Starting phenix.real_space_refine on Tue Aug 4 16:10:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/28wz_56931/08_2026/28wz_56931.cif Found real_map, /net/cci-nas-00/data/ceres_data/28wz_56931/08_2026/28wz_56931.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 { real_map_files = "/net/cci-nas-00/data/ceres_data/28wz_56931/08_2026/28wz_56931.map" default_real_map = "/net/cci-nas-00/data/ceres_data/28wz_56931/08_2026/28wz_56931.map" model { file = "/net/cci-nas-00/data/ceres_data/28wz_56931/08_2026/28wz_56931.cif" } default_model = "/net/cci-nas-00/data/ceres_data/28wz_56931/08_2026/28wz_56931.cif" } 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= 0.000 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 22 5.16 5 C 2951 2.51 5 N 808 2.21 5 O 847 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s 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: 4628 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1410 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 105} Link IDs: {'PTRANS': 7, 'TRANS': 215} Chain breaks: 1 Unresolved non-hydrogen bonds: 388 Unresolved non-hydrogen angles: 493 Unresolved non-hydrogen dihedrals: 323 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'HIS:plan': 3, 'TRP:plan': 1, 'GLU:plan': 13, 'GLN:plan1': 9, 'ASP:plan': 5, 'TYR:plan': 5, 'PHE:plan': 5, 'ARG:plan': 5, 'ASN:plan1': 3, 'PHE%COO:plan': 1} Unresolved non-hydrogen planarities: 232 Chain: "B" Number of atoms: 2792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2792 Classifications: {'peptide': 371} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 361} Chain breaks: 1 Unresolved non-hydrogen bonds: 237 Unresolved non-hydrogen angles: 304 Unresolved non-hydrogen dihedrals: 201 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'ASN:plan1': 2, 'GLN:plan1': 6, 'TYR:plan': 5, 'GLU:plan': 6, 'ASP:plan': 4, 'ARG:plan': 3, 'PHE:plan': 5, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 161 Chain: "C" Number of atoms: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 426 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 1, 'TRANS': 48} Time building chain proxies: 1.32, per 1000 atoms: 0.29 Number of scatterers: 4628 At special positions: 0 Unit cell: (65.85, 92.19, 108.872, 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 22 16.00 O 847 8.00 N 808 7.00 C 2951 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.39 Conformation dependent library (CDL) restraints added in 191.5 milliseconds 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1242 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 3 sheets defined 79.3% alpha, 1.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'A' and resid 575 through 592 Processing helix chain 'A' and resid 595 through 613 Processing helix chain 'A' and resid 618 through 633 Processing helix chain 'A' and resid 636 through 654 removed outlier: 3.696A pdb=" N GLN A 642 " --> pdb=" O GLU A 638 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN A 646 " --> pdb=" O GLN A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 658 through 674 removed outlier: 3.523A pdb=" N ALA A 664 " --> pdb=" O GLY A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 675 through 686 removed outlier: 3.609A pdb=" N THR A 681 " --> pdb=" O GLY A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 693 removed outlier: 3.565A pdb=" N ASP A 693 " --> pdb=" O GLU A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 694 through 709 Processing helix chain 'A' and resid 710 through 721 removed outlier: 3.816A pdb=" N PHE A 714 " --> pdb=" O ASN A 710 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N HIS A 720 " --> pdb=" O ARG A 716 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 748 removed outlier: 3.818A pdb=" N LEU A 728 " --> pdb=" O MET A 724 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LYS A 731 " --> pdb=" O TYR A 727 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N PHE A 732 " --> pdb=" O LEU A 728 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASP A 734 " --> pdb=" O ASP A 730 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ARG A 735 " --> pdb=" O LYS A 731 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LYS A 738 " --> pdb=" O ASP A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 754 through 762 Processing helix chain 'A' and resid 765 through 777 removed outlier: 3.668A pdb=" N CYS A 769 " --> pdb=" O GLY A 765 " (cutoff:3.500A) Proline residue: A 775 - end of helix Processing helix chain 'A' and resid 789 through 797 Processing helix chain 'B' and resid 8 through 20 removed outlier: 3.934A pdb=" N ASP B 18 " --> pdb=" O TYR B 14 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N SER B 19 " --> pdb=" O GLU B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 31 removed outlier: 3.684A pdb=" N ALA B 26 " --> pdb=" O GLY B 22 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU B 27 " --> pdb=" O ALA B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 75 Processing helix chain 'B' and resid 76 through 98 removed outlier: 3.578A pdb=" N ALA B 80 " --> pdb=" O ASP B 76 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LYS B 82 " --> pdb=" O