Starting phenix.real_space_refine on Fri Feb 14 16:53:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7q6z_13860/02_2025/7q6z_13860_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7q6z_13860/02_2025/7q6z_13860.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7q6z_13860/02_2025/7q6z_13860.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7q6z_13860/02_2025/7q6z_13860.map" model { file = "/net/cci-nas-00/data/ceres_data/7q6z_13860/02_2025/7q6z_13860_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7q6z_13860/02_2025/7q6z_13860_trim.cif" } resolution = 3.59 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.068 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Fe 1 7.16 5 S 36 5.16 5 C 3291 2.51 5 N 802 2.21 5 O 840 1.98 5 H 4784 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 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: 9754 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 7919 Classifications: {'peptide': 485} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 15, 'TRANS': 469} Chain breaks: 1 Chain: "B" Number of atoms: 1722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 1722 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 4, 'TRANS': 107} Chain breaks: 1 Chain: "A" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 113 Unusual residues: {'9V3': 1, 'CLR': 1, 'HEM': 1, 'PLM': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5233 SG CYS A 324 40.122 50.446 63.748 1.00 36.18 S Time building chain proxies: 5.24, per 1000 atoms: 0.54 Number of scatterers: 9754 At special positions: 0 Unit cell: (83.1, 84.208, 98.612, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 1 26.01 S 36 16.00 O 840 8.00 N 802 7.00 C 3291 6.00 H 4784 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 816 " - pdb=" SG CYS B 889 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.93 Conformation dependent library (CDL) restraints added in 674.5 milliseconds 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1110 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 4 sheets defined 72.5% alpha, 11.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'A' and resid 3 through 32 Processing helix chain 'A' and resid 32 through 41 Processing helix chain 'A' and resid 58 through 70 Processing helix chain 'A' and resid 70 through 89 Processing helix chain 'A' and resid 92 through 110 Processing helix chain 'A' and resid 110 through 130 removed outlier: 3.502A pdb=" N VAL A 114 " --> pdb=" O GLY A 110 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N MET A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE A 130 " --> pdb=" O CYS A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 149 Processing helix chain 'A' and resid 149 through 160 removed outlier: 3.714A pdb=" N TRP A 159 " --> pdb=" O VAL A 155 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N TYR A 160 " --> pdb=" O LYS A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 188 removed outlier: 3.709A pdb=" N TYR A 166 " --> pdb=" O THR A 162 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU A 178 " --> pdb=" O THR A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 209 Processing helix chain 'A' and resid 210 through 214 Processing helix chain 'A' and resid 221 through 230 Processing helix chain 'A' and resid 236 through 265 Processing helix chain 'A' and resid 266 through 273 Processing helix chain 'A' and resid 273 through 278 Processing helix chain 'A' and resid 281 through 314 removed outlier: 3.836A pdb=" N PHE A 304 " --> pdb=" O TYR A 300 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL A 306 " --> pdb=" O VAL A 302 " (cutoff:3.500A) Proline residue: A 307 - end of helix Processing helix chain 'A' and resid 330 through 337 Processing helix chain 'A' and resid 339 through 349 Processing helix chain 'A' and resid 350 through 355 removed outlier: 4.030A pdb=" N VAL A 354 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 380 removed outlier: 3.701A pdb=" N GLY A 380 " --> pdb=" O SER A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 408 Processing helix chain 'A' and resid 408 through 419 Processing helix chain 'A' and resid 420 through 449 removed outlier: 3.729A pdb=" N ARG A 426 " --> pdb=" O GLN A 422 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N CYS A 434 " --> pdb=" O ALA A 430 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU A 441 " --> pdb=" O SER A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 461 Processing helix chain 'A' and resid 467 through 488 Processing helix chain 'B' and resid 855 through 858 Processing helix chain 'B' and resid 880 through 884 removed outlier: 3.758A pdb=" N THR B 884 " --> pdb=" O PRO B 881 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AA2, first strand: chain 'B' and