain 'A' and resid 378 through 393 removed outlier: 3.586A pdb=" N VAL A 382 " --> pdb=" O GLY A 378 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY A 385 " --> pdb=" O LEU A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 452 Processing helix chain 'A' and resid 542 through 552 removed outlier: 3.664A pdb=" N MET A 552 " --> pdb=" O TYR A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 651 Processing helix chain 'A' and resid 688 through 692 Processing helix chain 'C' and resid 39 through 44 Processing helix chain 'E' and resid 23 through 27 Processing helix chain 'E' and resid 39 through 44 Processing helix chain 'E' and resid 51 through 60 Processing helix chain 'D' and resid 116 through 121 removed outlier: 3.991A pdb=" N LEU D 119 " --> pdb=" O ASN D 116 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASP D 121 " --> pdb=" O ALA D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 128 Processing helix chain 'D' and resid 137 through 145 removed outlier: 4.070A pdb=" N SER D 145 " --> pdb=" O ARG D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 189 removed outlier: 4.277A pdb=" N LEU D 170 " --> pdb=" O ARG D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 205 Processing helix chain 'D' and resid 209 through 214 Processing helix chain 'D' and resid 221 through 225 Processing helix chain 'D' and resid 235 through 241 Processing sheet with id=AA1, first strand: chain 'A' and resid 272 through 276 removed outlier: 6.528A pdb=" N GLU A 272 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N VAL A 341 " --> pdb=" O GLU A 272 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N SER A 274 " --> pdb=" O VAL A 341 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 348 through 355 removed outlier: 5.963A pdb=" N TYR A 348 " --> pdb=" O VAL A 412 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N VAL A 414 " --> pdb=" O TYR A 348 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N ARG A 350 " --> pdb=" O VAL A 414 " (cutoff:3.500A) removed outlier: 12.698A pdb=" N TYR A 416 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 9.758A pdb=" N ILE A 352 " --> pdb=" O TYR A 416 " (cutoff:3.500A) removed outlier: 12.395A pdb=" N VAL A 418 " --> pdb=" O ILE A 352 " (cutoff:3.500A) removed outlier: 9.708A pdb=" N PHE A 354 " --> pdb=" O VAL A 418 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 802 through 806 removed outlier: 6.429A pdb=" N LEU A 783 " --> pdb=" O TRP A 776 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N TRP A 776 " --> pdb=" O LEU A 783 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N PHE A 785 " --> pdb=" O LEU A 774 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N TYR A 608 " --> pdb=" O THR A 600 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE A 428 " --> pdb=" O PHE P1296 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N PHE P1296 " --> pdb=" O PHE A 428 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA P1294 " --> pdb=" O ILE A 430 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLY P1156 " --> pdb=" O ASP P1120 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ASP P1120 " --> pdb=" O GLY P1156 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 671 through 674 removed outlier: 5.293A pdb=" N ASP A 704 " --> pdb=" O ALA A 672 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N TYR A 674 " --> pdb=" O SER A 702 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N SER A 702 " --> pdb=" O TYR A 674 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 32 through 35 removed outlier: 3.667A pdb=" N MET E 64 " --> pdb=" O PHE E 74 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 32 through 35 removed outlier: 6.638A pdb=" N THR E 90 " --> pdb=" O ASN E 106 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ASN E 106 " --> pdb=" O THR E 90 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N THR E 92 " --> pdb=" O ILE E 104 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ILE E 104 " --> pdb=" O THR E 92 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N THR E 94 " --> pdb=" O THR E 102 " (cutoff:3.500A) 355 hydrogen bonds defined for protein. 954 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: 4.50 Time building geometry restraints manager: 4.