Starting phenix.real_space_refine on Thu Jul 2 02:33:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wg4_37502/07_2026/8wg4_37502.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wg4_37502/07_2026/8wg4_37502.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8wg4_37502/07_2026/8wg4_37502.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wg4_37502/07_2026/8wg4_37502.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wg4_37502/07_2026/8wg4_37502.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wg4_37502/07_2026/8wg4_37502.map" } resolution = 3.5 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= 0.004 sd= 0.067 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 46 5.16 5 C 3940 2.51 5 N 923 2.21 5 O 977 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5887 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 688, 5597 Classifications: {'peptide': 688} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 26, 'TRANS': 661} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ASN:plan1': 1, 'P1L:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 290 Unusual residues: {'LBN': 1, 'Y01': 7} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Time building chain proxies: 1.09, per 1000 atoms: 0.19 Number of scatterers: 5887 At special positions: 0 Unit cell: (88.7062, 88.7062, 104.269, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 46 16.00 P 1 15.00 O 977 8.00 N 923 7.00 C 3940 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 23 " - pdb=" SG CYS A 559 " 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: 0.36 Conformation dependent library (CDL) restraints added in 222.8 milliseconds 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1314 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 2 sheets defined 74.6% alpha, 3.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing helix chain 'A' and resid 31 through 35 Processing helix chain 'A' and resid 36 through 39 removed outlier: 4.469A pdb=" N GLY A 39 " --> pdb=" O LEU A 36 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 36 through 39' Processing helix chain 'A' and resid 40 through 66 removed outlier: 4.003A pdb=" N ALA A 46 " --> pdb=" O PRO A 42 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N LYS A 64 " --> pdb=" O SER A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 135 removed outlier: 3.649A pdb=" N PHE A 133 " --> pdb=" O LEU A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 145 Processing helix chain 'A' and resid 145 through 172 removed outlier: 3.715A pdb=" N VAL A 149 " --> pdb=" O GLY A 145 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL A 163 " --> pdb=" O ILE A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 179 removed outlier: 3.553A pdb=" N VAL A 176 " --> pdb=" O ILE A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 198 removed outlier: 5.670A pdb=" N ILE A 195 " --> pdb=" O ARG A 192 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ALA A 196 " --> pdb=" O THR A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 231 removed outlier: 3.612A pdb=" N LEU A 207 " --> pdb=" O ASN A 203 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LEU A 216 " --> pdb=" O ALA A 212 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ARG A 231 " --> pdb=" O THR A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 240 removed outlier: 3.532A pdb=" N LYS A 239 " --> pdb=" O ASP A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 264 removed outlier: 3.708A pdb=" N ILE A 256 " --> pdb=" O GLU A 252 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N PHE A 260 " --> pdb=" O ILE A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 306 removed outlier: 3.721A pdb=" N LYS A 304 " --> pdb=" O ASN A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 320 Processing helix chain 'A' and resid 331 through 355 removed outlier: 4.313A pdb=" N ASN A 355 " --> pdb=" O LYS A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 379 Processing helix chain 'A' and resid 403 through 407 Processing helix chain 'A' and resid 421 through 426 removed outlier: 5.068A pdb=" N ARG A 426 " --> pdb=" O LEU A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 448 removed outlier: 3.560A pdb=" N TRP A 431 " --> pdb=" O GLY A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 461 removed outlier: 3.650A pdb=" N ILE A 454 " --> pdb=" O THR A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 470 removed outlier: 3.515A pdb=" N TYR A 469 " --> pdb=" O PRO A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 497 removed outlier: 3.730A pdb=" N GLN A 477 " --> pdb=" O PRO A 473 " (cutoff:3.500A) Proline residue: A 480 - end of helix Proline residue: A 492 - end of helix Processing helix chain 'A' and resid 498 through 501 Processing helix chain 'A' and resid 506 through 527 Processing helix chain 'A' and resid 527 through 533 Processing helix chain 'A' and resid 536 through 546 Processing helix chain 'A' and resid 548 through 553 Processing helix chain 'A' and resid 553 through 561 removed outlier: 4.108A pdb=" N CYS A 559 " --> pdb=" O ILE A 555 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL A 560 " --> pdb=" O ARG A 556 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N PHE A 561 " --> pdb=" O PHE A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 578 Processing helix chain 'A' and resid 578 