Starting phenix.real_space_refine on Sat Feb 15 00:14:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8emv_28266/02_2025/8emv_28266.cif Found real_map, /net/cci-nas-00/data/ceres_data/8emv_28266/02_2025/8emv_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_28266/02_2025/8emv_28266.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8emv_28266/02_2025/8emv_28266.map" model { file = "/net/cci-nas-00/data/ceres_data/8emv_28266/02_2025/8emv_28266.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8emv_28266/02_2025/8emv_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 4.14, per 1000 atoms: 0.70 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: 1.61 Conformation dependent library (CDL) restraints added in 919.3 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: 0.77 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: 2.00 Time building geometry restraints manager: 1.78 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: 2.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 18.970 Find NCS groups from input model: 0.070 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:3.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.210 ------------------------------------------------------------------------------- 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 : 0.653 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: 0.2793 time to fit residues: 27.1752 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 : 0.759 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.110815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.086580 restraints weight = 9016.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.088930 restraints weight = 5944.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.090516 restraints weight = 4570.846| |-----------------------------------------------------------------------------| r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 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 : 0.699 Fit side-chains REVERT: A 291 MET cc_start: 0.8542 (ttm) cc_final: 0.8280 (ttm) REVERT: A 444 LYS cc_start: 0.8470 (tttm) cc_final: 0.8072 (tptm) REVERT: A 719 ILE cc_start: 0.9007 (OUTLIER) cc_final: 0.8756 (mm) REVERT: A 772 PHE cc_start: 0.7943 (t80) cc_final: 0.7718 (t80) outliers start: 5 outliers final: 3 residues processed: 77 average time/residue: 0.2229 time to fit residues: 22.4275 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 : 0.838 ------------------------------------------------------------------------------- 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 36 optimal weight: 0.1980 chunk 16 optimal weight: 4.9990 chunk 6 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 chunk 55 optimal weight: 0.0970 chunk 69 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 8 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 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 166 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.108972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.084497 restraints weight = 9121.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.086826 restraints weight = 6055.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.088041 restraints weight = 4672.758| |-----------------------------------------------------------------------------| r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6075 Z= 0.152 Angle : 0.500 6.252 8227 Z= 0.256 Chirality : 0.042 0.165 915 Planarity : 0.004 0.048 1071 Dihedral : 4.232 24.160 816 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.53 % Allowed : 10.86 % 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: -1.69 (0.29), residues: 739 helix: 0.15 (0.34), residues: 238 sheet: -1.07 (0.45), residues: 129 loop : -2.03 (0.29), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 131 HIS 0.002 0.000 HIS A 808 PHE 0.027 0.001 PHE A 197 TYR 0.010 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: 10 poor density : 71 time to evaluate : 0.696 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 291 MET cc_start: 0.8481 (ttm) cc_final: 0.8260 (ttm) REVERT: A 444 LYS cc_start: 0.8463 (tttm) cc_final: 0.7973 (tptm) REVERT: A 655 ASP cc_start: 0.8048 (p0) cc_final: 0.7574 (t0) outliers start: 10 outliers final: 7 residues processed: 77 average time/residue: 0.1943 time to fit residues: 20.2325 Evaluate side-chains 71 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 64 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASN 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 447 LEU Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 652 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 69 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 42 optimal weight: 0.2980 chunk 0 optimal weight: 6.9990 chunk 71 optimal weight: 0.3980 chunk 58 optimal weight: 0.0870 chunk 41 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 48 optimal weight: 0.6980 chunk 54 optimal weight: 0.9980 overall best weight: 0.4558 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.109889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.085658 restraints weight = 9302.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.087995 restraints weight = 6107.