ILE B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 130 removed outlier: 3.605A pdb=" N ALA B 110 " --> pdb=" O PRO B 106 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LYS B 128 " --> pdb=" O GLN B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 155 removed outlier: 3.589A pdb=" N GLU B 143 " --> pdb=" O GLU B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 158 No H-bonds generated for 'chain 'B' and resid 156 through 158' Processing helix chain 'B' and resid 163 through 183 removed outlier: 3.601A pdb=" N GLY B 167 " --> pdb=" O SER B 163 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N LEU B 169 " --> pdb=" O LYS B 165 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N PHE B 170 " --> pdb=" O TRP B 166 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE B 178 " --> pdb=" O GLN B 174 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LYS B 181 " --> pdb=" O LYS B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 186 No H-bonds generated for 'chain 'B' and resid 184 through 186' Processing helix chain 'B' and resid 187 through 198 removed outlier: 4.176A pdb=" N LEU B 191 " --> pdb=" O LEU B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 224 Processing helix chain 'B' and resid 225 through 240 Processing helix chain 'B' and resid 244 through 263 Proline residue: B 257 - end of helix Processing helix chain 'B' and resid 267 through 275 removed outlier: 3.540A pdb=" N LEU B 271 " --> pdb=" O THR B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 289 removed outlier: 3.613A pdb=" N ALA B 280 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL B 282 " --> pdb=" O GLN B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 306 removed outlier: 3.532A pdb=" N LYS B 300 " --> pdb=" O GLU B 296 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ALA B 303 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N PHE B 304 " --> pdb=" O LYS B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 334 removed outlier: 3.590A pdb=" N LYS B 316 " --> pdb=" O LEU B 312 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ILE B 319 " --> pdb=" O GLU B 315 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE B 320 " --> pdb=" O LYS B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 351 Processing helix chain 'B' and resid 356 through 371 Processing helix chain 'B' and resid 394 through 398 Processing helix chain 'C' and resid 50 through 62 removed outlier: 4.203A pdb=" N GLN C 55 " --> pdb=" O ASP C 51 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 752 through 753 removed outlier: 3.947A pdb=" N LEU A 752 " --> pdb=" O ILE A 788 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 265 through 266 Processing sheet with id=AA3, first strand: chain 'B' and resid 338 through 339 removed outlier: 3.521A pdb=" N LYS B 383 " --> pdb=" O SER B 378 " (cutoff:3.500A) 341 hydrogen bonds defined for protein. 1008 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: 0.75 Time building geometry restraints manager: 0.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1353 1.33 - 1.45: 682 1.45 - 1.57: 2646 1.57 - 1.69: 0 1.69 - 1.81: 35 Bond restraints: 4716 Sorted by residual: bond pdb=" C ARG A 749 " pdb=" N PRO A 750 " ideal model delta sigma weight residual 1.335 1.363 -0.028 1.28e-02 6.10e+03 4.86e+00 bond pdb=" CB PHE A 714 " pdb=" CG PHE A 714 " ideal model delta sigma weight residual 1.502 1.545 -0.043 2.30e-02 1.89e+03 3.45e+00 bond pdb=" CB ASN B 102 " pdb=" CG ASN B 102 " ideal model delta sigma weight residual 1.516 1.559 -0.043 2.50e-02 1.60e+03 3.02e+00 bond pdb=" CB CYS B 362 " pdb=" SG CYS B 362 " ideal model delta sigma weight residual 1.808 1.752 0.056 3.30e-02 9.18e+02 2.90e+00 bond pdb=" N ASN B 183 " pdb=" CA ASN B 183 " ideal model delta sigma weight residual 1.460 1.491 -0.031 1.83e-02 2.99e+03 2.81e+00 ... (remaining 4711 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 5768 1.92 - 3.85: 556 3.85 - 5.77: 68 5.77 - 7.69: 15 7.69 - 9.62: 4 Bond angle restraints: 6411 Sorted by residual: angle pdb=" N ASP C 50 " pdb=" CA ASP C 50 " pdb=" C ASP C 50 " ideal model delta sigma weight residual 111.56 121.18 -9.62 1.53e+00 4.27e-01 3.95e+01 angle pdb=" N PHE B 77 " pdb=" CA PHE B 77 " pdb=" C PHE B 77 " ideal model delta sigma weight residual 111.75 118.89 -7.14 1.28e+00 6.10e-01 3.11e+01 angle pdb=" N PRO A 694 " pdb=" CA PRO A 694 " pdb=" C PRO A 694 " ideal model delta sigma weight residual 112.47 121.73 -9.26 2.06e+00 2.36e-01 2.02e+01 angle pdb=" N ASP C 51 " pdb=" CA ASP C 51 " pdb=" C ASP C 51 " ideal model delta sigma weight residual 111.03 115.74 -4.71 1.11e+00 8.12e-01 1.80e+01 angle pdb=" CA ARG A 749 " pdb=" C ARG A 749 " pdb=" N PRO A 750 " ideal model delta sigma weight residual 118.44 124.84 -6.40 1.59e+00 3.96e-01 1.62e+01 ... (remaining 6406 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.18: 2600 17.18 - 34.35: 190 34.35 - 51.52: 26 51.52 - 68.70: 3 68.70 - 85.87: 6 Dihedral angle restraints: 2825 sinusoidal: 923 harmonic: 1902 Sorted by residual: dihedral pdb=" CA ASP C 50 " pdb=" C ASP C 50 " pdb=" N ASP C 51 " pdb=" CA ASP C 51 " ideal model delta harmonic sigma weight residual -180.00 -149.44 -30.56 0 5.00e+00 4.00e-02 3.74e+01 dihedral pdb=" CA ASP B 162 " pdb=" C ASP B 162 " pdb=" N SER B 163 " pdb=" CA SER B 163 " ideal model delta harmonic sigma weight residual -180.00 -150.00 -30.00 0 5.00e+00 4.00e-02 3.60e+01 dihedral pdb=" CA GLU C 49 " pdb=" C GLU C 49 " pdb=" N ASP C 50 " pdb=" CA ASP C 50 " ideal model delta harmonic sigma weight residual -180.00 -150.17 -29.83 0 5.00e+00 4.00e-02 3.56e+01 ... (remaining 2822 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 583 0.067 - 0.133: 123 0.133 - 0.200: 26 0.200 - 0.266: 6 0.266 - 0.333: 2 Chirality restraints: 740 Sorted by residual: chirality pdb=" CA ASP C 50 " pdb=" N ASP C 50 " pdb=" C ASP C 50 " pdb=" CB ASP C 50 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.77e+00 chirality pdb=" CA PHE A 732 " pdb=" N PHE A 732 " pdb=" C PHE A 732 " pdb=" CB PHE A 732 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" CA PHE A 662 " pdb=" N PHE A 662 " pdb=" C PHE A 662 " pdb=" CB PHE A 662 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.61e+00 ... (remaining 737 not shown) Planarity restraints: 834 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET A 724 " 0.016 2.00e-02 2.50e+03 3.20e-02 1.02e+01 pdb=" C MET A 724 " -0.055 2.00e-02 2.50e+03 pdb=" O MET A 724 " 0.020 2.00e-02 2.50e+03 pdb=" N SER A 725 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 640 " -0.014 2.00e-02 2.50e+03 2.85e-02 8.13e+00 pdb=" C PHE A 640 " 0.049 2.00e-02 2.50e+03 pdb=" O PHE A 640 " -0.018 2.00e-02 2.50e+03 pdb=" N ASN A 641 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 294 " 0.014 2.00e-02 2.50e+03 2.78e-02 7.74e+00 pdb=" C LEU B 294 " -0.048 2.00e-02 2.50e+03 pdb=" O LEU B 294 " 0.018 2.00e-02 2.50e+03 pdb=" N HIS B 295 " 0.016 2.00e-02 2.50e+03 ... (remaining 831 not shown) Histogram of nonbonded interaction distances: 2.62 - 3.08: 3155 3.08 - 3.53: 4851 3.53 - 3.99: 6857 3.99 - 4.44: 8512 4.44 - 4.90: 11984 Nonbonded interactions: 35359 Sorted by model distance: nonbonded pdb=" O ASP B 21 " pdb=" CA GLY B 22 " model vdw 2.621 2.752 nonbonded pdb=" N LEU C 30 " pdb=" O LEU C 30 " model vdw 2.631 2.496 nonbonded pdb=" N ASP C 17 " pdb=" O ASP C 17 " model vdw 2.631 2.496 nonbonded pdb=" N ASP B 356 " pdb=" O ASP B 356 " model vdw 2.632 2.496 nonbonded pdb=" C THR B 267 " pdb=" OG1 THR B 267 " model vdw 2.641 2.616 ... (remaining 35354 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: 1.630 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: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.670 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: 0.010 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6564 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 : 0.007 0.064 4716 Z= 0.352 Angle : 1.229 9.616 6411 Z= 0.781 Chirality : 0.061 0.333 740 Planarity : 0.010 0.086 834 Dihedral : 13.148 85.872 1583 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 0.23 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.26 % Favored : 95.43 % Rotamer: Outliers : 1.02 % Allowed : 2.80 % Favored : 96.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % 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: -1.72 (0.28), residues: 634 helix: -0.84 (0.19), residues: 461 sheet: -1.71 (1.45), residues: 10 loop : -1.51 (0.50), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.002 ARG B 323 TYR 0.034 0.006 TYR B 204 PHE 0.039 0.004 PHE A 732 TRP 0.016 0.006 TRP C 27 HIS 0.008 0.002 HIS B 264 Details of bonding type rmsd/Z covalent geometry : bond 0.00700 / 0.35 ( 4716) covalent geometry : angle 1.22868 / 0.78 ( 6411) hydrogen bonds : bond 0.25702 / 19.60 ( 341) hydrogen bonds : angle 8.79851 / 6.70 ( 1008) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 109 time to evaluate : 0.180 Fit side-chains revert: symmetry clash REVERT: A 720 HIS cc_start: 0.7748 (OUTLIER) cc_final: 0.6912 (t-90) REVERT: B 137 MET cc_start: 0.5800 (mmp) cc_final: 0.5131 (tpt) REVERT: B 242 ARG cc_start: 0.7513 (ttp-170) cc_final: 0.7219 (ttm-80) REVERT: B 307 ARG cc_start: 0.7186 (ttp80) cc_final: 0.6894 (ptm-80) outliers start: 4 outliers final: 3 residues processed: 113 average time/residue: 0.0847 time to fit residues: 11.8035 Evaluate side-chains 72 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 68 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 720 HIS Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 377 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 20.0000 chunk 17 optimal weight: 4.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 361 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 = 0.4401 r_free = 0.4401 target = 0.192105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.163028 restraints weight = 7398.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.166591 restraints weight = 4485.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.168963 restraints weight = 3157.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.170302 restraints weight = 2465.