through 587 Processing helix chain 'A' and resid 587 through 600 Processing helix chain 'A' and resid 603 through 614 Processing helix chain 'A' and resid 619 through 641 removed outlier: 3.554A pdb=" N CYS A 629 " --> pdb=" O ALA A 625 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N ILE A 639 " --> pdb=" O MET A 635 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N THR A 640 " --> pdb=" O THR A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 666 removed outlier: 4.543A pdb=" N PHE A 647 " --> pdb=" O ILE A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 703 removed outlier: 3.736A pdb=" N VAL A 681 " --> pdb=" O HIS A 677 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ASN A 682 " --> pdb=" O SER A 678 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLN A 683 " --> pdb=" O GLY A 679 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL A 684 " --> pdb=" O ALA A 680 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL A 685 " --> pdb=" O VAL A 681 " (cutoff:3.500A) Proline residue: A 688 - end of helix removed outlier: 3.629A pdb=" N PHE A 698 " --> pdb=" O TRP A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 707 through 730 removed outlier: 3.506A pdb=" N THR A 713 " --> pdb=" O THR A 709 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N PHE A 714 " --> pdb=" O SER A 710 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N LEU A 717 " --> pdb=" O THR A 713 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 269 through 276 removed outlier: 5.300A pdb=" N MET A 361 " --> pdb=" O CYS A 275 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 383 through 384 349 hydrogen bonds defined for protein. 987 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: 0.73 Time building geometry restraints manager: 0.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 884 1.32 - 1.44: 1649 1.44 - 1.57: 3456 1.57 - 1.70: 2 1.70 - 1.83: 66 Bond restraints: 6057 Sorted by residual: bond pdb=" CE1 HIS A 157 " pdb=" NE2 HIS A 157 " ideal model delta sigma weight residual 1.321 1.272 0.049 1.00e-02 1.00e+04 2.36e+01 bond pdb=" CG HIS A 157 " pdb=" CD2 HIS A 157 " ideal model delta sigma weight residual 1.354 1.322 0.032 1.10e-02 8.26e+03 8.23e+00 bond pdb=" C LEU A 36 " pdb=" N PRO A 37 " ideal model delta sigma weight residual 1.329 1.363 -0.034 1.25e-02 6.40e+03 7.34e+00 bond pdb=" C9 LBN A1201 " pdb=" O2 LBN A1201 " ideal model delta sigma weight residual 1.409 1.462 -0.053 2.00e-02 2.50e+03 6.96e+00 bond pdb=" CA SER A 699 " pdb=" CB SER A 699 " ideal model delta sigma weight residual 1.528 1.488 0.041 1.56e-02 4.11e+03 6.75e+00 ... (remaining 6052 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.30: 7447 2.30 - 4.59: 758 4.59 - 6.89: 30 6.89 - 9.19: 3 9.19 - 11.48: 1 Bond angle restraints: 8239 Sorted by residual: angle pdb=" CA ASN A 197 " pdb=" CB ASN A 197 " pdb=" CG ASN A 197 " ideal model delta sigma weight residual 112.60 118.20 -5.60 1.00e+00 1.00e+00 3.14e+01 angle pdb=" CA PHE A 479 " pdb=" CB PHE A 479 " pdb=" CG PHE A 479 " ideal model delta sigma weight residual 113.80 118.28 -4.48 1.00e+00 1.00e+00 2.01e+01 angle pdb=" CA TYR A 637 " pdb=" CB TYR A 637 " pdb=" CG TYR A 637 " ideal model delta sigma weight residual 113.90 105.89 8.01 1.80e+00 3.09e-01 1.98e+01 angle pdb=" CA HIS A 613 " pdb=" CB HIS A 613 " pdb=" CG HIS A 613 " ideal model delta sigma weight residual 113.80 109.38 4.42 1.00e+00 1.00e+00 1.95e+01 angle pdb=" C TYR A 264 " pdb=" CA TYR A 264 " pdb=" CB TYR A 264 " ideal model delta sigma weight residual 108.88 115.37 -6.49 1.50e+00 4.44e-01 1.87e+01 ... (remaining 8234 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.41: 3712 23.41 - 46.82: 173 46.82 - 70.24: 31 70.24 - 93.65: 6 93.65 - 117.06: 5 Dihedral angle restraints: 3927 sinusoidal: 1894 harmonic: 2033 Sorted by residual: dihedral pdb=" CB CYS A 23 " pdb=" SG CYS A 23 " pdb=" SG CYS A 559 " pdb=" CB CYS A 559 " ideal model delta sinusoidal sigma weight residual -86.00 -150.81 64.81 1 1.00e+01 1.00e-02 5.51e+01 dihedral pdb=" CA ILE A 28 " pdb=" C ILE A 28 " pdb=" N ARG A 29 " pdb=" CA ARG A 29 " ideal model delta harmonic sigma weight residual 180.00 -150.53 -29.47 0 5.00e+00 4.00e-02 3.47e+01 dihedral pdb=" CA ASP A 181 " pdb=" C ASP A 181 " pdb=" N LEU A 182 " pdb=" CA LEU A 182 " ideal model delta harmonic sigma weight residual -180.00 -153.61 -26.39 0 5.00e+00 4.00e-02 2.79e+01 ... (remaining 3924 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.070: 588 0.070 - 0.139: 286 0.139 - 0.209: 50 0.209 - 0.278: 7 0.278 - 0.348: 1 Chirality restraints: 932 Sorted by residual: chirality pdb=" CA ASN A 306 " pdb=" N ASN A 306 " pdb=" C ASN A 306 " pdb=" CB ASN A 306 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.03e+00 chirality pdb=" CA ASN A 438 " pdb=" N ASN A 438 " pdb=" C ASN A 438 " pdb=" CB ASN A 438 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CB ILE A 374 " pdb=" CA ILE A 374 " pdb=" CG1 ILE A 374 " pdb=" CG2 ILE A 374 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.69e+00 ... (remaining 929 not shown) Planarity restraints: 975 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 637 " -0.100 2.00e-02 2.50e+03 5.18e-02 5.37e+01 pdb=" CG TYR A 637 " 0.076 2.00e-02 2.50e+03 pdb=" CD1 TYR A 637 " 0.030 2.00e-02 2.50e+03 pdb=" CD2 TYR A 637 " 0.027 2.00e-02 2.50e+03 pdb=" CE1 TYR A 637 