Starting phenix.real_space_refine on Thu Nov 14 01:13:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9fcj_50317/11_2024/9fcj_50317.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9fcj_50317/11_2024/9fcj_50317.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9fcj_50317/11_2024/9fcj_50317.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9fcj_50317/11_2024/9fcj_50317.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9fcj_50317/11_2024/9fcj_50317.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9fcj_50317/11_2024/9fcj_50317.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.026 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: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 14 5.16 5 C 2010 2.51 5 N 524 2.21 5 O 625 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 3174 Number of models: 1 Model: "" Number of chains: 5 Chain: "C" Number of atoms: 607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 607 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "D" Number of atoms: 2508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2508 Classifications: {'peptide': 312} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 299} Chain breaks: 6 Chain: "D" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {' ZN': 1, 'JDA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "D" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1676 SG CYS D 440 37.181 76.326 21.625 1.00 9.31 S ATOM 1699 SG CYS D 443 38.872 76.870 18.330 1.00 10.42 S ATOM 2074 SG CYS D 506 40.932 75.662 21.048 1.00 8.96 S ATOM 2097 SG CYS D 509 39.780 79.274 21.029 1.00 9.66 S Time building chain proxies: 3.14, per 1000 atoms: 0.99 Number of scatterers: 3174 At special positions: 0 Unit cell: (66.78, 90.1, 58.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 14 16.00 O 625 8.00 N 524 7.00 C 2010 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.77 Conformation dependent library (CDL) restraints added in 385.9 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1000 " pdb="ZN ZN D1000 " - pdb=" SG CYS D 443 " pdb="ZN ZN D1000 " - pdb=" SG CYS D 509 " pdb="ZN ZN D1000 " - pdb=" SG CYS D 440 " pdb="ZN ZN D1000 " - pdb=" SG CYS D 506 " Number of angles added : 6 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 740 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 7 sheets defined 45.0% alpha, 30.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'C' and resid 22 through 35 removed outlier: 3.595A pdb=" N LYS C 33 " --> pdb=" O LYS C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 41 Processing helix chain 'C' and resid 55 through 60 Processing helix chain 'D' and resid 81 through 88 removed outlier: 4.142A pdb=" N ASN D 85 " --> pdb=" O GLY D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 101 removed outlier: 3.741A pdb=" N ILE D 95 " --> pdb=" O TYR D 91 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE D 101 " --> pdb=" O GLN D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 120 Processing helix chain 'D' and resid 144 through 166 Processing helix chain 'D' and resid 166 through 177 removed outlier: 3.787A pdb=" N ASP D 172 " --> pdb=" O GLU D 168 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLN D 177 " --> pdb=" O GLU D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 189 removed outlier: 3.962A pdb=" N LEU D 181 " --> pdb=" O GLN D 177 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR D 184 " --> pdb=" O ARG D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 220 Processing helix chain 'D' and resid 424 through 431 Processing helix chain 'D' and resid 484 through 494 Processing helix chain 'D' and resid 499 through 503 removed outlier: 3.685A pdb=" N LYS D 503 " --> pdb=" O GLY D 500 " (cutoff:3.500A) Processing helix chain 'D' and resid 564 through 568 Processing helix chain 'D' and resid 759 through 767 Processing helix chain 'D' and resid 768 through 772 Processing sheet with id=AA1, first strand: chain 'C' and resid 12 through 17 removed outlier: 9.096A pdb=" N LEU C 67 " --> pdb=" O GLN C 2 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N PHE C 4 " --> pdb=" O LEU C 67 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N LEU C 69 " --> pdb=" O PHE C 4 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N LYS C 6 " --> pdb=" O LEU C 69 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 74 through 75 Processing sheet with id=AA3, first strand: chain 'D' and resid 446 through 453 removed outlier: 6.395A pdb=" N GLN D 433 " --> pdb=" O ASP D 522 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 456 through 459 removed outlier: 6.118A pdb=" N ILE D 456 " --> pdb=" O HIS D 