Starting phenix.real_space_refine on Tue Aug 4 17:35:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/22av_68138/08_2026/22av_68138.cif Found real_map, /net/cci-nas-00/data/ceres_data/22av_68138/08_2026/22av_68138.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/22av_68138/08_2026/22av_68138.cif" } default_model = "/net/cci-nas-00/data/ceres_data/22av_68138/08_2026/22av_68138.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/22av_68138/08_2026/22av_68138.map" default_real_map = "/net/cci-nas-00/data/ceres_data/22av_68138/08_2026/22av_68138.map" } resolution = 3.34 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= 0.005 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 38 5.49 5 S 29 5.16 5 C 3313 2.51 5 N 937 2.21 5 O 1104 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 5421 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 4567 Classifications: {'peptide': 579} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 538} Chain breaks: 2 Unresolved non-hydrogen bonds: 109 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 99 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 3, 'GLN:plan1': 1, 'TRP:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 57 Chain: "B" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 827 Classifications: {'RNA': 39} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 3, 'rna3p_pur': 16, 'rna3p_pyr': 18} Link IDs: {'rna2p': 5, 'rna3p': 33} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Classifications: {'peptide': 1} Time building chain proxies: 1.21, per 1000 atoms: 0.22 Number of scatterers: 5421 At special positions: 0 Unit cell: (73.47, 77.19, 102.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 29 16.00 P 38 15.00 O 1104 8.00 N 937 7.00 C 3313 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: 0.47 Conformation dependent library (CDL) restraints added in 168.6 milliseconds 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1102 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 8 sheets defined 44.0% alpha, 11.7% beta 10 base pairs and 19 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'A' and resid 45 through 55 Processing helix chain 'A' and resid 62 through 71 Processing helix chain 'A' and resid 86 through 97 Processing helix chain 'A' and resid 97 through 104 removed outlier: 4.088A pdb=" N GLU A 101 " --> pdb=" O LYS A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 124 removed outlier: 3.500A pdb=" N GLU A 124 " --> pdb=" O TYR A 121 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 121 through 124' Processing helix chain 'A' and resid 132 through 138 Processing helix chain 'A' and resid 142 through 156 removed outlier: 3.715A pdb=" N PHE A 148 " --> pdb=" O LYS A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 165 Processing helix chain 'A' and resid 166 through 173 removed outlier: 3.653A pdb=" N LEU A 170 " --> pdb=" O MET A 166 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ASN A 173 " --> pdb=" O PRO A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 199 removed outlier: 3.814A pdb=" N GLN A 193 " --> pdb=" O SER A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 230 removed outlier: 3.661A pdb=" N TYR A 222 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N LEU A 223 " --> pdb=" O LYS A 219 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ARG A 230 " --> pdb=" O HIS A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 246 removed outlier: 3.856A pdb=" N ILE A 246 " --> pdb=" O ALA A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 277 removed outlier: 3.805A pdb=" N MET A 277 " --> pdb=" O ASP A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 287 removed outlier: 3.587A pdb=" N LYS A 286 " --> pdb=" O ASP A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 309 removed outlier: 4.534A pdb=" N GLY A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N LEU A 298 " --> pdb=" O GLN A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 340 removed outlier: 4.250A pdb=" N ALA A 330 " --> pdb=" O ILE A 326 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N VAL A 331 " --> pdb=" O