Starting phenix.real_space_refine on Wed Mar 4 04:14:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k30_62002/03_2026/9k30_62002.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k30_62002/03_2026/9k30_62002.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9k30_62002/03_2026/9k30_62002.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k30_62002/03_2026/9k30_62002.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9k30_62002/03_2026/9k30_62002.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k30_62002/03_2026/9k30_62002.map" } resolution = 3.17 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.058 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 334 5.49 5 Mg 1 5.21 5 S 19 5.16 5 C 5431 2.51 5 N 1929 2.21 5 O 2909 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10624 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3551 Classifications: {'peptide': 441} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 422} Chain breaks: 3 Chain: "B" Number of atoms: 6261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 6261 Classifications: {'RNA': 294} Modifications used: {'rna2p_pur': 15, 'rna2p_pyr': 13, 'rna3p_pur': 144, 'rna3p_pyr': 122} Link IDs: {'rna2p': 27, 'rna3p': 266} Chain breaks: 2 Chain: "C" Number of atoms: 583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 583 Classifications: {'DNA': 29} Link IDs: {'rna3p': 28} Chain: "D" Number of atoms: 227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 227 Classifications: {'DNA': 11} Link IDs: {'rna3p': 10} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1020 SG CYS A 125 31.529 83.927 77.087 1.00 90.03 S ATOM 1040 SG CYS A 128 27.886 84.496 76.209 1.00 91.19 S ATOM 1112 SG CYS A 139 30.618 86.444 74.477 1.00 91.01 S Time building chain proxies: 2.38, per 1000 atoms: 0.22 Number of scatterers: 10624 At special positions: 0 Unit cell: (83, 109.56, 152.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 19 16.00 P 334 15.00 Mg 1 11.99 O 2909 8.00 N 1929 7.00 C 5431 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: 0.87 Conformation dependent library (CDL) restraints added in 353.4 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 601 " pdb="ZN ZN A 601 " - pdb=" ND1 HIS A 142 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 139 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 125 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 128 " Number of angles added : 3 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 842 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 7 sheets defined 25.4% alpha, 27.7% beta 123 base pairs and 222 stacking pairs defined. Time for finding SS restraints: 1.53 Creating SS restraints... Processing helix chain 'A' and resid 17 through 27 Processing helix chain 'A' and resid 91 through 109 removed outlier: 3.732A pdb=" N ARG A 109 " --> pdb=" O CYS A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 176 removed outlier: 3.657A pdb=" N ARG A 164 " --> pdb=" O SER A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 198 Processing helix chain 'A' and resid 211 through 225 removed outlier: 3.588A pdb=" N ILE A 222 " --> pdb=" O LYS A 218 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU A 224 " --> pdb=" O ALA A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 314 removed outlier: 3.717A pdb=" N LEU A 313 " --> pdb=" O TYR A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 329 Processing helix chain 'A' and resid 336 through 347 removed outlier: 3.524A pdb=" N THR A 340 " --> pdb=" O TYR A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 363 removed outlier: 3.555A pdb=" N VAL A 359 " --> pdb=" O ASN A 355 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 6 removed outlier: 6.422A pdb=" N PHE A 4 " --> pdb=" O ILE A 40 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N LEU A 42 " --> pdb=" O PHE A 4 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N VAL A 6 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N VAL A 39 " --> pdb=" O LYS A 33 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 332 through 333 removed outlier: 6.858A pdb=" N ILE A 184 " --> pdb=" O SER A 333 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N VAL A 54 " --> pdb=" O ASN A 183 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N ILE A 185 " --> pdb=" O VAL A 54 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N VAL A 56 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ALA A 68 " --> pdb=" O GLY A 57 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE A 82 " --> pdb=" O