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 6468 1.03 - 1.23: 15 1.23 - 1.42: 3090 1.42 - 1.62: 3823 1.62 - 1.81: 48 Bond restraints: 13444 Sorted by residual: bond pdb=" C PHE A 737 " pdb=" O PHE A 737 " ideal model delta sigma weight residual 1.234 1.221 0.013 1.22e-02 6.72e+03 1.14e+00 bond pdb=" N GLY A 631 " pdb=" CA GLY A 631 " ideal model delta sigma weight residual 1.449 1.439 0.010 1.18e-02 7.18e+03 7.41e-01 bond pdb=" CA PRO D 206 " pdb=" C PRO D 206 " ideal model delta sigma weight residual 1.516 1.531 -0.014 1.75e-02 3.27e+03 6.86e-01 bond pdb=" C TRP A 576 " pdb=" N THR A 577 " ideal model delta sigma weight residual 1.331 1.344 -0.013 1.55e-02 4.16e+03 6.75e-01 bond pdb=" N GLN A 371 " pdb=" CA GLN A 371 " ideal model delta sigma weight residual 1.458 1.447 0.010 1.24e-02 6.50e+03 6.64e-01 ... (remaining 13439 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 22769 1.40 - 2.79: 1140 2.79 - 4.19: 123 4.19 - 5.59: 22 5.59 - 6.98: 3 Bond angle restraints: 24057 Sorted by residual: angle pdb=" N GLY A 756 " pdb=" CA GLY A 756 " pdb=" C GLY A 756 " ideal model delta sigma weight residual 115.34 108.94 6.40 1.67e+00 3.59e-01 1.47e+01 angle pdb=" N PHE A 478 " pdb=" CA PHE A 478 " pdb=" C PHE A 478 " ideal model delta sigma weight residual 111.36 107.35 4.01 1.09e+00 8.42e-01 1.36e+01 angle pdb=" N ARG D 212 " pdb=" CA ARG D 212 " pdb=" C ARG D 212 " ideal model delta sigma weight residual 112.45 107.80 4.65 1.39e+00 5.18e-01 1.12e+01 angle pdb=" N ASN A 579 " pdb=" CA ASN A 579 " pdb=" C ASN A 579 " ideal model delta sigma weight residual 107.67 114.65 -6.98 2.09e+00 2.29e-01 1.12e+01 angle pdb=" N THR A 577 " pdb=" CA THR A 577 " pdb=" C THR A 577 " ideal model delta sigma weight residual 109.24 114.52 -5.28 1.67e+00 3.59e-01 9.99e+00 ... (remaining 24052 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 6019 17.82 - 35.64: 200 35.64 - 53.46: 121 53.46 - 71.28: 46 71.28 - 89.10: 4 Dihedral angle restraints: 6390 sinusoidal: 3362 harmonic: 3028 Sorted by residual: dihedral pdb=" CB CYS A 690 " pdb=" SG CYS A 690 " pdb=" SG CYS A 700 " pdb=" CB CYS A 700 " ideal model delta sinusoidal sigma weight residual 93.00 131.29 -38.29 1 1.00e+01 1.00e-02 2.07e+01 dihedral pdb=" CA VAL A 660 " pdb=" C VAL A 660 " pdb=" N ARG A 661 " pdb=" CA ARG A 661 " ideal model delta harmonic sigma weight residual -180.00 -160.45 -19.55 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" CA PHE A 395 " pdb=" C PHE A 395 " pdb=" N GLU A 396 " pdb=" CA GLU A 396 " ideal model delta harmonic sigma weight residual 180.00 161.87 18.13 0 5.00e+00 4.00e-02 1.31e+01 ... (remaining 6387 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 591 0.034 - 0.068: 245 0.068 - 0.102: 99 0.102 - 0.136: 46 0.136 - 0.170: 12 Chirality restraints: 993 Sorted by residual: chirality pdb=" CA ILE P1167 " pdb=" N ILE P1167 " pdb=" C ILE P1167 " pdb=" CB ILE P1167 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.20e-01 chirality pdb=" CA ILE C 67 " pdb=" N ILE C 67 " pdb=" C ILE C 67 " pdb=" CB ILE C 67 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.03e-01 chirality pdb=" CA TRP D 191 " pdb=" N TRP D 191 " pdb=" C TRP D 191 " pdb=" CB TRP D 191 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.92e-01 ... (remaining 990 not shown) Planarity restraints: 2040 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 544 " 0.013 2.00e-02 2.50e+03 2.70e-02 7.28e+00 pdb=" C ALA A 544 " -0.047 2.00e-02 2.50e+03 pdb=" O ALA A 544 " 0.018 2.00e-02 2.50e+03 pdb=" N MET A 545 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 652 " 0.008 2.00e-02 2.50e+03 1.48e-02 6.58e+00 pdb=" CG PHE A 652 " 0.012 2.00e-02 2.50e+03 pdb=" CD1 PHE A 652 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE A 652 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE A 652 " -0.016 2.00e-02 2.50e+03 pdb=" CE2 PHE A 652 " 0.019 2.00e-02 2.50e+03 pdb=" CZ PHE A 652 " 0.007 2.00e-02 2.50e+03 pdb=" HD1 PHE A 652 " -0.029 2.00e-02 2.50e+03 pdb=" HD2 PHE A 652 " -0.005 2.00e-02 2.50e+03 pdb=" HE1 PHE A 652 " 0.022 2.00e-02 2.50e+03 pdb=" HE2 PHE A 652 " -0.018 2.00e-02 2.50e+03 pdb=" HZ PHE A 652 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 653 " -0.010 2.00e-02 2.50e+03 1.33e-02 5.34e+00 pdb=" CG TYR A 653 " -0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR A 653 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR A 653 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR A 653 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR A 653 " 0.015 2.00e-02 2.50e+03 pdb=" CZ TYR A 653 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 653 " -0.003 2.00e-02 2.50e+03 pdb=" HD1 TYR A 653 " 0.015 2.00e-02 2.50e+03 pdb=" HD2 TYR A 653 " 0.029 2.00e-02 2.50e+03 pdb=" HE1 TYR A 653 " 0.008 2.00e-02 2.50e+03 pdb=" HE2 TYR A 653 " -0.016 2.00e-02 2.50e+03 ... (remaining 2037 not shown) Histogram of nonbonded interaction distances: 1.46 - 2.09: 299 2.09 - 2.72: 22357 2.72 - 3.34: 35860 3.34 - 3.97: 46510 3.97 - 4.60: 71622 Nonbonded interactions: 176648 Sorted by model distance: nonbonded pdb=" HZ1 LYS A 310 " pdb=" OD1 ASP A 380 " model vdw 1.460 2.450 nonbonded