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR A 637 " 0.014 2.00e-02 2.50e+03 pdb=" CZ TYR A 637 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR A 637 " -0.062 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CAM Y01 A1207 " -0.020 2.00e-02 2.50e+03 4.13e-02 1.71e+01 pdb=" CAY Y01 A1207 " 0.071 2.00e-02 2.50e+03 pdb=" OAG Y01 A1207 " -0.029 2.00e-02 2.50e+03 pdb=" OAW Y01 A1207 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 69 " 0.048 2.00e-02 2.50e+03 2.46e-02 1.21e+01 pdb=" CG TYR A 69 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 TYR A 69 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR A 69 " -0.018 2.00e-02 2.50e+03 pdb=" CE1 TYR A 69 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR A 69 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 69 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 69 " 0.021 2.00e-02 2.50e+03 ... (remaining 972 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 1775 2.86 - 3.37: 5663 3.37 - 3.88: 8983 3.88 - 4.39: 10345 4.39 - 4.90: 17873 Nonbonded interactions: 44639 Sorted by model distance: nonbonded pdb=" ND2 ASN A 682 " pdb=" OAG Y01 A1207 " model vdw 2.353 3.120 nonbonded pdb=" NH2 ARG A 512 " pdb=" OAH Y01 A1207 " model vdw 2.437 3.120 nonbonded pdb=" OH TYR A 151 " pdb=" OD2 ASP A 659 " model vdw 2.530 3.040 nonbonded pdb=" OH TYR A 264 " pdb=" OD2 ASP A 378 " model vdw 2.577 3.040 nonbonded pdb=" O LEU A 527 " pdb=" OG SER A 531 " model vdw 2.589 3.040 ... (remaining 44634 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 0.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 5.370 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:0.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 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 : 0.009 0.053 6058 Z= 0.566 Angle : 1.353 11.484 8241 Z= 0.898 Chirality : 0.078 0.348 932 Planarity : 0.011 0.097 975 Dihedral : 14.755 117.059 2610 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 0.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.82 % Allowed : 6.12 % Favored : 92.07 % Cbeta Deviations : 0.15 % 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: -2.47 (0.29), residues: 679 helix: -1.68 (0.20), residues: 446 sheet: 0.57 (1.30), residues: 22 loop : -1.33 (0.44), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.003 ARG A 225 TYR 0.100 0.009 TYR A 637 PHE 0.035 0.007 PHE A 154 TRP 0.030 0.007 TRP A 206 HIS 0.025 0.005 HIS A 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00859 / 0.57 ( 6057) covalent geometry : angle 1.35197 / 0.90 ( 8239) SS BOND : bond 0.00473 / 0.25 ( 1) SS BOND : angle 3.97824 / 2.09 ( 2) hydrogen bonds : bond 0.21151 / 13.79 ( 349) hydrogen bonds : angle 8.35347 / 5.83 ( 987) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 99 time to evaluate : 0.137 Fit side-chains REVERT: A 69 TYR cc_start: 0.7908 (p90) cc_final: 0.7464 (p90) REVERT: A 143 LYS cc_start: 0.6429 (tptp) cc_final: 0.6045 (tptp) REVERT: A 181 ASP cc_start: 0.7692 (m-30) cc_final: 0.7461 (t0) REVERT: A 237 LEU cc_start: 0.5878 (OUTLIER) cc_final: 0.5591 (tp) REVERT: A 241 THR cc_start: 0.9239 (m) cc_final: 0.8906 (p) REVERT: A 252 GLU cc_start: 0.7348 (mt-10) cc_final: 0.6839 (mp0) REVERT: A 254 GLU cc_start: 0.7823 (mt-10) cc_final: 0.7522 (tp30) REVERT: A 310 MET cc_start: 0.6816 (mpt) cc_final: 0.6315 (mpp) REVERT: A 335 TYR cc_start: 0.7170 (t80) cc_final: 0.6755 (t80) REVERT: A 349 ARG cc_start: 0.7336 (mtm-85) cc_final: 0.6907 (mmm160) REVERT: A 445 LEU cc_start: 0.5617 (mt) cc_final: 0.5380 (mt) REVERT: A 548 LYS cc_start: 0.6310 (mtmm) cc_final: 0.6083 (pttt) REVERT: A 676 ILE cc_start: 0.7161 (OUTLIER) cc_final: 0.6934 (tp) REVERT: A 706 LEU cc_start: 0.8188 (mt) cc_final: 0.7952 (pp) REVERT: A 740 ASN cc_start: 0.6818 (t0) cc_final: 0.6609 (t0) outliers start: 11 outliers final: 2 residues processed: 107 average time/residue: 0.0608 time to fit residues: 8.6123 Evaluate side-chains 77 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 73 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain A residue 676 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 0.0870 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 27 optimal weight: 6.9990 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 123 ASN A 197 ASN A 202 ASN A 516 HIS A 565 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.163517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.122844 restraints weight = 6880.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.125268 restraints weight = 5034.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.127027 restraints weight = 4135.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.127875 restraints weight = 3666.