531 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N LYS D 533 " --> pdb=" O ILE D 456 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N VAL D 458 " --> pdb=" O LYS D 533 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N TYR D 778 " --> pdb=" O LEU D 532 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N VAL D 582 " --> pdb=" O TYR D 778 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N LEU D 780 " --> pdb=" O ALA D 580 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ALA D 580 " --> pdb=" O LEU D 780 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N TYR D 782 " --> pdb=" O LEU D 578 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N LEU D 578 " --> pdb=" O TYR D 782 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N LYS D 784 " --> pdb=" O TYR D 576 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N TYR D 576 " --> pdb=" O LYS D 784 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 456 through 459 removed outlier: 6.118A pdb=" N ILE D 456 " --> pdb=" O HIS D 531 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N LYS D 533 " --> pdb=" O ILE D 456 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N VAL D 458 " --> pdb=" O LYS D 533 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N TYR D 778 " --> pdb=" O LEU D 532 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N VAL D 582 " --> pdb=" O TYR D 778 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N LEU D 780 " --> pdb=" O ALA D 580 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ALA D 580 " --> pdb=" O LEU D 780 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N TYR D 782 " --> pdb=" O LEU D 578 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N LEU D 578 " --> pdb=" O TYR D 782 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N LYS D 784 " --> pdb=" O TYR D 576 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N TYR D 576 " --> pdb=" O LYS D 784 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N PHE D 579 " --> pdb=" O LYS D 599 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA D 596 " --> pdb=" O PHE D 750 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 504 through 506 Processing sheet with id=AA7, first strand: chain 'D' and resid 535 through 536 181 hydrogen bonds defined for protein. 459 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: 0.90 Time building geometry restraints manager: 0.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1006 1.34 - 1.46: 595 1.46 - 1.58: 1577 1.58 - 1.69: 0 1.69 - 1.81: 19 Bond restraints: 3197 Sorted by residual: bond pdb=" C12 JDA D1001 " pdb=" C13 JDA D1001 " ideal model delta sigma weight residual 1.371 1.352 0.019 2.00e-02 2.50e+03 9.38e-01 bond pdb=" C16 JDA D1001 " pdb=" C17 JDA D1001 " ideal model delta sigma weight residual 1.392 1.375 0.017 2.00e-02 2.50e+03 7.31e-01 bond pdb=" CB GLU C 51 " pdb=" CG GLU C 51 " ideal model delta sigma weight residual 1.520 1.544 -0.024 3.00e-02 1.11e+03 6.65e-01 bond pdb=" CG GLU C 51 " pdb=" CD GLU C 51 " ideal model delta sigma weight residual 1.516 1.535 -0.019 2.50e-02 1.60e+03 6.07e-01 bond pdb=" C PRO D 777 " pdb=" N TYR D 778 " ideal model delta sigma weight residual 1.329 1.315 0.014 1.79e-02 3.12e+03 6.00e-01 ... (remaining 3192 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 4241 1.65 - 3.31: 63 3.31 - 4.96: 5 4.96 - 6.62: 1 6.62 - 8.27: 2 Bond angle restraints: 4312 Sorted by residual: angle pdb=" CB MET D 524 " pdb=" CG MET D 524 " pdb=" SD MET D 524 " ideal model delta sigma weight residual 112.70 120.97 -8.27 3.00e+00 1.11e-01 7.60e+00 angle pdb=" C VAL C 17 " pdb=" N GLU C 18 " pdb=" CA GLU C 18 " ideal model delta sigma weight residual 122.15 129.70 -7.55 3.47e+00 8.31e-02 4.73e+00 angle pdb=" CB GLU C 51 " pdb=" CG GLU C 51 " pdb=" CD GLU C 51 " ideal model delta sigma weight residual 112.60 115.97 -3.37 1.70e+00 3.46e-01 3.92e+00 angle pdb=" CA LYS D 533 " pdb=" C LYS D 533 " pdb=" N CYS D 534 " ideal model delta sigma weight residual 114.76 116.96 -2.20 1.14e+00 7.69e-01 3.71e+00 angle pdb=" CA LYS D 533 " pdb=" C LYS D 533 " pdb=" O LYS D 533 " ideal model delta sigma weight residual 122.64 120.43 2.21 1.25e+00 6.40e-01 3.12e+00 ... (remaining 4307 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.37: 1709 17.37 - 34.73: 173 34.73 - 52.10: 52 52.10 - 69.46: 12 69.46 - 86.83: 5 Dihedral angle restraints: 1951 sinusoidal: 818 harmonic: 1133 Sorted by residual: dihedral pdb=" CG ARG D 517 " pdb=" CD ARG D 517 " pdb=" NE ARG D 517 " pdb=" CZ ARG D 517 " ideal model delta sinusoidal sigma weight residual -180.00 -136.99 -43.01 2 1.50e+01 4.44e-03 9.93e+00 dihedral pdb=" CB GLU D 760 " pdb=" CG GLU D 760 " pdb=" CD GLU D 760 " pdb=" OE1 GLU D 760 " ideal model delta sinusoidal sigma weight residual 0.00 -85.95 85.95 1 3.00e+01 1.11e-03 9.91e+00 dihedral pdb=" CA ASP D 463 " pdb=" CB ASP D 463 " pdb=" CG ASP D 463 " pdb=" OD1 ASP D 463 " ideal model delta sinusoidal sigma weight residual -30.00 -83.61 53.61 1 2.00e+01 2.50e-03 9.76e+00 ... (remaining 1948 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 317 0.026 - 0.052: 111 0.052 - 0.078: 42 0.078 - 0.104: 19 0.104 - 0.130: 9 Chirality restraints: 498 Sorted by residual: chirality pdb=" CA ILE C 36 " pdb=" N ILE C 36 " pdb=" C ILE C 36 " pdb=" CB ILE C 36 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.22e-01 chirality pdb=" CA VAL D 755 " pdb=" N VAL D 755 " pdb=" C VAL D 755 " pdb=" CB VAL D 755 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.63e-01 chirality pdb=" CA ILE D 552 " pdb=" N ILE D 552 " pdb=" C ILE D 552 " pdb=" CB ILE D 552 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.45e-01 ... (remaining 495 not shown) Planarity restraints: 541 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 JDA D1001 " 0.017 2.00e-02 2.50e+03 2.34e-02 1.09e+01 pdb=" C11 JDA D1001 " 0.015 2.00e-02 2.50e+03 pdb=" C5 JDA D1001 " -0.038 2.00e-02 2.50e+03 pdb=" C6 JDA D1001 " 0.007 2.00e-02 2.50e+03 pdb=" C7 JDA D1001 " 0.015 2.00e-02 2.50e+03 pdb=" C8 JDA D1001 " 0.017 2.00e-02 2.50e+03 pdb=" C9 JDA D1001 " 0.010 2.00e-02 2.50e+03 pdb=" N3 JDA D1001 " -0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" N JDA D1001 " -0.017 2.00e-02 2.50e+03 1.82e-02 7.44e+00 pdb=" C JDA D1001 " 0.033 2.00e-02 2.50e+03 pdb=" C1 JDA D1001 " -0.006 2.00e-02 2.50e+03 pdb=" C14 JDA D1001 " 0.012 2.00e-02 2.50e+03 pdb=" C2 JDA D1001 " -0.020 2.00e-02 2.50e+03 pdb=" C3 JDA D1001 " 0.008 2.00e-02 2.50e+03 pdb=" C4 JDA D1001 " 0.001 2.00e-02 2.50e+03 pdb=" N1 JDA D1001 " 0.015 2.00e-02 2.50e+03 pdb=" N2 JDA D1001 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 163 " 0.009 2.00e-02 2.50e+03 1.02e-02 1.83e+00 pdb=" CG PHE D 163 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 PHE D 163 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE D 163 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE D 163 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE D 163 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE D 163 " 0.000 2.00e-02 2.50e+03 ... (remaining 538 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 361 2.75 - 3.29: 2854 3.29 - 3.83: 5172 3.83 - 4.36: 6786 4.36 - 4.90: 11174 Nonbonded interactions: 26347 Sorted by model distance: nonbonded pdb=" O LEU C 73 " pdb=" OH TYR D 594 " model vdw 2.213 3.040 nonbonded pdb=" OE1 GLU D 202 " pdb=" O HOH D1101 " model vdw 2.233 3.040 nonbonded pdb=" O CYS D 102 " pdb=" O HOH D1102 " model vdw 2.234 3.040 nonbonded pdb=" O HOH D1109 " pdb=" O HOH D1112 " model vdw 2.276 3.040 nonbonded pdb=" NH1 ARG D 517 " pdb=" O HOH D1103 " model vdw 2.352 3.120 ... (remaining 26342 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 individual isotropic 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: 1.400 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: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.010 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 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 : 0.003 0.035 3197 Z= 0.196 Angle : 0.547 8.272 4312 Z= 0.291 Chirality : 0.036 0.130 498 Planarity : 0.004 0.031 541 Dihedral : 16.442 86.830 1211 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 0.56 % Allowed : 10.89 % Favored : 88.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.41), residues: 373 helix: 0.10 (0.42), residues: 140 sheet: 0.43 (0.46), residues: 102 loop : -0.09 (0.53), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 487 HIS 0.002 0.001 HIS C 68 PHE 0.024 0.002 PHE D 163 TYR 0.011 0.001 TYR D 504 ARG 0.005 0.001 ARG D 186 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 67 time to evaluate : 0.395 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 68 average time/residue: 1.4287 time to fit residues: 99.5310 Evaluate side-chains 64 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 63 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 455 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 32 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 29 optimal weight: 0.9980 chunk 11 optimal weight: 7.9990 chunk 18 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 158 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.1143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 3197 Z= 0.268 Angle : 0.555 5.965 4312 Z= 0.286 Chirality : 0.040 0.125 498 Planarity : 0.004 0.031 541 Dihedral : 5.339 41.254 426 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.96 % Allowed : 13.13 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.42), residues: 373 helix: 1.06 (0.42), residues: 143 sheet: 0.35 (0.45), residues: 104 loop : 0.28 (0.58), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 487 HIS 0.003 0.001 HIS D 584 PHE 0.012 0.002 PHE D 505 TYR 0.010 0.001 TYR D 782 ARG 0.007 0.001 ARG D 186 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 62 time to evaluate : 0.394 Fit side-chains outliers start: 7 outliers final: 2 residues processed: 66 average time/residue: 1.4244 time to fit residues: 96.3743 Evaluate side-chains 60 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 58 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain D residue 145 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 28 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 30 optimal weight: 8.9990 chunk 11 optimal weight: 5.9990 chunk 27 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 158 GLN D 198 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 3197 Z= 0.331 Angle : 0.558 5.832 4312 Z= 0.283 Chirality : 0.040 0.132 498 Planarity : 0.004 0.028 541 Dihedral : 5.359 42.546 424 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.40 % Allowed : 15.64 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.42), residues: 373 helix: 1.22 (0.42), residues: 143 sheet: 0.26 (0.46), residues: 104 loop : 0.19 (0.57), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 487 HIS 0.004 0.001 HIS D 584 PHE 0.012 0.002 PHE D 505 TYR 0.011 0.002 TYR D 504 ARG 0.005 0.001 ARG D 186 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 64 time to evaluate : 0.337 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 68 average time/residue: 1.4133 time to fit residues: 98.5951 Evaluate side-chains 66 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 62 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 770 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 16 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 36 optimal weight: 0.0770 chunk 18 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 overall best weight: 1.1142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 158 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3197 Z= 0.226 Angle : 0.532 10.675 4312 Z= 0.263 Chirality : 0.038 0.139 498 Planarity : 0.003 0.026 541 Dihedral : 5.185 42.025 424 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.07 % Allowed : 15.36 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.42), residues: 373 helix: 1.49 (0.42), residues: 143 sheet: 0.22 (0.46), residues: 104 loop : 0.24 (0.57), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 487 HIS 0.003 0.001 HIS D 584 PHE 0.009 0.002 PHE D 750 TYR 0.010 0.001 TYR D 504 ARG 0.004 0.001 ARG D 186 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 62 time to evaluate : 0.403 Fit side-chains REVERT: D 749 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8530 (mt) outliers start: 11 outliers final: 7 residues processed: 69 average time/residue: 1.3362 time to fit residues: 94.7001 Evaluate side-chains 67 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 59 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 535 PHE Chi-restraints excluded: chain D residue 565 GLU Chi-restraints excluded: chain D residue 749 LEU Chi-restraints excluded: chain D residue 770 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 15 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 18 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 158 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3197 Z= 0.266 Angle : 0.535 7.817 4312 Z= 0.266 Chirality : 0.039 0.130 498 Planarity : 0.003 0.027 541 Dihedral : 5.222 42.297 424 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.63 % Allowed : 14.80 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.43), residues: 373 helix: 1.57 (0.42), residues: 143 sheet: 0.19 (0.47), residues: 104 loop : 0.25 (0.57), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 487 HIS 0.004 0.001 HIS D 584 PHE 0.010 0.002 PHE D 505 TYR 0.011 0.001 TYR D 504 ARG 0.006 0.001 ARG D 186 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 56 time to evaluate : 0.385 Fit side-chains REVERT: D 433 GLN cc_start: 0.8005 (OUTLIER) cc_final: 0.7779 (mt0) REVERT: D 483 LYS cc_start: 0.8517 (OUTLIER) cc_final: 0.8269 (mmpt) REVERT: D 749 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8521 (mt) outliers start: 13 outliers final: 8 residues processed: 65 average time/residue: 1.1602 time to fit residues: 77.7487 Evaluate side-chains 69 