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.089591 restraints weight = 4695.361| |-----------------------------------------------------------------------------| r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6075 Z= 0.120 Angle : 0.473 5.991 8227 Z= 0.242 Chirality : 0.041 0.167 915 Planarity : 0.004 0.048 1071 Dihedral : 3.918 23.224 816 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.68 % Allowed : 11.62 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.30), residues: 739 helix: 0.65 (0.35), residues: 238 sheet: -0.79 (0.45), residues: 129 loop : -1.69 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 131 HIS 0.001 0.000 HIS A 808 PHE 0.029 0.001 PHE A 197 TYR 0.008 0.001 TYR A 746 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 84 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 73 time to evaluate : 0.702 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 444 LYS cc_start: 0.8447 (tttm) cc_final: 0.8010 (tptm) REVERT: A 655 ASP cc_start: 0.7991 (p0) cc_final: 0.7635 (t0) outliers start: 11 outliers final: 6 residues processed: 80 average time/residue: 0.1956 time to fit residues: 20.7330 Evaluate side-chains 70 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 64 time to evaluate : 0.670 ------------------------------------------------------------------------------- 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 334 THR Chi-restraints excluded: chain A residue 365 VAL 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 7 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 18 optimal weight: 9.9990 chunk 52 optimal weight: 0.2980 chunk 34 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.110295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.086396 restraints weight = 9141.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.088463 restraints weight = 6356.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.089716 restraints weight = 5046.855| |-----------------------------------------------------------------------------| r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6075 Z= 0.178 Angle : 0.490 6.236 8227 Z= 0.249 Chirality : 0.042 0.167 915 Planarity : 0.004 0.050 1071 Dihedral : 3.977 23.491 816 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.99 % Allowed : 13.46 % Favored : 84.56 % 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: -0.90 (0.31), residues: 739 helix: 0.86 (0.36), residues: 238 sheet: -0.90 (0.44), residues: 129 loop : -1.46 (0.31), residues: 372 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 0.010 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: 13 poor density : 66 time to evaluate : 0.723 Fit side-chains revert: symmetry clash REVERT: A 254 GLN cc_start: 0.8834 (OUTLIER) cc_final: 0.8632 (mm-40) REVERT: A 444 LYS cc_start: 0.8466 (tttm) cc_final: 0.8022 (tptm) REVERT: A 655 ASP cc_start: 0.8012 (p0) cc_final: 0.7676 (t0) outliers start: 13 outliers final: 9 residues processed: 74 average time/residue: 0.1868 time to fit residues: 18.6827 Evaluate side-chains 72 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.693 ------------------------------------------------------------------------------- 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 394 GLU Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 451 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 16 optimal weight: 0.0980 chunk 32 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 25 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 72 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 46 optimal weight: 10.0000 overall best weight: 1.5784 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.105932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.081207 restraints weight = 9150.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.083362 restraints weight = 6215.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.084661 restraints weight = 4869.305| |-----------------------------------------------------------------------------| r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6075 Z= 0.262 Angle : 0.534 6.555 8227 Z= 0.271 Chirality : 0.043 0.162 915 Planarity : 0.004 0.052 1071 Dihedral : 4.205 23.458 816 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 2.60 % Allowed : 14.07 % Favored : 83.33 % 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: -0.91 (0.31), residues: 739 helix: 0.91 (0.36), residues: 237 sheet: -0.83 (0.43), residues: 127 loop : -1.55 (0.31), residues: 375 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 0.029 0.001 PHE A 197 TYR 0.013 0.001 TYR A 299 ARG 0.003 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 81 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 64 time to evaluate : 0.645 Fit side-chains revert: symmetry clash REVERT: A 254 GLN cc_start: 0.8837 (OUTLIER) cc_final: 0.8629 (mm-40) REVERT: A 444 LYS cc_start: 0.8473 (tttm) cc_final: 0.8030 (tptm) REVERT: A 655 ASP cc_start: 0.8086 (p0) cc_final: 0.7684 (t0) REVERT: A 778 GLU cc_start: 0.7066 (pm20) cc_final: 0.6812 (pm20) outliers start: 17 outliers final: 12 residues processed: 75 average time/residue: 0.1903 time to fit residues: 18.9696 Evaluate side-chains 73 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 60 time to evaluate : 0.743 ------------------------------------------------------------------------------- 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 394 GLU 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 25 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 58 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.3173 r_free = 0.3173 target = 0.105607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.080336 restraints weight = 9137.