Starting phenix.real_space_refine on Wed Sep 25 13:26:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q6z_13860/09_2024/7q6z_13860_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q6z_13860/09_2024/7q6z_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q6z_13860/09_2024/7q6z_13860.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q6z_13860/09_2024/7q6z_13860.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q6z_13860/09_2024/7q6z_13860_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q6z_13860/09_2024/7q6z_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-5461/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: 5.54, per 1000 atoms: 0.57 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: 3.20 Conformation dependent library (CDL) restraints added in 645.0 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: 0.72 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: 3.68 Time building geometry restraints manager: 3.58 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: 2.000 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: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 25.740 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:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.550 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 0.690 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: 0.3598 time to fit residues: 43.5120 Evaluate side-chains 82 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 0.754 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6989 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 fitting. rotamer outliers: 4 poor density : 84 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 LEU cc_start: 0.7897 (tp) cc_final: 0.7317 (mt) REVERT: A 179 TYR cc_start: 0.8576 (m-80) cc_final: 0.8285 (m-10) REVERT: A 334 MET cc_start: 0.7657 (tmm) cc_final: 0.7435 (tmm) REVERT: A 370 MET cc_start: 0.6747 (tpp) cc_final: 0.5888 (tpt) REVERT: B 865 ARG cc_start: 0.7990 (ptm160) cc_final: 0.7653 (ptm160) outliers start: 4 outliers final: 4 residues processed: 86 average time/residue: 0.3417 time to fit residues: 38.4544 Evaluate side-chains 84 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 80 time to evaluate : 0.783 ------------------------------------------------------------------------------- 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 29 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 43 optimal weight: 0.2980 chunk 40 optimal weight: 0.9980 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7008 moved from start: 0.1222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 5133 Z= 0.303 Angle : 0.567 10.150 7004 Z= 0.292 Chirality : 0.041 0.448 751 Planarity : 0.004 0.038 839 Dihedral : 7.194 71.733 766 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.16 % Allowed : 7.95 % Favored : 90.89 % 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: 1.66 (0.36), residues: 589 helix: 2.32 (0.26), residues: 391 sheet: -1.20 (0.73), residues: 52 loop : -1.48 (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 180 ARG 0.002 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 fitting. rotamer outliers: 6 poor density : 84 time to evaluate : 0.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 MET cc_start: 0.7751 (mmm) cc_final: 0.7362 (mtp) REVERT: A 138 LEU cc_start: 0.7891 (tp) cc_final: 0.7314 (mt) REVERT: A 229 MET cc_start: 0.8197 (mtp) cc_final: 0.7955 (mtp) REVERT: A 370 MET cc_start: 0.6740 (tpp) cc_final: 0.5906 (tpt) REVERT: B 865 ARG cc_start: 0.7992 (ptm160) cc_final: 0.7686 (ptm160) outliers start: 6 outliers final: 5 residues processed: 87 average time/residue: 0.3565 time to fit residues: 41.1959 Evaluate side-chains 87 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 82 time to evaluate : 0.749 ------------------------------------------------------------------------------- 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 27 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 57 optimal weight: 0.6980 chunk 28 optimal weight: 0.0970 chunk 51 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 32 optimal weight: 0.2980 overall best weight: 0.5378 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6989 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 5133 Z= 0.239 Angle : 0.528 10.356 7004 Z= 0.272 Chirality : 0.040 0.460 751 Planarity : 0.004 0.037 839 Dihedral : 7.008 70.241 766 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.16 % Allowed : 9.50 % Favored : 89.34 % 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: 1.76 (0.36), residues: 589 helix: 2.39 (0.26), residues: 392 sheet: -1.33 (0.70), residues: 52 loop : -1.37 (0.48), 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 78 PHE 0.017 0.001 PHE A 17 TYR 0.016 0.002 TYR A 180 ARG 0.001 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 fitting. rotamer outliers: 6 poor density : 84 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 MET cc_start: 0.7747 (mmm) cc_final: 0.7307 (mtp) REVERT: A 138 LEU cc_start: 0.7902 (tp) cc_final: 0.7309 (mt) REVERT: A 172 THR cc_start: 0.7924 (OUTLIER) cc_final: 0.7688 (m) REVERT: A 370 MET cc_start: 0.6700 (tpp) cc_final: 0.5887 (tpt) REVERT: B 865 ARG cc_start: 0.7940 (ptm160) cc_final: 0.7676 (ptm160) outliers start: 6 outliers final: 5 residues processed: 88 average time/residue: 0.3270 time to fit residues: 38.0709 Evaluate side-chains 89 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 83 time to evaluate : 0.774 ------------------------------------------------------------------------------- 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 0 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 29 optimal weight: 0.0770 chunk 51 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 overall best weight: 0.7540 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7019 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 5133 Z= 0.309 Angle : 0.560 10.227 7004 Z= 0.290 Chirality : 0.041 0.457 751 Planarity : 0.004 0.038 839 Dihedral : 7.116 67.313 766 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.36 % Allowed : 11.05 % Favored : 87.60 % 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: 1.76 (0.36), residues: 589 helix: 2.31 (0.26), residues: 398 sheet: -1.59 (0.68), residues: 52 loop : -1.15 (0.50), residues: 139 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 0.017 0.002 PHE A 125 TYR 0.014 0.002 TYR A 166 ARG 0.002 0.000 ARG B 847 *********************** 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 90 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 83 time to evaluate : 0.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 MET cc_start: 0.7761 (mmm) cc_final: 0.7297 (mtp) REVERT: A 138 LEU cc_start: 0.7893 (tp) cc_final: 0.7316 (mt) REVERT: A 229 MET cc_start: 0.8357 (mtt) cc_final: 0.8139 (mtp) REVERT: A 370 MET cc_start: 0.6701 (tpp) cc_final: 0.5879 (tpt) outliers start: 7 outliers final: 6 residues processed: 87 average time/residue: 0.3274 time to fit residues: 37.8178 Evaluate side-chains 87 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 81 time to evaluate : 0.781 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 14 optimal weight: 0.7980 chunk 57 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 26 optimal weight: 0.3980 chunk 4 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 55 optimal weight: 0.6980 chunk 6 optimal weight: 0.1980 chunk 32 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 B 867 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6998 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 5133 Z= 0.243 Angle : 0.533 10.278 7004 Z= 0.275 Chirality : 0.040 0.454 751 Planarity : 0.004 0.037 839 Dihedral : 6.976 65.447 766 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % 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: 1.93 (0.36), residues: 589 helix: 2.42 (0.27), residues: 398 sheet: -1.55 (0.68), residues: 52 loop : -1.00 (0.51), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 63 HIS 0.004 0.001 HIS A 18 PHE 0.016 0.001 PHE A 17 TYR 0.015 0.002 TYR A 180 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 91 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 83 time to evaluate : 0.739 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: 0.7287 (mtp) REVERT: A 138 LEU cc_start: 0.7935 (tp) cc_final: 0.7348 (mt) REVERT: A 172 THR cc_start: 0.7932 (OUTLIER) cc_final: 0.7690 (m) REVERT: A 229 MET cc_start: 0.8384 (mtt) cc_final: 0.8034 (mtp) REVERT: A 292 GLN cc_start: 0.7650 (OUTLIER) cc_final: 0.6947 (mm-40) REVERT: A 370 MET cc_start: 0.6664 (tpp) cc_final: 0.5850 (tpt) REVERT: A 393 TRP cc_start: 0.8310 (t60) cc_final: 0.8088 (t60) REVERT: B 865 ARG cc_start: 0.7912 (ptm160) cc_final: 0.7659 (ptm160) outliers start: 8 outliers final: 4 residues processed: 87 average time/residue: 0.3268 time to fit residues: 37.6648 Evaluate side-chains 88 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 82 time to evaluate : 0.921 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 32 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 31 optimal weight: 0.0970 chunk 56 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 34 optimal weight: 0.3980 chunk 26 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 