VAL A 69 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N VAL A 71 " --> pdb=" O VAL A 80 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N VAL A 80 " --> pdb=" O VAL A 71 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 332 through 333 removed outlier: 6.858A pdb=" N ILE A 184 " --> pdb=" O SER A 333 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N VAL A 54 " --> pdb=" O ASN A 183 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N ILE A 185 " --> pdb=" O VAL A 54 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N VAL A 56 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ALA A 68 " --> pdb=" O GLY A 57 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE A 82 " --> pdb=" O VAL A 69 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N VAL A 71 " --> pdb=" O VAL A 80 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N VAL A 80 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 8.516A pdb=" N TYR A 381 " --> pdb=" O VAL A 81 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N LYS A 83 " --> pdb=" O TYR A 381 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N ILE A 383 " --> pdb=" O LYS A 83 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N GLN A 85 " --> pdb=" O ILE A 383 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N ASP A 87 " --> pdb=" O PRO A 385 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 394 through 399 removed outlier: 5.013A pdb=" N ALA A 432 " --> pdb=" O THR A 395 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N THR A 397 " --> pdb=" O ILE A 430 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ILE A 430 " --> pdb=" O THR A 397 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 405 through 408 Processing sheet with id=AA6, first strand: chain 'A' and resid 448 through 455 removed outlier: 3.565A pdb=" N ALA A 439 " --> pdb=" O ILE A 454 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N MET A 466 " --> pdb=" O LEU A 442 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 503 through 507 removed outlier: 3.504A pdb=" N ALA A 507 " --> pdb=" O ILE A 496 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N LYS A 497 " --> pdb=" O SER A 488 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE A 486 " --> pdb=" O ASN A 499 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N TYR A 516 " --> pdb=" O THR A 473 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N GLU A 475 " --> pdb=" O LEU A 514 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N LEU A 514 " --> pdb=" O GLU A 475 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N ASN A 477 " --> pdb=" O THR A 512 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N THR A 512 " --> pdb=" O ASN A 477 " (cutoff:3.500A) 126 hydrogen bonds defined for protein. 354 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 298 hydrogen bonds 548 hydrogen bond angles 0 basepair planarities 123 basepair parallelities 222 stacking parallelities Total time for adding SS restraints: 2.77 Time building geometry restraints manager: 1.23 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: 1652 1.34 - 1.46: 4642 1.46 - 1.58: 4508 1.58 - 1.70: 684 1.70 - 1.82: 27 Bond restraints: 11513 Sorted by residual: bond pdb=" C LEU A 157 " pdb=" N PRO A 158 " ideal model delta sigma weight residual 1.331 1.371 -0.039 8.70e-03 1.32e+04 2.06e+01 bond pdb=" C ILE A 179 " pdb=" N PRO A 180 " ideal model delta sigma weight residual 1.335 1.372 -0.037 8.70e-03 1.32e+04 1.82e+01 bond pdb=" O5' A B 338 " pdb=" C5' A B 338 " ideal model delta sigma weight residual 1.420 1.478 -0.058 1.50e-02 4.44e+03 1.47e+01 bond pdb=" C ILE A 349 " pdb=" N PRO A 350 " ideal model delta sigma weight residual 1.330 1.376 -0.046 1.22e-02 6.72e+03 1.41e+01 bond pdb=" O5' C B 285 " pdb=" C5' C B 285 " ideal model delta sigma weight residual 1.420 1.475 -0.055 1.50e-02 4.44e+03 1.37e+01 ... (remaining 11508 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.14: 14977 2.14 - 4.28: 2015 4.28 - 6.42: 124 6.42 - 8.56: 14 8.56 - 10.70: 2 Bond angle restraints: 17132 Sorted by residual: angle pdb=" CA ASP A 366 " pdb=" CB ASP A 366 " pdb=" CG ASP A 366 " ideal model delta sigma weight residual 112.60 118.04 -5.44 1.00e+00 1.00e+00 2.96e+01 angle pdb=" C TYR A 365 " pdb=" CA TYR A 365 " pdb=" CB TYR A 365 " ideal model delta sigma weight residual 110.42 121.12 -10.70 1.99e+00 2.53e-01 2.89e+01 angle pdb=" C TYR A 336 " pdb=" CA TYR A 336 " pdb=" CB TYR A 336 " ideal model delta sigma weight residual 109.33 118.47 -9.14 1.97e+00 2.58e-01 