GLU A 327 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE A 332 " --> pdb=" O ASP A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 385 Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 397 through 404 Processing helix chain 'A' and resid 405 through 409 Processing helix chain 'A' and resid 413 through 418 removed outlier: 4.288A pdb=" N GLN A 417 " --> pdb=" O LEU A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 538 removed outlier: 4.272A pdb=" N ILE A 533 " --> pdb=" O LEU A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 546 No H-bonds generated for 'chain 'A' and resid 544 through 546' Processing helix chain 'A' and resid 564 through 574 removed outlier: 3.772A pdb=" N ASN A 573 " --> pdb=" O ASN A 569 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASN A 574 " --> pdb=" O VAL A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 609 removed outlier: 4.040A pdb=" N ILE A 608 " --> pdb=" O GLN A 605 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N TYR A 609 " --> pdb=" O GLU A 606 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 605 through 609' Processing helix chain 'A' and resid 623 through 632 removed outlier: 3.652A pdb=" N THR A 632 " --> pdb=" O LYS A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 641 Processing helix chain 'A' and resid 642 through 652 removed outlier: 3.872A pdb=" N LEU A 652 " --> pdb=" O GLN A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 691 through 702 removed outlier: 3.533A pdb=" N MET A 702 " --> pdb=" O TYR A 698 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 116 through 117 removed outlier: 3.623A pdb=" N THR A 77 " --> pdb=" O GLN A 161 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN A 161 " --> pdb=" O THR A 77 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 181 through 182 removed outlier: 8.077A pdb=" N ILE A 236 " --> pdb=" O THR A 583 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N THR A 583 " --> pdb=" O ILE A 236 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N VAL A 238 " --> pdb=" O ILE A 581 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 250 through 253 Processing sheet with id=AA4, first strand: chain 'A' and resid 262 through 268 removed outlier: 6.970A pdb=" N TYR A 262 " --> pdb=" O ALA A 311 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N GLY A 313 " --> pdb=" O TYR A 262 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N ARG A 264 " --> pdb=" O GLY A 313 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ARG A 315 " --> pdb=" O ARG A 264 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N LEU A 266 " --> pdb=" O ARG A 315 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N VAL A 317 " --> pdb=" O LEU A 266 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ASP A 268 " --> pdb=" O VAL A 317 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N SER A 319 " --> pdb=" O ASP A 268 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 366 through 367 removed outlier: 3.652A pdb=" N VAL A 366 " --> pdb=" O PHE A 374 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 521 through 522 removed outlier: 6.730A pdb=" N LEU A 560 " --> pdb=" O VAL A 587 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE A 585 " --> pdb=" O MET A 562 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 619 through 622 Processing sheet with id=AA8, first strand: chain 'A' and resid 655 through 656 162 hydrogen bonds defined for protein. 429 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 27 hydrogen bonds 50 hydrogen bond angles 0 basepair planarities 10 basepair parallelities 19 stacking parallelities Total time for adding SS restraints: 0.88 Time building geometry restraints manager: 0.