Starting phenix.real_space_refine on Tue Aug 4 17:46:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8phw_17677/08_2026/8phw_17677.cif Found real_map, /net/cci-nas-00/data/ceres_data/8phw_17677/08_2026/8phw_17677.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8phw_17677/08_2026/8phw_17677.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8phw_17677/08_2026/8phw_17677.cif" model { file = "/net/cci-nas-00/data/ceres_data/8phw_17677/08_2026/8phw_17677.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8phw_17677/08_2026/8phw_17677.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8phw_17677/08_2026/8phw_17677.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8phw_17677/08_2026/8phw_17677.map" } resolution = 3.6 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= 0.022 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: 4 Type Number sf(0) Gaussians S 36 5.16 5 C 3500 2.51 5 N 847 2.21 5 O 976 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5359 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3528 Classifications: {'peptide': 454} Link IDs: {'PTRANS': 15, 'TRANS': 438} Chain breaks: 7 Chain: "H" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 972 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 3, 'TRANS': 124} Chain: "L" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 800 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "A" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'FY5': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'Y01': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.32, per 1000 atoms: 0.25 Number of scatterers: 5359 At special positions: 0 Unit cell: (87.72, 94.86, 104.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 36 16.00 O 976 8.00 N 847 7.00 C 3500 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 430 " - pdb=" SG CYS A 530 " distance=2.03 Simple disulfide: pdb=" SG CYS A 465 " - pdb=" SG CYS A 485 " distance=2.03 Simple disulfide: pdb=" SG CYS A 474 " - pdb=" SG CYS A 524 " distance=2.03 Simple disulfide: pdb=" SG CYS A 599 " - pdb=" SG CYS A 613 " distance=2.03 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.04 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.04 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: 0.38 Conformation dependent library (CDL) restraints added in 114.5 milliseconds 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1246 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 6 sheets defined 46.4% alpha, 12.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 27 through 52 removed outlier: 3.742A pdb=" N ALA A 40 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS A 41 " --> pdb=" O SER A 37 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA A 45 " --> pdb=" O LYS A 41 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ILE A 46 " --> pdb=" O THR A 42 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N SER A 50 " --> pdb=" O ILE A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 80 removed outlier: 3.860A pdb=" N PHE A 68 " --> pdb=" O SER A 64 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N PHE A 73 " --> pdb=" O ILE A 69 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N GLU A 74 " --> pdb=" O ASP A 70 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ASN A 77 " --> pdb=" O PHE A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 117 removed outlier: 4.217A pdb=" N GLY A 100 " --> pdb=" O LEU A 96 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N CYS A 101 " --> pdb=" O ILE A 97 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N PHE A 102 " --> pdb=" O GLY A 98 " (cutoff:3.500A) Proline residue: A 114 - end of helix removed outlier: 3.612A pdb=" N PHE A 117 " --> pdb=" O LEU A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 185 removed outlier: 3.718A pdb=" N GLY A 184 " --> pdb=" O LEU A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 199 removed outlier: 3.743A pdb=" N LEU A 193 " --> pdb=" O VAL A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 217 removed outlier: 3.891A pdb=" N MET A 217 " --> pdb=" O ASN A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 231 removed outlier: 4.153A pdb=" N ILE A 221 " --> pdb=" O MET A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 245 Processing helix chain 'A' and resid 257 through 274 removed outlier: 4.055A pdb=" N ASN A 261 " --> pdb=" O ALA A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 340 through 366 removed outlier: 3.595A pdb=" N GLN A 348 " --> pdb=" O LEU A 344 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N SER A 351 " --> pdb=" O LEU A 347 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N PHE A 360 " --> pdb=" O PHE A 356 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N LYS A 361 " --> pdb=" O THR A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 381 Processing helix chain 'A' and resid 381 through 400 removed outlier: 3.875A pdb=" N GLY A 394 " --> pdb=" O MET A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 423 removed outlier: 3.522A pdb=" N ALA A 408 " --> pdb=" O THR A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 487 Processing helix chain 'A' and resid 527 through 559 removed outlier: 3.685A pdb=" N THR A 531 " --> pdb=" O ASP A 527 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N TYR A 535 " --> pdb=" O THR A 531 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N PHE A 536 " --> pdb=" O ARG A 532 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU A 550 " --> pdb=" O PHE A 546 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N GLY A 551 " --> pdb=" O PHE A 547 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N THR A 553 " --> pdb=" O ALA A 549 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N SER A 554 " --> pdb=" O LEU A 550 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N VAL A 556 " --> pdb=" O GLY A 552 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N MET A 557 " --> pdb=" O THR A 553 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE A 559 " --> pdb=" O HIS A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 597 Proline residue: A 588 - end of helix Processing helix chain 'A' and resid 617 through 646 removed outlier: 3.665A pdb=" N LEU A 639 " --> pdb=" O SER A 635 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 434 through 435 removed outlier: 7.052A pdb=" N SER A 434 " --> pdb=" O THR A 480 