2.15e+01 angle pdb=" N TYR A 102 " pdb=" CA TYR A 102 " pdb=" CB TYR A 102 " ideal model delta sigma weight residual 110.12 116.88 -6.76 1.47e+00 4.63e-01 2.11e+01 angle pdb=" CA THR A 16 " pdb=" CB THR A 16 " pdb=" OG1 THR A 16 " ideal model delta sigma weight residual 109.60 102.73 6.87 1.50e+00 4.44e-01 2.10e+01 ... (remaining 17127 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.31: 6324 30.31 - 60.62: 596 60.62 - 90.93: 211 90.93 - 121.25: 1 121.25 - 151.56: 1 Dihedral angle restraints: 7133 sinusoidal: 5836 harmonic: 1297 Sorted by residual: dihedral pdb=" C5' G B 168 " pdb=" C4' G B 168 " pdb=" C3' G B 168 " pdb=" O3' G B 168 " ideal model delta sinusoidal sigma weight residual 147.00 98.22 48.78 1 8.00e+00 1.56e-02 5.12e+01 dihedral pdb=" O4' U B -9 " pdb=" C2' U B -9 " pdb=" C1' U B -9 " pdb=" C3' U B -9 " ideal model delta sinusoidal sigma weight residual 25.00 -22.22 47.22 1 8.00e+00 1.56e-02 4.81e+01 dihedral pdb=" C5' U B 299 " pdb=" C4' U B 299 " pdb=" C3' U B 299 " pdb=" O3' U B 299 " ideal model delta sinusoidal sigma weight residual 147.00 101.55 45.45 1 8.00e+00 1.56e-02 4.48e+01 ... (remaining 7130 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.128: 1703 0.128 - 0.256: 466 0.256 - 0.385: 0 0.385 - 0.513: 0 0.513 - 0.641: 5 Chirality restraints: 2174 Sorted by residual: chirality pdb=" P DC C -9 " pdb=" OP1 DC C -9 " pdb=" OP2 DC C -9 " pdb=" O5' DC C -9 " both_signs ideal model delta sigma weight residual True 2.35 -2.99 -0.64 2.00e-01 2.50e+01 1.03e+01 chirality pdb=" P DC D -1 " pdb=" OP1 DC D -1 " pdb=" OP2 DC D -1 " pdb=" O5' DC D -1 " both_signs ideal model delta sigma weight residual True 2.35 2.99 -0.64 2.00e-01 2.50e+01 1.02e+01 chirality pdb=" P C B 144 " pdb=" OP1 C B 144 " pdb=" OP2 C B 144 " pdb=" O5' C B 144 " both_signs ideal model delta sigma weight residual True 2.41 -2.98 -0.57 2.00e-01 2.50e+01 8.26e+00 ... (remaining 2171 not shown) Planarity restraints: 949 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 34 " -0.155 9.50e-02 1.11e+02 7.01e-02 3.72e+00 pdb=" NE ARG A 34 " 0.005 2.00e-02 2.50e+03 pdb=" CZ ARG A 34 " 0.017 2.00e-02 2.50e+03 pdb=" NH1 ARG A 34 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 34 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 414 " -0.120 9.50e-02 1.11e+02 5.41e-02 2.30e+00 pdb=" NE ARG A 414 " 0.012 2.00e-02 2.50e+03 pdb=" CZ ARG A 414 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG A 414 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A 414 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG D 1 " -0.014 2.00e-02 2.50e+03 6.17e-03 1.14e+00 pdb=" N9 DG D 1 " 0.015 2.00e-02 2.50e+03 pdb=" C8 DG D 1 " 0.002 2.00e-02 2.50e+03 pdb=" N7 DG D 1 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DG D 1 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DG D 1 " -0.004 2.00e-02 2.50e+03 pdb=" O6 DG D 1 " -0.002 2.00e-02 2.50e+03 pdb=" N1 DG D 1 " 0.000 2.00e-02 2.50e+03 pdb=" C2 DG D 1 " 0.001 2.00e-02 2.50e+03 pdb=" N2 DG D 1 " 0.000 2.00e-02 2.50e+03 pdb=" N3 DG D 1 " 0.003 2.00e-02 2.50e+03 pdb=" C4 DG D 1 " 0.000 2.00e-02 2.50e+03 ... (remaining 946 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 20 2.55 - 3.14: 6649 3.14 - 3.72: 18518 3.72 - 4.31: 27549 4.31 - 4.90: 36921 Nonbonded interactions: 89657 Sorted by model distance: nonbonded pdb=" OP1 G B 275 " pdb="MG MG B 501 " model vdw 1.959 2.170 nonbonded pdb=" OP1 A B 276 " pdb="MG MG B 501 " model vdw 2.265 2.170 nonbonded pdb=" O TYR A 309 " pdb=" N GLN A 312 " model vdw 2.431 3.120 nonbonded pdb=" O2' U B 236 " pdb=" O2' C B 355 " model vdw 2.464 3.040 nonbonded pdb=" OE1 GLN A 52 " pdb=" O2' A B 411 " model vdw 2.468 3.040 ... (remaining 89652 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: 1.270 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: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.160 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:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 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 : 0.011 0.083 11517 Z= 0.700 Angle : 1.394 10.703 17135 Z= 0.880 Chirality : 0.097 0.641 2174 Planarity : 0.004 0.070 949 Dihedral : 21.380 151.557 6291 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 0.