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1612 1.34 - 1.46: 1186 1.46 - 1.58: 2708 1.58 - 1.70: 75 1.70 - 1.82: 49 Bond restraints: 5630 Sorted by residual: bond pdb=" N VAL A 348 " pdb=" CA VAL A 348 " ideal model delta sigma weight residual 1.458 1.494 -0.037 1.35e-02 5.49e+03 7.37e+00 bond pdb=" N SER A 349 " pdb=" CA SER A 349 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.20e-02 6.94e+03 4.82e+00 bond pdb=" CA SER A 349 " pdb=" CB SER A 349 " ideal model delta sigma weight residual 1.530 1.504 0.026 1.56e-02 4.11e+03 2.69e+00 bond pdb=" N3 C B 50 " pdb=" C4 C B 50 " ideal model delta sigma weight residual 1.335 1.328 0.007 7.00e-03 2.04e+04 8.90e-01 bond pdb=" CG1 ILE A 326 " pdb=" CD1 ILE A 326 " ideal model delta sigma weight residual 1.513 1.478 0.035 3.90e-02 6.57e+02 8.18e-01 ... (remaining 5625 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.37: 7423 1.37 - 2.75: 348 2.75 - 4.12: 47 4.12 - 5.49: 10 5.49 - 6.87: 4 Bond angle restraints: 7832 Sorted by residual: angle pdb=" C1' C B 63 " pdb=" N1 C B 63 " pdb=" C2 C B 63 " ideal model delta sigma weight residual 118.80 122.75 -3.95 1.10e+00 8.26e-01 1.29e+01 angle pdb=" N VAL A 348 " pdb=" CA VAL A 348 " pdb=" C VAL A 348 " ideal model delta sigma weight residual 112.29 108.97 3.32 9.40e-01 1.13e+00 1.25e+01 angle pdb=" O5' G B 55 " pdb=" C5' G B 55 " pdb=" C4' G B 55 " ideal model delta sigma weight residual 109.40 112.10 -2.70 8.00e-01 1.56e+00 1.14e+01 angle pdb=" O5' A B 60 " pdb=" C5' A B 60 " pdb=" C4' A B 60 " ideal model delta sigma weight residual 109.40 112.05 -2.65 8.00e-01 1.56e+00 1.10e+01 angle pdb=" O5' C B 67 " pdb=" C5' C B 67 " pdb=" C4' C B 67 " ideal model delta sigma weight residual 109.40 112.04 -2.64 8.00e-01 1.56e+00 1.09e+01 ... (remaining 7827 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.26: 3121 20.26 - 40.51: 249 40.51 - 60.77: 73 60.77 - 81.03: 44 81.03 - 101.28: 2 Dihedral angle restraints: 3489 sinusoidal: 1795 harmonic: 1694 Sorted by residual: dihedral pdb=" O4' C B 50 " pdb=" C1' C B 50 " pdb=" N1 C B 50 " pdb=" C2 C B 50 " ideal model delta sinusoidal sigma weight residual -160.00 -58.72 -101.28 1 1.50e+01 4.44e-03 5.10e+01 dihedral pdb=" CA SER A 155 " pdb=" C SER A 155 " pdb=" N GLY A 156 " pdb=" CA GLY A 156 " ideal model delta harmonic sigma weight residual 180.00 -159.87 -20.13 0 5.00e+00 4.00e-02 1.62e+01 dihedral pdb=" CA GLY A 156 " pdb=" C GLY A 156 " pdb=" N ASN A 157 " pdb=" CA ASN A 157 " ideal model delta harmonic sigma weight residual -180.00 -163.89 -16.11 0 5.00e+00 4.00e-02 1.04e+01 ... (remaining 3486 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 674 0.047 - 0.094: 155 0.094 - 0.141: 73 0.141 - 0.188: 7 0.188 - 0.235: 1 Chirality restraints: 910 Sorted by residual: chirality pdb=" CG LEU A 249 " pdb=" CB LEU A 249 " pdb=" CD1 LEU A 249 " pdb=" CD2 LEU A 249 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CA VAL A 348 " pdb=" N VAL A 348 " pdb=" C VAL A 348 " pdb=" CB VAL A 348 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 8.86e-01 chirality pdb=" CB ILE A 326 " pdb=" CA ILE A 326 " pdb=" CG1 ILE A 326 " pdb=" CG2 ILE A 326 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.72e-01 ... (remaining 907 not shown) Planarity restraints: 858 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 531 " 0.027 5.00e-02 4.00e+02 4.08e-02 2.67e+00 pdb=" N PRO A 532 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 532 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 532 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' G B 7 " 0.019 2.00e-02 2.50e+03 9.42e-03 2.66e+00 pdb=" N9 G B 7 " -0.025 2.00e-02 2.50e+03 pdb=" C8 G B 7 " -0.001 2.00e-02 2.50e+03 pdb=" N7 G B 7 " 0.001 2.00e-02 2.50e+03 pdb=" C5 G B 7 " 0.004 2.00e-02 2.50e+03 pdb=" C6 G B 7 " 0.003 2.00e-02 2.50e+03 pdb=" O6 G B 7 " 0.001 2.00e-02 2.50e+03 pdb=" N1 G B 7 " 0.003 2.00e-02 2.50e+03 pdb=" C2 G B 7 " -0.001 2.00e-02 2.50e+03 pdb=" N2 G B 7 " -0.001 2.00e-02 2.50e+03 pdb=" N3 G B 7 " -0.004 2.00e-02 2.50e+03 pdb=" C4 G B 7 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 347 " 0.008 2.00e-02 2.50e+03 1.60e-02 2.55e+00 pdb=" C ASP A 347 " -0.028 2.00e-02 2.50e+03 pdb=" O ASP A 347 " 0.010 2.00e-02 2.50e+03 pdb=" N VAL A 348 " 0.009 2.00e-02 2.50e+03 ... (remaining 855 not shown) Histogram of nonbonded interaction distances: 2.47 - 2.95: 2333 2.95 - 3.44: 5538 3.44 - 3.93: 9219 3.93 - 4.41: 10488 4.41 - 4.90: 16284 Nonbonded interactions: 43862 Sorted by model distance: nonbonded pdb=" O ASP