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N HIS A 520 " --> pdb=" O CYS A 474 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 6 through 10 removed outlier: 4.208A pdb=" N GLN H 6 " --> pdb=" O SER H 28 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N SER H 28 " --> pdb=" O GLN H 6 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 48 through 54 removed outlier: 6.837A pdb=" N TRP H 39 " --> pdb=" O VAL H 51 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N SER H 53 " --> pdb=" O ILE H 37 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N ILE H 37 " --> pdb=" O SER H 53 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 5 through 7 Processing sheet with id=AA5, first strand: chain 'L' and resid 54 through 55 removed outlier: 3.777A pdb=" N SER L 54 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N TYR L 50 " --> pdb=" O SER L 54 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N LEU L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N GLN L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 54 through 55 removed outlier: 3.777A pdb=" N SER L 54 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N TYR L 50 " --> pdb=" O SER L 54 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N LEU L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N GLN L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) 264 hydrogen bonds defined for protein. 750 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: 0.64 Time building geometry restraints manager: 0.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 822 1.32 - 1.45: 1624 1.45 - 1.57: 2991 1.57 - 1.70: 1 1.70 - 1.82: 53 Bond restraints: 5491 Sorted by residual: bond pdb=" O20 FY5 A 701 " pdb=" S21 FY5 A 701 " ideal model delta sigma weight residual 1.673 1.603 0.070 2.00e-02 2.50e+03 1.21e+01 bond pdb=" C THR A 186 " pdb=" N PRO A 187 " ideal model delta sigma weight residual 1.331 1.351 -0.020 7.90e-03 1.60e+04 6.28e+00 bond pdb=" C18 FY5 A 701 " pdb=" O20 FY5 A 701 " ideal model delta sigma weight residual 1.372 1.421 -0.049 2.00e-02 2.50e+03 6.04e+00 bond pdb=" N VAL L 34 " pdb=" CA VAL L 34 " ideal model delta sigma weight residual 1.459 1.441 0.018 1.25e-02 6.40e+03 2.09e+00 bond pdb=" C SER H 36 " pdb=" N ILE H 37 " ideal model delta sigma weight residual 1.334 1.316 0.017 1.24e-02 6.50e+03 1.98e+00 ... (remaining 5486 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.36: 7000 1.36 - 2.72: 372 2.72 - 4.07: 56 4.07 - 5.43: 18 5.43 - 6.79: 6 Bond angle restraints: 7452 Sorted by residual: angle pdb=" N ILE A 428 " pdb=" CA ILE A 428 " pdb=" C ILE A 428 " ideal model delta sigma weight residual 112.83 108.67 4.16 9.90e-01 1.02e+00 1.77e+01 angle pdb=" N TYR H 63 " pdb=" CA TYR H 63 " pdb=" C TYR H 63 " ideal model delta sigma weight residual 108.34 112.26 -3.92 1.31e+00 5.83e-01 8.93e+00 angle pdb=" C SER L 51 " pdb=" N ALA L 52 " pdb=" CA ALA L 52 " ideal model delta sigma weight residual 121.54 127.23 -5.69 1.91e+00 2.74e-01 8.89e+00 angle pdb=" CA TYR A 590 " pdb=" CB TYR A 590 " pdb=" CG TYR A 590 " ideal model delta sigma weight residual 113.90 119.01 -5.11 1.80e+00 3.09e-01 8.05e+00 angle pdb=" C ASN A 403 " pdb=" CA ASN A 403 " pdb=" CB ASN A 403 " ideal model delta sigma weight residual 110.42 115.50 -5.08 1.99e+00 2.53e-01 6.51e+00 ... (remaining 7447 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.98: 2730 11.98 - 23.96: 278 23.96 - 35.94: 107 35.94 - 47.92: 36 47.92 - 59.90: 11 Dihedral angle restraints: 3162 sinusoidal: 1199 harmonic: 1963 Sorted by residual: dihedral pdb=" CA CYS A 607 " pdb=" C CYS A 607 " pdb=" N GLY A 608 " pdb=" CA GLY A 608 " ideal model delta harmonic sigma weight residual 180.00 152.90 27.10 0 5.00e+00 4.00e-02 2.94e+01 dihedral pdb=" CA GLY A 608 " pdb=" C GLY A 608 " pdb=" N THR A 609 " pdb=" CA THR A 609 " ideal model delta harmonic sigma weight residual -180.00 -154.57 -25.43 0 5.00e+00 4.00e-02 2.59e+01 dihedral pdb=" CA ASN A 617 " pdb=" C ASN A 617 " pdb=" N SER A 618 " pdb=" CA SER A 618 " ideal model delta harmonic sigma weight residual -180.00 -157.20 -22.80 0 5.00e+00 4.00e-02 2.08e+01 ... (remaining 3159 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 496 0.029 - 0.058: 229 0.058 - 0.087: 76 0.087 - 0.115: 37 0.115 - 0.144: 9 Chirality restraints: 847 Sorted by residual: chirality pdb=" CA VAL A 473 " pdb=" N VAL A 473 " pdb=" C VAL A 473 " pdb=" CB VAL A 473 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.14 2.00e-01 2.50e+01 5.20e-01 chirality pdb=" CA THR A 186 " pdb=" N THR A 186 " pdb=" C THR A 186 " pdb=" CB THR A 186 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.14 2.00e-01 2.50e+01 4.97e-01 chirality pdb=" CA PRO A 220 " pdb=" N PRO A 220 " pdb=" C PRO A 220 " pdb=" CB PRO A 220 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.67e-01 ... (remaining 844 not shown) Planarity restraints: 905 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 219 " -0.038 5.00e-02 4.00e+02 5.77e-02 5.32e+00 pdb=" N PRO A 220 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO A 220 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 220 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY H 106 " -0.030 5.00e-02 4.00e+02 4.59e-02 3.37e+00 pdb=" N PRO H 107 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO H 107 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO H 107 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 590 " -0.013 2.00e-02 2.50e+03 1.01e-02 2.05e+00 pdb=" CG TYR A 590 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 TYR A 590 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR A 590 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR A 590 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR A 590 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 590 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 590 " -0.001 2.00e-02 2.50e+03 ... (remaining 902 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 793 2.75 - 3.29: 5508 3.29 - 3.82: 8421 3.82 - 4.36: 9687 4.36 - 4.90: 16556 Nonbonded interactions: 40965 Sorted by model distance: nonbonded pdb=" O CYS A 101 " pdb=" OG SER A 269 " model vdw 2.209 3.040 nonbonded pdb=" O ALA A 415 " pdb=" OG SER A 418 " model vdw 2.221 3.040 nonbonded pdb=" OD1 ASP L 83 " pdb=" OH TYR L 87 " model vdw 2.235 3.040 nonbonded pdb=" NH2 ARG H 70 " pdb=" O SER H 88 " model vdw 2.248 3.120 nonbonded pdb=" O CYS A 474 " pdb=" N ALA A 519 " model vdw 2.252 3.120 ... (remaining 40960 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.790 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: 0.130 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.710 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 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:0.