chunk 33 optimal weight: 0.1980 chunk 17 optimal weight: 0.7980 chunk 11 optimal weight: 0.2980 overall best weight: 0.3178 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6965 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5133 Z= 0.173 Angle : 0.514 10.526 7004 Z= 0.264 Chirality : 0.039 0.464 751 Planarity : 0.004 0.036 839 Dihedral : 6.779 63.415 766 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.74 % Allowed : 10.85 % 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: 2.08 (0.36), residues: 589 helix: 2.52 (0.27), residues: 398 sheet: -1.43 (0.68), residues: 52 loop : -0.93 (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 0.016 0.001 PHE A 17 TYR 0.016 0.001 TYR A 180 ARG 0.001 0.000 ARG A 459 *********************** 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 94 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 85 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 MET cc_start: 0.7758 (mmm) cc_final: 0.7258 (mtp) REVERT: A 138 LEU cc_start: 0.7927 (tp) cc_final: 0.7334 (mt) REVERT: A 172 THR cc_start: 0.7865 (OUTLIER) cc_final: 0.7635 (m) REVERT: A 229 MET cc_start: 0.8343 (mtt) cc_final: 0.8029 (mtp) REVERT: A 370 MET cc_start: 0.6620 (tpp) cc_final: 0.5852 (tpt) outliers start: 9 outliers final: 7 residues processed: 90 average time/residue: 0.3178 time to fit residues: 37.8823 Evaluate side-chains 88 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 80 time to evaluate : 0.787 ------------------------------------------------------------------------------- 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 261 MET 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 11 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 chunk 38 optimal weight: 0.5980 chunk 28 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 chunk 44 optimal weight: 0.6980 chunk 51 optimal weight: 0.6980 chunk 54 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 chunk 31 optimal weight: 0.0980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6982 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 5133 Z= 0.240 Angle : 0.545 10.405 7004 Z= 0.279 Chirality : 0.040 0.464 751 Planarity : 0.004 0.035 839 Dihedral : 6.870 61.501 766 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 1.74 % Allowed : 11.24 % 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: 1.96 (0.36), residues: 589 helix: 2.53 (0.26), residues: 392 sheet: -1.49 (0.68), residues: 52 loop : -1.14 (0.51), residues: 145 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 0.016 0.001 PHE A 17 TYR 0.014 0.001 TYR A 180 ARG 0.001 0.000 ARG B 865 *********************** 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 94 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 85 time to evaluate : 0.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 HIS cc_start: 0.7840 (OUTLIER) cc_final: 0.6400 (t-90) REVERT: A 102 MET cc_start: 0.7761 (mmm) cc_final: 0.7233 (mtp) REVERT: A 138 LEU cc_start: 0.7931 (tp) cc_final: 0.7338 (mt) REVERT: A 334 MET cc_start: 0.7570 (tmm) cc_final: 0.7205 (tmm) REVERT: A 370 MET cc_start: 0.6632 (tpp) cc_final: 0.5836 (tpt) REVERT: B 865 ARG cc_start: 0.7617 (ptm160) cc_final: 0.7416 (ptm160) REVERT: B 875 GLN cc_start: 0.6847 (tp-100) cc_final: 0.6493 (tt0) outliers start: 9 outliers final: 7 residues processed: 90 average time/residue: 0.3226 time to fit residues: 38.3813 Evaluate side-chains 89 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 81 time to evaluate : 0.744 ------------------------------------------------------------------------------- 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: 2.9990 chunk 41 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 50 optimal weight: 0.2980 chunk 52 optimal weight: 0.0970 chunk 34 optimal weight: 0.9990 chunk 56 optimal weight: 0.5980 chunk 26 optimal weight: 0.3980 chunk 38 optimal weight: 0.5980 chunk 58 optimal weight: 0.2980 overall best weight: 0.3378 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6959 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5133 Z= 0.179 Angle : 0.521 10.511 7004 Z= 0.264 Chirality : 0.039 0.466 751 Planarity : 0.003 0.035 839 Dihedral : 6.730 59.022 766 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.74 % Allowed : 12.02 % 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: 2.11 (0.36), residues: 589 helix: 2.64 (0.26), residues: 392 sheet: -1.45 (0.68), residues: 52 loop : -1.07 (0.51), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 63 HIS 0.002 0.000 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 *********************** 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 94 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 85 time to evaluate : 0.