resid 26 through 30 removed outlier: 3.855A pdb=" N GLN B 26 " --> pdb=" O SER B 819 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N VAL B 28 " --> pdb=" O THR B 817 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER B 30 " --> pdb=" O SER B 815 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N SER B 815 " --> pdb=" O SER B 30 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU B 812 " --> pdb=" O MET B 876 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 851 through 853 removed outlier: 6.802A pdb=" N TRP B 830 " --> pdb=" O VAL B 842 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N ILE B 844 " --> pdb=" O VAL B 828 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N VAL B 828 " --> pdb=" O ILE B 844 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLY B 892 " --> pdb=" O ASP B 827 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA B 891 " --> pdb=" O TYR B 903 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 851 through 853 removed outlier: 6.802A pdb=" N TRP B 830 " --> pdb=" O VAL B 842 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N ILE B 844 " --> pdb=" O VAL B 828 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N VAL B 828 " --> pdb=" O ILE B 844 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLY B 892 " --> pdb=" O ASP B 827 " (cutoff:3.500A) 354 hydrogen bonds defined for protein. 1023 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: 3.51 Time building geometry restraints manager: 3.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.09: 4771 1.09 - 1.34: 1451 1.34 - 1.58: 3635 1.58 - 1.83: 55 1.83 - 2.08: 5 Bond restraints: 9917 Sorted by residual: bond pdb=" C8 9V3 A 603 " pdb=" S 9V3 A 603 " ideal model delta sigma weight residual 1.720 1.967 -0.247 2.00e-02 2.50e+03 1.52e+02 bond pdb=" C8 9V3 A 603 " pdb=" C9 9V3 A 603 " ideal model delta sigma weight residual 1.359 1.549 -0.190 2.00e-02 2.50e+03 8.99e+01 bond pdb=" C10 9V3 A 603 " pdb=" C11 9V3 A 603 " ideal model delta sigma weight residual 1.358 1.229 0.129 2.00e-02 2.50e+03 4.13e+01 bond pdb=" C5 9V3 A 603 " pdb=" N1 9V3 A 603 " ideal model delta sigma weight residual 1.358 1.475 -0.117 2.00e-02 2.50e+03 3.44e+01 bond pdb=" C7 9V3 A 603 " pdb=" C8 9V3 A 603 " ideal model delta sigma weight residual 1.489 1.394 0.095 2.00e-02 2.50e+03 2.25e+01 ... (remaining 9912 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.15: 17768 7.15 - 14.31: 7 14.31 - 21.46: 0 21.46 - 28.62: 0 28.62 - 35.77: 6 Bond angle restraints: 17781 Sorted by residual: angle pdb=" N MET A 1 " pdb=" CA MET A 1 " pdb=" HA MET A 1 " ideal model delta sigma weight residual 110.00 74.23 35.77 3.00e+00 1.11e-01 1.42e+02 angle pdb=" C MET A 1 " pdb=" CA MET A 1 " pdb=" HA MET A 1 " ideal model delta sigma weight residual 110.00 74.41 35.59 3.00e+00 1.11e-01 1.41e+02 angle pdb=" CB THR A 332 " pdb=" CA THR A 332 " pdb=" HA THR A 332 " ideal model delta sigma weight residual 109.00 74.03 34.97 3.00e+00 1.11e-01 1.36e+02 angle pdb=" N THR A 332 " pdb=" CA THR A 332 " pdb=" HA THR A 332 " ideal model delta sigma weight residual 110.00 75.32 34.68 3.00e+00 1.11e-01 1.34e+02 angle pdb=" C THR A 332 " pdb=" CA THR A 332 " pdb=" HA THR A 332 " ideal model delta sigma weight residual 109.00 74.95 34.05 3.00e+00 1.11e-01 1.29e+02 ... (remaining 17776 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 4288 17.96 - 35.92: 319 35.92 - 53.88: 105 53.88 - 71.84: 20 71.84 - 89.80: 6 Dihedral angle restraints: 4738 sinusoidal: 2490 harmonic: 2248 Sorted by residual: dihedral pdb=" C2B HEM A 602 " pdb=" C3B HEM A 602 " pdb=" CAB HEM A 602 " pdb=" CBB HEM A 602 " ideal model delta sinusoidal sigma weight residual 0.00 46.64 -46.64 2 1.00e+01 1.00e-02 2.54e+01 dihedral pdb=" CA MET A 334 " pdb=" C MET A 334 " pdb=" N TRP A 335 " pdb=" CA TRP A 335 " ideal model delta harmonic sigma weight residual 180.00 160.98 19.02 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA TYR A 300 " pdb=" C TYR A 300 " pdb=" N LEU A 301 " pdb=" CA LEU A 301 " ideal model delta harmonic sigma weight residual 180.00 161.59 18.41 0 5.00e+00 4.00e-02 1.36e+01 ... (remaining 4735 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 727 0.093 - 0.186: 21 0.186 - 0.279: 0 0.279 - 0.372: 2 0.372 - 0.465: 1 Chirality restraints: 751 Sorted by residual: chirality pdb=" CA MET A 1 " pdb=" N MET A 1 " pdb=" C MET A 1 " pdb=" CB MET A 1 " both_signs ideal model delta sigma weight residual False 2.57 2.10 0.46 2.00e-01 2.50e+01 5.40e+00 chirality pdb=" CA THR A 332 " pdb=" N THR A 332 " pdb=" C THR A 332 " pdb=" CB THR A 332 " both_signs ideal model delta sigma weight residual False 2.53 2.17 0.36 2.00e-01 2.50e+01 3.24e+00 chirality pdb=" C12 9V3 A 603 " pdb=" C13 9V3 A 603 " pdb=" C9 9V3 A 603 " pdb=" N1 9V3 A 603 " both_signs ideal model delta sigma weight residual False -2.36 -2.68 0.32 2.00e-01 2.50e+01 2.59e+00 ... (remaining 748 not shown) Planarity restraints: 1413 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 113 " -0.009 2.00e-02 2.50e+03 1.78e-02 3.15e+00 pdb=" C GLY A 113 " 0.031 2.00e-02 2.50e+03 pdb=" O GLY A 113 " -0.011 2.00e-02 2.50e+03 pdb=" N VAL A 114 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 306 " -0.022 5.00e-02 4.00e+02 3.31e-02 1.75e+00 pdb=" N PRO A 307 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO A 307 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 307 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 17 " -0.012 2.00e-02 2.50e+03 6.51e-03 1.27e+00 pdb=" CG PHE A 17 " 0.011 2.00e-02 2.50e+03 pdb=" CD1 PHE A 17 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE A 17 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 PHE A 17 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 17 " -0.010 2.00e-02 2.50e+03 pdb=" CZ PHE A 17 " 0.001 2.00e-02 2.50e+03 pdb=" HD1 PHE A 17 " -0.000 2.00e-02 2.50e+03 pdb=" HD2 PHE A 17 " 0.001 2.00e-02 2.50e+03 pdb=" HE1 PHE A 17 " -0.000 2.00e-02 2.50e+03 pdb=" HE2 PHE A 17 " -0.002 2.00e-02 2.50e+03 pdb=" HZ PHE A 17 " -0.001 2.00e-02 2.50e+03 ... (remaining 1410 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.18: 396 2.18 - 2.78: 18718 2.78 - 3.39: 27645 3.39 - 3.99: 34634 3.99 - 4.60: 54177 Nonbonded interactions: 135570 Sorted by model distance: nonbonded pdb=" O TYR A 349 " pdb=" H TYR A 351 " model vdw 1.569 2.450 nonbonded pdb=" O SER A 14 " pdb=" HD1 HIS A 18 " model vdw 1.662 2.450 nonbonded pdb=" OE1 GLU B 882 " pdb=" H GLU B 882 " model vdw 1.663 2.450 nonbonded pdb=" HA MET A 1 " pdb=" HB2 MET A 1 " model vdw 1.688 1.952 nonbonded pdb=" O THR B 846 " pdb="HH11 ARG B 865 " model vdw 1.695 2.450 ... (remaining 135565 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.160 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 24.340 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6986 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 : 0.008 0.247 5133 Z= 0.483 Angle : 0.688 13.229 7004 Z= 0.345 Chirality : 0.043 0.465 751 Planarity : 0.003 0.033 839 Dihedral : 14.584 89.798 1837 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.36), residues: 589 helix: 2.24 (0.27), residues: 381 sheet: -1.00 (0.83), residues: 52 loop : -1.10 (0.49), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 388 HIS 0.006 0.001 HIS A 18 PHE 0.012 0.002 PHE A 17 TYR 0.014 0.002 TYR A 166 ARG 0.003 0.000 ARG B 847 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 LEU cc_start: 0.7902 (tp) cc_final: 0.7305 (mt) REVERT: A 334 MET cc_start: 0.7452 (tmm) cc_final: 0.7142 (tmm) REVERT: A 370 MET cc_start: 0.6733 (tpp) cc_final: 0.5853 (tpt) outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.3486 time to fit residues: 41.9763 Evaluate side-chains 82 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 49 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 17 optimal weight: 0.1980 chunk 28 optimal weight: 0.0970 chunk 34 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.167339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.131402 restraints weight = 15215.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.137730 restraints weight = 8580.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.142050 restraints weight = 5949.228| |-----------------------------------------------------------------------------| r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6948 moved from start: 0.0936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 5133 Z= 0.282 Angle : 0.567 10.051 7004 Z= 0.297 Chirality : 0.041 0.451 751 Planarity : 0.004 0.039 839 Dihedral : 7.632 79.238 766 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 0.78 % Allowed : 6.20 % Favored : 93.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.36), residues: 589 helix: 2.30 (0.26), residues: 391 sheet: -1.03 (0.80), residues: 52 loop : -1.22 (0.49), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 63 HIS 0.004 0.001 HIS A 343 PHE 0.020 0.002 PHE A 17 TYR 0.017 0.002 TYR A 180 ARG 0.003 0.000 ARG A 176 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 84 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 LEU cc_start: 0.7849 (tp) cc_final: 0.7271 (mt) REVERT: A 179 TYR cc_start: 0.8554 (m-80) cc_final: 0.8260 (m-10) REVERT: A 334 MET cc_start: 0.7642 (tmm) cc_final: 0.7413 (tmm) REVERT: A 370 MET cc_start: 0.6725 (tpp) cc_final: 0.5849 (tpt) REVERT: B 865 ARG cc_start: 0.7980 (ptm160) cc_final: 0.7645 (ptm160) outliers start: 4 outliers final: 4 residues processed: 86 average time/residue: 0.3548 time to fit residues: 39.4781 Evaluate side-chains 84 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 80 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 17 PHE Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain B residue 840 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 13 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 chunk 8 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.165363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.130506 restraints weight = 15781.