A 347 " pdb=" OD1 ASP A 347 " model vdw 2.466 3.040 nonbonded pdb=" OD1 ASP A 215 " pdb=" N VAL A 216 " model vdw 2.509 3.120 nonbonded pdb=" O4' C B 63 " pdb=" C6 C B 63 " model vdw 2.550 2.672 nonbonded pdb=" O VAL A 570 " pdb=" OD1 ASN A 574 " model vdw 2.556 3.040 nonbonded pdb=" O4' C B 52 " pdb=" C6 C B 52 " model vdw 2.574 2.672 ... (remaining 43857 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.690 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:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6566 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5630 Z= 0.148 Angle : 0.658 6.868 7832 Z= 0.410 Chirality : 0.051 0.235 910 Planarity : 0.005 0.041 858 Dihedral : 17.167 101.282 2387 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Rotamer: Outliers : 0.20 % Allowed : 0.40 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.37), residues: 573 helix: 0.45 (0.39), residues: 193 sheet: -2.28 (0.49), residues: 91 loop : -0.31 (0.39), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 411 TYR 0.025 0.002 TYR A 83 PHE 0.019 0.002 PHE A 422 TRP 0.009 0.001 TRP A 357 HIS 0.012 0.001 HIS A 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.15 ( 5630) covalent geometry : angle 0.65755 / 0.41 ( 7832) hydrogen bonds : bond 0.20122 / 13.44 ( 189) hydrogen bonds : angle 7.82542 / 5.64 ( 479) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 133 time to evaluate : 0.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 290 LEU cc_start: 0.7284 (tp) cc_final: 0.6371 (tp) outliers start: 1 outliers final: 0 residues processed: 134 average time/residue: 0.0680 time to fit residues: 12.2697 Evaluate side-chains 89 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 54 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 56 optimal weight: 0.0000 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 58 optimal weight: 9.9990 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 697 HIS ** 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 = 0.3838 r_free = 0.3838 target = 0.100287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.079527 restraints weight = 17549.761| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 4.76 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 5630 Z= 0.144 Angle : 0.668 10.391 7832 Z= 0.334 Chirality : 0.042 0.164 910 Planarity : 0.005 0.045 858 Dihedral : 17.118 98.626 1268 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.63 % Allowed : 11.11 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.36), residues: 573 helix: 0.56 (0.39), residues: 189 sheet: -1.88 (0.51), residues: 89 loop : -0.33 (0.38), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 545 TYR 0.016 0.001 TYR A 698 PHE 0.021 0.002 PHE A 99 TRP 0.009 0.001 TRP A 63 HIS 0.006 0.001 HIS A 697 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.14 ( 5630) covalent geometry : angle 0.66783 / 0.33 ( 7832) hydrogen bonds : bond 0.05332 / 3.43 ( 189) hydrogen bonds : angle 6.07022 / 4.37 ( 479) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 96 time to evaluate : 0.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 258 GLU cc_start: 0.9275 (mm-30) cc_final: 0.8774 (mp0) REVERT: A 404 MET cc_start: 0.8773 (mmp) cc_final: 0.8493 (mmp) REVERT: A 694 GLU cc_start: 0.9124 (tp30) cc_final: 0.8892 (tp30) REVERT: A 698 TYR cc_start: 0.9204 (m-80) cc_final: 0.8965 (m-80) REVERT: A 700 ARG cc_start: 0.7140 (tmm160) cc_final: 0.6844 (tmm160) outliers start: 13 outliers final: 6 residues processed: 102 average time/residue: 0.0721 time to fit residues: 9.8370 Evaluate side-chains 93 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 87 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 422 PHE Chi-restraints excluded: chain A residue 424 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 11 optimal weight: 4.9990 chunk 48 optimal weight: 0.0470 chunk 42 optimal weight: 0.1980 chunk 55 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 9 optimal weight: 8.9990 chunk 6 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 overall best weight: 1.2082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 