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.171550 restraints weight = 2096.559| |-----------------------------------------------------------------------------| r_work (final): 0.4183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6639 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4716 Z= 0.174 Angle : 0.672 10.865 6411 Z= 0.366 Chirality : 0.040 0.128 740 Planarity : 0.004 0.044 834 Dihedral : 7.455 59.925 686 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.73 % Favored : 95.11 % Rotamer: Outliers : 2.54 % Allowed : 10.69 % Favored : 86.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % 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: 0.54 (0.33), residues: 634 helix: 0.79 (0.22), residues: 475 sheet: -1.39 (1.46), residues: 10 loop : -0.63 (0.58), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 703 TYR 0.020 0.002 TYR B 179 PHE 0.017 0.002 PHE A 732 TRP 0.008 0.001 TRP C 43 HIS 0.008 0.001 HIS B 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.17 ( 4716) covalent geometry : angle 0.67183 / 0.37 ( 6411) hydrogen bonds : bond 0.05927 / 4.42 ( 341) hydrogen bonds : angle 5.37067 / 4.11 ( 1008) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 0.210 Fit side-chains revert: symmetry clash REVERT: A 720 HIS cc_start: 0.7675 (OUTLIER) cc_final: 0.7116 (t-90) REVERT: B 123 ASP cc_start: 0.6118 (m-30) cc_final: 0.4286 (t70) REVERT: B 137 MET cc_start: 0.5815 (mmp) cc_final: 0.4772 (tpt) outliers start: 10 outliers final: 7 residues processed: 87 average time/residue: 0.0849 time to fit residues: 9.2868 Evaluate side-chains 75 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 719 CYS Chi-restraints excluded: chain A residue 720 HIS Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 377 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 20 optimal weight: 0.0050 chunk 60 optimal weight: 5.9990 chunk 30 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 6 optimal weight: 10.0000 chunk 48 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 50 optimal weight: 0.7980 chunk 59 optimal weight: 0.0970 overall best weight: 0.4792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 228 GLN B 361 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.195757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.166246 restraints weight = 7410.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.170138 restraints weight = 4372.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.172738 restraints weight = 3018.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.174397 restraints weight = 2326.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.175533 restraints weight = 1940.945| |-----------------------------------------------------------------------------| r_work (final): 0.4210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6568 moved from start: 0.3695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4716 Z= 0.136 Angle : 0.588 11.957 6411 Z= 0.312 Chirality : 0.037 0.125 740 Planarity : 0.004 0.055 834 Dihedral : 6.797 59.909 686 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.10 % Favored : 95.74 % Rotamer: Outliers : 2.80 % Allowed : 13.74 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % 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 (0.34), residues: 634 helix: 1.22 (0.23), residues: 476 sheet: -1.38 (1.44), residues: 10 loop : -0.38 (0.61), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 688 TYR 0.020 0.001 TYR B 179 PHE 0.011 0.001 PHE A 662 TRP 0.007 0.001 TRP C 43 HIS 0.004 0.001 HIS B 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.14 ( 4716) covalent geometry : angle 0.58785 / 0.31 ( 6411) hydrogen bonds : bond 0.04629 / 3.45 ( 341) hydrogen bonds : angle 4.83353 / 3.70 ( 1008) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.102 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 720 HIS cc_start: 0.7850 (OUTLIER) cc_final: 0.7131 (t-90) REVERT: B 123 ASP cc_start: 0.5824 (m-30) cc_final: 0.4094 (t70) REVERT: B 137 MET cc_start: 0.5577 (mmp) cc_final: 0.4643 (tpt) REVERT: B 232 TYR cc_start: 0.6951 (m-10) cc_final: 0.6710 (m-10) REVERT: C 43 TRP cc_start: 0.4939 (p-90) cc_final: 0.4711 (p-90) outliers start: 11 outliers final: 8 residues processed: 82 average time/residue: 0.0448 time to fit residues: 4.8093 Evaluate side-chains 74 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 65 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 719 CYS Chi-restraints excluded: chain A residue 720 HIS Chi-restraints excluded: chain A residue 745 ILE Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 377 ILE Chi-restraints excluded: chain C residue 50 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 29 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 26 optimal weight: 8.9990 chunk 60 optimal weight: 10.0000 chunk 11 optimal weight: 0.9980 chunk 28 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 = 0.4413 r_free = 0.4413 target = 0.193464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.163582 restraints weight = 7589.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.167447 restraints weight = 4489.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.169949 restraints weight = 3115.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.171688 restraints weight = 2425.