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 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 : 0.005 0.070 5497 Z= 0.233 Angle : 0.723 6.790 7464 Z= 0.423 Chirality : 0.041 0.144 847 Planarity : 0.005 0.058 905 Dihedral : 12.493 59.901 1898 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 6.20 % Allowed : 7.75 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.65 (0.26), residues: 669 helix: -1.77 (0.25), residues: 283 sheet: -1.50 (0.57), residues: 81 loop : -3.36 (0.26), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 70 TYR 0.025 0.002 TYR A 590 PHE 0.010 0.001 PHE A 537 TRP 0.014 0.002 TRP A 254 HIS 0.003 0.001 HIS A 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.23 ( 5491) covalent geometry : angle 0.72217 / 0.42 ( 7452) SS BOND : bond 0.00428 / 0.31 ( 6) SS BOND : angle 1.12052 / 0.55 ( 12) hydrogen bonds : bond 0.13904 / 9.20 ( 256) hydrogen bonds : angle 5.86732 / 4.15 ( 750) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 137 time to evaluate : 0.178 Fit side-chains revert: symmetry clash REVERT: A 58 ARG cc_start: 0.6762 (OUTLIER) cc_final: 0.6160 (ttp80) REVERT: A 170 MET cc_start: 0.7729 (ttm) cc_final: 0.7378 (ttm) REVERT: A 218 ILE cc_start: 0.7663 (mm) cc_final: 0.7459 (tt) REVERT: A 253 ARG cc_start: 0.7567 (OUTLIER) cc_final: 0.6436 (mtm110) REVERT: A 386 PHE cc_start: 0.8258 (t80) cc_final: 0.7730 (t80) REVERT: A 390 MET cc_start: 0.7207 (mtm) cc_final: 0.6897 (mtm) REVERT: A 417 MET cc_start: 0.6765 (mmm) cc_final: 0.6395 (mmm) REVERT: A 601 LYS cc_start: 0.7751 (tttp) cc_final: 0.7317 (tttp) REVERT: A 631 MET cc_start: 0.6745 (tpp) cc_final: 0.6223 (tpp) REVERT: H 32 PHE cc_start: 0.8359 (t80) cc_final: 0.8126 (t80) REVERT: L 18 ASP cc_start: 0.5539 (m-30) cc_final: 0.5334 (m-30) REVERT: L 43 LYS cc_start: 0.7818 (mmtm) cc_final: 0.7601 (mmtm) outliers start: 36 outliers final: 16 residues processed: 167 average time/residue: 0.0524 time to fit residues: 11.8852 Evaluate side-chains 147 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 129 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ARG Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 224 PHE Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 253 ARG Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 421 PHE Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 629 SER Chi-restraints excluded: chain H residue 25 CYS Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 111 TRP Chi-restraints excluded: chain L residue 96 LEU Chi-restraints excluded: chain L residue 105 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 49 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.0060 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.144173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.123989 restraints weight = 9171.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.127920 restraints weight = 4518.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.130466 restraints weight = 2783.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.132074 restraints weight = 1990.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.133272 restraints weight = 1585.103| |-----------------------------------------------------------------------------| r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7135 moved from start: 0.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5497 Z= 0.142 Angle : 0.606 7.553 7464 Z= 0.312 Chirality : 0.042 0.247 847 Planarity : 0.005 0.058 905 Dihedral : 8.386 58.687 793 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 6.37 % Allowed : 14.80 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.69 (0.30), residues: 669 helix: 0.30 (0.29), residues: 296 sheet: -1.02 (0.60), residues: 78 loop : -2.72 (0.29), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 614 TYR 0.015 0.001 TYR A 625 PHE 0.022 0.001 PHE A 73 TRP 0.009 0.001 TRP A 470 HIS 0.002 0.001 HIS A 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 ( 5491) covalent geometry : angle 0.60482 / 0.31 ( 7452) SS BOND : bond 0.00421 / 0.31 ( 6) SS BOND : angle 1.24473 / 0.63 ( 12) hydrogen bonds : bond 0.04772 / 3.10 ( 256) hydrogen bonds : angle 4.52252 / 3.34 ( 750) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 132 time to evaluate : 0.110 Fit side-chains revert: symmetry clash REVERT: A 170 MET cc_start: 0.7681 (ttm) cc_final: 0.7467 (ttm) REVERT: A 173 TYR cc_start: 0.7477 (m-80) cc_final: 0.7238 (m-80) REVERT: A 217 MET cc_start: 0.7921 (mmp) cc_final: 0.7514 (mmp) REVERT: A 253 ARG cc_start: 0.7577 (OUTLIER) cc_final: 0.6596 (mtm110) REVERT: A 386 PHE cc_start: 0.8091 (t80) cc_final: 0.7397 (t80) REVERT: A 390 MET cc_start: 0.7096 (mtm) cc_final: 0.6779 (mtm) REVERT: A 404 THR cc_start: 0.6277 (OUTLIER) cc_final: 0.5964 (m) REVERT: A 416 VAL cc_start: 0.7325 (t) cc_final: 0.7124 (p) REVERT: A 417 MET cc_start: 0.6615 (mmm) cc_final: 0.6301 (mmm) REVERT: A 533 LYS cc_start: 0.7948 (mttm) cc_final: 0.7695 (mttm) REVERT: A 545 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7877 (mm) REVERT: A 601 LYS cc_start: 0.7615 (tttp) cc_final: 0.7214 (tttp) REVERT: A 631 MET cc_start: 0.6754 (tpp) cc_final: 0.6232 (tpp) REVERT: H 32 PHE cc_start: 0.8296 (t80) cc_final: 0.8033 (t80) REVERT: L 18 ASP cc_start: 0.6022 (m-30) cc_final: 0.5712 (m-30) REVERT: L 43 LYS cc_start: 0.7699 (mmtm) cc_final: 0.7495 (mmtm) outliers start: 37 outliers final: 19 residues processed: 157 average time/residue: 0.0513 time to fit residues: 10.9889 Evaluate side-chains 148 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 126 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 224 PHE Chi-restraints excluded: chain A residue 253 ARG Chi-restraints excluded: chain A residue 340 MET Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 421 PHE Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain H residue 25 CYS Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 58 SER Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 111 TRP Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 92 SER Chi-restraints excluded: chain L residue 96 LEU Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain L residue 105 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 58 optimal weight: 0.0060 chunk 51 optimal weight: 0.9990 chunk 61 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 65.8333 > 50:) chunk 40 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 36 optimal weight: 4.9990 chunk 5 optimal weight: 0.2980 chunk 52 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 7 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 = 0.3874 r_free = 0.3874 target = 0.143929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.123847 restraints weight = 9132.