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.082482 restraints weight = 6020.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.084115 restraints weight = 4669.027| |-----------------------------------------------------------------------------| r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6075 Z= 0.165 Angle : 0.498 7.097 8227 Z= 0.253 Chirality : 0.042 0.166 915 Planarity : 0.004 0.050 1071 Dihedral : 4.014 22.344 816 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.29 % Allowed : 14.53 % 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: -0.64 (0.31), residues: 739 helix: 1.18 (0.36), residues: 233 sheet: -0.96 (0.44), residues: 124 loop : -1.27 (0.31), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 54 HIS 0.002 0.000 HIS A 808 PHE 0.032 0.001 PHE A 197 TYR 0.010 0.001 TYR A 746 ARG 0.003 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 79 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 64 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 444 LYS cc_start: 0.8480 (tttm) cc_final: 0.8093 (tptm) REVERT: A 655 ASP cc_start: 0.7975 (p0) cc_final: 0.7651 (t0) REVERT: A 778 GLU cc_start: 0.7086 (pm20) cc_final: 0.6873 (pm20) outliers start: 15 outliers final: 12 residues processed: 73 average time/residue: 0.1953 time to fit residues: 19.1092 Evaluate side-chains 71 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 0.726 ------------------------------------------------------------------------------- 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 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 394 GLU 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 24 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 73 optimal weight: 7.9990 chunk 4 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 43 optimal weight: 0.2980 chunk 54 optimal weight: 0.3980 chunk 47 optimal weight: 0.0060 chunk 60 optimal weight: 0.9990 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.111927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.087546 restraints weight = 9096.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.089800 restraints weight = 6026.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.091211 restraints weight = 4680.658| |-----------------------------------------------------------------------------| r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2190 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= 0.129 Angle : 0.481 7.507 8227 Z= 0.245 Chirality : 0.041 0.160 915 Planarity : 0.004 0.050 1071 Dihedral : 3.833 21.330 816 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.68 % Allowed : 15.14 % 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: 1.33 (0.36), residues: 233 sheet: -0.89 (0.43), residues: 124 loop : -1.11 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 776 HIS 0.001 0.000 HIS A 808 PHE 0.030 0.001 PHE A 197 TYR 0.008 0.001 TYR A 746 ARG 0.002 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 76 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.666 Fit side-chains revert: symmetry clash REVERT: A 444 LYS cc_start: 0.8463 (tttm) cc_final: 0.8102 (tptm) REVERT: A 655 ASP cc_start: 0.7906 (p0) cc_final: 0.7634 (t0) REVERT: A 778 GLU cc_start: 0.7061 (pm20) cc_final: 0.6841 (pm20) outliers start: 11 outliers final: 10 residues processed: 71 average time/residue: 0.2322 time to fit residues: 21.2264 Evaluate side-chains 70 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 60 time to evaluate : 0.693 ------------------------------------------------------------------------------- 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 394 GLU Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 468 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 18 optimal weight: 0.1980 chunk 16 optimal weight: 5.9990 chunk 36 optimal weight: 0.1980 chunk 55 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 46 optimal weight: 10.0000 chunk 24 optimal weight: 0.7980 chunk 23 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 29 optimal weight: 0.4980 chunk 49 optimal weight: 7.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.3239 r_free = 0.3239 target = 0.110672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.086232 restraints weight = 9136.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.088506 restraints weight = 6101.