128 HIS ** A 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 193 GLN ** A 697 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.096903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.075809 restraints weight = 18007.541| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 4.68 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5630 Z= 0.147 Angle : 0.642 14.325 7832 Z= 0.314 Chirality : 0.042 0.205 910 Planarity : 0.005 0.049 858 Dihedral : 17.210 95.583 1268 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.84 % Allowed : 13.54 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.36), residues: 573 helix: 0.76 (0.40), residues: 187 sheet: -1.62 (0.56), residues: 82 loop : -0.38 (0.37), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 79 TYR 0.013 0.001 TYR A 51 PHE 0.018 0.002 PHE A 148 TRP 0.009 0.001 TRP A 63 HIS 0.004 0.001 HIS A 697 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 ( 5630) covalent geometry : angle 0.64246 / 0.31 ( 7832) hydrogen bonds : bond 0.04485 / 2.82 ( 189) hydrogen bonds : angle 5.55773 / 4.01 ( 479) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 87 time to evaluate : 0.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 MET cc_start: 0.9703 (tpp) cc_final: 0.9202 (mpp) REVERT: A 329 GLU cc_start: 0.8696 (OUTLIER) cc_final: 0.7570 (mp0) REVERT: A 392 MET cc_start: 0.9035 (OUTLIER) cc_final: 0.8821 (mtm) REVERT: A 586 LYS cc_start: 0.7592 (tttp) cc_final: 0.7166 (tttt) REVERT: A 631 LEU cc_start: 0.9318 (mm) cc_final: 0.9106 (mm) REVERT: A 694 GLU cc_start: 0.9281 (tp30) cc_final: 0.8964 (tp30) REVERT: A 698 TYR cc_start: 0.9274 (m-80) cc_final: 0.8692 (m-80) outliers start: 19 outliers final: 11 residues processed: 96 average time/residue: 0.0694 time to fit residues: 9.0074 Evaluate side-chains 93 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 80 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 299 GLN Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 392 MET Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 422 PHE Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 546 MET Chi-restraints excluded: chain A residue 606 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 26 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 57 optimal weight: 20.0000 chunk 9 optimal weight: 9.9990 chunk 58 optimal weight: 10.0000 chunk 48 optimal weight: 0.5980 chunk 34 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 96 ASN ** A 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 193 GLN A 697 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.097191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.076937 restraints weight = 17480.462| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 4.56 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5630 Z= 0.124 Angle : 0.604 11.872 7832 Z= 0.298 Chirality : 0.041 0.182 910 Planarity : 0.004 0.047 858 Dihedral : 17.246 94.294 1268 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 3.64 % Allowed : 16.57 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.36), residues: 573 helix: 0.79 (0.40), residues: 187 sheet: -1.61 (0.57), residues: 80 loop : -0.33 (0.37), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 695 TYR 0.012 0.001 TYR A 83 PHE 0.021 0.002 PHE A 148 TRP 0.013 0.001 TRP A 357 HIS 0.005 0.001 HIS A 697 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.12 ( 5630) covalent geometry : angle 0.60367 / 0.30 ( 7832) hydrogen bonds : bond 0.03925 / 2.45 ( 189) hydrogen bonds : angle 5.29901 / 3.82 ( 479) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 86 time to evaluate : 0.