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.127716 restraints weight = 4492.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.130306 restraints weight = 2784.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.132020 restraints weight = 1986.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.132845 restraints weight = 1563.181| |-----------------------------------------------------------------------------| r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7149 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5497 Z= 0.148 Angle : 0.597 7.226 7464 Z= 0.304 Chirality : 0.042 0.164 847 Planarity : 0.004 0.043 905 Dihedral : 7.437 57.975 784 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 5.68 % Allowed : 19.10 % Favored : 75.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.97 (0.32), residues: 669 helix: 1.07 (0.31), residues: 296 sheet: -0.94 (0.60), residues: 83 loop : -2.47 (0.31), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 614 TYR 0.016 0.001 TYR L 50 PHE 0.014 0.001 PHE A 73 TRP 0.009 0.001 TRP A 254 HIS 0.002 0.001 HIS A 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.15 ( 5491) covalent geometry : angle 0.59562 / 0.30 ( 7452) SS BOND : bond 0.00472 / 0.34 ( 6) SS BOND : angle 1.15528 / 0.60 ( 12) hydrogen bonds : bond 0.04570 / 3.00 ( 256) hydrogen bonds : angle 4.35018 / 3.22 ( 750) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 136 time to evaluate : 0.190 Fit side-chains revert: symmetry clash REVERT: A 58 ARG cc_start: 0.6794 (OUTLIER) cc_final: 0.6230 (ttp80) REVERT: A 97 ILE cc_start: 0.8147 (tt) cc_final: 0.7943 (tt) REVERT: A 170 MET cc_start: 0.7664 (ttm) cc_final: 0.7454 (ttm) REVERT: A 173 TYR cc_start: 0.7493 (m-80) cc_final: 0.7234 (m-80) REVERT: A 253 ARG cc_start: 0.7667 (OUTLIER) cc_final: 0.7138 (mtm110) REVERT: A 386 PHE cc_start: 0.8040 (t80) cc_final: 0.7280 (t80) REVERT: A 390 MET cc_start: 0.7191 (mtm) cc_final: 0.6798 (mtm) REVERT: A 440 MET cc_start: 0.6750 (OUTLIER) cc_final: 0.6519 (ttp) REVERT: A 533 LYS cc_start: 0.7949 (mttm) cc_final: 0.7700 (mttm) REVERT: A 545 LEU cc_start: 0.8112 (OUTLIER) cc_final: 0.7829 (mm) REVERT: A 601 LYS cc_start: 0.7480 (tttp) cc_final: 0.7082 (tttp) REVERT: A 631 MET cc_start: 0.6782 (tpp) cc_final: 0.6250 (tpp) REVERT: L 18 ASP cc_start: 0.6056 (m-30) cc_final: 0.5839 (m-30) REVERT: L 43 LYS cc_start: 0.7663 (mmtm) cc_final: 0.7456 (mmtm) outliers start: 33 outliers final: 25 residues processed: 155 average time/residue: 0.0587 time to fit residues: 12.3660 Evaluate side-chains 161 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 132 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ARG Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 253 ARG Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 340 MET Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 421 PHE Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 440 MET Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain H residue 25 CYS Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 58 SER Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 111 TRP Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 96 LEU Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain L residue 105 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 25 optimal weight: 0.7980 chunk 39 optimal weight: 0.5980 chunk 3 optimal weight: 0.4980 chunk 28 optimal weight: 0.4980 chunk 62 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 7 optimal weight: 0.5980 chunk 57 optimal weight: 0.3980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 7 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 = 0.3897 r_free = 0.3897 target = 0.145962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.126659 restraints weight = 9087.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.130381 restraints weight = 4577.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.132863 restraints weight = 2866.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.134481 restraints weight = 2057.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.135407 restraints weight = 1626.212| |-----------------------------------------------------------------------------| r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7112 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5497 Z= 0.132 Angle : 0.588 7.654 7464 Z= 0.296 Chirality : 0.041 0.155 847 Planarity : 0.004 0.043 905 Dihedral : 7.051 60.313 782 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 6.88 % Allowed : 19.10 % Favored : 74.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.72 (0.32), residues: 669 helix: 1.33 (0.31), residues: 296 sheet: -0.49 (0.62), residues: 78 loop : -2.49 (0.31), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 614 TYR 0.014 0.001 TYR L 50 PHE 0.013 0.001 PHE A 73 TRP 0.008 0.001 TRP A 254 HIS 0.002 0.001 HIS A 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 ( 5491) covalent geometry : angle 0.58593 / 0.29 ( 7452) SS BOND : bond 0.00497 / 0.37 ( 6) SS BOND : angle 1.27071 / 0.64 ( 12) hydrogen bonds : bond 0.04180 / 2.74 ( 256) hydrogen bonds : angle 4.21854 / 3.13 ( 750) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 128 time to evaluate : 0.107 Fit side-chains REVERT: A 58 ARG cc_start: 0.6769 (OUTLIER) cc_final: 0.6263 (ttp80) REVERT: A 253 ARG cc_start: 0.7716 (OUTLIER) cc_final: 0.7097 (mtm110) REVERT: A 386 PHE cc_start: 0.7935 (t80) cc_final: 0.7242 (t80) REVERT: A 390 MET cc_start: 0.6982 (mtm) cc_final: 0.6744 (mtm) REVERT: A 463 CYS cc_start: 0.6155 (t) cc_final: 0.5465 (t) REVERT: A 533 LYS cc_start: 0.7858 (mttm) cc_final: 0.7646 (mttm) REVERT: A 545 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7870 (mm) REVERT: A 601 LYS cc_start: 0.7407 (tttp) cc_final: 0.7074 (tttp) REVERT: A 631 MET cc_start: 0.6703 (tpp) cc_final: 0.6228 (tpp) REVERT: L 18 ASP cc_start: 0.6030 (m-30) cc_final: 0.5781 (m-30) REVERT: L 43 LYS cc_start: 0.7633 (mmtm) cc_final: 0.7411 (mmtm) REVERT: L 97 ILE cc_start: 0.6667 (OUTLIER) cc_final: 0.6141 (mm) outliers start: 40 outliers final: 26 residues processed: 155 average time/residue: 0.0410 time to fit residues: 8.5775 Evaluate side-chains 155 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 125 time to evaluate : 0.