Starting phenix.real_space_refine on Mon Jul 28 14:37:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7q6z_13860/07_2025/7q6z_13860_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7q6z_13860/07_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_13860/07_2025/7q6z_13860.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7q6z_13860/07_2025/7q6z_13860.map" model { file = "/net/cci-nas-00/data/ceres_data/7q6z_13860/07_2025/7q6z_13860_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7q6z_13860/07_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-5711/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: 6.22, per 1000 atoms: 0.64 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: 3.34 Conformation dependent library (CDL) restraints added in 735.9 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: 0.89 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: 3.83 Time building geometry restraints manager: 3.81 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: 1.980 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: 0.180 Extract box with map and model: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 28.040 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:3.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.530 ------------------------------------------------------------------------------- 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 5135 Z= 0.374 Angle : 0.688 13.229 7006 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 Details of bonding type rmsd hydrogen bonds : bond 0.15397 ( 342) hydrogen bonds : angle 7.51231 ( 1023) SS BOND : bond 0.00180 ( 1) SS BOND : angle 0.51118 ( 2) covalent geometry : bond 0.00781 ( 5133) covalent geometry : angle 0.68781 ( 7004) Misc. bond : bond 0.00665 ( 1) *********************** 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 : 0.728 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: 0.3680 time to fit residues: 44.1079 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 : 0.798 ------------------------------------------------------------------------------- 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 = 43)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.131380 restraints weight = 15215.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.137697 restraints weight = 8594.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.142015 restraints weight = 5964.867| |-----------------------------------------------------------------------------| r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6949 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 5135 Z= 0.194 Angle : 0.567 10.051 7006 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 Details of bonding type rmsd hydrogen bonds : bond 0.05015 ( 342) hydrogen bonds : angle 5.63069 ( 1023) SS BOND : bond 0.00124 ( 1) SS BOND : angle 0.85641 ( 2) covalent geometry : bond 0.00449 ( 5133) covalent geometry : angle 0.56707 ( 7004) Misc. bond : bond 0.01269 ( 1) *********************** 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 : 0.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 LEU cc_start: 0.7848 (tp) cc_final: 0.7270 (mt) REVERT: A 179 TYR cc_start: 0.8552 (m-80) cc_final: 0.8258 (m-10) REVERT: A 334 MET cc_start: 0.7642 (tmm) cc_final: 0.7414 (tmm) REVERT: A 370 MET cc_start: 0.6725 (tpp) cc_final: 0.5850 (tpt) REVERT: B 865 ARG cc_start: 0.7980 (ptm160) cc_final: 0.7644 (ptm160) outliers start: 4 outliers final: 4 residues processed: 86 average time/residue: 0.3477 time to fit residues: 39.0237 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 : 0.810 ------------------------------------------------------------------------------- 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: 0.9990 chunk 53 optimal weight: 0.9990 chunk 52 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 46 optimal weight: 0.5980 chunk 12 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 chunk 8 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3774 r_free = 0.3774 target = 0.166235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.131532 restraints weight = 15728.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.137436 restraints weight = 9031.