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.172482 restraints weight = 2027.829| |-----------------------------------------------------------------------------| r_work (final): 0.4169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6637 moved from start: 0.4032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4716 Z= 0.147 Angle : 0.596 13.269 6411 Z= 0.310 Chirality : 0.038 0.122 740 Planarity : 0.004 0.060 834 Dihedral : 6.264 50.385 685 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.94 % Favored : 95.90 % Rotamer: Outliers : 3.05 % Allowed : 15.52 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: 1.27 (0.34), residues: 634 helix: 1.24 (0.23), residues: 477 sheet: -1.45 (1.51), residues: 10 loop : -0.07 (0.61), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 688 TYR 0.011 0.001 TYR B 322 PHE 0.016 0.002 PHE A 732 TRP 0.006 0.001 TRP C 43 HIS 0.004 0.001 HIS B 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.15 ( 4716) covalent geometry : angle 0.59592 / 0.31 ( 6411) hydrogen bonds : bond 0.04415 / 3.29 ( 341) hydrogen bonds : angle 4.81152 / 3.69 ( 1008) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 67 time to evaluate : 0.176 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 720 HIS cc_start: 0.7721 (OUTLIER) cc_final: 0.7092 (t-90) REVERT: B 123 ASP cc_start: 0.5798 (m-30) cc_final: 0.3997 (t70) REVERT: B 137 MET cc_start: 0.5612 (mmp) cc_final: 0.4575 (tpt) REVERT: B 210 VAL cc_start: 0.5304 (OUTLIER) cc_final: 0.5054 (m) outliers start: 12 outliers final: 8 residues processed: 75 average time/residue: 0.0885 time to fit residues: 8.5288 Evaluate side-chains 74 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 719 CYS Chi-restraints excluded: chain A residue 720 HIS Chi-restraints excluded: chain A residue 745 ILE Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 377 ILE Chi-restraints excluded: chain C residue 50 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 40 optimal weight: 0.5980 chunk 25 optimal weight: 30.0000 chunk 63 optimal weight: 0.8980 chunk 36 optimal weight: 0.6980 chunk 24 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 26 optimal weight: 10.0000 chunk 33 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 12 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 658 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.192564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.163884 restraints weight = 7390.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.167341 restraints weight = 4488.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.169741 restraints weight = 3188.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.171353 restraints weight = 2510.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.172301 restraints weight = 2101.558| |-----------------------------------------------------------------------------| r_work (final): 0.4182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6609 moved from start: 0.4300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4716 Z= 0.131 Angle : 0.571 13.858 6411 Z= 0.292 Chirality : 0.036 0.121 740 Planarity : 0.004 0.062 834 Dihedral : 5.894 46.397 685 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.31 % Favored : 96.53 % Rotamer: Outliers : 2.54 % Allowed : 17.05 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: 1.45 (0.35), residues: 634 helix: 1.34 (0.23), residues: 482 sheet: -0.93 (1.59), residues: 10 loop : 0.02 (0.62), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 116 TYR 0.011 0.001 TYR B 179 PHE 0.013 0.001 PHE A 662 TRP 0.006 0.001 TRP B 166 HIS 0.003 0.000 HIS B 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.13 ( 4716) covalent geometry : angle 0.57139 / 0.29 ( 6411) hydrogen bonds : bond 0.04059 / 3.02 ( 341) hydrogen bonds : angle 4.68953 / 3.60 ( 1008) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 68 time to evaluate : 0.174 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 682 GLU cc_start: 0.6610 (mm-30) cc_final: 0.6299 (mm-30) REVERT: A 720 HIS cc_start: 0.7768 (OUTLIER) cc_final: 0.7136 (t70) REVERT: B 137 MET cc_start: 0.5381 (mmp) cc_final: 0.4849 (tpt) outliers start: 10 outliers final: 7 residues processed: 75 average time/residue: 0.0509 time to fit residues: 5.0215 Evaluate side-chains 69 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 61 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 719 CYS Chi-restraints excluded: chain A residue 720 HIS Chi-restraints excluded: chain A residue 745 ILE Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain C residue 50 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 62 optimal weight: 0.9990 chunk 57 optimal weight: 0.6980 chunk 31 optimal weight: 5.9990 chunk 21 optimal weight: 20.0000 chunk 30 optimal weight: 3.9990 chunk 22 optimal weight: 30.0000 chunk 51 optimal weight: 0.9980 chunk 2 optimal weight: 8.9990 chunk 17 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 658 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.191929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.163401 restraints weight = 7536.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.167001 restraints weight = 4586.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.169334 restraints weight = 3220.