pdb=" HD1 HIS A 533 " pdb=" OD1 ASP A 568 " model vdw 1.479 2.450 nonbonded pdb=" H GLU A 396 " pdb=" O LYS A 419 " model vdw 1.481 2.450 nonbonded pdb=" O ASP P1270 " pdb="HH12 ARG P1273 " model vdw 1.484 2.450 nonbonded pdb="HD22 ASN E 71 " pdb=" O ASN E 96 " model vdw 1.535 2.450 ... (remaining 176643 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.840 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: 0.220 Extract box with map and model: 0.500 Check model and map are aligned: 0.080 Set scattering table: 0.140 Process input model: 31.030 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6494 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 0.024 6978 Z= 0.166 Angle : 0.839 6.984 9438 Z= 0.514 Chirality : 0.048 0.170 993 Planarity : 0.005 0.027 1228 Dihedral : 10.502 89.098 2476 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % 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: 0.94 (0.28), residues: 819 helix: -0.22 (0.41), residues: 116 sheet: 1.37 (0.26), residues: 357 loop : 0.22 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP P1042 HIS 0.002 0.001 HIS A 533 PHE 0.013 0.001 PHE A 652 TYR 0.019 0.002 TYR A 416 ARG 0.012 0.001 ARG A 314 Details of bonding type rmsd hydrogen bonds : bond 0.12660 ( 351) hydrogen bonds : angle 7.84154 ( 954) SS BOND : bond 0.00417 ( 2) SS BOND : angle 0.79721 ( 4) covalent geometry : bond 0.00296 ( 6976) covalent geometry : angle 0.83897 ( 9434) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 242 time to evaluate : 1.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 355 GLU cc_start: 0.9006 (mt-10) cc_final: 0.8652 (mm-30) REVERT: A 362 ASP cc_start: 0.8985 (t70) cc_final: 0.8729 (t0) REVERT: A 390 ASN cc_start: 0.9511 (m-40) cc_final: 0.9270 (m110) REVERT: A 430 ILE cc_start: 0.8925 (tt) cc_final: 0.8705 (tt) REVERT: A 441 GLN cc_start: 0.8785 (tt0) cc_final: 0.8426 (pm20) REVERT: A 515 LEU cc_start: 0.9372 (tp) cc_final: 0.9092 (pp) REVERT: A 607 GLU cc_start: 0.9542 (mt-10) cc_final: 0.9330 (mm-30) REVERT: A 709 ASN cc_start: 0.8791 (m110) cc_final: 0.8443 (m110) REVERT: A 745 TRP cc_start: 0.8303 (p90) cc_final: 0.8093 (p90) REVERT: E 64 MET cc_start: 0.9210 (mtp) cc_final: 0.8950 (mmm) REVERT: D 115 THR cc_start: 0.7078 (m) cc_final: 0.6419 (p) REVERT: D 117 MET cc_start: 0.9113 (mmm) cc_final: 0.8697 (mmm) REVERT: D 171 LYS cc_start: 0.9402 (mmtt) cc_final: 0.8841 (mmmt) REVERT: D 176 LYS cc_start: 0.9205 (mtmt) cc_final: 0.8783 (tppt) REVERT: D 178 GLU cc_start: 0.9023 (mm-30) cc_final: 0.7669 (mm-30) outliers start: 0 outliers final: 0 residues processed: 242 average time/residue: 0.5024 time to fit residues: 152.9278 Evaluate side-chains 164 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 7.9990 chunk 63 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 21 optimal weight: 0.0040 chunk 42 optimal weight: 7.9990 chunk 34 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 25 optimal weight: 10.0000 chunk 40 optimal weight: 7.9990 chunk 49 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 overall best weight: 2.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 506 ASN A 533 HIS A 579 ASN D 139 HIS ** P1064 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.114676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.082496 restraints weight = 66134.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.085171 restraints weight = 33289.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.086711 restraints weight = 18645.606| |-----------------------------------------------------------------------------| r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.3260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 6978 Z= 0.189 Angle : 0.615 12.644 9438 Z= 0.349 Chirality : 0.044 0.218 993 Planarity : 0.005 0.052 1228 Dihedral : 5.180 55.540 943 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % 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: 0.77 (0.28), residues: 819 helix: 0.80 (0.45), residues: 132 sheet: 0.97 (0.26), residues: 352 loop : 0.00 (0.34), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 745 HIS 0.007 0.002 HIS D 139 PHE 0.022 0.002 PHE P1296 TYR 0.013 0.001 TYR A 416 ARG 0.004 0.001 ARG A 592 Details of bonding type rmsd hydrogen bonds : bond 0.04653 ( 351) hydrogen bonds : angle 6.61041 ( 954) SS BOND : bond 0.00558 ( 2) SS BOND : angle 2.58163 ( 4) covalent geometry : bond 0.00373 ( 6976) covalent geometry : angle 0.61278 ( 9434) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 1.