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.141363 restraints weight = 6345.853| |-----------------------------------------------------------------------------| r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6995 moved from start: 0.1176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 5135 Z= 0.197 Angle : 0.558 10.152 7006 Z= 0.288 Chirality : 0.040 0.448 751 Planarity : 0.004 0.037 839 Dihedral : 7.177 72.761 766 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.16 % Allowed : 7.75 % Favored : 91.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.36), residues: 589 helix: 2.35 (0.26), residues: 391 sheet: -1.16 (0.74), residues: 52 loop : -1.44 (0.48), residues: 146 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 0.002 PHE A 17 TYR 0.016 0.002 TYR A 180 ARG 0.002 0.000 ARG B 847 Details of bonding type rmsd hydrogen bonds : bond 0.04655 ( 342) hydrogen bonds : angle 5.23582 ( 1023) SS BOND : bond 0.00221 ( 1) SS BOND : angle 0.65130 ( 2) covalent geometry : bond 0.00460 ( 5133) covalent geometry : angle 0.55817 ( 7004) Misc. bond : bond 0.01734 ( 1) *********************** 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 89 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 83 time to evaluate : 0.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 MET cc_start: 0.7712 (mmm) cc_final: 0.7345 (mtp) REVERT: A 138 LEU cc_start: 0.7874 (tp) cc_final: 0.7305 (mt) REVERT: A 229 MET cc_start: 0.8216 (mtp) cc_final: 0.7987 (mtp) REVERT: A 370 MET cc_start: 0.6730 (tpp) cc_final: 0.5893 (tpt) REVERT: B 865 ARG cc_start: 0.7974 (ptm160) cc_final: 0.7664 (ptm160) outliers start: 6 outliers final: 5 residues processed: 86 average time/residue: 0.3346 time to fit residues: 38.3906 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 : 0.704 ------------------------------------------------------------------------------- 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: 1.9990 chunk 19 optimal weight: 0.9980 chunk 52 optimal weight: 0.4980 chunk 18 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 21 optimal weight: 0.2980 chunk 24 optimal weight: 0.9980 chunk 50 optimal weight: 0.5980 chunk 35 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3782 r_free = 0.3782 target = 0.166806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.132295 restraints weight = 15693.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.138248 restraints weight = 9037.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.142231 restraints weight = 6325.295| |-----------------------------------------------------------------------------| r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7005 moved from start: 0.1376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 5135 Z= 0.181 Angle : 0.539 10.425 7006 Z= 0.278 Chirality : 0.040 0.457 751 Planarity : 0.004 0.037 839 Dihedral : 7.081 70.504 766 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.16 % Allowed : 9.30 % Favored : 89.53 % 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: 1.73 (0.36), residues: 589 helix: 2.37 (0.26), residues: 392 sheet: -1.32 (0.70), residues: 52 loop : -1.40 (0.48), 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 0.017 0.001 PHE A 17 TYR 0.015 0.002 TYR A 180 ARG 0.002 0.000 ARG B 847 Details of bonding type rmsd hydrogen bonds : bond 0.04427 ( 342) hydrogen bonds : angle 5.03098 ( 1023) SS BOND : bond 0.00216 ( 1) SS BOND : angle 0.55232 ( 2) covalent geometry : bond 0.00424 ( 5133) covalent geometry : angle 0.53894 ( 7004) Misc. bond : bond 0.01359 ( 1) *********************** 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 : 0.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 MET cc_start: 0.7759 (mmm) cc_final: 0.7323 (mtp) REVERT: A 138 LEU cc_start: 0.7917 (tp) cc_final: 0.7329 (mt) REVERT: A 172 THR cc_start: 0.7962 (OUTLIER) cc_final: 0.7731 (m) REVERT: A 334 MET cc_start: 0.7598 (tmm) cc_final: 0.7376 (tmm) REVERT: A 370 MET cc_start: 0.6710 (tpp) cc_final: 0.5901 (tpt) outliers start: 6 outliers final: 5 residues processed: 88 average time/residue: 0.3340 time to fit residues: 38.9882 Evaluate side-chains 88 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 82 time to evaluate : 0.703 ------------------------------------------------------------------------------- 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: 0.9990 chunk 41 optimal weight: 0.9990 chunk 57 optimal weight: 0.0980 chunk 56 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 45 optimal weight: 0.0050 chunk 46 optimal weight: 0.5980 chunk 25 optimal weight: 0.9990 chunk 58 optimal weight: 0.4980 chunk 33 optimal weight: 0.9990 overall best weight: 0.4194 ------------------------------------------------------------------------------- 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 = 0.3809 r_free = 0.3809 target = 0.169827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.134575 restraints weight = 15517.