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.170956 restraints weight = 2518.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.171847 restraints weight = 2113.674| |-----------------------------------------------------------------------------| r_work (final): 0.4187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6631 moved from start: 0.4510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4716 Z= 0.138 Angle : 0.592 12.349 6411 Z= 0.303 Chirality : 0.037 0.121 740 Planarity : 0.004 0.064 834 Dihedral : 5.517 43.285 683 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.10 % Favored : 95.74 % Rotamer: Outliers : 3.56 % Allowed : 16.28 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: 1.41 (0.34), residues: 634 helix: 1.30 (0.23), residues: 487 sheet: -0.41 (1.85), residues: 10 loop : -0.04 (0.64), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 703 TYR 0.010 0.001 TYR B 322 PHE 0.015 0.002 PHE A 662 TRP 0.051 0.004 TRP C 43 HIS 0.003 0.001 HIS A 712 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.14 ( 4716) covalent geometry : angle 0.59234 / 0.30 ( 6411) hydrogen bonds : bond 0.04043 / 3.01 ( 341) hydrogen bonds : angle 4.72789 / 3.64 ( 1008) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 63 time to evaluate : 0.193 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 682 GLU cc_start: 0.6734 (mm-30) cc_final: 0.6426 (mm-30) REVERT: A 720 HIS cc_start: 0.7851 (OUTLIER) cc_final: 0.7188 (t70) REVERT: A 724 MET cc_start: 0.7099 (mmm) cc_final: 0.6874 (mtm) REVERT: B 137 MET cc_start: 0.5478 (mmp) cc_final: 0.4903 (tpt) REVERT: B 210 VAL cc_start: 0.5415 (OUTLIER) cc_final: 0.5163 (m) outliers start: 14 outliers final: 9 residues processed: 71 average time/residue: 0.0706 time to fit residues: 6.5795 Evaluate side-chains 68 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 719 CYS Chi-restraints excluded: chain A residue 720 HIS Chi-restraints excluded: chain A residue 745 ILE Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 240 CYS Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 377 ILE Chi-restraints excluded: chain C residue 50 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 10 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 chunk 3 optimal weight: 10.0000 chunk 61 optimal weight: 6.9990 chunk 58 optimal weight: 0.0040 chunk 32 optimal weight: 5.9990 chunk 49 optimal weight: 0.4980 chunk 54 optimal weight: 0.9990 chunk 22 optimal weight: 30.0000 chunk 7 optimal weight: 9.9990 chunk 29 optimal weight: 3.9990 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 658 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.193041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.164768 restraints weight = 7440.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.168311 restraints weight = 4503.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.170675 restraints weight = 3163.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.172305 restraints weight = 2468.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.173104 restraints weight = 2067.044| |-----------------------------------------------------------------------------| r_work (final): 0.4202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6592 moved from start: 0.4688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4716 Z= 0.126 Angle : 0.577 12.093 6411 Z= 0.295 Chirality : 0.036 0.124 740 Planarity : 0.004 0.065 834 Dihedral : 5.355 40.231 683 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.10 % Favored : 95.74 % Rotamer: Outliers : 3.05 % Allowed : 17.56 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: 1.56 (0.35), residues: 634 helix: 1.41 (0.23), residues: 486 sheet: -0.31 (1.86), residues: 10 loop : 0.03 (0.64), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 703 TYR 0.016 0.001 TYR B 232 PHE 0.012 0.001 PHE A 662 TRP 0.028 0.002 TRP C 39 HIS 0.003 0.000 HIS A 712 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.13 ( 4716) covalent geometry : angle 0.57687 / 0.30 ( 6411) hydrogen bonds : bond 0.03837 / 2.85 ( 341) hydrogen bonds : angle 4.66821 / 3.60 ( 1008) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 61 time to evaluate : 0.174 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 720 HIS cc_start: 0.7749 (OUTLIER) cc_final: 0.7090 (t70) REVERT: B 137 MET cc_start: 0.5422 (mmp) cc_final: 0.4901 (tpt) REVERT: B 277 MET cc_start: 0.5208 (mpp) cc_final: 0.4926 (mmm) outliers start: 12 outliers final: 8 residues processed: 67 average time/residue: 0.0714 time to fit residues: 6.2989 Evaluate side-chains 68 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 59 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 719 CYS Chi-restraints excluded: chain A residue 720 HIS Chi-restraints excluded: chain A residue 745 ILE Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 377 ILE Chi-restraints excluded: chain C residue 50 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 40 optimal weight: 0.9980 chunk 3 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 47 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 58 optimal weight: 0.0010 chunk 21 optimal weight: 10.0000 chunk 10 optimal weight: 0.9990 overall best weight: 0.6788 ------------------------------------------------------------------------------- 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 = 0.4421 r_free = 0.4421 target = 0.193841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.165653 restraints weight = 7509.