Starting phenix.real_space_refine on Sun Dec 29 15:38:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8emv_28266/12_2024/8emv_28266.cif Found real_map, /net/cci-nas-00/data/ceres_data/8emv_28266/12_2024/8emv_28266.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8emv_28266/12_2024/8emv_28266.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8emv_28266/12_2024/8emv_28266.map" model { file = "/net/cci-nas-00/data/ceres_data/8emv_28266/12_2024/8emv_28266.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8emv_28266/12_2024/8emv_28266.cif" } resolution = 3.6 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5939 atoms to isotropic. 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 Ca 1 9.91 5 S 31 5.16 5 C 3795 2.51 5 N 1013 2.21 5 O 1109 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 5949 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 747, 5948 Classifications: {'peptide': 747} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 47, 'TRANS': 699} Chain breaks: 3 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 36 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.52, per 1000 atoms: 0.76 Number of scatterers: 5949 At special positions: 0 Unit cell: (62.64, 98.28, 103.68, 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) Ca 1 19.99 S 31 16.00 O 1109 8.00 N 1013 7.00 C 3795 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: 1.35 Conformation dependent library (CDL) restraints added in 933.0 milliseconds 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1418 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 6 sheets defined 33.3% alpha, 16.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'A' and resid 19 through 25 removed outlier: 3.743A pdb=" N ARG A 24 " --> pdb=" O GLU A 20 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY A 25 " --> pdb=" O THR A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 78 No H-bonds generated for 'chain 'A' and resid 76 through 78' Processing helix chain 'A' and resid 83 through 91 Processing helix chain 'A' and resid 127 through 140 Processing helix chain 'A' and resid 148 through 163 removed outlier: 3.503A pdb=" N PHE A 152 " --> pdb=" O SER A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 179 removed outlier: 4.287A pdb=" N ILE A 175 " --> pdb=" O PRO A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 194 removed outlier: 3.641A pdb=" N GLU A 187 " --> pdb=" O LYS A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 208 Processing helix chain 'A' and resid 209 through 221 Processing helix chain 'A' and resid 223 through 233 removed outlier: 3.662A pdb=" N ASP A 227 " --> pdb=" O ARG A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 253 Processing helix chain 'A' and resid 268 through 280 removed outlier: 4.887A pdb=" N LEU A 274 " --> pdb=" O SER A 270 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N LEU A 275 " --> pdb=" O GLN A 271 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ILE A 276 " --> pdb=" O ALA A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 288 removed outlier: 3.736A pdb=" N GLU A 287 " --> pdb=" O GLN A 283 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ARG A 288 " --> pdb=" O GLN A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 300 removed outlier: 3.639A pdb=" N ARG A 298 " --> pdb=" O GLU A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 324 No H-bonds generated for 'chain 'A' and resid 322 through 324' Processing helix chain 'A' and resid 347 through 357 removed outlier: 3.927A pdb=" N ARG A 351 " --> pdb=" O VAL A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 399 Processing helix chain 'A' and resid 418 through 434 removed outlier: 3.672A pdb=" N PHE A 433 " --> pdb=" O CYS A 429 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY A 434 " --> pdb=" O ARG A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 611 Processing helix chain 'A' and resid 622 through 632 Processing helix chain 'A' and resid 632 through 641 Processing helix chain 'A' and resid 661 through 666 Processing helix chain 'A' and resid 680 through 690 