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.140756 restraints weight = 8961.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.144906 restraints weight = 6314.418| |-----------------------------------------------------------------------------| r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6966 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5135 Z= 0.140 Angle : 0.506 10.152 7006 Z= 0.259 Chirality : 0.039 0.451 751 Planarity : 0.003 0.036 839 Dihedral : 6.817 66.699 766 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.36 % Allowed : 10.27 % Favored : 88.37 % 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: 2.01 (0.36), residues: 589 helix: 2.50 (0.26), residues: 398 sheet: -1.38 (0.69), residues: 52 loop : -1.08 (0.50), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 63 HIS 0.004 0.001 HIS A 18 PHE 0.016 0.001 PHE A 17 TYR 0.016 0.001 TYR A 180 ARG 0.001 0.000 ARG A 176 Details of bonding type rmsd hydrogen bonds : bond 0.04106 ( 342) hydrogen bonds : angle 4.76698 ( 1023) SS BOND : bond 0.00259 ( 1) SS BOND : angle 0.51658 ( 2) covalent geometry : bond 0.00321 ( 5133) covalent geometry : angle 0.50550 ( 7004) Misc. bond : bond 0.00521 ( 1) *********************** 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 : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 MET cc_start: 0.7736 (mmm) cc_final: 0.7251 (mtp) REVERT: A 138 LEU cc_start: 0.7915 (tp) cc_final: 0.7325 (mt) REVERT: A 229 MET cc_start: 0.8317 (mtt) cc_final: 0.8089 (mtp) REVERT: A 292 GLN cc_start: 0.7529 (OUTLIER) cc_final: 0.7274 (mm-40) REVERT: A 300 TYR cc_start: 0.7918 (m-80) cc_final: 0.7651 (m-80) REVERT: A 370 MET cc_start: 0.6649 (tpp) cc_final: 0.5837 (tpt) REVERT: A 393 TRP cc_start: 0.8264 (t60) cc_final: 0.8012 (t60) outliers start: 7 outliers final: 5 residues processed: 89 average time/residue: 0.3557 time to fit residues: 41.3747 Evaluate side-chains 87 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 81 time to evaluate : 0.782 ------------------------------------------------------------------------------- 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 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: 0.6980 chunk 58 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 chunk 43 optimal weight: 0.5980 chunk 44 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 17 optimal weight: 0.0980 chunk 54 optimal weight: 0.8980 chunk 55 optimal weight: 0.4980 chunk 14 optimal weight: 0.3980 chunk 42 optimal weight: 0.9980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.170073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.134471 restraints weight = 15659.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.140665 restraints weight = 9024.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.144657 restraints weight = 6349.396| |-----------------------------------------------------------------------------| r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6981 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5135 Z= 0.145 Angle : 0.520 10.629 7006 Z= 0.267 Chirality : 0.040 0.468 751 Planarity : 0.003 0.035 839 Dihedral : 6.722 64.961 766 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.16 % Allowed : 11.43 % Favored : 87.