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.127997 restraints weight = 3415.222| |-----------------------------------------------------------------------------| r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6058 Z= 0.152 Angle : 0.654 8.629 8241 Z= 0.336 Chirality : 0.042 0.137 932 Planarity : 0.004 0.034 975 Dihedral : 10.308 81.198 1320 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.15 % Allowed : 10.08 % Favored : 87.77 % 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: 0.09 (0.32), residues: 679 helix: 0.65 (0.24), residues: 446 sheet: 2.40 (1.90), residues: 10 loop : -1.15 (0.42), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 293 TYR 0.020 0.002 TYR A 637 PHE 0.021 0.002 PHE A 298 TRP 0.010 0.001 TRP A 128 HIS 0.003 0.001 HIS A 422 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 ( 6057) covalent geometry : angle 0.65331 / 0.34 ( 8239) SS BOND : bond 0.00136 / 0.07 ( 1) SS BOND : angle 1.64011 / 0.87 ( 2) hydrogen bonds : bond 0.05622 / 3.88 ( 349) hydrogen bonds : angle 4.91672 / 3.43 ( 987) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.275 Fit side-chains REVERT: A 205 LEU cc_start: 0.7340 (OUTLIER) cc_final: 0.6504 (tt) REVERT: A 237 LEU cc_start: 0.7442 (OUTLIER) cc_final: 0.7178 (tp) REVERT: A 292 GLU cc_start: 0.7400 (tt0) cc_final: 0.7092 (tt0) REVERT: A 445 LEU cc_start: 0.7165 (mt) cc_final: 0.6941 (mt) REVERT: A 609 ASN cc_start: 0.8087 (t0) cc_final: 0.7288 (t0) outliers start: 13 outliers final: 7 residues processed: 94 average time/residue: 0.0770 time to fit residues: 9.8521 Evaluate side-chains 77 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 650 MET Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 737 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 33 optimal weight: 8.9990 chunk 57 optimal weight: 0.2980 chunk 23 optimal weight: 7.9990 chunk 50 optimal weight: 1.9990 chunk 53 optimal weight: 7.9990 chunk 46 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- 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 = 0.3744 r_free = 0.3744 target = 0.160413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.122332 restraints weight = 6884.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.122148 restraints weight = 5153.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.122718 restraints weight = 4680.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.122874 restraints weight = 4236.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.123136 restraints weight = 4142.769| |-----------------------------------------------------------------------------| r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 6058 Z= 0.183 Angle : 0.643 8.406 8241 Z= 0.325 Chirality : 0.042 0.144 932 Planarity : 0.004 0.038 975 Dihedral : 9.152 59.774 1318 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.47 % Allowed : 13.22 % Favored : 83.31 % 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: 0.51 (0.32), residues: 679 helix: 1.14 (0.24), residues: 447 sheet: 1.07 (1.76), residues: 10 loop : -1.33 (0.41), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 608 TYR 0.016 0.002 TYR A 264 PHE 0.015 0.002 PHE A 730 TRP 0.008 0.001 TRP A 431 HIS 0.004 0.001 HIS A 516 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.18 ( 6057) covalent geometry : angle 0.64258 / 0.32 ( 8239) SS BOND : bond 0.00278 / 0.15 ( 1) SS BOND : angle 1.21772 / 0.64 ( 2) hydrogen bonds : bond 0.05557 / 3.80 ( 349) hydrogen bonds : angle 4.68945 / 3.28 ( 987) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 69 time to evaluate : 0.224 Fit side-chains revert: symmetry clash REVERT: A 181 ASP cc_start: 0.6818 (t0) cc_final: 0.6591 (t0) REVERT: A 310 MET cc_start: 0.6706 (mpp) cc_final: 0.6470 (mmt) REVERT: A 445 LEU cc_start: 0.7121 (mt) cc_final: 0.6869 (mt) REVERT: A 628 MET cc_start: 0.7426 (mmm) cc_final: 0.7092 (mmp) outliers start: 21 outliers final: 15 residues processed: 83 average time/residue: 0.0841 time to fit residues: 9.3759 Evaluate side-chains 78 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 63 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 51 CYS Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain A residue 650 MET Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 737 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 12 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 66 optimal weight: 9.9990 chunk 46 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 2 optimal weight: 0.0060 chunk 20 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 chunk 26 optimal weight: 7.9990 overall best weight: 0.9198 ------------------------------------------------------------------------------- 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 = 0.3767 r_free = 0.3767 target = 0.162426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.122279 restraints weight = 6883.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.124451 restraints weight = 5090.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.126028 restraints weight = 4223.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.126823 restraints weight = 3761.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.127423 restraints weight = 3523.866| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.3116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6058 Z= 0.148 Angle : 0.582 7.936 8241 Z= 0.290 Chirality : 0.040 0.137 932 Planarity : 0.004 0.039 975 Dihedral : 8.719 64.500 1314 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.64 % Allowed : 14.71 % Favored : 81.65 % 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: 0.79 (0.32), residues: 679 helix: 1.42 (0.24), residues: 451 sheet: 0.74 (1.67), residues: 10 loop : -1.41 (0.40), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 293 TYR 0.022 0.001 TYR A 496 PHE 0.013 0.002 PHE A 549 TRP 0.008 0.001 TRP A 67 HIS 0.003 0.001 HIS A 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 ( 6057) covalent geometry : angle 0.58194 / 0.29 ( 8239) SS BOND : bond 0.00233 / 0.12 ( 1) SS BOND : angle 1.05296 / 0.55 ( 2) hydrogen bonds : bond 0.04911 / 3.40 ( 349) hydrogen bonds : angle 4.43921 / 3.09 ( 987) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 74 time to evaluate : 0.176 Fit side-chains revert: symmetry clash REVERT: A 178 PHE cc_start: 0.8137 (OUTLIER) cc_final: 0.6926 (m-80) REVERT: A 181 ASP cc_start: 0.6776 (t0) cc_final: 0.6067 (t0) REVERT: A 335 TYR cc_start: 0.7411 (t80) cc_final: 0.7016 (t80) REVERT: A 445 LEU cc_start: 0.7102 (mt) cc_final: 0.6841 (mt) REVERT: A 544 LEU cc_start: 0.6754 (OUTLIER) cc_final: 0.6542 (tt) REVERT: A 606 GLU cc_start: 0.7546 (OUTLIER) cc_final: 0.7117 (mp0) REVERT: A 628 MET cc_start: 0.7795 (mmm) cc_final: 0.7183 (mmp) outliers start: 22 outliers final: 16 residues processed: 87 average time/residue: 0.0729 time to fit residues: 8.7323 Evaluate side-chains 88 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 69 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 51 CYS Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 178 PHE Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 596 ILE Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain A residue 650 MET Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 701 MET Chi-restraints excluded: chain A residue 703 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 66 optimal weight: 9.9990 chunk 1 optimal weight: 0.7980 chunk 50 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 chunk 46 optimal weight: 0.1980 chunk 36 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3770 r_free = 0.3770 target = 0.162855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.122212 restraints weight = 6997.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.124540 restraints weight = 5083.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.126084 restraints weight = 4168.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.127108 restraints weight = 3684.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.127786 restraints weight = 3418.162| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.3355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6058 Z= 0.130 Angle : 0.548 7.531 8241 Z= 0.272 Chirality : 0.039 0.135 932 Planarity : 0.004 0.041 975 Dihedral : 8.546 67.168 1314 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 4.79 % Allowed : 15.04 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.14 (0.33), residues: 679 helix: 1.72 (0.25), residues: 446 sheet: 0.47 (1.64), residues: 10 loop : -1.26 (0.41), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 556 TYR 0.018 0.001 TYR A 496 PHE 0.013 0.001 PHE A 549 TRP 0.005 0.001 TRP A 431 HIS 0.002 0.001 HIS A 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 ( 6057) covalent geometry : angle 0.54804 / 0.27 ( 8239) SS BOND : bond 0.00165 / 0.09 ( 1) SS BOND : angle 1.08167 / 0.57 ( 2) hydrogen bonds : bond 0.04639 / 3.22 ( 349) hydrogen bonds : angle 4.29307 / 2.98 ( 987) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 75 time to evaluate : 0.220 Fit side-chains REVERT: A 178 PHE cc_start: 0.8125 (OUTLIER) cc_final: 0.6939 (m-80) REVERT: A 181 ASP cc_start: 0.6717 (t0) cc_final: 0.6438 (t70) REVERT: A 292 GLU cc_start: 0.7277 (tt0) cc_final: 0.6556 (tt0) REVERT: A 445 LEU cc_start: 0.7061 (mt) cc_final: 0.6795 (mt) REVERT: A 606 GLU cc_start: 0.7560 (OUTLIER) cc_final: 0.7092 (mp0) outliers start: 29 outliers final: 21 residues processed: 92 average time/residue: 0.0653 time to fit residues: 8.2303 Evaluate side-chains 92 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 69 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 51 CYS Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 178 PHE Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 348 ARG Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 515 MET Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain A residue 596 ILE Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain A residue 650 MET Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 701 MET Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 737 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 38 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 24 optimal weight: 8.9990 chunk 15 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 32 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 472 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.161873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.120797 restraints weight = 6965.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.123230 restraints weight = 4979.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.124858 restraints weight = 4057.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.125506 restraints weight = 3598.