Processing helix chain 'A' and resid 702 through 706 removed outlier: 3.674A pdb=" N ARG A 706 " --> pdb=" O GLU A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 816 No H-bonds generated for 'chain 'A' and resid 814 through 816' Processing helix chain 'A' and resid 868 through 881 removed outlier: 4.689A pdb=" N ALA A 878 " --> pdb=" O ARG A 874 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N LEU A 879 " --> pdb=" O GLN A 875 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 65 removed outlier: 4.116A pdb=" N THR A 55 " --> pdb=" O THR A 42 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N THR A 42 " --> pdb=" O THR A 55 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N SER A 26 " --> pdb=" O LEU A 43 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 326 through 328 Processing sheet with id=AA3, first strand: chain 'A' and resid 387 through 388 removed outlier: 6.706A pdb=" N VAL A 361 " --> pdb=" O SER A 411 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N GLU A 413 " --> pdb=" O VAL A 361 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N LEU A 363 " --> pdb=" O GLU A 413 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 598 through 599 removed outlier: 5.978A pdb=" N GLU A 598 " --> pdb=" O MET A 617 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N SER A 619 " --> pdb=" O GLU A 598 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LEU A 644 " --> pdb=" O GLU A 616 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER A 618 " --> pdb=" O LEU A 644 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU A 671 " --> pdb=" O SER A 645 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 781 through 786 removed outlier: 4.518A pdb=" N LYS A 785 " --> pdb=" O ASN A 726 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ASN A 726 " --> pdb=" O LYS A 785 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LEU A 839 " --> pdb=" O ILE A 733 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N GLY A 735 " --> pdb=" O ALA A 837 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ALA A 837 " --> pdb=" O GLY A 735 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 759 through 763 removed outlier: 5.058A pdb=" N LYS A 761 " --> pdb=" O VAL A 749 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL A 749 " --> pdb=" O LYS A 761 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N ARG A 763 " --> pdb=" O VAL A 747 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N VAL A 747 " --> pdb=" O ARG A 763 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N GLU A 800 " --> pdb=" O PHE A 805 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N PHE A 805 " --> pdb=" O GLU A 800 " (cutoff:3.500A) 201 hydrogen bonds defined for protein. 570 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.70 Time building geometry restraints manager: 1.58 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: 1898 1.34 - 1.45: 878 1.45 - 1.57: 3246 1.57 - 1.69: 0 1.69 - 1.81: 53 Bond restraints: 6075 Sorted by residual: bond pdb=" C PRO A 370 " pdb=" N PRO A 371 " ideal model delta sigma weight residual 1.336 1.390 -0.054 1.20e-02 6.94e+03 2.04e+01 bond pdb=" C PRO A 454 " pdb=" N SER A 455 " ideal model delta sigma weight residual 1.329 1.233 0.095 3.03e-02 1.09e+03 9.92e+00 bond pdb=" C LEU A 835 " pdb=" N PRO A 836 " ideal model delta sigma weight residual 1.333 1.349 -0.016 1.17e-02 7.31e+03 1.99e+00 bond pdb=" CB CYS A 669 " pdb=" SG CYS A 669 " ideal model delta sigma weight residual 1.808 1.763 0.045 3.30e-02 9.18e+02 1.85e+00 bond pdb=" C LEU A 453 " pdb=" N PRO A 454 " ideal model delta sigma weight residual 1.330 1.346 -0.016 1.25e-02 6.40e+03 1.72e+00 ... (remaining 6070 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 7808 1.66 - 3.31: 353 3.31 - 4.97: 54 4.97 - 6.63: 6 6.63 - 8.28: 6 Bond angle restraints: 8227 Sorted by residual: angle pdb=" C SER A 200 " pdb=" N GLU A 201 " pdb=" CA GLU A 201 " ideal model delta sigma weight residual 121.54 129.14 -7.60 1.91e+00 2.74e-01 1.59e+01 angle pdb=" C GLY A 380 " pdb=" N PHE A 381 " pdb=" CA PHE A 381 " ideal