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.36), residues: 589 helix: 2.52 (0.26), residues: 398 sheet: -1.40 (0.68), residues: 52 loop : -1.02 (0.50), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 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 839 Details of bonding type rmsd hydrogen bonds : bond 0.04038 ( 342) hydrogen bonds : angle 4.70584 ( 1023) SS BOND : bond 0.00257 ( 1) SS BOND : angle 0.44110 ( 2) covalent geometry : bond 0.00333 ( 5133) covalent geometry : angle 0.52023 ( 7004) Misc. bond : bond 0.00772 ( 1) *********************** 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 89 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 83 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 MET cc_start: 0.7765 (mmm) cc_final: 0.7270 (mtp) REVERT: A 138 LEU cc_start: 0.7928 (tp) cc_final: 0.7345 (mt) REVERT: A 172 THR cc_start: 0.7934 (OUTLIER) cc_final: 0.7695 (m) REVERT: A 229 MET cc_start: 0.8334 (mtt) cc_final: 0.8055 (mtp) REVERT: A 300 TYR cc_start: 0.7919 (m-80) cc_final: 0.7679 (m-80) REVERT: A 370 MET cc_start: 0.6649 (tpp) cc_final: 0.5851 (tpt) outliers start: 6 outliers final: 4 residues processed: 86 average time/residue: 0.3534 time to fit residues: 39.9010 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 : 0.803 ------------------------------------------------------------------------------- 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: 0.7980 chunk 56 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 52 optimal weight: 0.7980 chunk 15 optimal weight: 0.5980 chunk 37 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 9 optimal weight: 0.0980 chunk 6 optimal weight: 0.0980 chunk 24 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.169785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.135082 restraints weight = 15545.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.141177 restraints weight = 8876.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.145272 restraints weight = 6209.667| |-----------------------------------------------------------------------------| r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6981 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5135 Z= 0.144 Angle : 0.512 10.190 7006 Z= 0.261 Chirality : 0.039 0.454 751 Planarity : 0.003 0.035 839 Dihedral : 6.651 62.732 766 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.55 % Allowed : 11.24 % 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: 2.12 (0.36), residues: 589 helix: 2.56 (0.26), residues: 398 sheet: -1.36 (0.68), residues: 52 loop : -0.99 (0.51), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 63 HIS 0.003 0.001 HIS A 18 PHE 0.018 0.001 PHE A 125 TYR 0.015 0.001 TYR A 180 ARG 0.002 0.000 ARG B 839 Details of bonding type rmsd hydrogen bonds : bond 0.03998 ( 342) hydrogen bonds : angle 4.66057 ( 1023) SS BOND : bond 0.00252 ( 1) SS BOND : angle 0.41129 ( 2) covalent geometry : bond 0.00333 ( 5133) covalent geometry : angle 0.51166 ( 7004) Misc. bond : bond 0.00761 ( 1) *********************** 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 93 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 85 time to evaluate : 0.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 MET cc_start: 0.7791 (mmm) cc_final: 0.7276 (mtp) REVERT: A 138 LEU cc_start: 0.7941 (tp) cc_final: 0.7359 (mt) REVERT: A 172 THR cc_start: 0.7945 (OUTLIER) cc_final: 0.7708 (m) REVERT: A 229 MET cc_start: 0.8313 (mtt) cc_final: 0.7955 (mtp) REVERT: A 300 TYR cc_start: 0.7873 (m-80) cc_final: 0.7641 (m-80) REVERT: A 370 MET cc_start: 0.6628 (tpp) cc_final: 0.5839 (tpt) REVERT: A 481 HIS cc_start: 0.7634 (OUTLIER) cc_final: 0.7234 (t-90) REVERT: B 875 GLN cc_start: 0.6672 (tp-100) cc_final: 0.6290 (tt0) outliers start: 8 outliers final: 5 residues processed: 89 average time/residue: 0.3451 time to fit residues: 40.2298 Evaluate side-chains 91 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 84 time to evaluate : 0.794 ------------------------------------------------------------------------------- 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: 0.4980 chunk 47 optimal weight: 0.9990 chunk 51 optimal weight: 0.0670 chunk 19 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 44 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 chunk 6 optimal weight: 0.0970 overall best weight: 0.4316 ------------------------------------------------------------------------------- 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 = 0.3804 r_free = 0.3804 target = 0.169402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.134957 restraints weight = 15691.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.141052 restraints weight = 8961.