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 2.02 % Allowed : 9.85 % Favored : 88.13 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.07 (0.34), residues: 433 helix: -2.05 (0.40), residues: 102 sheet: -1.39 (0.50), residues: 104 loop : -2.35 (0.34), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 34 TYR 0.012 0.002 TYR A 336 PHE 0.005 0.001 PHE A 331 TRP 0.011 0.002 TRP A 342 HIS 0.001 0.001 HIS A 142 Details of bonding type rmsd covalent geometry : bond 0.01118 (11513) covalent geometry : angle 1.39326 (17132) hydrogen bonds : bond 0.19264 ( 416) hydrogen bonds : angle 7.49832 ( 902) metal coordination : bond 0.04212 ( 4) metal coordination : angle 3.83734 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 100 time to evaluate : 0.223 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 317 LYS cc_start: 0.9048 (ttpt) cc_final: 0.8831 (ttpp) REVERT: A 340 THR cc_start: 0.8632 (m) cc_final: 0.8393 (p) REVERT: A 347 PHE cc_start: 0.8343 (m-80) cc_final: 0.8053 (m-80) REVERT: A 366 ASP cc_start: 0.6222 (OUTLIER) cc_final: 0.1056 (t0) outliers start: 8 outliers final: 0 residues processed: 105 average time/residue: 0.1167 time to fit residues: 16.4841 Evaluate side-chains 55 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 54 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 366 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 49 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 10 ASN A 123 ASN A 133 GLN A 182 ASN A 198 ASN ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 338 GLN A 343 GLN A 493 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.076277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.057862 restraints weight = 33955.434| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 2.03 r_work: 0.2920 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 11517 Z= 0.248 Angle : 0.667 7.439 17135 Z= 0.349 Chirality : 0.038 0.210 2174 Planarity : 0.004 0.020 949 Dihedral : 22.165 138.946 5350 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.03 % Allowed : 16.67 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.37), residues: 433 helix: 0.42 (0.48), residues: 109 sheet: -1.06 (0.46), residues: 115 loop : -1.68 (0.37), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 104 TYR 0.020 0.002 TYR A 212 PHE 0.015 0.002 PHE A 331 TRP 0.008 0.003 TRP A 342 HIS 0.003 0.001 HIS A 142 Details of bonding type rmsd covalent geometry : bond 0.00499 (11513) covalent geometry : angle 0.66709 (17132) hydrogen bonds : bond 0.06166 ( 416) hydrogen bonds : angle 3.87216 ( 902) metal coordination : bond 0.01498 ( 4) metal coordination : angle 1.50883 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 57 time to evaluate : 0.218 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 ASN cc_start: 0.8769 (OUTLIER) cc_final: 0.8282 (m110) REVERT: A 347 PHE cc_start: 0.8360 (m-80) cc_final: 0.8139 (m-80) REVERT: A 351 LYS cc_start: 0.9087 (OUTLIER) cc_final: 0.8884 (mttt) outliers start: 12 outliers final: 6 residues processed: 64 average time/residue: 0.1034 time to fit residues: 9.2412 Evaluate side-chains 56 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 48 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ASN Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 351 LYS Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 379 ASP Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 512 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 69 optimal weight: 7.9990 chunk 27 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 45 optimal weight: 6.9990 chunk 48 optimal weight: 6.9990 chunk 53 optimal weight: 5.9990 chunk 56 optimal weight: 6.9990 chunk 71 optimal weight: 10.0000 chunk 47 optimal weight: 10.0000 chunk 54 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.073688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.055515 restraints weight = 34666.348| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 2.07 r_work: 0.2873 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.3095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 11517 Z= 0.299 Angle : 0.644 7.855 17135 Z= 0.335 Chirality : 0.037 0.224 2174 Planarity : 0.004 0.028 949 Dihedral : 22.343 138.809 5348 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 4.80 % Allowed : 17.17 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.38), residues: 433 helix: 0.81 (0.50), residues: 109 sheet: -1.14 (0.45), residues: 121 loop : -1.65 (0.39), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 344 TYR 0.020 0.002 TYR A 212 PHE 0.009 0.002 PHE A 331 TRP 0.009 0.002 TRP A 342 HIS 0.003 0.001 HIS A 142 Details of bonding type rmsd covalent geometry : bond 0.00595 (11513) covalent geometry : angle 0.64356 (17132) hydrogen bonds : bond 0.06374 ( 416) hydrogen bonds : angle 3.75340 ( 902) metal coordination : bond 