model delta sigma weight residual 122.82 128.33 -5.51 1.42e+00 4.96e-01 1.50e+01 angle pdb=" N LEU A 835 " pdb=" CA LEU A 835 " pdb=" C LEU A 835 " ideal model delta sigma weight residual 109.81 117.69 -7.88 2.21e+00 2.05e-01 1.27e+01 angle pdb=" N PRO A 370 " pdb=" CA PRO A 370 " pdb=" C PRO A 370 " ideal model delta sigma weight residual 110.70 114.57 -3.87 1.22e+00 6.72e-01 1.00e+01 angle pdb=" CA PRO A 370 " pdb=" C PRO A 370 " pdb=" N PRO A 371 " ideal model delta sigma weight residual 117.93 121.50 -3.57 1.20e+00 6.94e-01 8.86e+00 ... (remaining 8222 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.47: 3225 16.47 - 32.94: 405 32.94 - 49.41: 65 49.41 - 65.88: 23 65.88 - 82.35: 7 Dihedral angle restraints: 3725 sinusoidal: 1539 harmonic: 2186 Sorted by residual: dihedral pdb=" CA LYS A 238 " pdb=" C LYS A 238 " pdb=" N PRO A 239 " pdb=" CA PRO A 239 " ideal model delta harmonic sigma weight residual 180.00 -150.53 -29.47 0 5.00e+00 4.00e-02 3.47e+01 dihedral pdb=" CA LYS A 236 " pdb=" C LYS A 236 " pdb=" N GLY A 237 " pdb=" CA GLY A 237 " ideal model delta harmonic sigma weight residual 180.00 155.95 24.05 0 5.00e+00 4.00e-02 2.31e+01 dihedral pdb=" CA PRO A 239 " pdb=" C PRO A 239 " pdb=" N TYR A 240 " pdb=" CA TYR A 240 " ideal model delta harmonic sigma weight residual 180.00 -160.69 -19.31 0 5.00e+00 4.00e-02 1.49e+01 ... (remaining 3722 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 548 0.039 - 0.078: 254 0.078 - 0.117: 77 0.117 - 0.156: 26 0.156 - 0.195: 10 Chirality restraints: 915 Sorted by residual: chirality pdb=" CB VAL A 116 " pdb=" CA VAL A 116 " pdb=" CG1 VAL A 116 " pdb=" CG2 VAL A 116 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.19 2.00e-01 2.50e+01 9.46e-01 chirality pdb=" CB VAL A 621 " pdb=" CA VAL A 621 " pdb=" CG1 VAL A 621 " pdb=" CG2 VAL A 621 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 9.22e-01 chirality pdb=" CA LEU A 835 " pdb=" N LEU A 835 " pdb=" C LEU A 835 " pdb=" CB LEU A 835 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.71e-01 ... (remaining 912 not shown) Planarity restraints: 1071 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 369 " 0.046 5.00e-02 4.00e+02 6.97e-02 7.77e+00 pdb=" N PRO A 370 " -0.120 5.00e-02 4.00e+02 pdb=" CA PRO A 370 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 370 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 111 " -0.041 5.00e-02 4.00e+02 6.07e-02 5.89e+00 pdb=" N PRO A 112 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO A 112 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 112 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 321 " -0.037 5.00e-02 4.00e+02 5.56e-02 4.95e+00 pdb=" N PRO A 322 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO A 322 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 322 " -0.031 5.00e-02 4.00e+02 ... (remaining 1068 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 2031 2.85 - 3.36: 5011 3.36 - 3.88: 9084 3.88 - 4.39: 10476 4.39 - 4.90: 18462 Nonbonded interactions: 45064 Sorted by model distance: nonbonded pdb=" N ASP A 225 " pdb=" OD1 ASP A 225 " model vdw 2.339 3.120 nonbonded pdb=" O SER A 591 " pdb=" OG SER A 591 " model vdw 2.340 3.040 nonbonded pdb=" OE1 GLU A 577 " pdb=" OG SER A 581 " model vdw 2.356 3.040 nonbonded pdb=" N ASP A 125 " pdb=" OD1 ASP A 125 " model vdw 2.377 3.120 nonbonded pdb=" O SER A 404 " pdb=" OG SER A 404 " model vdw 2.382 3.040 ... (remaining 45059 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 18.360 Find NCS groups from input model: 0.060 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:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.095 6075 Z= 0.453 Angle : 0.813 8.282 8227 Z= 0.461 Chirality : 0.052 0.195 915 Planarity : 0.007 0.070 1071 Dihedral : 15.162 82.355 2307 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % 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: -4.26 (0.24), residues: 739 helix: -3.01 (0.23), residues: 235 sheet: -2.29 (0.41), residues: 124 loop : -2.89 (0.26), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 54 HIS 0.005 0.001 HIS A 808 