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 HIS cc_start: 0.7780 (OUTLIER) cc_final: 0.6408 (t-90) REVERT: A 102 MET cc_start: 0.7748 (mmm) cc_final: 0.7237 (mtp) REVERT: A 138 LEU cc_start: 0.7875 (tp) cc_final: 0.7303 (mt) REVERT: A 172 THR cc_start: 0.7879 (OUTLIER) cc_final: 0.7646 (m) REVERT: A 229 MET cc_start: 0.8350 (mtt) cc_final: 0.8027 (mtp) REVERT: A 334 MET cc_start: 0.7454 (tmm) cc_final: 0.7149 (tmm) REVERT: A 370 MET cc_start: 0.6593 (tpp) cc_final: 0.5809 (tpt) REVERT: A 481 HIS cc_start: 0.7588 (OUTLIER) cc_final: 0.7198 (t-90) REVERT: B 875 GLN cc_start: 0.6813 (tp-100) cc_final: 0.6510 (tt0) outliers start: 9 outliers final: 5 residues processed: 90 average time/residue: 0.3208 time to fit residues: 38.2206 Evaluate side-chains 93 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 85 time to evaluate : 0.694 ------------------------------------------------------------------------------- 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 54 optimal weight: 0.9980 chunk 46 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 chunk 37 optimal weight: 0.0970 chunk 49 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 43 optimal weight: 0.3980 chunk 6 optimal weight: 0.3980 chunk 13 optimal weight: 0.5980 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6966 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5133 Z= 0.202 Angle : 0.525 10.448 7004 Z= 0.266 Chirality : 0.039 0.464 751 Planarity : 0.004 0.035 839 Dihedral : 6.680 56.646 766 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.74 % Allowed : 12.02 % 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: 2.16 (0.36), residues: 589 helix: 2.68 (0.26), residues: 392 sheet: -1.45 (0.68), residues: 52 loop : -1.06 (0.52), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 63 HIS 0.003 0.000 HIS A 343 PHE 0.016 0.001 PHE A 17 TYR 0.015 0.001 TYR A 180 ARG 0.001 0.000 ARG B 865 ********************** 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 91 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 82 time to evaluate : 0.706 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 HIS cc_start: 0.7837 (OUTLIER) cc_final: 0.6378 (t-90) REVERT: A 102 MET cc_start: 0.7759 (mmm) cc_final: 0.7237 (mtp) REVERT: A 138 LEU cc_start: 0.7920 (tp) cc_final: 0.7338 (mt) REVERT: A 229 MET cc_start: 0.8318 (mtt) cc_final: 0.7983 (mtp) REVERT: A 334 MET cc_start: 0.7399 (tmm) cc_final: 0.7175 (tmm) REVERT: A 370 MET cc_start: 0.6624 (tpp) cc_final: 0.5848 (tpt) REVERT: B 875 GLN cc_start: 0.6834 (tp-100) cc_final: 0.6517 (tt0) outliers start: 9 outliers final: 6 residues processed: 87 average time/residue: 0.3226 time to fit residues: 37.2087 Evaluate side-chains 88 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 81 time to evaluate : 0.706 ------------------------------------------------------------------------------- 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 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 46 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 5 optimal weight: 0.4980 chunk 8 optimal weight: 0.0470 chunk 41 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 chunk 31 optimal weight: 0.3980 chunk 40 optimal weight: 0.6980 overall best weight: 0.4878 ------------------------------------------------------------------------------- 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 = 0.3808 r_free = 0.3808 target = 0.169657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.135390 restraints weight = 15461.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.141428 restraints weight = 8914.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.145447 restraints weight = 6241.720| |-----------------------------------------------------------------------------| r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6963 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5133 Z= 0.221 Angle : 0.537 10.506 7004 Z= 0.272 Chirality : 0.040 0.466 751 Planarity : 0.004 0.034 839 Dihedral : 6.694 55.538 766 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.36 % Allowed : 12.21 % 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: 2.10 (0.36), residues: 589 helix: 2.67 (0.26), residues: 391 sheet: -1.47 (0.68), residues: 52 loop : -1.16 (0.52), residues: 146 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 0.015 0.001 TYR A 180 ARG 0.001 0.000 ARG B 847 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2958.14 seconds wall clock time: 51 minutes 58.84 seconds (3118.84 seconds total)