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ARG Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 224 PHE Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 253 ARG Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 340 MET Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 421 PHE Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 629 SER Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 58 SER Chi-restraints excluded: chain H residue 86 MET Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 99 CYS Chi-restraints excluded: chain H residue 111 TRP Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 96 LEU Chi-restraints excluded: chain L residue 97 ILE Chi-restraints excluded: chain L residue 105 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 31 optimal weight: 1.9990 chunk 65 optimal weight: 0.0970 chunk 45 optimal weight: 0.7980 chunk 49 optimal weight: 0.6980 chunk 41 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 30 optimal weight: 3.9990 chunk 58 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 445 ASN H 42 GLN ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.145381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.125767 restraints weight = 9136.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.129628 restraints weight = 4512.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.132176 restraints weight = 2790.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.133804 restraints weight = 1997.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.134919 restraints weight = 1581.323| |-----------------------------------------------------------------------------| r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7121 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5497 Z= 0.140 Angle : 0.601 8.019 7464 Z= 0.299 Chirality : 0.041 0.169 847 Planarity : 0.004 0.043 905 Dihedral : 7.033 61.307 781 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 6.71 % Allowed : 20.14 % Favored : 73.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.66 (0.32), residues: 669 helix: 1.41 (0.31), residues: 296 sheet: -0.70 (0.60), residues: 81 loop : -2.43 (0.31), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 614 TYR 0.016 0.001 TYR L 50 PHE 0.012 0.001 PHE A 73 TRP 0.009 0.001 TRP A 254 HIS 0.002 0.001 HIS A 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 ( 5491) covalent geometry : angle 0.59926 / 0.30 ( 7452) SS BOND : bond 0.00624 / 0.46 ( 6) SS BOND : angle 1.22826 / 0.62 ( 12) hydrogen bonds : bond 0.04178 / 2.74 ( 256) hydrogen bonds : angle 4.15495 / 3.09 ( 750) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 132 time to evaluate : 0.183 Fit side-chains revert: symmetry clash REVERT: A 58 ARG cc_start: 0.6775 (OUTLIER) cc_final: 0.6243 (ttp80) REVERT: A 173 TYR cc_start: 0.7388 (m-80) cc_final: 0.7149 (m-80) REVERT: A 253 ARG cc_start: 0.7674 (OUTLIER) cc_final: 0.7021 (mtm110) REVERT: A 386 PHE cc_start: 0.7919 (t80) cc_final: 0.7242 (t80) REVERT: A 390 MET cc_start: 0.7070 (mtm) cc_final: 0.6794 (mtm) REVERT: A 463 CYS cc_start: 0.6234 (t) cc_final: 0.5575 (t) REVERT: A 533 LYS cc_start: 0.7911 (mttm) cc_final: 0.7694 (mttm) REVERT: A 545 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7868 (mm) REVERT: A 601 LYS cc_start: 0.7407 (tttp) cc_final: 0.7041 (tttp) REVERT: A 631 MET cc_start: 0.6825 (tpp) cc_final: 0.6301 (tpp) REVERT: H 93 ASP cc_start: 0.7052 (m-30) cc_final: 0.6811 (m-30) REVERT: H 121 TYR cc_start: 0.7139 (m-80) cc_final: 0.6854 (m-80) REVERT: L 18 ASP cc_start: 0.6076 (m-30) cc_final: 0.5756 (m-30) REVERT: L 43 LYS cc_start: 0.7646 (mmtm) cc_final: 0.7409 (mmtm) REVERT: L 97 ILE cc_start: 0.6702 (OUTLIER) cc_final: 0.6196 (mm) outliers start: 39 outliers final: 28 residues processed: 157 average time/residue: 0.0625 time to fit residues: 13.2707 Evaluate side-chains 163 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 131 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 58 ARG Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 224 PHE Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 253 ARG Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 421 PHE Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 629 SER Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 86 MET Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 111 TRP Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 96 LEU Chi-restraints excluded: chain L residue 97 ILE Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain L residue 105 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 16 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 chunk 10 optimal weight: 0.0770 chunk 64 optimal weight: 0.5980 chunk 15 optimal weight: 0.0050 chunk 23 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 overall best weight: 0.4352 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 544 ASN H 42 GLN ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.146517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.126615 restraints weight = 9115.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.130592 restraints weight = 4437.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.133196 restraints weight = 2708.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.134880 restraints weight = 1920.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.135884 restraints weight = 1501.073| |-----------------------------------------------------------------------------| r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7104 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5497 Z= 0.120 Angle : 0.592 8.346 7464 Z= 0.291 Chirality : 0.041 0.139 847 Planarity : 0.004 0.044 905 Dihedral : 6.875 62.421 781 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 6.20 % Allowed : 20.48 % Favored : 73.