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.169198 restraints weight = 4525.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.171563 restraints weight = 3174.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.173015 restraints weight = 2472.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.174260 restraints weight = 2085.959| |-----------------------------------------------------------------------------| r_work (final): 0.4212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6571 moved from start: 0.4872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4716 Z= 0.131 Angle : 0.586 11.780 6411 Z= 0.302 Chirality : 0.036 0.128 740 Planarity : 0.005 0.068 834 Dihedral : 5.295 37.557 683 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.10 % Favored : 95.74 % Rotamer: Outliers : 3.31 % Allowed : 18.32 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: 1.51 (0.35), residues: 634 helix: 1.37 (0.23), residues: 486 sheet: -0.06 (1.93), residues: 10 loop : -0.03 (0.63), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 703 TYR 0.012 0.001 TYR B 232 PHE 0.013 0.002 PHE A 662 TRP 0.020 0.002 TRP C 43 HIS 0.003 0.000 HIS A 712 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 ( 4716) covalent geometry : angle 0.58593 / 0.30 ( 6411) hydrogen bonds : bond 0.03953 / 2.92 ( 341) hydrogen bonds : angle 4.72946 / 3.65 ( 1008) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 63 time to evaluate : 0.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 682 GLU cc_start: 0.6653 (mm-30) cc_final: 0.6417 (mm-30) REVERT: A 720 HIS cc_start: 0.7755 (OUTLIER) cc_final: 0.7056 (t70) REVERT: B 137 MET cc_start: 0.5390 (mmp) cc_final: 0.4908 (tpt) REVERT: B 353 GLU cc_start: 0.7464 (tm-30) cc_final: 0.7169 (pp20) outliers start: 13 outliers final: 7 residues processed: 71 average time/residue: 0.0651 time to fit residues: 6.1381 Evaluate side-chains 66 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 719 CYS Chi-restraints excluded: chain A residue 720 HIS Chi-restraints excluded: chain A residue 745 ILE Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain C residue 50 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 6 optimal weight: 10.0000 chunk 61 optimal weight: 0.0470 chunk 40 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 18 optimal weight: 8.9990 chunk 16 optimal weight: 4.9990 chunk 2 optimal weight: 20.0000 chunk 23 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 overall best weight: 0.9282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 658 ASN ** B 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 247 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.192298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.164281 restraints weight = 7360.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.167774 restraints weight = 4403.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.170076 restraints weight = 3079.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.171707 restraints weight = 2399.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.172651 restraints weight = 2002.126| |-----------------------------------------------------------------------------| r_work (final): 0.4198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6611 moved from start: 0.4967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4716 Z= 0.142 Angle : 0.612 11.746 6411 Z= 0.313 Chirality : 0.038 0.129 740 Planarity : 0.004 0.067 834 Dihedral : 5.227 34.379 683 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.42 % Favored : 95.43 % Rotamer: Outliers : 2.54 % Allowed : 19.59 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 0.16 % 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: 1.42 (0.35), residues: 634 helix: 1.33 (0.23), residues: 486 sheet: -0.33 (1.85), residues: 10 loop : -0.14 (0.63), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 703 TYR 0.012 0.001 TYR B 179 PHE 0.023 0.002 PHE C 19 TRP 0.020 0.002 TRP C 43 HIS 0.003 0.001 HIS A 712 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 ( 4716) covalent geometry : angle 0.61227 / 0.31 ( 6411) hydrogen bonds : bond 0.03947 / 2.92 ( 341) hydrogen bonds : angle 4.79739 / 3.70 ( 1008) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 0.172 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 682 GLU cc_start: 0.6653 (mm-30) cc_final: 0.6415 (mm-30) REVERT: A 720 HIS cc_start: 0.7841 (OUTLIER) cc_final: 0.7253 (t70) REVERT: B 137 MET cc_start: 0.5456 (mmp) cc_final: 0.5015 (tpt) REVERT: B 210 VAL cc_start: 0.5405 (OUTLIER) cc_final: 0.5101 (m) REVERT: B 353 GLU cc_start: 0.7435 (tm-30) cc_final: 0.7170 (pp20) outliers start: 10 outliers final: 7 residues processed: 63 average time/residue: 0.0502 time to fit residues: 4.2194 Evaluate side-chains 64 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 719 CYS Chi-restraints excluded: chain A residue 720 HIS Chi-restraints excluded: chain A residue 745 ILE Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 247 ASN Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 352 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 51 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 22 optimal weight: 30.0000 chunk 61 optimal weight: 2.9990 chunk 38 optimal weight: 0.0470 chunk 58 optimal weight: 0.3980 chunk 4 optimal weight: 9.9990 overall best weight: 0.6480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 247 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.195431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.166883 restraints weight = 7460.