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.145220 restraints weight = 6241.916| |-----------------------------------------------------------------------------| r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6949 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5135 Z= 0.140 Angle : 0.517 10.382 7006 Z= 0.263 Chirality : 0.039 0.462 751 Planarity : 0.003 0.034 839 Dihedral : 6.600 61.163 766 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.36 % Allowed : 11.82 % 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: 2.18 (0.36), residues: 589 helix: 2.61 (0.26), residues: 398 sheet: -1.37 (0.68), residues: 52 loop : -0.96 (0.52), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 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 847 Details of bonding type rmsd hydrogen bonds : bond 0.03956 ( 342) hydrogen bonds : angle 4.60224 ( 1023) SS BOND : bond 0.00249 ( 1) SS BOND : angle 0.40483 ( 2) covalent geometry : bond 0.00322 ( 5133) covalent geometry : angle 0.51705 ( 7004) Misc. bond : bond 0.00665 ( 1) *********************** 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 93 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 86 time to evaluate : 0.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 MET cc_start: 0.7760 (mmm) cc_final: 0.7225 (mtp) REVERT: A 138 LEU cc_start: 0.7913 (tp) cc_final: 0.7334 (mt) REVERT: A 172 THR cc_start: 0.7895 (OUTLIER) cc_final: 0.7653 (m) REVERT: A 229 MET cc_start: 0.8333 (mtt) cc_final: 0.7986 (mtp) REVERT: A 300 TYR cc_start: 0.7865 (m-80) cc_final: 0.7629 (m-80) REVERT: A 370 MET cc_start: 0.6603 (tpp) cc_final: 0.5819 (tpt) REVERT: A 481 HIS cc_start: 0.7609 (OUTLIER) cc_final: 0.7215 (t-90) REVERT: B 875 GLN cc_start: 0.6684 (tp-100) cc_final: 0.6419 (tt0) outliers start: 7 outliers final: 5 residues processed: 90 average time/residue: 0.3454 time to fit residues: 40.8343 Evaluate side-chains 91 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 84 time to evaluate : 0.758 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 23 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 53 optimal weight: 0.5980 chunk 42 optimal weight: 0.4980 chunk 41 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3784 r_free = 0.3784 target = 0.167288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.132728 restraints weight = 15699.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.138658 restraints weight = 9046.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.142397 restraints weight = 6392.898| |-----------------------------------------------------------------------------| r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7004 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 5135 Z= 0.199 Angle : 0.559 10.437 7006 Z= 0.285 Chirality : 0.041 0.467 751 Planarity : 0.004 0.034 839 Dihedral : 6.805 60.587 766 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.55 % Allowed : 11.24 % 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: 1.93 (0.36), residues: 589 helix: 2.54 (0.26), residues: 392 sheet: -1.44 (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 0.002 PHE A 17 TYR 0.017 0.002 TYR B 888 ARG 0.002 0.000 ARG B 847 Details of bonding type rmsd hydrogen bonds : bond 0.04184 ( 342) hydrogen bonds : angle 4.71278 ( 1023) SS BOND : bond 0.00241 ( 1) SS BOND : angle 0.53625 ( 2) covalent geometry : bond 0.00467 ( 5133) covalent geometry : angle 0.55854 ( 7004) Misc. bond : bond 0.01793 ( 1) *********************** 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 93 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 85 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 MET cc_start: 0.7764 (mmm) cc_final: 0.7247 (mtp) REVERT: A 138 LEU cc_start: 0.7942 (tp) cc_final: 0.7362 (mt) REVERT: A 370 MET cc_start: 0.6655 (tpp) cc_final: 0.5864 (tpt) REVERT: B 875 GLN cc_start: 0.6798 (tp-100) cc_final: 0.6481 (tt0) outliers start: 8 outliers final: 7 residues processed: 90 average time/residue: 0.3417 time to fit residues: 40.2542 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 : 0.758 ------------------------------------------------------------------------------- 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: 0.0980 chunk 54 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 27 optimal weight: 0.6980 chunk 5 optimal weight: 0.5980 chunk 21 optimal weight: 0.0970 chunk 40 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 overall best weight: 0.4178 ------------------------------------------------------------------------------- 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 = 0.3810 r_free = 0.3810 target = 0.170122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.135671 restraints weight = 15652.