0.02151 ( 4) metal coordination : angle 2.04534 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 52 time to evaluate : 0.155 Fit side-chains revert: symmetry clash REVERT: A 200 ASP cc_start: 0.8963 (m-30) cc_final: 0.7972 (t0) REVERT: A 215 ASP cc_start: 0.8666 (m-30) cc_final: 0.8465 (m-30) REVERT: A 221 LEU cc_start: 0.8364 (mt) cc_final: 0.8159 (pp) REVERT: A 306 THR cc_start: 0.8721 (OUTLIER) cc_final: 0.8344 (m) REVERT: A 326 ASP cc_start: 0.8448 (m-30) cc_final: 0.8201 (m-30) REVERT: A 347 PHE cc_start: 0.8434 (m-80) cc_final: 0.7973 (m-80) REVERT: A 501 GLN cc_start: 0.7604 (pm20) cc_final: 0.7400 (pm20) outliers start: 19 outliers final: 12 residues processed: 65 average time/residue: 0.0924 time to fit residues: 8.7915 Evaluate side-chains 57 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 44 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 379 ASP Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 490 CYS Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 522 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 45 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 53 optimal weight: 5.9990 chunk 7 optimal weight: 6.9990 chunk 26 optimal weight: 7.9990 chunk 4 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 183 ASN ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 353 HIS A 524 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.073998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.055954 restraints weight = 34473.454| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 2.06 r_work: 0.2884 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.3293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 11517 Z= 0.249 Angle : 0.603 7.516 17135 Z= 0.310 Chirality : 0.034 0.201 2174 Planarity : 0.004 0.026 949 Dihedral : 22.301 137.887 5348 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 3.79 % Allowed : 18.69 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.38), residues: 433 helix: 0.95 (0.51), residues: 109 sheet: -1.12 (0.46), residues: 116 loop : -1.59 (0.38), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 344 TYR 0.012 0.002 TYR A 44 PHE 0.009 0.001 PHE A 331 TRP 0.010 0.002 TRP A 342 HIS 0.002 0.001 HIS A 142 Details of bonding type rmsd covalent geometry : bond 0.00492 (11513) covalent geometry : angle 0.60321 (17132) hydrogen bonds : bond 0.05819 ( 416) hydrogen bonds : angle 3.50633 ( 902) metal coordination : bond 0.01703 ( 4) metal coordination : angle 1.52526 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 45 time to evaluate : 0.221 Fit side-chains revert: symmetry clash REVERT: A 98 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.8330 (mp0) REVERT: A 326 ASP cc_start: 0.8396 (m-30) cc_final: 0.8051 (m-30) REVERT: A 347 PHE cc_start: 0.8386 (m-80) cc_final: 0.7979 (m-80) outliers start: 15 outliers final: 8 residues processed: 54 average time/residue: 0.0883 time to fit residues: 7.1522 Evaluate side-chains 51 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 98 GLU Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 379 ASP Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 522 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 43 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 39 optimal weight: 6.9990 chunk 15 optimal weight: 0.7980 chunk 35 optimal weight: 4.9990 chunk 7 optimal weight: 7.9990 chunk 37 optimal weight: 2.9990 chunk 48 optimal weight: 6.9990 chunk 74 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 353 HIS A 437 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.075050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.056873 restraints weight = 34422.435| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 1.97 r_work: 0.2917 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.3473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 11517 Z= 0.177 Angle : 0.558 6.983 17135 Z= 0.286 Chirality : 0.031 0.181 2174 Planarity : 0.003 0.025 949 Dihedral : 22.245 138.549 5348 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 3.28 % Allowed : 19.44 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.38), residues: 433 helix: 1.13 (0.50), residues: 108 sheet: -1.00 (0.47), residues: 114 loop : -1.40 (0.38), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 412 TYR 0.015 0.001 TYR A 212 PHE 0.007 0.001 PHE A 331 TRP 0.008 0.001 TRP A 342 HIS 0.001 0.001 HIS A 353 Details of bonding type rmsd covalent geometry : bond 0.00351 (11513) covalent geometry : angle 0.55797 (17132) hydrogen bonds : bond 0.05269 ( 