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 MET cc_start: 0.9704 (tpp) cc_final: 0.8892 (mpp) REVERT: A 329 GLU cc_start: 0.8642 (OUTLIER) cc_final: 0.7550 (mp0) REVERT: A 367 MET cc_start: 0.8922 (tmm) cc_final: 0.8652 (tpp) REVERT: A 399 GLU cc_start: 0.9191 (pm20) cc_final: 0.8958 (pm20) REVERT: A 586 LYS cc_start: 0.7639 (tttp) cc_final: 0.7231 (tttt) REVERT: A 694 GLU cc_start: 0.9275 (tp30) cc_final: 0.8832 (tp30) REVERT: A 698 TYR cc_start: 0.9236 (m-80) cc_final: 0.8556 (m-80) outliers start: 18 outliers final: 13 residues processed: 95 average time/residue: 0.0685 time to fit residues: 8.8340 Evaluate side-chains 92 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 78 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 299 GLN Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 392 MET Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 422 PHE Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 546 MET Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain A residue 697 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 10 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 58 optimal weight: 10.0000 chunk 38 optimal weight: 0.2980 chunk 29 optimal weight: 0.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 616 ASN ** A 697 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.096040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.075589 restraints weight = 18055.797| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 4.59 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 5630 Z= 0.145 Angle : 0.622 8.899 7832 Z= 0.309 Chirality : 0.044 0.332 910 Planarity : 0.005 0.052 858 Dihedral : 17.267 92.892 1268 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.23 % Allowed : 18.38 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.36), residues: 573 helix: 0.69 (0.40), residues: 182 sheet: -1.61 (0.57), residues: 78 loop : -0.34 (0.36), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 700 TYR 0.012 0.001 TYR A 83 PHE 0.030 0.002 PHE A 99 TRP 0.008 0.001 TRP A 63 HIS 0.003 0.001 HIS A 697 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.14 ( 5630) covalent geometry : angle 0.62180 / 0.31 ( 7832) hydrogen bonds : bond 0.04101 / 2.50 ( 189) hydrogen bonds : angle 5.29961 / 3.85 ( 479) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 81 time to evaluate : 0.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 MET cc_start: 0.9705 (tpp) cc_final: 0.8948 (mpp) REVERT: A 277 MET cc_start: 0.9165 (mtp) cc_final: 0.8690 (mmm) REVERT: A 329 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.7423 (mp0) REVERT: A 367 MET cc_start: 0.8966 (tmm) cc_final: 0.8747 (tpp) REVERT: A 392 MET cc_start: 0.8893 (OUTLIER) cc_final: 0.8669 (mtm) REVERT: A 586 LYS cc_start: 0.7552 (tttp) cc_final: 0.7075 (tttt) outliers start: 16 outliers final: 11 residues processed: 87 average time/residue: 0.0685 time to fit residues: 8.0437 Evaluate side-chains 91 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 78 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 299 GLN Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 392 MET Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 422 PHE Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 546 MET Chi-restraints excluded: chain A residue 606 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 13 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 10 optimal weight: 0.8980 chunk 12 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 47 optimal weight: 0.0670 chunk 50 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 57 optimal weight: 20.0000 overall best weight: 0.8320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 193 GLN A 697 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.096633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.076225 restraints weight = 18242.521| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 4.63 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5630 Z= 0.124 Angle : 0.614 12.910 7832 Z= 0.300 Chirality : 0.044 0.397 910 Planarity : 0.005 0.049 858 Dihedral : 17.284 92.219 1268 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.43 % Allowed : 18.59 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.36), residues: 573 helix: 0.72 (0.40), residues: 182 sheet: -1.47 (0.55), residues: 85 loop : -0.30 (0.36), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 230 TYR 0.017 0.001 TYR A 698 PHE 0.027 0.002 PHE A 148 TRP 0.008 0.001 TRP A 357 HIS 0.012 0.001 HIS A 697 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.12 ( 5630) covalent geometry : angle 0.61409 / 0.30 ( 7832) hydrogen bonds : bond 0.03709 / 2.30 ( 189) hydrogen bonds : angle 5.21763 / 3.75 ( 479) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 80 time to evaluate : 0.