PHE 0.018 0.002 PHE A 799 TYR 0.019 0.002 TYR A 648 ARG 0.012 0.001 ARG A 73 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.707 Fit side-chains REVERT: A 228 LYS cc_start: 0.8684 (tttt) cc_final: 0.8369 (tptp) REVERT: A 291 MET cc_start: 0.8471 (ttm) cc_final: 0.8129 (ttm) REVERT: A 444 LYS cc_start: 0.8438 (tttm) cc_final: 0.8071 (tptm) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.2630 time to fit residues: 25.7988 Evaluate side-chains 56 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 62 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 58 optimal weight: 0.6980 chunk 22 optimal weight: 8.9990 chunk 35 optimal weight: 2.9990 chunk 43 optimal weight: 8.9990 chunk 67 optimal weight: 0.7980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 ASN A 166 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6075 Z= 0.166 Angle : 0.524 5.390 8227 Z= 0.277 Chirality : 0.042 0.151 915 Planarity : 0.005 0.045 1071 Dihedral : 4.677 25.876 816 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 0.76 % Allowed : 10.40 % Favored : 88.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.65 (0.27), residues: 739 helix: -0.95 (0.31), residues: 237 sheet: -1.78 (0.41), residues: 130 loop : -2.29 (0.28), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 131 HIS 0.002 0.000 HIS A 808 PHE 0.030 0.001 PHE A 197 TYR 0.012 0.001 TYR A 820 ARG 0.003 0.000 ARG A 73 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 74 time to evaluate : 0.705 Fit side-chains REVERT: A 291 MET cc_start: 0.8540 (ttm) cc_final: 0.8252 (ttm) REVERT: A 444 LYS cc_start: 0.8460 (tttm) cc_final: 0.8075 (tptm) REVERT: A 719 ILE cc_start: 0.9010 (OUTLIER) cc_final: 0.8792 (mm) REVERT: A 772 PHE cc_start: 0.7890 (t80) cc_final: 0.7665 (t80) outliers start: 5 outliers final: 3 residues processed: 77 average time/residue: 0.2166 time to fit residues: 21.7438 Evaluate side-chains 66 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 62 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 652 THR Chi-restraints excluded: chain A residue 719 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 37 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 18 optimal weight: 0.2980 chunk 67 optimal weight: 0.9980 chunk 72 optimal weight: 5.9990 chunk 59 optimal weight: 5.9990 chunk 66 optimal weight: 0.7980 chunk 22 optimal weight: 0.0770 chunk 54 optimal weight: 0.7980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6075 Z= 0.137 Angle : 0.496 6.354 8227 Z= 0.254 Chirality : 0.041 0.167 915 Planarity : 0.004 0.048 1071 Dihedral : 4.198 24.048 816 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.38 % Allowed : 11.01 % Favored : 87.61 % 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: -1.71 (0.29), residues: 739 helix: 0.12 (0.34), residues: 238 sheet: -1.09 (0.45), residues: 129 loop : -2.03 (0.29), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 131 HIS 0.002 0.000 HIS A 808 PHE 0.028 0.001 PHE A 197 TYR 0.009 0.001 TYR A 299 ARG 0.003 0.000 ARG A 73 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 72 time to evaluate : 0.719 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 291 MET cc_start: 0.8465 (ttm) cc_final: 0.8229 (ttm) REVERT: A 444 LYS cc_start: 0.8446 (tttm) cc_final: 0.7969 (tptm) REVERT: A 655 ASP cc_start: 0.8016 (p0) cc_final: 0.7571 (t0) outliers start: 9 outliers final: 5 residues processed: 77 average time/residue: 0.1921 time to fit residues: 19.8083 Evaluate side-chains 68 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 63 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASN Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 451 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 66 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 7 optimal weight: 0.7980 chunk 32 optimal weight: 5.9990 chunk 45 optimal weight: 6.9990 chunk 67 optimal weight: 0.9990 chunk 71 optimal weight: 0.6980 chunk 35 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 19 optimal weight: 0.3980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6075 Z= 0.152 Angle : 0.491 5.943 8227 Z= 