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.136343 restraints weight = 9124.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.140322 restraints weight = 6457.084| |-----------------------------------------------------------------------------| r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7015 moved from start: 0.1228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 5133 Z= 0.328 Angle : 0.580 10.181 7004 Z= 0.300 Chirality : 0.041 0.448 751 Planarity : 0.004 0.039 839 Dihedral : 7.275 71.646 766 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.16 % Allowed : 8.33 % Favored : 90.50 % 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: 1.59 (0.36), residues: 589 helix: 2.27 (0.26), residues: 391 sheet: -1.24 (0.74), residues: 52 loop : -1.50 (0.48), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 63 HIS 0.005 0.001 HIS A 343 PHE 0.016 0.002 PHE A 17 TYR 0.015 0.002 TYR A 166 ARG 0.003 0.000 ARG B 847 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 84 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 MET cc_start: 0.7739 (mmm) cc_final: 0.7362 (mtp) REVERT: A 138 LEU cc_start: 0.7887 (tp) cc_final: 0.7312 (mt) REVERT: A 229 MET cc_start: 0.8211 (mtp) cc_final: 0.7963 (mtp) REVERT: A 370 MET cc_start: 0.6749 (tpp) cc_final: 0.5911 (tpt) outliers start: 6 outliers final: 5 residues processed: 87 average time/residue: 0.3243 time to fit residues: 37.2896 Evaluate side-chains 87 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 82 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 17 PHE Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain B residue 840 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 38 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 50 optimal weight: 0.6980 chunk 35 optimal weight: 0.5980 chunk 30 optimal weight: 0.8980 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 150 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.165309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.130802 restraints weight = 15725.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.136692 restraints weight = 9050.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.140516 restraints weight = 6364.965| |-----------------------------------------------------------------------------| r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7011 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 5133 Z= 0.303 Angle : 0.558 10.343 7004 Z= 0.289 Chirality : 0.041 0.456 751 Planarity : 0.004 0.038 839 Dihedral : 7.197 70.113 766 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.16 % Allowed : 10.27 % Favored : 88.57 % 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: 1.63 (0.36), residues: 589 helix: 2.28 (0.26), residues: 392 sheet: -1.41 (0.70), residues: 52 loop : -1.39 (0.49), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 63 HIS 0.004 0.001 HIS A 343 PHE 0.017 0.002 PHE A 17 TYR 0.015 0.002 TYR A 166 ARG 0.002 0.000 ARG B 847 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 84 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 MET cc_start: 0.7738 (mmm) cc_final: 0.7311 (mtp) REVERT: A 138 LEU cc_start: 0.7892 (tp) cc_final: 0.7308 (mt) REVERT: A 172 THR cc_start: 0.7970 (OUTLIER) cc_final: 0.7720 (m) REVERT: A 370 MET cc_start: 0.6722 (tpp) cc_final: 0.5898 (tpt) outliers start: 6 outliers final: 5 residues processed: 88 average time/residue: 0.3312 time to fit residues: 38.5630 Evaluate side-chains 89 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 83 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 17 PHE Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain B residue 840 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 44 optimal weight: 0.9980 chunk 41 optimal weight: 0.7980 chunk 57 optimal weight: 0.0470 chunk 56 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 46 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 chunk 58 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 GLN A 292 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.165672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.131013 restraints weight = 15631.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.136964 restraints weight = 9001.