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 355 GLU cc_start: 0.9118 (mt-10) cc_final: 0.8566 (mm-30) REVERT: A 390 ASN cc_start: 0.9523 (m-40) cc_final: 0.9296 (m110) REVERT: A 417 LYS cc_start: 0.9297 (tttt) cc_final: 0.8951 (ttmm) REVERT: A 422 ASN cc_start: 0.8170 (m-40) cc_final: 0.7842 (m-40) REVERT: A 447 ASP cc_start: 0.8425 (m-30) cc_final: 0.8032 (p0) REVERT: A 550 TYR cc_start: 0.8438 (m-10) cc_final: 0.8199 (m-10) REVERT: A 571 THR cc_start: 0.8580 (t) cc_final: 0.7764 (t) REVERT: A 579 ASN cc_start: 0.8250 (m-40) cc_final: 0.7830 (m110) REVERT: A 760 TYR cc_start: 0.7732 (m-80) cc_final: 0.7312 (m-10) REVERT: E 64 MET cc_start: 0.9109 (mtp) cc_final: 0.8732 (mmm) REVERT: E 105 ASP cc_start: 0.7633 (t70) cc_final: 0.7377 (t70) REVERT: D 115 THR cc_start: 0.7397 (m) cc_final: 0.6544 (p) REVERT: D 117 MET cc_start: 0.9267 (mmm) cc_final: 0.8859 (mmm) REVERT: D 139 HIS cc_start: 0.9272 (m-70) cc_final: 0.8985 (m90) REVERT: D 171 LYS cc_start: 0.9369 (mmtt) cc_final: 0.9015 (mmmt) REVERT: D 172 ASP cc_start: 0.8928 (m-30) cc_final: 0.8396 (p0) REVERT: D 176 LYS cc_start: 0.9260 (mtmt) cc_final: 0.8856 (tppt) REVERT: D 178 GLU cc_start: 0.8663 (mm-30) cc_final: 0.7867 (mm-30) outliers start: 0 outliers final: 0 residues processed: 183 average time/residue: 0.4807 time to fit residues: 112.8052 Evaluate side-chains 148 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 48 optimal weight: 10.0000 chunk 69 optimal weight: 30.0000 chunk 9 optimal weight: 2.9990 chunk 44 optimal weight: 7.9990 chunk 57 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 chunk 60 optimal weight: 8.9990 chunk 43 optimal weight: 0.8980 chunk 3 optimal weight: 5.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P1064 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.112343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.079714 restraints weight = 70066.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.081220 restraints weight = 31632.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.082872 restraints weight = 20715.614| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.4462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 6978 Z= 0.243 Angle : 0.629 7.680 9438 Z= 0.356 Chirality : 0.044 0.155 993 Planarity : 0.005 0.039 1228 Dihedral : 5.380 56.832 943 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.14 % Allowed : 1.69 % Favored : 98.17 % 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: -0.10 (0.27), residues: 819 helix: 0.24 (0.42), residues: 129 sheet: 0.35 (0.25), residues: 353 loop : -0.52 (0.32), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 776 HIS 0.010 0.002 HIS D 139 PHE 0.017 0.002 PHE E 74 TYR 0.014 0.002 TYR A 609 ARG 0.006 0.001 ARG A 367 Details of bonding type rmsd hydrogen bonds : bond 0.04236 ( 351) hydrogen bonds : angle 6.22102 ( 954) SS BOND : bond 0.00625 ( 2) SS BOND : angle 1.49907 ( 4) covalent geometry : bond 0.00481 ( 6976) covalent geometry : angle 0.62851 ( 9434) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 156 time to evaluate : 1.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 355 GLU cc_start: 0.9114 (mt-10) cc_final: 0.8630 (mm-30) REVERT: A 361 LYS cc_start: 0.8332 (tttt) cc_final: 0.8026 (mtpt) REVERT: A 447 ASP cc_start: 0.8476 (m-30) cc_final: 0.8123 (p0) REVERT: A 760 TYR cc_start: 0.7941 (m-80) cc_final: 0.7569 (m-10) REVERT: E 64 MET cc_start: 0.8870 (mtp) cc_final: 0.8642 (mmm) REVERT: E 105 ASP cc_start: 0.7860 (t70) cc_final: 0.7628 (t70) REVERT: D 115 THR cc_start: 0.7773 (m) cc_final: 0.6840 (p) REVERT: D 117 MET cc_start: 0.9202 (mmm) cc_final: 0.8842 (mmm) REVERT: P 1258 MET cc_start: 0.7991 (mmm) cc_final: 0.7339 (mmm) REVERT: P 1267 GLU cc_start: 0.8838 (mp0) cc_final: 0.8501 (mp0) outliers start: 1 outliers final: 0 residues processed: 156 average time/residue: 0.6215 time to fit residues: 129.6790 Evaluate side-chains 134 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 1.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 30 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 16 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 25 optimal weight: 10.0000 chunk 81 optimal weight: 8.9990 chunk 65 optimal weight: 2.9990 chunk 40 optimal weight: 8.9990 chunk 20 optimal weight: 5.9990 chunk 67 optimal weight: 0.6980 chunk 56 optimal weight: 3.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 34 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.113721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.076308 restraints weight = 67080.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.080695 restraints weight = 29053.