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.126212 restraints weight = 3388.886| |-----------------------------------------------------------------------------| r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.3384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 6058 Z= 0.183 Angle : 0.601 7.266 8241 Z= 0.299 Chirality : 0.041 0.138 932 Planarity : 0.004 0.041 975 Dihedral : 8.701 70.765 1314 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 5.29 % Allowed : 15.21 % Favored : 79.50 % 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: 0.93 (0.33), residues: 679 helix: 1.54 (0.25), residues: 450 sheet: 0.50 (1.66), residues: 10 loop : -1.35 (0.41), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 556 TYR 0.017 0.002 TYR A 496 PHE 0.015 0.002 PHE A 154 TRP 0.008 0.001 TRP A 431 HIS 0.004 0.001 HIS A 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.18 ( 6057) covalent geometry : angle 0.60052 / 0.30 ( 8239) SS BOND : bond 0.00317 / 0.17 ( 1) SS BOND : angle 0.82778 / 0.44 ( 2) hydrogen bonds : bond 0.05213 / 3.58 ( 349) hydrogen bonds : angle 4.41014 / 3.07 ( 987) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 74 time to evaluate : 0.130 Fit side-chains revert: symmetry clash REVERT: A 178 PHE cc_start: 0.8095 (OUTLIER) cc_final: 0.6979 (m-80) REVERT: A 383 LYS cc_start: 0.7428 (ptpt) cc_final: 0.6564 (mttp) REVERT: A 445 LEU cc_start: 0.7129 (mt) cc_final: 0.6847 (mt) REVERT: A 606 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.7199 (mp0) outliers start: 32 outliers final: 24 residues processed: 94 average time/residue: 0.0638 time to fit residues: 8.1815 Evaluate side-chains 96 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 70 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 51 CYS Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 178 PHE Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 348 ARG Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 411 TYR Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 496 TYR Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain A residue 650 MET Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 701 MET Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 727 HIS Chi-restraints excluded: chain A residue 737 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 33 optimal weight: 7.9990 chunk 42 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 35 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 66 optimal weight: 9.9990 chunk 55 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 5 optimal weight: 4.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- 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 = 0.3755 r_free = 0.3755 target = 0.160952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.120513 restraints weight = 6991.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.122776 restraints weight = 5146.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.124108 restraints weight = 4278.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.124836 restraints weight = 3828.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.125547 restraints weight = 3602.109| |-----------------------------------------------------------------------------| r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.3486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 6058 Z= 0.168 Angle : 0.592 8.067 8241 Z= 0.292 Chirality : 0.040 0.135 932 Planarity : 0.004 0.040 975 Dihedral : 8.640 73.149 1314 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 5.45 % Allowed : 15.04 % Favored : 79.50 % 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: 1.00 (0.33), residues: 679 helix: 1.58 (0.25), residues: 450 sheet: 0.43 (1.65), residues: 10 loop : -1.27 (0.41), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 556 TYR 0.017 0.001 TYR A 496 PHE 0.015 0.002 PHE A 154 TRP 0.007 0.001 TRP A 431 HIS 0.003 0.001 HIS A 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.17 ( 6057) covalent geometry : angle 0.59171 / 0.29 ( 8239) SS BOND : bond 0.00258 / 0.14 ( 1) SS BOND : angle 0.83003 / 0.44 ( 2) hydrogen bonds : bond 0.05038 / 3.46 ( 349) hydrogen bonds : angle 4.36398 / 3.04 ( 987) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 72 time to evaluate : 0.207 Fit side-chains revert: symmetry clash REVERT: A 178 PHE cc_start: 0.8086 (OUTLIER) cc_final: 0.6981 (m-80) REVERT: A 383 LYS cc_start: 0.7257 (ptpt) cc_final: 0.6402 (mttp) REVERT: A 445 LEU cc_start: 0.7105 (mt) cc_final: 0.6856 (mt) REVERT: A 583 MET cc_start: 0.7586 (mmm) cc_final: 0.7218 (mmt) REVERT: A 606 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7240 (mp0) outliers start: 33 outliers final: 29 residues processed: 93 average time/residue: 0.0652 time to fit residues: 8.3903 Evaluate side-chains 101 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 70 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 51 CYS Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 178 PHE Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 348 ARG Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 411 TYR Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 496 TYR Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 515 MET Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain A residue 596 ILE Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain A residue 650 MET Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 701 MET Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 727 HIS Chi-restraints excluded: chain A residue 737 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 3 optimal weight: 0.7980 chunk 25 optimal weight: 0.0070 chunk 36 optimal weight: 0.5980 chunk 63 optimal weight: 2.9990 chunk 27 optimal weight: 7.9990 chunk 66 optimal weight: 10.0000 chunk 65 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 52 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- 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 = 0.3810 r_free = 0.3810 target = 0.165635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.126243 restraints weight = 6902.