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 MET cc_start: 0.9697 (tpp) cc_final: 0.8989 (mpp) REVERT: A 277 MET cc_start: 0.9082 (mtp) cc_final: 0.8651 (mmm) REVERT: A 329 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.7069 (mp0) REVERT: A 367 MET cc_start: 0.8957 (tmm) cc_final: 0.8740 (tpp) REVERT: A 392 MET cc_start: 0.8906 (OUTLIER) cc_final: 0.8631 (mtm) REVERT: A 586 LYS cc_start: 0.7548 (tttp) cc_final: 0.7062 (tttt) outliers start: 17 outliers final: 9 residues processed: 88 average time/residue: 0.0634 time to fit residues: 7.5513 Evaluate side-chains 86 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 299 GLN Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 392 MET Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 422 PHE Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 546 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 19 optimal weight: 0.7980 chunk 51 optimal weight: 4.9990 chunk 16 optimal weight: 0.3980 chunk 10 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 36 optimal weight: 7.9990 chunk 44 optimal weight: 0.8980 chunk 50 optimal weight: 0.0670 chunk 20 optimal weight: 0.9990 chunk 24 optimal weight: 0.0170 overall best weight: 0.4356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 157 ASN A 193 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.097024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.076195 restraints weight = 17995.331| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 4.67 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.2909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5630 Z= 0.111 Angle : 0.612 13.925 7832 Z= 0.297 Chirality : 0.042 0.177 910 Planarity : 0.005 0.064 858 Dihedral : 17.254 92.062 1268 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.03 % Allowed : 19.39 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.36), residues: 573 helix: 0.82 (0.41), residues: 182 sheet: -1.52 (0.52), residues: 90 loop : -0.22 (0.37), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 700 TYR 0.013 0.001 TYR A 698 PHE 0.031 0.002 PHE A 148 TRP 0.008 0.001 TRP A 127 HIS 0.002 0.000 HIS A 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 ( 5630) covalent geometry : angle 0.61165 / 0.30 ( 7832) hydrogen bonds : bond 0.03546 / 2.18 ( 189) hydrogen bonds : angle 5.07362 / 3.69 ( 479) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 0.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 MET cc_start: 0.9701 (tpp) cc_final: 0.9004 (mpp) REVERT: A 136 LEU cc_start: 0.9157 (tp) cc_final: 0.8928 (pp) REVERT: A 196 GLU cc_start: 0.8703 (tm-30) cc_final: 0.8296 (mm-30) REVERT: A 197 MET cc_start: 0.8890 (ptp) cc_final: 0.8577 (ptm) REVERT: A 277 MET cc_start: 0.9080 (mtp) cc_final: 0.8713 (mmm) REVERT: A 294 GLN cc_start: 0.9259 (mm-40) cc_final: 0.9057 (mm-40) REVERT: A 329 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.6738 (mp0) REVERT: A 367 MET cc_start: 0.8937 (tmm) cc_final: 0.8706 (tpp) REVERT: A 392 MET cc_start: 0.8903 (OUTLIER) cc_final: 0.8578 (mtm) REVERT: A 586 LYS cc_start: 0.7533 (tttp) cc_final: 0.7102 (tttt) REVERT: A 631 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.9002 (mm) outliers start: 15 outliers final: 10 residues processed: 86 average time/residue: 0.0567 time to fit residues: 6.6879 Evaluate side-chains 91 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 78 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 299 GLN Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 392 MET Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 422 PHE Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 546 MET Chi-restraints excluded: chain A residue 631 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 10 optimal weight: 0.4980 chunk 38 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 49 optimal weight: 10.0000 chunk 30 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 = 0.3793 r_free = 0.3793 target = 