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.083433 restraints weight = 17882.272| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.4757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6978 Z= 0.139 Angle : 0.515 5.559 9438 Z= 0.286 Chirality : 0.042 0.146 993 Planarity : 0.004 0.036 1228 Dihedral : 5.112 58.693 943 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % 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: -0.06 (0.28), residues: 819 helix: 0.60 (0.43), residues: 128 sheet: 0.27 (0.26), residues: 342 loop : -0.48 (0.32), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 191 HIS 0.003 0.001 HIS D 139 PHE 0.009 0.001 PHE E 74 TYR 0.012 0.001 TYR A 416 ARG 0.003 0.000 ARG D 173 Details of bonding type rmsd hydrogen bonds : bond 0.03535 ( 351) hydrogen bonds : angle 5.79597 ( 954) SS BOND : bond 0.00547 ( 2) SS BOND : angle 1.33279 ( 4) covalent geometry : bond 0.00278 ( 6976) covalent geometry : angle 0.51478 ( 9434) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 1.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 355 GLU cc_start: 0.9158 (mt-10) cc_final: 0.8636 (mm-30) REVERT: A 390 ASN cc_start: 0.9505 (m-40) cc_final: 0.9251 (m110) REVERT: A 428 PHE cc_start: 0.8706 (t80) cc_final: 0.8125 (t80) REVERT: A 447 ASP cc_start: 0.8377 (m-30) cc_final: 0.8076 (p0) REVERT: A 488 ARG cc_start: 0.8942 (ptt180) cc_final: 0.8293 (mtm110) REVERT: A 608 TYR cc_start: 0.9161 (p90) cc_final: 0.8698 (p90) REVERT: A 760 TYR cc_start: 0.7830 (m-80) cc_final: 0.7558 (m-10) REVERT: E 105 ASP cc_start: 0.7689 (t70) cc_final: 0.7472 (t0) REVERT: D 115 THR cc_start: 0.7820 (m) cc_final: 0.6847 (p) REVERT: D 117 MET cc_start: 0.9167 (mmm) cc_final: 0.8797 (mmm) REVERT: P 1046 MET cc_start: 0.8357 (mpp) cc_final: 0.7870 (mpp) REVERT: P 1258 MET cc_start: 0.7942 (mmm) cc_final: 0.7615 (mmm) REVERT: P 1267 GLU cc_start: 0.8864 (mp0) cc_final: 0.8655 (mp0) outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.5767 time to fit residues: 117.1095 Evaluate side-chains 142 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 9 optimal weight: 2.9990 chunk 50 optimal weight: 0.0270 chunk 47 optimal weight: 6.9990 chunk 53 optimal weight: 4.9990 chunk 80 optimal weight: 10.0000 chunk 15 optimal weight: 0.7980 chunk 79 optimal weight: 20.0000 chunk 37 optimal weight: 0.0770 chunk 59 optimal weight: 10.0000 chunk 30 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 overall best weight: 0.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 GLN A 579 ASN D 196 ASN P1271 ASN P1295 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.114780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.077963 restraints weight = 68350.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.082433 restraints weight = 29131.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.085278 restraints weight = 17753.844| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.4935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6978 Z= 0.100 Angle : 0.480 4.478 9438 Z= 0.264 Chirality : 0.042 0.151 993 Planarity : 0.004 0.036 1228 Dihedral : 4.882 56.818 943 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.28), residues: 819 helix: 0.87 (0.44), residues: 130 sheet: 0.34 (0.26), residues: 336 loop : -0.30 (0.33), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 191 HIS 0.002 0.001 HIS D 139 PHE 0.007 0.001 PHE P1296 TYR 0.009 0.001 TYR D 177 ARG 0.003 0.000 ARG A 592 Details of bonding type rmsd hydrogen bonds : bond 0.03232 ( 351) hydrogen bonds : angle 5.52243 ( 954) SS BOND : bond 0.00470 ( 2) SS BOND : angle 1.16025 ( 4) covalent geometry : bond 0.00204 ( 6976) covalent geometry : angle 0.47963 ( 9434) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 1.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 355 GLU cc_start: 0.9100 (mt-10) cc_final: 0.8538 (mm-30) REVERT: A 361 LYS cc_start: 0.8189 (tttt) cc_final: 0.7887 (mtpt) REVERT: A 417 LYS cc_start: 0.9326 (tttt) cc_final: 0.9110 (mmtm) REVERT: A 428 PHE cc_start: 0.8671 (t80) cc_final: 0.8368 (t80) REVERT: A 511 THR cc_start: 0.9057 (t) cc_final: 0.8854 (t) REVERT: A 569 ASP cc_start: 0.8123 (m-30) cc_final: 0.7917 (m-30) REVERT: A 760 TYR cc_start: 0.7722 (m-80) cc_final: 0.7521 (m-10) REVERT: E 105 ASP cc_start: 0.7675 (t70) cc_final: 0.7418 (t0) REVERT: D 115 THR cc_start: 0.7831 (m) cc_final: 0.6861 (p) REVERT: D 117 MET cc_start: 0.9164 (mmm) cc_final: 0.8829 (mmm) REVERT: D 171 LYS cc_start: 0.9436 (mmtt) cc_final: 0.8989 (tppt) REVERT: P 1046 MET cc_start: 0.8348 (mpp) cc_final: 0.7872 (mpp) REVERT: P 1258 MET cc_start: 0.7969 (mmm) cc_final: 0.7644 (mmm) REVERT: P 1267 GLU cc_start: 0.8886 (mp0) cc_final: 0.8667 (mp0) outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.4494 time to fit residues: 92.1555 Evaluate side-chains 139 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 50 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 38 optimal weight: 9.9990 chunk 71 optimal weight: 30.0000 chunk 81 optimal weight: 0.8980 chunk 83 optimal weight: 7.9990 chunk 4 optimal weight: 0.8980 chunk 65 optimal weight: 0.8980 chunk 55 optimal weight: 0.5980 chunk 54 optimal weight: 2.9990 chunk 40 optimal weight: 6.