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.127903 restraints weight = 5205.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.127958 restraints weight = 4119.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.128834 restraints weight = 3934.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.129335 restraints weight = 3538.099| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.3720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6058 Z= 0.122 Angle : 0.540 8.124 8241 Z= 0.265 Chirality : 0.038 0.131 932 Planarity : 0.004 0.040 975 Dihedral : 8.245 72.378 1314 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 4.46 % Allowed : 17.36 % Favored : 78.18 % 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: 1.30 (0.33), residues: 679 helix: 1.84 (0.25), residues: 451 sheet: 0.11 (1.57), residues: 10 loop : -1.22 (0.41), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 608 TYR 0.017 0.001 TYR A 496 PHE 0.015 0.001 PHE A 549 TRP 0.006 0.001 TRP A 420 HIS 0.002 0.001 HIS A 516 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 ( 6057) covalent geometry : angle 0.53967 / 0.26 ( 8239) SS BOND : bond 0.00206 / 0.11 ( 1) SS BOND : angle 0.75296 / 0.40 ( 2) hydrogen bonds : bond 0.04382 / 3.04 ( 349) hydrogen bonds : angle 4.16179 / 2.89 ( 987) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 73 time to evaluate : 0.222 Fit side-chains revert: symmetry clash REVERT: A 178 PHE cc_start: 0.8096 (OUTLIER) cc_final: 0.6968 (m-80) REVERT: A 348 ARG cc_start: 0.7630 (OUTLIER) cc_final: 0.6906 (ttm110) REVERT: A 383 LYS cc_start: 0.7246 (ptpt) cc_final: 0.6468 (mttp) REVERT: A 445 LEU cc_start: 0.7085 (mt) cc_final: 0.6808 (mt) REVERT: A 583 MET cc_start: 0.7591 (mmm) cc_final: 0.7324 (mmt) REVERT: A 593 MET cc_start: 0.5533 (mtt) cc_final: 0.4996 (ttm) REVERT: A 606 GLU cc_start: 0.7539 (OUTLIER) cc_final: 0.7104 (mp0) outliers start: 27 outliers final: 20 residues processed: 91 average time/residue: 0.0641 time to fit residues: 8.2313 Evaluate side-chains 95 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 72 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 178 PHE Chi-restraints excluded: chain A residue 348 ARG Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 411 TYR Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain A residue 576 SER Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain A residue 650 MET Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 701 MET Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 737 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 20 optimal weight: 0.0370 chunk 67 optimal weight: 0.0010 chunk 54 optimal weight: 4.9990 chunk 46 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 52 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 chunk 7 optimal weight: 3.9990 chunk 58 optimal weight: 0.6980 chunk 42 optimal weight: 0.7980 overall best weight: 0.4264 ------------------------------------------------------------------------------- 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 = 0.3934 r_free = 0.3934 target = 0.175293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.133766 restraints weight = 7020.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.136774 restraints weight = 4664.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.138743 restraints weight = 3657.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.140111 restraints weight = 3170.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 14)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.140260 restraints weight = 2929.811| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.3920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6058 Z= 0.108 Angle : 0.527 8.358 8241 Z= 0.254 Chirality : 0.037 0.132 932 Planarity : 0.003 0.040 975 Dihedral : 7.970 74.676 1314 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.47 % Allowed : 18.51 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.54 (0.33), residues: 679 helix: 2.02 (0.25), residues: 451 sheet: -0.03 (1.56), residues: 10 loop : -1.11 (0.41), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 134 TYR 0.017 0.001 TYR A 496 PHE 0.013 0.001 PHE A 549 TRP 0.006 0.001 TRP A 420 HIS 0.001 0.000 HIS A 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 ( 6057) covalent geometry : angle 0.52663 / 0.25 ( 8239) SS BOND : bond 0.00125 / 0.07 ( 1) SS BOND : angle 0.66932 / 0.36 ( 2) hydrogen bonds : bond 0.04101 / 2.85 ( 349) hydrogen bonds : angle 4.07917 / 2.84 ( 987) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 75 time to evaluate : 0.218 Fit side-chains revert: symmetry clash REVERT: A 348 ARG cc_start: 0.7561 (OUTLIER) cc_final: 0.6863 (ttm110) REVERT: A 383 LYS cc_start: 0.7028 (ptpt) cc_final: 0.6454 (mttp) REVERT: A 445 LEU cc_start: 0.7063 (mt) cc_final: 0.6769 (mt) REVERT: A 583 MET cc_start: 0.7564 (mmm) cc_final: 0.7288 (mmt) REVERT: A 593 MET cc_start: 0.5432 (mtt) cc_final: 0.4988 (ttm) REVERT: A 606 GLU cc_start: 0.7528 (OUTLIER) cc_final: 0.7092 (mp0) outliers start: 21 outliers final: 16 residues processed: 89 average time/residue: 0.0652 time to fit residues: 8.2299 Evaluate side-chains 91 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 