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.49 (0.33), residues: 669 helix: 1.55 (0.31), residues: 293 sheet: -0.77 (0.60), residues: 83 loop : -2.26 (0.32), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 614 TYR 0.012 0.001 TYR L 50 PHE 0.024 0.001 PHE H 32 TRP 0.007 0.001 TRP A 254 HIS 0.003 0.001 HIS A 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 ( 5491) covalent geometry : angle 0.59077 / 0.29 ( 7452) SS BOND : bond 0.00491 / 0.36 ( 6) SS BOND : angle 1.03913 / 0.55 ( 12) hydrogen bonds : bond 0.03863 / 2.54 ( 256) hydrogen bonds : angle 4.05194 / 3.01 ( 750) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 133 time to evaluate : 0.159 Fit side-chains revert: symmetry clash REVERT: A 58 ARG cc_start: 0.6728 (OUTLIER) cc_final: 0.6205 (ttp80) REVERT: A 253 ARG cc_start: 0.7674 (OUTLIER) cc_final: 0.7035 (mtm110) REVERT: A 386 PHE cc_start: 0.7890 (t80) cc_final: 0.7207 (t80) REVERT: A 390 MET cc_start: 0.7116 (mtm) cc_final: 0.6818 (mtm) REVERT: A 463 CYS cc_start: 0.6215 (t) cc_final: 0.5551 (t) REVERT: A 533 LYS cc_start: 0.7905 (mttm) cc_final: 0.7572 (mttm) REVERT: A 545 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7810 (mm) REVERT: A 601 LYS cc_start: 0.7296 (tttp) cc_final: 0.6953 (tttp) REVERT: A 631 MET cc_start: 0.6825 (tpp) cc_final: 0.6300 (tpp) REVERT: L 18 ASP cc_start: 0.6052 (m-30) cc_final: 0.5731 (m-30) REVERT: L 43 LYS cc_start: 0.7616 (mmtm) cc_final: 0.7391 (mmtm) REVERT: L 97 ILE cc_start: 0.6712 (OUTLIER) cc_final: 0.6220 (mm) outliers start: 36 outliers final: 25 residues processed: 157 average time/residue: 0.0530 time to fit residues: 11.1578 Evaluate side-chains 160 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 131 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 58 ARG Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 224 PHE Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 253 ARG Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 340 MET Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 575 HIS Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 629 SER Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 58 SER Chi-restraints excluded: chain H residue 86 MET Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 111 TRP Chi-restraints excluded: chain L residue 96 LEU Chi-restraints excluded: chain L residue 97 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 64 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 6 optimal weight: 0.5980 chunk 16 optimal weight: 0.3980 chunk 40 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 38 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 chunk 55 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 42 GLN ** L 7 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 = 0.3883 r_free = 0.3883 target = 0.145585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.125600 restraints weight = 9198.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.129449 restraints weight = 4562.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.132052 restraints weight = 2834.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.133760 restraints weight = 2018.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.134869 restraints weight = 1588.749| |-----------------------------------------------------------------------------| r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7118 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5497 Z= 0.145 Angle : 0.607 7.336 7464 Z= 0.303 Chirality : 0.042 0.172 847 Planarity : 0.004 0.044 905 Dihedral : 6.798 62.207 778 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 6.20 % Allowed : 20.14 % Favored : 73.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.53 (0.32), residues: 669 helix: 1.46 (0.31), residues: 296 sheet: -0.73 (0.60), residues: 83 loop : -2.28 (0.32), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 614 TYR 0.017 0.001 TYR L 50 PHE 0.024 0.001 PHE H 32 TRP 0.010 0.001 TRP A 254 HIS 0.002 0.001 HIS A 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 ( 5491) covalent geometry : angle 0.60525 / 0.30 ( 7452) SS BOND : bond 0.00606 / 0.45 ( 6) SS BOND : angle 1.39691 / 0.73 ( 12) hydrogen bonds : bond 0.04124 / 2.70 ( 256) hydrogen bonds : angle 4.12081 / 3.06 ( 750) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 135 time to evaluate : 0.186 Fit side-chains revert: symmetry clash REVERT: A 253 ARG cc_start: 0.7636 (OUTLIER) cc_final: 0.6995 (mtm110) REVERT: A 386 PHE cc_start: 0.7907 (t80) cc_final: 0.7240 (t80) REVERT: A 390 MET cc_start: 0.7079 (mtm) cc_final: 0.6814 (mtm) REVERT: A 463 CYS cc_start: 0.6244 (t) cc_final: 0.5632 (t) REVERT: A 533 LYS cc_start: 0.7983 (mttm) cc_final: 0.7652 (mttm) REVERT: A 545 LEU cc_start: 0.8097 (OUTLIER) cc_final: 0.7828 (mm) REVERT: A 601 LYS cc_start: 0.7367 (tttp) cc_final: 0.7011 (tttp) REVERT: A 631 MET cc_start: 0.6804 (tpp) cc_final: 0.6297 (tpp) REVERT: H 121 TYR cc_start: 0.7156 (m-80) cc_final: 0.6862 (m-80) REVERT: L 18 ASP cc_start: 0.6069 (m-30) cc_final: 0.5727 (m-30) REVERT: L 43 LYS cc_start: 0.7630 (mmtm) cc_final: 0.7388 (mmtm) REVERT: L 97 ILE cc_start: 0.6729 (OUTLIER) cc_final: 0.6225 (mm) outliers start: 36 outliers final: 30 residues processed: 155 average time/residue: 0.0590 time to fit residues: 12.5803 Evaluate side-chains 169 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 136 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 224 PHE Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 253 ARG Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 340 MET Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 575 HIS Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 629 SER Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 58 SER Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 86 MET Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 111 TRP Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 96 LEU Chi-restraints excluded: chain L residue 97 ILE Chi-restraints excluded: chain L residue 105 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 50 optimal weight: 4.9990 chunk 21 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 29 optimal weight: 0.1980 chunk 12 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 43 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 7 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 = 0.3880 r_free = 0.3880 target = 0.145349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.125401 restraints weight = 9028.