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 11 LYS Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 433 GLN Chi-restraints excluded: chain D residue 483 LYS Chi-restraints excluded: chain D residue 535 PHE Chi-restraints excluded: chain D residue 565 GLU Chi-restraints excluded: chain D residue 749 LEU Chi-restraints excluded: chain D residue 770 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 9 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 35 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 158 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 3197 Z= 0.323 Angle : 0.562 7.433 4312 Z= 0.280 Chirality : 0.040 0.133 498 Planarity : 0.004 0.027 541 Dihedral : 5.345 42.698 424 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.91 % Allowed : 14.80 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.42), residues: 373 helix: 1.35 (0.42), residues: 143 sheet: 0.10 (0.47), residues: 104 loop : 0.22 (0.57), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 487 HIS 0.004 0.001 HIS D 584 PHE 0.011 0.002 PHE D 750 TYR 0.012 0.002 TYR D 504 ARG 0.005 0.001 ARG D 186 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 60 time to evaluate : 0.378 Fit side-chains REVERT: D 483 LYS cc_start: 0.8502 (OUTLIER) cc_final: 0.8250 (mmpt) REVERT: D 749 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8531 (mt) outliers start: 14 outliers final: 8 residues processed: 69 average time/residue: 1.2512 time to fit residues: 88.7684 Evaluate side-chains 71 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 11 LYS Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 483 LYS Chi-restraints excluded: chain D residue 535 PHE Chi-restraints excluded: chain D residue 565 GLU Chi-restraints excluded: chain D residue 749 LEU Chi-restraints excluded: chain D residue 770 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 20 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 14 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 158 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3197 Z= 0.193 Angle : 0.501 7.612 4312 Z= 0.251 Chirality : 0.037 0.128 498 Planarity : 0.003 0.029 541 Dihedral : 5.102 41.603 424 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.35 % Allowed : 15.64 % Favored : 81.01 % 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: 1.09 (0.43), residues: 373 helix: 1.69 (0.42), residues: 142 sheet: 0.15 (0.47), residues: 104 loop : 0.29 (0.57), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP D 487 HIS 0.003 0.001 HIS D 584 PHE 0.008 0.001 PHE D 453 TYR 0.010 0.001 TYR D 504 ARG 0.006 0.001 ARG D 186 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 0.381 Fit side-chains REVERT: C 48 LYS cc_start: 0.8001 (mptp) cc_final: 0.7799 (mmtt) REVERT: D 483 LYS cc_start: 0.8487 (OUTLIER) cc_final: 0.8267 (mmpt) REVERT: D 749 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8522 (mt) outliers start: 12 outliers final: 7 residues processed: 65 average time/residue: 1.1140 time to fit residues: 74.7479 Evaluate side-chains 65 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 483 LYS Chi-restraints excluded: chain D residue 535 PHE Chi-restraints excluded: chain D residue 565 GLU Chi-restraints excluded: chain D residue 749 LEU Chi-restraints excluded: chain D residue 770 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 18 optimal weight: 6.9990 chunk 3 optimal weight: 0.0070 chunk 28 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 35 optimal weight: 6.9990 chunk 32 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 14 optimal weight: 9.9990 chunk 26 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 overall best weight: 0.6800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 158 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3197 Z= 0.168 Angle : 0.512 11.197 4312 Z= 0.250 Chirality : 0.037 0.131 498 Planarity : 0.003 0.026 541 Dihedral : 4.947 41.218 424 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.51 % Allowed : 16.76 % Favored : 80.73 % 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: 1.29 (0.43), residues: 373 helix: 1.91 (0.42), residues: 142 sheet: 0.23 (0.49), residues: 104 loop : 0.36 (0.57), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP D 487 HIS 0.003 0.001 HIS D 584 PHE 0.008 0.001 PHE D 453 TYR 0.012 0.001 TYR D 576 ARG 0.006 0.000 ARG D 186 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.384 Fit side-chains REVERT: C 48 LYS cc_start: 0.7970 (mptp) cc_final: 0.7761 (mmtt) REVERT: D 455 ASP cc_start: 0.7500 (p0) cc_final: 0.7140 (p0) REVERT: D 483 LYS cc_start: 0.8477 (OUTLIER) cc_final: 0.8260 (mmpt) REVERT: D 749 