416) hydrogen bonds : angle 3.29467 ( 902) metal coordination : bond 0.01176 ( 4) metal coordination : angle 1.00214 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 45 time to evaluate : 0.165 Fit side-chains revert: symmetry clash REVERT: A 98 GLU cc_start: 0.8633 (OUTLIER) cc_final: 0.8416 (mp0) REVERT: A 200 ASP cc_start: 0.8608 (m-30) cc_final: 0.7721 (t0) REVERT: A 221 LEU cc_start: 0.8271 (mt) cc_final: 0.8029 (pp) REVERT: A 326 ASP cc_start: 0.8455 (m-30) cc_final: 0.7976 (m-30) REVERT: A 347 PHE cc_start: 0.8433 (m-80) cc_final: 0.8003 (m-80) REVERT: A 456 MET cc_start: 0.8552 (mmm) cc_final: 0.8342 (mmm) outliers start: 13 outliers final: 9 residues processed: 54 average time/residue: 0.0913 time to fit residues: 7.2108 Evaluate side-chains 52 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 42 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 98 GLU Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 379 ASP Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 490 CYS Chi-restraints excluded: chain A residue 512 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 68 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 chunk 46 optimal weight: 6.9990 chunk 14 optimal weight: 10.0000 chunk 49 optimal weight: 5.9990 chunk 17 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 70 optimal weight: 10.0000 chunk 0 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 44 optimal weight: 10.0000 overall best weight: 3.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.073325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.055259 restraints weight = 34631.172| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 2.11 r_work: 0.2866 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.3629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 11517 Z= 0.301 Angle : 0.631 7.708 17135 Z= 0.322 Chirality : 0.036 0.208 2174 Planarity : 0.004 0.027 949 Dihedral : 22.290 137.363 5348 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 4.29 % Allowed : 18.94 % Favored : 76.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.38), residues: 433 helix: 0.98 (0.49), residues: 110 sheet: -1.14 (0.47), residues: 114 loop : -1.65 (0.38), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 22 TYR 0.011 0.002 TYR A 212 PHE 0.007 0.001 PHE A 331 TRP 0.012 0.002 TRP A 342 HIS 0.003 0.001 HIS A 353 Details of bonding type rmsd covalent geometry : bond 0.00594 (11513) covalent geometry : angle 0.63090 (17132) hydrogen bonds : bond 0.06260 ( 416) hydrogen bonds : angle 3.38632 ( 902) metal coordination : bond 0.02058 ( 4) metal coordination : angle 2.09894 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 43 time to evaluate : 0.215 Fit side-chains revert: symmetry clash REVERT: A 200 ASP cc_start: 0.8471 (m-30) cc_final: 0.7520 (t0) REVERT: A 221 LEU cc_start: 0.8346 (mt) cc_final: 0.8122 (pp) REVERT: A 326 ASP cc_start: 0.8502 (m-30) cc_final: 0.8032 (m-30) REVERT: A 347 PHE cc_start: 0.8458 (m-80) cc_final: 0.8037 (m-80) outliers start: 17 outliers final: 10 residues processed: 56 average time/residue: 0.0920 time to fit residues: 7.6162 Evaluate side-chains 48 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 38 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 379 ASP Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 490 CYS Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 522 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 67 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 54 optimal weight: 6.9990 chunk 2 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 28 optimal weight: 7.9990 chunk 59 optimal weight: 7.9990 chunk 73 optimal weight: 6.9990 chunk 7 optimal weight: 4.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 10 ASN ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.072500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.054510 restraints weight = 34470.092| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 2.14 r_work: 0.2847 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.3771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 11517 Z= 0.359 Angle : 0.674 8.085 17135 Z= 0.344 Chirality : 0.038 0.225 2174 Planarity : 0.005 0.031 949 Dihedral : 22.381 136.571 5348 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 3.79 % Allowed : 20.20 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.52 (0.38), residues: 433 helix: 0.74 (0.49), residues: 109 sheet: -1.29 (0.46), residues: 114 loop : -1.78 (0.38), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 22 TYR 