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.140944 restraints weight = 6345.023| |-----------------------------------------------------------------------------| r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6997 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 5133 Z= 0.274 Angle : 0.546 10.246 7004 Z= 0.283 Chirality : 0.040 0.463 751 Planarity : 0.004 0.039 839 Dihedral : 7.096 67.413 766 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.36 % Allowed : 10.66 % Favored : 87.98 % 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: 1.77 (0.36), residues: 589 helix: 2.31 (0.26), residues: 398 sheet: -1.54 (0.68), residues: 52 loop : -1.14 (0.51), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 63 HIS 0.004 0.001 HIS A 343 PHE 0.018 0.002 PHE A 125 TYR 0.014 0.002 TYR A 166 ARG 0.002 0.000 ARG B 839 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 85 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 MET cc_start: 0.7727 (mmm) cc_final: 0.7272 (mtp) REVERT: A 138 LEU cc_start: 0.7865 (tp) cc_final: 0.7285 (mt) REVERT: A 172 THR cc_start: 0.7937 (OUTLIER) cc_final: 0.7688 (m) REVERT: A 292 GLN cc_start: 0.7645 (OUTLIER) cc_final: 0.6948 (mm-40) REVERT: A 370 MET cc_start: 0.6687 (tpp) cc_final: 0.5857 (tpt) outliers start: 7 outliers final: 5 residues processed: 90 average time/residue: 0.3266 time to fit residues: 39.0443 Evaluate side-chains 90 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 83 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 17 PHE Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 292 GLN Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain B residue 840 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 15 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 43 optimal weight: 0.6980 chunk 44 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 14 optimal weight: 0.4980 chunk 42 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 GLN B 867 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.165826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.131731 restraints weight = 15790.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.137656 restraints weight = 9081.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.141816 restraints weight = 6349.610| |-----------------------------------------------------------------------------| r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6989 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 5133 Z= 0.268 Angle : 0.557 10.555 7004 Z= 0.288 Chirality : 0.040 0.462 751 Planarity : 0.004 0.039 839 Dihedral : 7.067 65.996 766 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 0.97 % Allowed : 11.82 % Favored : 87.21 % 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: 1.83 (0.36), residues: 589 helix: 2.36 (0.26), residues: 397 sheet: -1.56 (0.67), residues: 52 loop : -1.09 (0.51), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 63 HIS 0.004 0.001 HIS A 343 PHE 0.016 0.001 PHE A 17 TYR 0.014 0.002 TYR A 166 ARG 0.002 0.000 ARG B 865 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 81 time to evaluate : 0.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 MET cc_start: 0.7743 (mmm) cc_final: 0.7273 (mtp) REVERT: A 138 LEU cc_start: 0.7868 (tp) cc_final: 0.7293 (mt) REVERT: A 172 THR cc_start: 0.7926 (OUTLIER) cc_final: 0.7675 (m) REVERT: A 370 MET cc_start: 0.6672 (tpp) cc_final: 0.5859 (tpt) REVERT: B 865 ARG cc_start: 0.7899 (ptm160) cc_final: 0.7668 (ptm160) outliers start: 5 outliers final: 4 residues processed: 84 average time/residue: 0.3337 time to fit residues: 37.2589 Evaluate side-chains 83 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 78 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 17 PHE Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 376 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 11 optimal weight: 0.6980 chunk 56 optimal weight: 0.7980 chunk 21 optimal weight: 0.5980 chunk 52 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 chunk 37 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 9 optimal weight: 0.3980 chunk 6 optimal weight: 0.4980 chunk 24 optimal weight: 0.9980 chunk 34 optimal weight: 0.3980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 GLN B 867 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.167548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.133223 restraints weight = 15676.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.139292 restraints weight = 9021.