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.141878 restraints weight = 8923.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.145785 restraints weight = 6227.150| |-----------------------------------------------------------------------------| r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6962 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 5135 Z= 0.141 Angle : 0.538 10.529 7006 Z= 0.274 Chirality : 0.040 0.466 751 Planarity : 0.003 0.034 839 Dihedral : 6.678 59.036 766 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.55 % Allowed : 11.82 % Favored : 86.63 % 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: 2.01 (0.36), residues: 589 helix: 2.59 (0.26), residues: 392 sheet: -1.40 (0.68), residues: 52 loop : -1.25 (0.51), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 63 HIS 0.004 0.001 HIS A 78 PHE 0.016 0.001 PHE A 17 TYR 0.022 0.002 TYR B 888 ARG 0.001 0.000 ARG B 860 Details of bonding type rmsd hydrogen bonds : bond 0.04031 ( 342) hydrogen bonds : angle 4.57487 ( 1023) SS BOND : bond 0.00235 ( 1) SS BOND : angle 0.42769 ( 2) covalent geometry : bond 0.00323 ( 5133) covalent geometry : angle 0.53813 ( 7004) Misc. bond : bond 0.00545 ( 1) ********************** 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 93 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 85 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 HIS cc_start: 0.7788 (OUTLIER) cc_final: 0.6319 (t-90) REVERT: A 102 MET cc_start: 0.7733 (mmm) cc_final: 0.7216 (mtp) REVERT: A 138 LEU cc_start: 0.7874 (tp) cc_final: 0.7314 (mt) REVERT: A 172 THR cc_start: 0.7892 (OUTLIER) cc_final: 0.7656 (m) REVERT: A 229 MET cc_start: 0.8357 (mtt) cc_final: 0.8053 (mtp) REVERT: A 370 MET cc_start: 0.6598 (tpp) cc_final: 0.5837 (tpt) REVERT: A 481 HIS cc_start: 0.7628 (OUTLIER) cc_final: 0.7235 (t-90) REVERT: B 875 GLN cc_start: 0.6756 (tp-100) cc_final: 0.6484 (tt0) outliers start: 8 outliers final: 5 residues processed: 90 average time/residue: 0.3481 time to fit residues: 41.2733 Evaluate side-chains 93 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 85 time to evaluate : 0.827 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 21 optimal weight: 0.1980 chunk 26 optimal weight: 0.0980 chunk 3 optimal weight: 3.9990 chunk 20 optimal weight: 0.0980 chunk 0 optimal weight: 2.9990 chunk 16 optimal weight: 0.4980 chunk 14 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 chunk 9 optimal weight: 0.1980 chunk 25 optimal weight: 0.5980 chunk 12 optimal weight: 0.6980 overall best weight: 0.2180 ------------------------------------------------------------------------------- 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 = 0.3831 r_free = 0.3831 target = 0.172403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.138468 restraints weight = 15362.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.144596 restraints weight = 8686.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.148782 restraints weight = 6045.597| |-----------------------------------------------------------------------------| r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6913 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 : 0.002 0.040 5135 Z= 0.111 Angle : 0.514 10.483 7006 Z= 0.261 Chirality : 0.039 0.463 751 Planarity : 0.003 0.034 839 Dihedral : 6.466 55.037 766 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.74 % Favored : 96.10 % 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: 2.23 (0.36), residues: 589 helix: 2.74 (0.26), residues: 392 sheet: -1.23 (0.69), residues: 52 loop : -1.14 (0.51), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 63 HIS 0.011 0.001 HIS A 32 PHE 0.015 0.001 PHE A 17 TYR 0.019 0.001 TYR B 888 ARG 0.001 0.000 ARG A 348 Details of bonding type rmsd hydrogen bonds : bond 0.03827 ( 342) hydrogen bonds : angle 4.44838 ( 1023) SS BOND : bond 0.00269 ( 1) SS BOND : angle 0.34355 ( 2) covalent geometry : bond 0.00247 ( 5133) covalent geometry : angle 0.51447 ( 7004) Misc. bond : bond 0.00291 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4044.09 seconds wall clock time: 69 minutes 48.19 seconds (4188.19 seconds total)