0.014 0.002 TYR A 212 PHE 0.007 0.002 PHE A 331 TRP 0.010 0.002 TRP A 342 HIS 0.003 0.001 HIS A 142 Details of bonding type rmsd covalent geometry : bond 0.00712 (11513) covalent geometry : angle 0.67339 (17132) hydrogen bonds : bond 0.06631 ( 416) hydrogen bonds : angle 3.54487 ( 902) metal coordination : bond 0.02607 ( 4) metal coordination : angle 2.28917 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 39 time to evaluate : 0.245 Fit side-chains REVERT: A 10 ASN cc_start: 0.8959 (OUTLIER) cc_final: 0.8737 (m-40) REVERT: A 200 ASP cc_start: 0.8466 (m-30) cc_final: 0.8236 (m-30) REVERT: A 326 ASP cc_start: 0.8397 (m-30) cc_final: 0.7950 (m-30) REVERT: A 347 PHE cc_start: 0.8450 (m-80) cc_final: 0.8066 (m-80) REVERT: A 456 MET cc_start: 0.8583 (mmm) cc_final: 0.8309 (mmm) outliers start: 15 outliers final: 11 residues processed: 52 average time/residue: 0.0819 time to fit residues: 6.4635 Evaluate side-chains 50 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 38 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ASN Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 379 ASP Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 490 CYS Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 522 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 6 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 56 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 44 optimal weight: 10.0000 chunk 35 optimal weight: 0.9990 chunk 61 optimal weight: 7.9990 chunk 60 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.074588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.056385 restraints weight = 34433.073| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 2.04 r_work: 0.2894 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.3834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11517 Z= 0.199 Angle : 0.578 7.132 17135 Z= 0.295 Chirality : 0.032 0.176 2174 Planarity : 0.004 0.029 949 Dihedral : 22.345 136.242 5348 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.77 % Allowed : 21.97 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.38), residues: 433 helix: 0.88 (0.49), residues: 108 sheet: -1.03 (0.48), residues: 114 loop : -1.61 (0.38), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 412 TYR 0.009 0.001 TYR A 102 PHE 0.008 0.001 PHE A 331 TRP 0.003 0.001 TRP A 342 HIS 0.001 0.000 HIS A 142 Details of bonding type rmsd covalent geometry : bond 0.00394 (11513) covalent geometry : angle 0.57756 (17132) hydrogen bonds : bond 0.05333 ( 416) hydrogen bonds : angle 3.30663 ( 902) metal coordination : bond 0.01440 ( 4) metal coordination : angle 1.31465 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.201 Fit side-chains REVERT: A 326 ASP cc_start: 0.8350 (m-30) cc_final: 0.7947 (m-30) REVERT: A 456 MET cc_start: 0.8547 (mmm) cc_final: 0.8291 (mmm) outliers start: 7 outliers final: 7 residues processed: 44 average time/residue: 0.0919 time to fit residues: 5.9988 Evaluate side-chains 46 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 39 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 379 ASP Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 490 CYS Chi-restraints excluded: chain A residue 512 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 43 optimal weight: 0.4980 chunk 0 optimal weight: 7.9990 chunk 59 optimal weight: 7.9990 chunk 21 optimal weight: 3.9990 chunk 67 optimal weight: 6.9990 chunk 71 optimal weight: 10.0000 chunk 49 optimal weight: 6.9990 chunk 31 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 75 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 overall best weight: 3.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 10 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.073363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.055236 restraints weight = 34541.587| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 2.11 r_work: 0.2869 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.3911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 11517 Z= 0.294 Angle : 0.637 12.705 17135 Z= 0.323 Chirality : 0.035 0.204 2174 Planarity : 0.004 0.035 949 Dihedral : 22.362 135.996 5348 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 3.03 % Allowed : 21.46 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.38), residues: 433 helix: 0.74 (0.50), residues: 108 sheet: -1.13 (0.48), residues: 114 loop : -1.70 (0.38), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 346 TYR 0.009 0.002 TYR A 336 PHE 0.046 0.003 PHE A 347 TRP 0.005 0.002 TRP A 156 HIS 0.002 