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.090020 restraints weight = 4736.596| |-----------------------------------------------------------------------------| r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6075 Z= 0.175 Angle : 0.498 7.600 8227 Z= 0.252 Chirality : 0.042 0.153 915 Planarity : 0.004 0.051 1071 Dihedral : 3.904 21.625 816 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.99 % Allowed : 15.14 % Favored : 82.87 % 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: -0.40 (0.31), residues: 739 helix: 1.36 (0.35), residues: 233 sheet: -0.84 (0.43), residues: 124 loop : -1.10 (0.31), residues: 382 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 0.033 0.001 PHE A 197 TYR 0.009 0.001 TYR A 746 ARG 0.004 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 73 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 60 time to evaluate : 0.677 Fit side-chains revert: symmetry clash REVERT: A 413 GLU cc_start: 0.7937 (tt0) cc_final: 0.7675 (tt0) REVERT: A 444 LYS cc_start: 0.8464 (tttm) cc_final: 0.8107 (tptm) REVERT: A 655 ASP cc_start: 0.7920 (p0) cc_final: 0.7635 (t0) outliers start: 13 outliers final: 13 residues processed: 68 average time/residue: 0.2066 time to fit residues: 18.5343 Evaluate side-chains 71 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 58 time to evaluate : 0.668 ------------------------------------------------------------------------------- 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 187 GLU Chi-restraints excluded: chain A residue 286 LEU 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 394 GLU 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 62 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 42 optimal weight: 0.0870 chunk 26 optimal weight: 4.9990 chunk 38 optimal weight: 0.9980 chunk 53 optimal weight: 0.4980 chunk 20 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 64 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 467 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.111322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.086980 restraints weight = 9150.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.089237 restraints weight = 6041.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.090676 restraints weight = 4681.104| |-----------------------------------------------------------------------------| r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6075 Z= 0.147 Angle : 0.489 7.943 8227 Z= 0.247 Chirality : 0.041 0.153 915 Planarity : 0.004 0.050 1071 Dihedral : 3.807 20.811 816 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.99 % Allowed : 14.98 % Favored : 83.03 % 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: -0.27 (0.31), residues: 739 helix: 1.49 (0.35), residues: 233 sheet: -0.80 (0.43), residues: 124 loop : -1.02 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 54 HIS 0.001 0.000 HIS A 808 PHE 0.032 0.001 PHE A 197 TYR 0.009 0.001 TYR A 746 ARG 0.003 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 73 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 60 time to evaluate : 0.685 Fit side-chains revert: symmetry clash REVERT: A 413 GLU cc_start: 0.7914 (tt0) cc_final: 0.7678 (tt0) REVERT: A 444 LYS cc_start: 0.8488 (tttm) cc_final: 0.8140 (tptm) REVERT: A 655 ASP cc_start: 0.7925 (p0) cc_final: 0.7650 (t0) outliers start: 13 outliers final: 13 residues processed: 68 average time/residue: 0.2258 time to fit residues: 19.7411 Evaluate side-chains 69 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 56 time to evaluate : 0.671 ------------------------------------------------------------------------------- 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 187 GLU Chi-restraints excluded: chain A residue 286 LEU 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 394 GLU 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 68 optimal weight: 0.8980 chunk 43 optimal weight: 0.6980 chunk 34 optimal weight: 0.5980 chunk 19 optimal weight: 0.0980 chunk 47 optimal weight: 1.9990 chunk 40 optimal weight: 0.0030 chunk 73 optimal weight: 7.9990 chunk 55 optimal weight: 2.9990 chunk 27 optimal weight: 6.9990 chunk 64 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 overall best weight: 0.4390 ------------------------------------------------------------------------------- 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 = 0.3254 r_free = 0.3254 target = 0.111382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.084882 restraints weight = 9439.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.087852 restraints weight = 5446.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.089834 restraints weight = 3887.700| |-----------------------------------------------------------------------------| r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6075 Z= 0.124 Angle : 0.481 7.983 8227 Z= 0.242 Chirality : 0.041 0.147 915 Planarity : 0.004 0.049 1071 Dihedral : 3.667 20.265 816 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.53 % Allowed : 15.60 % Favored : 82.87 % 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 (0.31), residues: 739 helix: 1.59 (0.35), residues: 233 sheet: -0.78 (0.43), residues: 124 loop : -0.92 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 776 HIS 0.001 0.000 HIS A 808 PHE 0.027 0.001 PHE A 197 TYR 0.008 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: 1932.73 seconds wall clock time: 35 minutes 23.65 seconds (2123.65 seconds total)