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.129216 restraints weight = 4496.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.131781 restraints weight = 2802.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.133263 restraints weight = 2003.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.134456 restraints weight = 1616.073| |-----------------------------------------------------------------------------| r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7123 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5497 Z= 0.150 Angle : 0.636 8.880 7464 Z= 0.314 Chirality : 0.042 0.162 847 Planarity : 0.004 0.045 905 Dihedral : 6.824 62.467 778 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 6.37 % Allowed : 20.31 % Favored : 73.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.55 (0.32), residues: 669 helix: 1.48 (0.31), residues: 293 sheet: -0.63 (0.61), residues: 81 loop : -2.31 (0.31), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 614 TYR 0.016 0.001 TYR L 50 PHE 0.024 0.001 PHE H 32 TRP 0.010 0.001 TRP A 254 HIS 0.002 0.001 HIS A 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 ( 5491) covalent geometry : angle 0.63393 / 0.31 ( 7452) SS BOND : bond 0.00590 / 0.44 ( 6) SS BOND : angle 1.34691 / 0.71 ( 12) hydrogen bonds : bond 0.04201 / 2.76 ( 256) hydrogen bonds : angle 4.14967 / 3.08 ( 750) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 131 time to evaluate : 0.118 Fit side-chains revert: symmetry clash REVERT: A 58 ARG cc_start: 0.6774 (OUTLIER) cc_final: 0.6130 (ttp80) REVERT: A 253 ARG cc_start: 0.7612 (OUTLIER) cc_final: 0.6964 (mtm110) REVERT: A 386 PHE cc_start: 0.7923 (t80) cc_final: 0.7227 (t80) REVERT: A 390 MET cc_start: 0.7080 (mtm) cc_final: 0.6794 (mtm) REVERT: A 463 CYS cc_start: 0.6258 (t) cc_final: 0.5636 (t) REVERT: A 533 LYS cc_start: 0.7994 (mttm) cc_final: 0.7684 (mttm) REVERT: A 545 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7827 (mm) REVERT: A 601 LYS cc_start: 0.7357 (tttp) cc_final: 0.7004 (tttp) REVERT: A 631 MET cc_start: 0.6801 (tpp) cc_final: 0.6297 (tpp) REVERT: H 93 ASP cc_start: 0.7067 (m-30) cc_final: 0.6850 (m-30) REVERT: H 121 TYR cc_start: 0.7147 (m-80) cc_final: 0.6862 (m-80) REVERT: L 18 ASP cc_start: 0.6064 (m-30) cc_final: 0.5727 (m-30) REVERT: L 43 LYS cc_start: 0.7627 (mmtm) cc_final: 0.7387 (mmtm) REVERT: L 97 ILE cc_start: 0.6724 (OUTLIER) cc_final: 0.6301 (mm) outliers start: 37 outliers final: 33 residues processed: 152 average time/residue: 0.0623 time to fit residues: 12.7888 Evaluate side-chains 167 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 130 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 58 ARG Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 224 PHE Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 253 ARG Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 340 MET Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 421 PHE Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 575 HIS Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 629 SER Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 58 SER Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 86 MET Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 111 TRP Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 96 LEU Chi-restraints excluded: chain L residue 97 ILE Chi-restraints excluded: chain L residue 105 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 12 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 43 optimal weight: 0.4980 chunk 11 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 17 optimal weight: 0.0980 chunk 6 optimal weight: 0.9980 chunk 18 optimal weight: 0.0170 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 7 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 = 0.3909 r_free = 0.3909 target = 0.146996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.127532 restraints weight = 9129.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.131438 restraints weight = 4542.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.133964 restraints weight = 2797.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.135613 restraints weight = 1986.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.136430 restraints weight = 1559.999| |-----------------------------------------------------------------------------| r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7095 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5497 Z= 0.127 Angle : 0.612 7.583 7464 Z= 0.302 Chirality : 0.041 0.155 847 Planarity : 0.004 0.045 905 Dihedral : 6.686 63.178 778 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 6.20 % Allowed : 19.97 % Favored : 73.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.49 (0.33), residues: 669 helix: 1.50 (0.31), residues: 296 sheet: -0.76 (0.60), residues: 83 loop : -2.22 (0.32), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 58 TYR 0.013 0.001 TYR L 50 PHE 0.025 0.001 PHE H 32 TRP 0.007 0.001 TRP A 470 HIS 0.002 0.001 HIS A 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 ( 5491) covalent geometry : angle 0.61048 / 0.30 ( 7452) SS BOND : bond 0.00532 / 0.39 ( 6) SS BOND : angle 1.20569 / 0.64 ( 12) hydrogen bonds : bond 0.03898 / 2.56 ( 256) hydrogen bonds : angle 4.03367 / 3.00 ( 750) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 131 time to evaluate : 0.139 Fit side-chains revert: symmetry clash REVERT: A 58 ARG cc_start: 0.6761 (OUTLIER) cc_final: 0.6156 (ttp80) REVERT: A 169 TYR cc_start: 0.7072 (t80) cc_final: 0.6861 (t80) REVERT: A 253 ARG cc_start: 0.7660 (OUTLIER) cc_final: 0.7028 (mtm110) REVERT: A 386 PHE cc_start: 0.7870 (t80) cc_final: 0.7214 (t80) REVERT: A 390 MET cc_start: 0.7004 (mtm) cc_final: 0.6768 (mtm) REVERT: A 463 CYS cc_start: 0.6135 (t) cc_final: 0.5518 (t) REVERT: A 533 LYS cc_start: 0.7974 (mttm) cc_final: 0.7706 (mttm) REVERT: A 545 LEU cc_start: 0.8064 (OUTLIER) cc_final: 0.7800 (mm) REVERT: A 601 LYS cc_start: 0.7237 (tttp) cc_final: 0.6934 (tttp) REVERT: A 631 MET cc_start: 0.6775 (tpp) cc_final: 0.6288 (tpp) REVERT: H 121 TYR cc_start: 0.7102 (m-80) cc_final: 0.6872 (m-80) REVERT: L 18 ASP cc_start: 0.6049 (m-30) cc_final: 0.5721 (m-30) REVERT: L 43 LYS cc_start: 0.7604 (mmtm) cc_final: 0.7366 (mmtm) REVERT: L 97 ILE cc_start: 0.6681 (OUTLIER) cc_final: 0.6280 (mm) outliers start: 36 outliers final: 31 residues processed: 151 average time/residue: 0.0617 time to fit residues: 