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.143465 restraints weight = 6308.529| |-----------------------------------------------------------------------------| r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6977 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5133 Z= 0.228 Angle : 0.542 10.161 7004 Z= 0.277 Chirality : 0.039 0.447 751 Planarity : 0.004 0.038 839 Dihedral : 6.945 63.809 766 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.55 % Allowed : 11.43 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.36), residues: 589 helix: 2.49 (0.27), residues: 392 sheet: -1.47 (0.68), residues: 52 loop : -1.24 (0.50), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 63 HIS 0.003 0.001 HIS A 18 PHE 0.016 0.001 PHE A 17 TYR 0.015 0.001 TYR A 180 ARG 0.001 0.000 ARG B 860 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 83 time to evaluate : 0.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 MET cc_start: 0.7749 (mmm) cc_final: 0.7258 (mtp) REVERT: A 138 LEU cc_start: 0.7916 (tp) cc_final: 0.7340 (mt) REVERT: A 172 THR cc_start: 0.7894 (OUTLIER) cc_final: 0.7654 (m) REVERT: A 370 MET cc_start: 0.6643 (tpp) cc_final: 0.5867 (tpt) REVERT: B 875 GLN cc_start: 0.6807 (tp-100) cc_final: 0.6304 (tt0) outliers start: 8 outliers final: 6 residues processed: 88 average time/residue: 0.3446 time to fit residues: 40.0464 Evaluate side-chains 86 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 79 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 17 PHE Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 481 HIS Chi-restraints excluded: chain B residue 840 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 42 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 51 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 55 optimal weight: 0.6980 chunk 21 optimal weight: 0.3980 chunk 49 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.166925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.132655 restraints weight = 15712.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.138543 restraints weight = 9064.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.142611 restraints weight = 6385.715| |-----------------------------------------------------------------------------| r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6988 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 5133 Z= 0.274 Angle : 0.558 10.436 7004 Z= 0.286 Chirality : 0.040 0.463 751 Planarity : 0.004 0.038 839 Dihedral : 7.001 62.332 766 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.55 % Allowed : 11.63 % Favored : 86.82 % 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: 1.84 (0.36), residues: 589 helix: 2.46 (0.26), residues: 392 sheet: -1.50 (0.68), residues: 52 loop : -1.28 (0.50), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 63 HIS 0.004 0.001 HIS A 343 PHE 0.016 0.001 PHE A 17 TYR 0.017 0.002 TYR A 351 ARG 0.002 0.000 ARG B 847 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 84 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 HIS cc_start: 0.7962 (OUTLIER) cc_final: 0.6390 (t-90) REVERT: A 102 MET cc_start: 0.7745 (mmm) cc_final: 0.7222 (mtp) REVERT: A 138 LEU cc_start: 0.7925 (tp) cc_final: 0.7347 (mt) REVERT: A 370 MET cc_start: 0.6657 (tpp) cc_final: 0.5870 (tpt) REVERT: B 865 ARG cc_start: 0.7639 (ptm160) cc_final: 0.7428 (ptm160) REVERT: B 875 GLN cc_start: 0.6927 (tp-100) cc_final: 0.6487 (tt0) outliers start: 8 outliers final: 7 residues processed: 89 average time/residue: 0.3361 time to fit residues: 39.4948 Evaluate side-chains 89 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 81 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 17 PHE Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 481 HIS Chi-restraints excluded: chain B residue 840 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 23 optimal weight: 4.9990 chunk 48 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 28 optimal weight: 0.5980 chunk 45 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 GLN A 343 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.164784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.130598 restraints weight = 15766.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.136348 restraints weight = 9164.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.139938 restraints weight = 6505.311| |-----------------------------------------------------------------------------| r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7039 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 5133 Z= 0.327 Angle : 0.591 10.405 7004 Z= 0.303 Chirality : 0.041 0.466 751 Planarity : 0.004 0.038 839 Dihedral : 7.198 61.623 766 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 1.55 % Allowed : 12.40 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.36), residues: 589 helix: 2.36 (0.26), residues: 392 sheet: -1.54 (0.68), residues: 52 loop : -1.41 (0.49), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 63 HIS 0.004 0.001 HIS A 343 PHE 0.016 0.002 PHE A 17 TYR 0.013 0.002 TYR A 166 ARG 0.002 0.000 ARG B 847 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 83 time to evaluate : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 MET cc_start: 0.7762 (mmm) cc_final: 0.7256 (mtp) REVERT: A 138 LEU cc_start: 0.7942 (tp) cc_final: 0.7378 (mt) REVERT: A 172 THR cc_start: 0.7998 (OUTLIER) cc_final: 0.7745 (m) REVERT: A 334 MET cc_start: 0.7834 (tmm) cc_final: 0.7521 (ttm) REVERT: A 370 MET cc_start: 0.6694 (tpp) cc_final: 0.5897 (tpt) REVERT: B 865 ARG cc_start: 0.7711 (ptm160) cc_final: 0.7502 (ptm160) REVERT: B 875 GLN cc_start: 0.6942 (tp-100) cc_final: 0.6460 (tt0) outliers start: 8 outliers final: 6 residues processed: 87 average time/residue: 0.3274 time to fit residues: 37.4621 Evaluate side-chains 89 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 82 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 17 PHE Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 481 HIS Chi-restraints excluded: chain B residue 840 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 43 optimal weight: 0.0770 chunk 54 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 5 optimal weight: 0.3980 chunk 21 optimal weight: 0.3980 chunk 40 optimal weight: 2.9990 chunk 39 optimal weight: 0.3980 chunk 13 optimal weight: 0.9980 overall best weight: 0.3938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.167105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.133524 restraints weight = 15587.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.139527 restraints weight = 8902.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.143509 restraints weight = 6207.071| |-----------------------------------------------------------------------------| r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6957 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5133 Z= 0.192 Angle : 0.527 10.522 7004 Z= 0.267 Chirality : 0.039 0.465 751 Planarity : 0.004 0.038 839 Dihedral : 6.890 59.044 766 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.90 % Favored : 95.93 % Rotamer: Outliers : 1.36 % Allowed : 12.40 % 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: 1.92 (0.36), residues: 589 helix: 2.53 (0.27), residues: 392 sheet: -1.43 (0.68), residues: 52 loop : -1.29 (0.50), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 63 HIS 0.003 0.001 HIS A 343 PHE 0.016 0.001 PHE A 17 TYR 0.020 0.001 TYR B 888 ARG 0.002 0.000 ARG B 860 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 82 time to evaluate : 0.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 MET cc_start: 0.7656 (mmm) cc_final: 0.7165 (mtp) REVERT: A 138 LEU cc_start: 0.7926 (tp) cc_final: 0.7334 (mt) REVERT: A 172 THR cc_start: 0.7838 (OUTLIER) cc_final: 0.7597 (m) REVERT: A 334 MET cc_start: 0.7699 (tmm) cc_final: 0.7485 (tmm) REVERT: A 370 MET cc_start: 0.6614 (tpp) cc_final: 0.5846 (tpt) REVERT: A 438 MET cc_start: 0.7389 (tpp) cc_final: 0.6633 (tpp) REVERT: B 875 GLN cc_start: 0.6875 (tp-100) cc_final: 0.6466 (tt0) outliers start: 7 outliers final: 6 residues processed: 86 average time/residue: 0.3440 time to fit residues: 38.7962 Evaluate side-chains 84 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 77 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 17 PHE Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 481 HIS Chi-restraints excluded: chain B residue 840 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 21 optimal weight: 0.0970 chunk 26 optimal weight: 0.2980 chunk 3 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 chunk 9 optimal weight: 0.0770 chunk 25 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 overall best weight: 0.3736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.168128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.134715 restraints weight = 15382.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.140735 restraints weight = 8787.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.144859 restraints weight = 6127.534| |-----------------------------------------------------------------------------| r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6955 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5133 Z= 0.190 Angle : 0.523 10.476 7004 Z= 0.265 Chirality : 0.039 0.465 751 Planarity : 0.004 0.038 839 Dihedral : 6.752 56.474 766 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.41 % Favored : 95.42 % Rotamer: Outliers : 1.55 % Allowed : 12.02 % Favored : 86.43 % 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: 2.04 (0.36), residues: 589 helix: 2.70 (0.27), residues: 385 sheet: -1.44 (0.68), residues: 52 loop : -1.27 (0.50), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 63 HIS 0.010 0.001 HIS A 32 PHE 0.016 0.001 PHE A 17 TYR 0.016 0.001 TYR A 180 ARG 0.001 0.000 ARG B 865 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3709.24 seconds wall clock time: 66 minutes 11.50 seconds (3971.50 seconds total)