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 579 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.115316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.083082 restraints weight = 68550.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.085173 restraints weight = 32508.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.086661 restraints weight = 18533.558| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.5202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6978 Z= 0.099 Angle : 0.475 4.297 9438 Z= 0.258 Chirality : 0.042 0.150 993 Planarity : 0.004 0.036 1228 Dihedral : 4.693 54.555 943 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % 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: 0.23 (0.29), residues: 819 helix: 0.93 (0.45), residues: 130 sheet: 0.36 (0.26), residues: 344 loop : -0.23 (0.34), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 745 HIS 0.002 0.001 HIS D 139 PHE 0.010 0.001 PHE P1296 TYR 0.010 0.001 TYR D 177 ARG 0.002 0.000 ARG P1205 Details of bonding type rmsd hydrogen bonds : bond 0.03040 ( 351) hydrogen bonds : angle 5.31964 ( 954) SS BOND : bond 0.00420 ( 2) SS BOND : angle 1.10674 ( 4) covalent geometry : bond 0.00203 ( 6976) covalent geometry : angle 0.47419 ( 9434) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 355 GLU cc_start: 0.9041 (mt-10) cc_final: 0.8516 (mm-30) REVERT: A 428 PHE cc_start: 0.8672 (t80) cc_final: 0.8263 (t80) REVERT: A 608 TYR cc_start: 0.9004 (p90) cc_final: 0.8531 (p90) REVERT: A 760 TYR cc_start: 0.7704 (m-80) cc_final: 0.7499 (m-10) REVERT: E 105 ASP cc_start: 0.7651 (t70) cc_final: 0.7433 (t0) REVERT: D 115 THR cc_start: 0.7829 (m) cc_final: 0.7088 (p) REVERT: D 117 MET cc_start: 0.9189 (mmm) cc_final: 0.8877 (mmm) REVERT: D 139 HIS cc_start: 0.9240 (m-70) cc_final: 0.8740 (m90) REVERT: P 1046 MET cc_start: 0.8386 (mpp) cc_final: 0.7929 (mpp) REVERT: P 1258 MET cc_start: 0.7672 (mmm) cc_final: 0.7302 (mmm) REVERT: P 1267 GLU cc_start: 0.8918 (mp0) cc_final: 0.8709 (mp0) REVERT: P 1276 LEU cc_start: 0.9297 (mp) cc_final: 0.8934 (tp) outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.4610 time to fit residues: 93.2590 Evaluate side-chains 136 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 34 optimal weight: 0.9990 chunk 15 optimal weight: 0.0020 chunk 48 optimal weight: 9.9990 chunk 21 optimal weight: 0.0980 chunk 45 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 50 optimal weight: 10.0000 overall best weight: 0.8192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 441 GLN A 579 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.115464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.079320 restraints weight = 66617.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.083810 restraints weight = 28125.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.086692 restraints weight = 17055.713| |-----------------------------------------------------------------------------| r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.5418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6978 Z= 0.101 Angle : 0.473 5.463 9438 Z= 0.259 Chirality : 0.043 0.163 993 Planarity : 0.003 0.037 1228 Dihedral : 4.692 62.823 943 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.29), residues: 819 helix: 1.10 (0.45), residues: 130 sheet: 0.27 (0.26), residues: 345 loop : 0.00 (0.35), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 191 HIS 0.002 0.001 HIS D 139 PHE 0.011 0.001 PHE P1296 TYR 0.010 0.001 TYR A 416 ARG 0.002 0.000 ARG P1297 Details of bonding type rmsd hydrogen bonds : bond 0.02959 ( 351) hydrogen bonds : angle 5.21833 ( 954) SS BOND : bond 0.00538 ( 2) SS BOND : angle 1.57996 ( 4) covalent geometry : bond 0.00208 ( 6976) covalent geometry : angle 0.47217 ( 9434) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 304 MET cc_start: 0.8497 (ttm) cc_final: 0.7952 (tpp) REVERT: A 308 ILE cc_start: 0.9450 (mt) cc_final: 0.9133 (tp) REVERT: A 428 PHE cc_start: 0.8601 (t80) cc_final: 0.8388 (t80) REVERT: A 550 TYR cc_start: 0.8529 (m-10) cc_final: 0.8293 (m-10) REVERT: A 760 TYR cc_start: 0.7658 (m-80) cc_final: 0.7425 (m-10) REVERT: D 115 THR cc_start: 0.7866 (m) cc_final: 0.7038 (p) REVERT: D 117 MET cc_start: 0.9139 (mmm) cc_final: 0.8849 (mmm) REVERT: P 1046 MET cc_start: 0.8347 (mpp) cc_final: 0.7869 (mpp) REVERT: P 1258 MET cc_start: 0.7817 (mmm) cc_final: 0.7483 (mmm) REVERT: P 1267 GLU cc_start: 0.8921 (mp0) cc_final: 0.8692 (mp0) REVERT: P 1276 LEU cc_start: 0.9259 (mp) cc_final: 0.9014 (tp) outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.4392 time to fit residues: 90.8765 Evaluate side-chains 143 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 3 optimal weight: 2.9990 chunk 69 optimal weight: 8.9990 chunk 70 optimal weight: 5.9990 chunk 13 optimal weight: 8.9990 chunk 15 optimal weight: 0.6980 chunk 66 optimal weight: 0.0970 chunk 22 optimal weight: 5.9990 chunk 59 optimal weight: 9.9990 chunk 64 optimal weight: 1.9990 chunk 40 optimal weight: 8.9990 chunk 78 optimal weight: 3.