12.5842 Evaluate side-chains 165 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 130 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 58 ARG Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 253 ARG Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 340 MET Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 575 HIS Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 629 SER Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 58 SER Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 86 MET Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 111 TRP Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 96 LEU Chi-restraints excluded: chain L residue 97 ILE Chi-restraints excluded: chain L residue 105 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 10 optimal weight: 0.0070 chunk 62 optimal weight: 0.0980 chunk 21 optimal weight: 0.9980 chunk 56 optimal weight: 0.5980 chunk 17 optimal weight: 0.0970 chunk 49 optimal weight: 0.6980 chunk 1 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 overall best weight: 0.2996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 7 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 = 0.3933 r_free = 0.3933 target = 0.148882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.129279 restraints weight = 9145.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.133130 restraints weight = 4539.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.135697 restraints weight = 2814.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.137350 restraints weight = 1997.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.138482 restraints weight = 1566.257| |-----------------------------------------------------------------------------| r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 moved from start: 0.2878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 5497 Z= 0.109 Angle : 0.594 7.765 7464 Z= 0.293 Chirality : 0.040 0.176 847 Planarity : 0.004 0.044 905 Dihedral : 6.514 63.673 778 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 5.34 % Allowed : 21.34 % Favored : 73.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.34 (0.33), residues: 669 helix: 1.55 (0.31), residues: 291 sheet: -0.34 (0.61), residues: 78 loop : -2.10 (0.32), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 58 TYR 0.010 0.001 TYR A 625 PHE 0.025 0.001 PHE H 32 TRP 0.009 0.001 TRP A 470 HIS 0.003 0.001 HIS A 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 ( 5491) covalent geometry : angle 0.59330 / 0.29 ( 7452) SS BOND : bond 0.00419 / 0.31 ( 6) SS BOND : angle 1.01410 / 0.55 ( 12) hydrogen bonds : bond 0.03583 / 2.34 ( 256) hydrogen bonds : angle 3.91401 / 2.91 ( 750) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 129 time to evaluate : 0.111 Fit side-chains revert: symmetry clash REVERT: A 58 ARG cc_start: 0.6740 (OUTLIER) cc_final: 0.6116 (ttp80) REVERT: A 169 TYR cc_start: 0.7056 (t80) cc_final: 0.6850 (t80) REVERT: A 463 CYS cc_start: 0.5986 (t) cc_final: 0.5366 (t) REVERT: A 533 LYS cc_start: 0.7983 (mttm) cc_final: 0.7711 (mttm) REVERT: A 545 LEU cc_start: 0.8034 (OUTLIER) cc_final: 0.7796 (mm) REVERT: A 601 LYS cc_start: 0.7122 (tttp) cc_final: 0.6869 (tttp) REVERT: A 631 MET cc_start: 0.6774 (tpp) cc_final: 0.6298 (tpp) REVERT: L 18 ASP cc_start: 0.5988 (m-30) cc_final: 0.5667 (m-30) REVERT: L 43 LYS cc_start: 0.7556 (mmtm) cc_final: 0.7334 (mmtm) REVERT: L 97 ILE cc_start: 0.6669 (OUTLIER) cc_final: 0.6221 (mm) outliers start: 31 outliers final: 23 residues processed: 146 average time/residue: 0.0520 time to fit residues: 10.2193 Evaluate side-chains 150 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 124 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 58 ARG Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 340 MET Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 575 HIS Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 629 SER Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 58 SER Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 86 MET Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 111 TRP Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 96 LEU Chi-restraints excluded: chain L residue 97 ILE Chi-restraints excluded: chain L residue 105 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 47 optimal weight: 0.9980 chunk 53 optimal weight: 4.9990 chunk 10 optimal weight: 0.5980 chunk 15 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 30 optimal weight: 0.0060 chunk 13 optimal weight: 0.5980 chunk 58 optimal weight: 4.9990 chunk 22 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 12 optimal weight: 0.0070 overall best weight: 0.3814 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 4 GLN ** L 7 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 = 0.3927 r_free = 0.3927 target = 0.148439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.128822 restraints weight = 9084.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.132700 restraints weight = 4538.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.135308 restraints weight = 2826.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.136951 restraints weight = 2008.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.138076 restraints weight = 1575.183| |-----------------------------------------------------------------------------| r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7063 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5497 Z= 0.119 Angle : 0.607 7.779 7464 Z= 0.301 Chirality : 0.041 0.216 847 Planarity : 0.004 0.042 905 Dihedral : 6.083 63.298 770 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 4.82 % Allowed : 22.03 % Favored : 73.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.33 (0.32), residues: 669 helix: 1.56 (0.31), residues: 288 sheet: -0.50 (0.59), residues: 83 loop : -2.01 (0.32), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 58 TYR 0.012 0.001 TYR L 50 PHE 0.025 0.001 PHE H 32 TRP 0.008 0.001 TRP A 470 HIS 0.002 0.001 HIS A 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 ( 5491) covalent geometry : angle 0.60498 / 0.30 ( 7452) SS BOND : bond 0.00527 / 0.38 ( 6) SS BOND : angle 1.29409 / 0.72 ( 12) hydrogen bonds : bond 0.03720 / 2.42 ( 256) hydrogen bonds : angle 3.95548 / 2.95 ( 750) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1147.59 seconds wall clock time: 20 minutes 19.43 seconds (1219.43 seconds total)