0.251 Chirality : 0.041 0.167 915 Planarity : 0.004 0.049 1071 Dihedral : 4.044 23.756 816 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.99 % Allowed : 11.77 % Favored : 86.24 % 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: -1.19 (0.30), residues: 739 helix: 0.63 (0.35), residues: 238 sheet: -0.89 (0.45), residues: 131 loop : -1.74 (0.30), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 776 HIS 0.002 0.000 HIS A 808 PHE 0.028 0.001 PHE A 197 TYR 0.010 0.001 TYR A 299 ARG 0.002 0.000 ARG A 73 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 70 time to evaluate : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 444 LYS cc_start: 0.8421 (tttm) cc_final: 0.7988 (tptm) REVERT: A 655 ASP cc_start: 0.8012 (p0) cc_final: 0.7590 (t0) outliers start: 13 outliers final: 8 residues processed: 79 average time/residue: 0.1966 time to fit residues: 20.4915 Evaluate side-chains 70 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 62 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASN Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 451 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 59 optimal weight: 1.9990 chunk 40 optimal weight: 0.2980 chunk 1 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 29 optimal weight: 0.1980 chunk 61 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 36 optimal weight: 7.9990 chunk 64 optimal weight: 5.9990 chunk 18 optimal weight: 10.0000 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6075 Z= 0.194 Angle : 0.502 6.348 8227 Z= 0.255 Chirality : 0.042 0.163 915 Planarity : 0.004 0.050 1071 Dihedral : 4.086 23.722 816 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.14 % Allowed : 13.46 % Favored : 84.40 % 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: -1.06 (0.31), residues: 739 helix: 0.70 (0.35), residues: 244 sheet: -0.95 (0.44), residues: 129 loop : -1.59 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 54 HIS 0.002 0.001 HIS A 808 PHE 0.028 0.001 PHE A 197 TYR 0.011 0.001 TYR A 299 ARG 0.003 0.000 ARG A 73 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 254 GLN cc_start: 0.8901 (OUTLIER) cc_final: 0.8643 (mm-40) REVERT: A 444 LYS cc_start: 0.8431 (tttm) cc_final: 0.8006 (tptm) REVERT: A 655 ASP cc_start: 0.7995 (p0) cc_final: 0.7626 (t0) outliers start: 14 outliers final: 11 residues processed: 75 average time/residue: 0.1915 time to fit residues: 19.1448 Evaluate side-chains 74 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASN Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 254 GLN Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 468 LYS Chi-restraints excluded: chain A residue 652 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 24 optimal weight: 0.4980 chunk 64 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 6075 Z= 0.396 Angle : 0.600 6.269 8227 Z= 0.307 Chirality : 0.046 0.156 915 Planarity : 0.004 0.054 1071 Dihedral : 4.601 25.030 816 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 2.45 % Allowed : 14.07 % Favored : 83.49 % 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: -1.17 (0.30), residues: 739 helix: 0.69 (0.35), residues: 238 sheet: -1.03 (0.42), residues: 128 loop : -1.68 (0.30), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 54 HIS 0.005 0.001 HIS A 808 PHE 0.028 0.002 PHE A 197 TYR 0.016 0.002 TYR A 299 ARG 0.005 0.000 ARG A 73 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 58 time to evaluate : 0.698 Fit side-chains revert: symmetry clash REVERT: A 444 LYS cc_start: 0.8439 (tttm) cc_final: 0.8076 (tptm) REVERT: A 655 ASP cc_start: 0.8054 (p0) cc_final: 0.7635 (t0) REVERT: A 778 GLU cc_start: 0.7126 (pm20) cc_final: 0.6869 (pm20) outliers start: 16 outliers final: 12 residues processed: 69 average time/residue: 0.1977 time to fit residues: 18.3832 Evaluate side-chains 67 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 55 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASN Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 468 LYS Chi-restraints excluded: chain A residue 614 CYS Chi-restraints excluded: chain A residue 652 