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 579 ASN D 226 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.113275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.080809 restraints weight = 68297.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.083352 restraints weight = 29982.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.084883 restraints weight = 18225.529| |-----------------------------------------------------------------------------| r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.5658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6978 Z= 0.161 Angle : 0.513 5.167 9438 Z= 0.284 Chirality : 0.042 0.160 993 Planarity : 0.004 0.036 1228 Dihedral : 4.839 63.306 943 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % 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: 0.04 (0.29), residues: 819 helix: 0.69 (0.44), residues: 130 sheet: 0.19 (0.26), residues: 345 loop : -0.25 (0.34), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 745 HIS 0.003 0.001 HIS D 139 PHE 0.011 0.001 PHE A 490 TYR 0.012 0.001 TYR A 416 ARG 0.003 0.000 ARG A 367 Details of bonding type rmsd hydrogen bonds : bond 0.03159 ( 351) hydrogen bonds : angle 5.28822 ( 954) SS BOND : bond 0.00290 ( 2) SS BOND : angle 1.10468 ( 4) covalent geometry : bond 0.00318 ( 6976) covalent geometry : angle 0.51241 ( 9434) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 1.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 ILE cc_start: 0.9523 (mt) cc_final: 0.9220 (tp) REVERT: A 428 PHE cc_start: 0.8461 (t80) cc_final: 0.8203 (t80) REVERT: A 760 TYR cc_start: 0.7836 (m-80) cc_final: 0.7504 (m-10) REVERT: D 115 THR cc_start: 0.7939 (m) cc_final: 0.7094 (p) REVERT: D 117 MET cc_start: 0.9106 (mmm) cc_final: 0.8777 (mmm) REVERT: P 1046 MET cc_start: 0.8398 (mpp) cc_final: 0.7958 (mpp) REVERT: P 1258 MET cc_start: 0.7479 (mmm) cc_final: 0.7073 (mmm) REVERT: P 1276 LEU cc_start: 0.9243 (mp) cc_final: 0.8841 (tp) outliers start: 0 outliers final: 0 residues processed: 148 average time/residue: 0.4525 time to fit residues: 86.1697 Evaluate side-chains 129 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 60 optimal weight: 8.9990 chunk 51 optimal weight: 0.9980 chunk 69 optimal weight: 20.0000 chunk 64 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 70 optimal weight: 9.9990 chunk 40 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 46 optimal weight: 4.9990 chunk 79 optimal weight: 20.0000 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 579 ASN ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P1271 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.111775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.079193 restraints weight = 67547.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.082174 restraints weight = 33180.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.082975 restraints weight = 18386.528| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.5930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6978 Z= 0.198 Angle : 0.560 6.510 9438 Z= 0.310 Chirality : 0.042 0.163 993 Planarity : 0.004 0.045 1228 Dihedral : 5.026 55.948 943 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.29), residues: 819 helix: 0.20 (0.44), residues: 129 sheet: 0.15 (0.27), residues: 346 loop : -0.55 (0.34), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 745 HIS 0.005 0.001 HIS D 139 PHE 0.011 0.002 PHE D 144 TYR 0.012 0.001 TYR A 416 ARG 0.004 0.001 ARG A 366 Details of bonding type rmsd hydrogen bonds : bond 0.03397 ( 351) hydrogen bonds : angle 5.51661 ( 954) SS BOND : bond 0.00189 ( 2) SS BOND : angle 0.99867 ( 4) covalent geometry : bond 0.00390 ( 6976) covalent geometry : angle 0.55999 ( 9434) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 598 LYS cc_start: 0.9567 (ptmt) cc_final: 0.9318 (ptmt) REVERT: A 608 TYR cc_start: 0.8979 (p90) cc_final: 0.8496 (p90) REVERT: A 711 MET cc_start: 0.8997 (ppp) cc_final: 0.8786 (ppp) REVERT: A 760 TYR cc_start: 0.7896 (m-80) cc_final: 0.7535 (m-10) REVERT: D 117 MET cc_start: 0.9076 (mmm) cc_final: 0.8754 (tmm) REVERT: P 1258 MET cc_start: 