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8530 (mt) outliers start: 9 outliers final: 6 residues processed: 63 average time/residue: 1.1632 time to fit residues: 75.6298 Evaluate side-chains 65 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 483 LYS Chi-restraints excluded: chain D residue 535 PHE Chi-restraints excluded: chain D residue 565 GLU Chi-restraints excluded: chain D residue 749 LEU Chi-restraints excluded: chain D residue 770 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 30 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 34 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 3 optimal weight: 0.0670 chunk 23 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 158 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3197 Z= 0.178 Angle : 0.521 11.404 4312 Z= 0.253 Chirality : 0.037 0.129 498 Planarity : 0.003 0.026 541 Dihedral : 4.924 41.161 424 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.51 % Allowed : 16.48 % Favored : 81.01 % 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: 1.39 (0.43), residues: 373 helix: 2.01 (0.42), residues: 142 sheet: 0.27 (0.49), residues: 104 loop : 0.39 (0.57), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP D 487 HIS 0.003 0.001 HIS D 584 PHE 0.008 0.001 PHE D 579 TYR 0.012 0.001 TYR D 576 ARG 0.006 0.001 ARG D 186 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 58 time to evaluate : 0.372 Fit side-chains REVERT: C 48 LYS cc_start: 0.7986 (mptp) cc_final: 0.7782 (mmtt) REVERT: D 455 ASP cc_start: 0.7476 (p0) cc_final: 0.7119 (p0) REVERT: D 483 LYS cc_start: 0.8475 (OUTLIER) cc_final: 0.8261 (mmpt) REVERT: D 749 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8528 (mt) outliers start: 9 outliers final: 4 residues processed: 64 average time/residue: 1.1858 time to fit residues: 78.2353 Evaluate side-chains 63 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 57 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 483 LYS Chi-restraints excluded: chain D residue 535 PHE Chi-restraints excluded: chain D residue 749 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 23 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 3 optimal weight: 0.4980 chunk 5 optimal weight: 0.6980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 158 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3197 Z= 0.251 Angle : 0.551 10.870 4312 Z= 0.268 Chirality : 0.038 0.129 498 Planarity : 0.003 0.029 541 Dihedral : 5.091 41.742 424 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.79 % Allowed : 17.04 % Favored : 80.17 % 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: 1.25 (0.43), residues: 373 helix: 1.83 (0.42), residues: 142 sheet: 0.22 (0.49), residues: 104 loop : 0.40 (0.57), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 487 HIS 0.004 0.001 HIS D 584 PHE 0.009 0.002 PHE D 750 TYR 0.016 0.001 TYR D 576 ARG 0.005 0.001 ARG D 186 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 0.386 Fit side-chains REVERT: D 455 ASP cc_start: 0.7516 (p0) cc_final: 0.7169 (p0) REVERT: D 483 LYS cc_start: 0.8475 (OUTLIER) cc_final: 0.8243 (mmpt) REVERT: D 749 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8538 (mt) outliers start: 10 outliers final: 4 residues processed: 64 average time/residue: 1.1612 time to fit residues: 76.6271 Evaluate side-chains 64 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 483 LYS Chi-restraints excluded: chain D residue 535 PHE Chi-restraints excluded: chain D residue 749 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 26 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 37 optimal weight: 0.5980 chunk 0 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 158 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.132309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.104874 restraints weight = 3396.064| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 1.84 r_work: 0.2982 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3197 Z= 0.200 Angle : 0.549 13.421 4312 Z= 0.265 Chirality : 0.037 0.131 498 Planarity : 0.003 0.028 541 Dihedral : 5.013 41.331 424 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.23 % Allowed : 17.88 % Favored : 79.89 % 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: 1.37 (0.44), residues: 373 helix: 1.96 (0.42), residues: 142 sheet: 0.22 (0.49), residues: 104 loop : 0.46 (0.58), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP D 487 HIS 0.003 0.001 HIS D 584 PHE 0.007 0.001 PHE D 579 TYR 0.012 0.001 TYR D 576 ARG 0.005 0.000 ARG D 186 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1900.65 seconds wall clock time: 34 minutes 55.96 seconds (2095.96 seconds total)