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 69 optimal weight: 0.8980 chunk 8 optimal weight: 5.9990 chunk 40 optimal weight: 4.9990 chunk 52 optimal weight: 0.6980 chunk 60 optimal weight: 4.9990 chunk 39 optimal weight: 0.0370 chunk 71 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 chunk 43 optimal weight: 0.3980 chunk 32 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6075 Z= 0.127 Angle : 0.496 7.807 8227 Z= 0.251 Chirality : 0.042 0.163 915 Planarity : 0.004 0.050 1071 Dihedral : 4.070 21.652 816 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.99 % Allowed : 14.83 % Favored : 83.18 % 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: -0.70 (0.31), residues: 739 helix: 1.17 (0.36), residues: 233 sheet: -1.05 (0.43), residues: 124 loop : -1.31 (0.31), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 665 HIS 0.001 0.000 HIS A 808 PHE 0.010 0.001 PHE A 799 TYR 0.008 0.001 TYR A 746 ARG 0.002 0.000 ARG A 470 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 254 GLN cc_start: 0.8877 (OUTLIER) cc_final: 0.8660 (mm-40) REVERT: A 291 MET cc_start: 0.8460 (ttm) cc_final: 0.8025 (tpp) REVERT: A 444 LYS cc_start: 0.8428 (tttm) cc_final: 0.8068 (tptm) REVERT: A 655 ASP cc_start: 0.7994 (p0) cc_final: 0.7652 (t0) outliers start: 13 outliers final: 10 residues processed: 73 average time/residue: 0.2202 time to fit residues: 20.9340 Evaluate side-chains 70 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASN Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 254 GLN Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 468 LYS Chi-restraints excluded: chain A residue 652 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 42 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 14 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 chunk 35 optimal weight: 0.0870 chunk 6 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 overall best weight: 1.5964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6075 Z= 0.263 Angle : 0.544 7.466 8227 Z= 0.276 Chirality : 0.043 0.160 915 Planarity : 0.004 0.052 1071 Dihedral : 4.248 23.098 816 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.45 % Allowed : 14.07 % Favored : 83.49 % 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: -0.76 (0.31), residues: 739 helix: 1.01 (0.35), residues: 239 sheet: -0.92 (0.43), residues: 122 loop : -1.37 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 54 HIS 0.003 0.001 HIS A 808 PHE 0.013 0.001 PHE A 799 TYR 0.013 0.001 TYR A 299 ARG 0.003 0.000 ARG A 470 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 59 time to evaluate : 0.796 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 254 GLN cc_start: 0.8884 (OUTLIER) cc_final: 0.6999 (mm110) REVERT: A 444 LYS cc_start: 0.8437 (tttm) cc_final: 0.8077 (tptm) REVERT: A 655 ASP cc_start: 0.8066 (p0) cc_final: 0.7670 (t0) outliers start: 16 outliers final: 11 residues processed: 70 average time/residue: 0.2109 time to fit residues: 19.5220 Evaluate side-chains 70 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASN Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 254 GLN Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 468 LYS Chi-restraints excluded: chain A residue 614 CYS Chi-restraints excluded: chain A residue 652 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 62 optimal weight: 1.9990 chunk 66 optimal weight: 0.4980 chunk 68 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 52 optimal weight: 0.6980 chunk 20 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 42 optimal weight: 0.0000 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6075 Z= 0.142 Angle : 0.509 7.775 8227 Z= 0.256 Chirality : 0.042 0.160 915 Planarity : 0.004 0.052 1071 Dihedral : 3.986 21.517 816 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.83 % Allowed : 14.98 % Favored : 83.18 % 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: -0.44 (0.31), residues: 739 helix: 1.39 (0.36), residues: 232 sheet: -0.90 (0.44), residues: 124 loop : -1.15 (0.32), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 665 HIS 0.001 