0.7436 (mmm) cc_final: 0.7053 (mmm) REVERT: P 1267 GLU cc_start: 0.8865 (mp0) cc_final: 0.8624 (mp0) REVERT: P 1276 LEU cc_start: 0.9109 (mp) cc_final: 0.8796 (tp) outliers start: 0 outliers final: 0 residues processed: 145 average time/residue: 0.4802 time to fit residues: 88.7654 Evaluate side-chains 125 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 10 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 38 optimal weight: 9.9990 chunk 24 optimal weight: 4.9990 chunk 37 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 chunk 20 optimal weight: 7.9990 chunk 1 optimal weight: 0.6980 chunk 58 optimal weight: 0.8980 chunk 45 optimal weight: 0.3980 chunk 47 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 579 ASN D 139 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.114215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.082603 restraints weight = 68158.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.084545 restraints weight = 32900.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.085992 restraints weight = 19922.796| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.5983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6978 Z= 0.098 Angle : 0.489 5.676 9438 Z= 0.264 Chirality : 0.043 0.171 993 Planarity : 0.004 0.037 1228 Dihedral : 4.602 46.867 943 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 0.03 (0.29), residues: 819 helix: 0.72 (0.44), residues: 130 sheet: 0.22 (0.27), residues: 349 loop : -0.33 (0.35), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 576 HIS 0.006 0.001 HIS D 139 PHE 0.030 0.001 PHE A 428 TYR 0.012 0.001 TYR D 177 ARG 0.002 0.000 ARG A 391 Details of bonding type rmsd hydrogen bonds : bond 0.02995 ( 351) hydrogen bonds : angle 5.18702 ( 954) SS BOND : bond 0.00188 ( 2) SS BOND : angle 0.97676 ( 4) covalent geometry : bond 0.00206 ( 6976) covalent geometry : angle 0.48839 ( 9434) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 ILE cc_start: 0.9535 (mt) cc_final: 0.9241 (tp) REVERT: A 598 LYS cc_start: 0.9544 (ptmt) cc_final: 0.9293 (ptmt) REVERT: A 608 TYR cc_start: 0.9027 (p90) cc_final: 0.8543 (p90) REVERT: A 711 MET cc_start: 0.9055 (ppp) cc_final: 0.8796 (ppp) REVERT: A 768 MET cc_start: 0.8042 (ptp) cc_final: 0.7627 (ptt) REVERT: E 105 ASP cc_start: 0.7996 (t0) cc_final: 0.7766 (t0) REVERT: D 117 MET cc_start: 0.9232 (mmm) cc_final: 0.8754 (mmm) REVERT: D 178 GLU cc_start: 0.8427 (mm-30) cc_final: 0.7862 (mm-30) REVERT: P 1046 MET cc_start: 0.8473 (mpp) cc_final: 0.7997 (mpp) REVERT: P 1258 MET cc_start: 0.7660 (mmm) cc_final: 0.7269 (mmm) REVERT: P 1267 GLU cc_start: 0.8920 (mp0) cc_final: 0.8696 (mp0) REVERT: P 1276 LEU cc_start: 0.9247 (mp) cc_final: 0.8624 (tp) REVERT: P 1295 ASN cc_start: 0.9058 (p0) cc_final: 0.8849 (m-40) outliers start: 0 outliers final: 0 residues processed: 145 average time/residue: 0.4963 time to fit residues: 93.2815 Evaluate side-chains 131 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 61 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 55 optimal weight: 0.8980 chunk 80 optimal weight: 20.0000 chunk 21 optimal weight: 0.5980 chunk 76 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 45 optimal weight: 10.0000 chunk 65 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 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 579 ASN D 139 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.113433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.081374 restraints weight = 67853.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.083801 restraints weight = 30146.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.085873 restraints weight = 18541.272| |-----------------------------------------------------------------------------| r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.6112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6978 Z= 0.118 Angle : 0.480 5.545 9438 Z= 0.262 Chirality : 0.042 0.159 993 Planarity : 0.004 0.037 1228 Dihedral : 4.455 36.937 943 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 0.07 (0.29), residues: 819 helix: 0.87 (0.44), residues: 129 sheet: 0.30 (0.27), residues: 339 loop : -0.42 (0.34), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 745 HIS 0.003 0.001 HIS D 139 PHE 0.018 0.001 PHE A 428 TYR 0.010 0.001 TYR A 416 ARG 0.004 0.000 ARG A 391 Details of bonding type rmsd hydrogen bonds : bond 0.02978 ( 351) hydrogen bonds : angle 5.16494 ( 954) SS BOND : bond 0.00150 ( 2) SS BOND : angle 0.82942 ( 4) covalent geometry : bond 0.00239 ( 6976) covalent geometry : angle 0.47971 ( 9434) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5191.18 seconds wall clock time: 90 minutes 58.86 seconds (5458.86 seconds total)