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.170543 restraints weight = 4435.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.173039 restraints weight = 3092.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.174805 restraints weight = 2392.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.175796 restraints weight = 1979.579| |-----------------------------------------------------------------------------| r_work (final): 0.4207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6579 moved from start: 0.5079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4716 Z= 0.127 Angle : 0.592 11.426 6411 Z= 0.305 Chirality : 0.037 0.132 740 Planarity : 0.004 0.068 834 Dihedral : 5.196 37.815 683 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.26 % Favored : 95.58 % Rotamer: Outliers : 2.04 % Allowed : 20.10 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 0.16 % 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: 1.45 (0.35), residues: 634 helix: 1.38 (0.24), residues: 486 sheet: -0.34 (1.83), residues: 10 loop : -0.22 (0.63), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 703 TYR 0.012 0.001 TYR B 322 PHE 0.013 0.002 PHE C 19 TRP 0.017 0.002 TRP C 43 HIS 0.003 0.000 HIS A 712 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.13 ( 4716) covalent geometry : angle 0.59231 / 0.30 ( 6411) hydrogen bonds : bond 0.03817 / 2.82 ( 341) hydrogen bonds : angle 4.76212 / 3.68 ( 1008) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.181 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 682 GLU cc_start: 0.6573 (mm-30) cc_final: 0.6348 (mm-30) REVERT: A 720 HIS cc_start: 0.7790 (OUTLIER) cc_final: 0.7287 (t70) REVERT: B 137 MET cc_start: 0.5442 (mmp) cc_final: 0.5002 (tpt) REVERT: B 353 GLU cc_start: 0.7467 (tm-30) cc_final: 0.7217 (pp20) outliers start: 8 outliers final: 7 residues processed: 59 average time/residue: 0.0595 time to fit residues: 4.7218 Evaluate side-chains 59 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 51 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 719 CYS Chi-restraints excluded: chain A residue 720 HIS Chi-restraints excluded: chain A residue 745 ILE Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 247 ASN Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 352 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 18 optimal weight: 1.9990 chunk 21 optimal weight: 10.0000 chunk 51 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 28 optimal weight: 20.0000 chunk 55 optimal weight: 2.9990 chunk 1 optimal weight: 20.0000 chunk 26 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 chunk 25 optimal weight: 8.9990 chunk 47 optimal weight: 0.7980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 247 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.191666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.162162 restraints weight = 7563.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.165987 restraints weight = 4446.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.168565 restraints weight = 3082.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.170057 restraints weight = 2376.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.171292 restraints weight = 2000.410| |-----------------------------------------------------------------------------| r_work (final): 0.4158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6680 moved from start: 0.5025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 4716 Z= 0.173 Angle : 0.628 12.019 6411 Z= 0.324 Chirality : 0.039 0.135 740 Planarity : 0.005 0.069 834 Dihedral : 5.235 35.272 683 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.89 % Favored : 94.95 % Rotamer: Outliers : 2.54 % Allowed : 19.85 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 0.16 % 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: 1.27 (0.35), residues: 634 helix: 1.24 (0.23), residues: 486 sheet: -0.55 (1.82), residues: 10 loop : -0.26 (0.64), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 703 TYR 0.013 0.002 TYR B 322 PHE 0.018 0.002 PHE A 662 TRP 0.021 0.002 TRP C 43 HIS 0.004 0.001 HIS B 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.17 ( 4716) covalent geometry : angle 0.62756 / 0.32 ( 6411) hydrogen bonds : bond 0.04139 / 3.07 ( 341) hydrogen bonds : angle 4.95505 / 3.83 ( 1008) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 915.92 seconds wall clock time: 16 minutes 28.67 seconds (988.67 seconds total)