0.000 HIS A 808 PHE 0.010 0.001 PHE A 799 TYR 0.009 0.001 TYR A 746 ARG 0.003 0.000 ARG A 470 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 0.711 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 254 GLN cc_start: 0.8898 (OUTLIER) cc_final: 0.8646 (mm-40) REVERT: A 315 LEU cc_start: 0.8064 (OUTLIER) cc_final: 0.7761 (tt) REVERT: A 413 GLU cc_start: 0.7947 (tt0) cc_final: 0.7734 (tt0) REVERT: A 444 LYS cc_start: 0.8433 (tttm) cc_final: 0.8123 (tptm) REVERT: A 655 ASP cc_start: 0.7941 (p0) cc_final: 0.7653 (t0) outliers start: 12 outliers final: 9 residues processed: 72 average time/residue: 0.2175 time to fit residues: 20.2769 Evaluate side-chains 71 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 60 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASN Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 254 GLN Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 468 LYS Chi-restraints excluded: chain A residue 652 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 33 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 73 optimal weight: 0.0000 chunk 67 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 45 optimal weight: 0.2980 chunk 35 optimal weight: 0.7980 chunk 46 optimal weight: 8.9990 chunk 62 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 overall best weight: 1.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6075 Z= 0.211 Angle : 0.523 7.780 8227 Z= 0.265 Chirality : 0.042 0.156 915 Planarity : 0.004 0.053 1071 Dihedral : 4.087 22.103 816 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.83 % Allowed : 15.44 % Favored : 82.72 % 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: -0.52 (0.31), residues: 739 helix: 1.24 (0.35), residues: 239 sheet: -0.79 (0.43), residues: 122 loop : -1.24 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 54 HIS 0.002 0.001 HIS A 808 PHE 0.011 0.001 PHE A 799 TYR 0.011 0.001 TYR A 299 ARG 0.002 0.000 ARG A 470 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 0.654 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 254 GLN cc_start: 0.8913 (OUTLIER) cc_final: 0.8654 (mm-40) REVERT: A 291 MET cc_start: 0.8615 (ttm) cc_final: 0.8119 (tpp) REVERT: A 444 LYS cc_start: 0.8431 (tttm) cc_final: 0.8121 (tptm) REVERT: A 655 ASP cc_start: 0.7984 (p0) cc_final: 0.7641 (t0) outliers start: 12 outliers final: 10 residues processed: 69 average time/residue: 0.2237 time to fit residues: 19.9144 Evaluate side-chains 68 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASN Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 254 GLN Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 468 LYS Chi-restraints excluded: chain A residue 652 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 54 optimal weight: 1.9990 chunk 8 optimal weight: 0.3980 chunk 16 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 7 optimal weight: 0.3980 chunk 10 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 42 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.109201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.084687 restraints weight = 8940.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.086765 restraints weight = 6042.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.088337 restraints weight = 4744.293| |-----------------------------------------------------------------------------| r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6075 Z= 0.143 Angle : 0.512 7.990 8227 Z= 0.255 Chirality : 0.042 0.156 915 Planarity : 0.004 0.051 1071 Dihedral : 3.915 20.933 816 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.68 % Allowed : 15.60 % Favored : 82.72 % 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: -0.29 (0.31), residues: 739 helix: 1.51 (0.36), residues: 233 sheet: -0.83 (0.43), residues: 124 loop : -1.05 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP A 776 HIS 0.001 0.000 HIS A 415 PHE 0.010 0.001 PHE A 799 TYR 0.009 0.001 TYR A 746 ARG 0.004 0.000 ARG A 470 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1510.23 seconds wall clock time: 28 minutes 13.41 seconds (1693.41 seconds total)