0.001 HIS A 142 Details of bonding type rmsd covalent geometry : bond 0.00582 (11513) covalent geometry : angle 0.63642 (17132) hydrogen bonds : bond 0.06113 ( 416) hydrogen bonds : angle 3.41334 ( 902) metal coordination : bond 0.02172 ( 4) metal coordination : angle 1.97793 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 35 time to evaluate : 0.209 Fit side-chains REVERT: A 326 ASP cc_start: 0.8394 (m-30) cc_final: 0.7996 (m-30) REVERT: A 456 MET cc_start: 0.8585 (mmm) cc_final: 0.8328 (mmm) outliers start: 12 outliers final: 10 residues processed: 45 average time/residue: 0.0884 time to fit residues: 5.9796 Evaluate side-chains 45 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 35 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 379 ASP Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 490 CYS Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 522 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 10 optimal weight: 3.9990 chunk 20 optimal weight: 10.0000 chunk 19 optimal weight: 7.9990 chunk 47 optimal weight: 10.0000 chunk 48 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 51 optimal weight: 6.9990 chunk 30 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.073650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.055584 restraints weight = 33904.213| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 2.04 r_work: 0.2880 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.3920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 11517 Z= 0.235 Angle : 0.608 11.191 17135 Z= 0.309 Chirality : 0.033 0.188 2174 Planarity : 0.004 0.036 949 Dihedral : 22.390 135.659 5348 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 3.03 % Allowed : 21.21 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.39), residues: 433 helix: 0.66 (0.49), residues: 110 sheet: -1.09 (0.48), residues: 114 loop : -1.69 (0.39), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 484 TYR 0.009 0.001 TYR A 336 PHE 0.040 0.003 PHE A 347 TRP 0.004 0.001 TRP A 342 HIS 0.002 0.001 HIS A 142 Details of bonding type rmsd covalent geometry : bond 0.00466 (11513) covalent geometry : angle 0.60735 (17132) hydrogen bonds : bond 0.05797 ( 416) hydrogen bonds : angle 3.36872 ( 902) metal coordination : bond 0.01973 ( 4) metal coordination : angle 1.94054 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 35 time to evaluate : 0.224 Fit side-chains REVERT: A 326 ASP cc_start: 0.8376 (m-30) cc_final: 0.7964 (m-30) REVERT: A 456 MET cc_start: 0.8572 (mmm) cc_final: 0.8321 (mmm) outliers start: 12 outliers final: 11 residues processed: 44 average time/residue: 0.0906 time to fit residues: 5.9313 Evaluate side-chains 46 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 35 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 379 ASP Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 490 CYS Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 522 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 44 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 47 optimal weight: 10.0000 chunk 55 optimal weight: 6.9990 chunk 72 optimal weight: 10.0000 chunk 62 optimal weight: 7.9990 chunk 71 optimal weight: 10.0000 chunk 9 optimal weight: 3.9990 chunk 54 optimal weight: 7.9990 chunk 58 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.072033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.054055 restraints weight = 34989.176| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 2.21 r_work: 0.2840 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.4015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.059 11517 Z= 0.423 Angle : 0.722 10.464 17135 Z= 0.365 Chirality : 0.040 0.238 2174 Planarity : 0.005 0.040 949 Dihedral : 22.451 135.025 5348 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 2.78 % Allowed : 21.46 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.71 (0.38), residues: 433 helix: 0.51 (0.49), residues: 109 sheet: -1.36 (0.47), residues: 114 loop : -1.88 (0.38), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 22 TYR 0.011 0.002 TYR A 212 PHE 0.032 0.003 PHE A 347 TRP 0.006 0.002 TRP A 156 HIS 0.003 0.001 HIS A 142 Details of bonding type rmsd covalent geometry : bond 0.00837 (11513) covalent geometry : angle 0.72113 (17132) hydrogen bonds : bond 0.07026 ( 416) hydrogen bonds : angle 3.59525 ( 902) metal coordination : bond 0.03090 ( 4) metal coordination : angle 2.84940 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2198.34 seconds wall clock time: 38 minutes 26.59 seconds (2306.59 seconds total)