73 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 348 ARG Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 411 TYR Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain A residue 596 ILE Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain A residue 650 MET Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain A residue 701 MET Chi-restraints excluded: chain A residue 703 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 38 optimal weight: 1.9990 chunk 19 optimal weight: 0.1980 chunk 13 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 66 optimal weight: 9.9990 chunk 63 optimal weight: 0.8980 chunk 11 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3867 r_free = 0.3867 target = 0.169834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.128402 restraints weight = 6988.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.131040 restraints weight = 4910.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.132451 restraints weight = 3988.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.133635 restraints weight = 3548.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.134465 restraints weight = 3269.447| |-----------------------------------------------------------------------------| r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.3947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6058 Z= 0.125 Angle : 0.548 7.923 8241 Z= 0.266 Chirality : 0.038 0.132 932 Planarity : 0.003 0.040 975 Dihedral : 7.991 73.065 1314 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.47 % Allowed : 18.68 % Favored : 77.85 % 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: 1.52 (0.33), residues: 679 helix: 2.03 (0.25), residues: 451 sheet: -0.11 (1.55), residues: 10 loop : -1.17 (0.41), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 608 TYR 0.016 0.001 TYR A 496 PHE 0.013 0.001 PHE A 549 TRP 0.005 0.001 TRP A 420 HIS 0.002 0.001 HIS A 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 ( 6057) covalent geometry : angle 0.54831 / 0.27 ( 8239) SS BOND : bond 0.00156 / 0.08 ( 1) SS BOND : angle 0.64464 / 0.34 ( 2) hydrogen bonds : bond 0.04372 / 3.03 ( 349) hydrogen bonds : angle 4.10126 / 2.85 ( 987) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 75 time to evaluate : 0.212 Fit side-chains revert: symmetry clash REVERT: A 348 ARG cc_start: 0.7541 (OUTLIER) cc_final: 0.6736 (ttm110) REVERT: A 383 LYS cc_start: 0.7002 (ptpt) cc_final: 0.6473 (mttp) REVERT: A 445 LEU cc_start: 0.7110 (mt) cc_final: 0.6814 (mt) REVERT: A 583 MET cc_start: 0.7593 (mmm) cc_final: 0.7319 (mmt) REVERT: A 593 MET cc_start: 0.5470 (mtt) cc_final: 0.5078 (ttm) REVERT: A 602 ARG cc_start: 0.6669 (ptp90) cc_final: 0.6435 (ttm170) REVERT: A 606 GLU cc_start: 0.7517 (OUTLIER) cc_final: 0.7130 (mp0) outliers start: 21 outliers final: 18 residues processed: 90 average time/residue: 0.0675 time to fit residues: 8.4115 Evaluate side-chains 93 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 73 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 348 ARG Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 411 TYR Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 596 ILE Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain A residue 650 MET Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain A residue 701 MET Chi-restraints excluded: chain A residue 703 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 1 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 8 optimal weight: 0.0870 chunk 35 optimal weight: 2.9990 chunk 64 optimal weight: 0.0010 chunk 37 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 overall best weight: 1.0168 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 739 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.171833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.131357 restraints weight = 6997.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.133154 restraints weight = 5043.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.133073 restraints weight = 3922.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.133993 restraints weight = 3823.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.134151 restraints weight = 3502.359| |-----------------------------------------------------------------------------| r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.3905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6058 Z= 0.152 Angle : 0.577 7.847 8241 Z= 0.281 Chirality : 0.039 0.134 932 Planarity : 0.004 0.039 975 Dihedral : 8.152 72.375 1314 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.97 % Allowed : 18.35 % Favored : 77.69 % 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: 1.39 (0.33), residues: 679 helix: 1.93 (0.25), residues: 449 sheet: -0.00 (1.57), residues: 10 loop : -1.22 (0.41), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 556 TYR 0.016 0.001 TYR A 335 PHE 0.013 0.002 PHE A 549 TRP 0.007 0.001 TRP A 420 HIS 0.004 0.001 HIS A 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.15 ( 6057) covalent geometry : angle 0.57653 / 0.28 ( 8239) SS BOND : bond 0.00196 / 0.10 ( 1) SS BOND : angle 0.68961 / 0.36 ( 2) hydrogen bonds : bond 0.04772 / 3.29 ( 349) hydrogen bonds : angle 4.18005 / 2.92 ( 987) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1045.02 seconds wall clock time: 18 minutes 45.47 seconds (1125.47 seconds total)