0.095355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.074918 restraints weight = 17950.992| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 4.59 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.3047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 5630 Z= 0.134 Angle : 0.611 12.587 7832 Z= 0.297 Chirality : 0.041 0.159 910 Planarity : 0.004 0.047 858 Dihedral : 17.267 90.457 1268 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.23 % Allowed : 19.80 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.36), residues: 573 helix: 0.86 (0.41), residues: 183 sheet: -1.45 (0.53), residues: 90 loop : -0.18 (0.37), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 301 TYR 0.013 0.001 TYR A 698 PHE 0.027 0.001 PHE A 148 TRP 0.021 0.001 TRP A 357 HIS 0.003 0.001 HIS A 697 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.13 ( 5630) covalent geometry : angle 0.61139 / 0.30 ( 7832) hydrogen bonds : bond 0.03608 / 2.22 ( 189) hydrogen bonds : angle 5.07079 / 3.68 ( 479) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 79 time to evaluate : 0.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 MET cc_start: 0.9703 (tpp) cc_final: 0.9005 (mpp) REVERT: A 196 GLU cc_start: 0.8745 (tm-30) cc_final: 0.8367 (mm-30) REVERT: A 197 MET cc_start: 0.8910 (ptp) cc_final: 0.8611 (ptm) REVERT: A 277 MET cc_start: 0.9073 (mtp) cc_final: 0.8769 (mmm) REVERT: A 294 GLN cc_start: 0.9266 (mm-40) cc_final: 0.8921 (mm-40) REVERT: A 329 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.6639 (mp0) REVERT: A 367 MET cc_start: 0.9000 (tmm) cc_final: 0.8743 (tpp) REVERT: A 392 MET cc_start: 0.8939 (OUTLIER) cc_final: 0.8615 (mtm) REVERT: A 694 GLU cc_start: 0.9355 (tp30) cc_final: 0.8939 (tp30) REVERT: A 698 TYR cc_start: 0.9309 (m-80) cc_final: 0.8438 (m-80) outliers start: 16 outliers final: 10 residues processed: 85 average time/residue: 0.0660 time to fit residues: 7.7466 Evaluate side-chains 87 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 75 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 157 ASN Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 299 GLN Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 392 MET Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 422 PHE Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 583 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 12 optimal weight: 9.9990 chunk 1 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 42 optimal weight: 1.9990 chunk 7 optimal weight: 0.0020 chunk 28 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 chunk 39 optimal weight: 4.9990 chunk 30 optimal weight: 0.7980 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 193 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.096280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.075500 restraints weight = 17927.332| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 4.64 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.3138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5630 Z= 0.114 Angle : 0.641 14.543 7832 Z= 0.302 Chirality : 0.043 0.334 910 Planarity : 0.004 0.046 858 Dihedral : 17.268 90.177 1268 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.23 % Allowed : 20.20 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.36), residues: 573 helix: 0.84 (0.41), residues: 182 sheet: -1.36 (0.52), residues: 90 loop : -0.16 (0.37), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 79 TYR 0.011 0.001 TYR A 83 PHE 0.026 0.001 PHE A 148 TRP 0.012 0.001 TRP A 357 HIS 0.002 0.000 HIS A 697 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.11 ( 5630) covalent geometry : angle 0.64113 / 0.30 ( 7832) hydrogen bonds : bond 0.03431 / 2.10 ( 189) hydrogen bonds : angle 5.05017 / 3.63 ( 479) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 75 time to evaluate : 0.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 MET cc_start: 0.9691 (tpp) cc_final: 0.9004 (mpp) REVERT: A 136 LEU cc_start: 0.9084 (tp) cc_final: 0.8792 (pp) REVERT: A 196 GLU cc_start: 0.8744 (tm-30) cc_final: 0.8350 (mm-30) REVERT: A 277 MET cc_start: 0.9053 (mtp) cc_final: 0.8802 (mmm) REVERT: A 294 GLN cc_start: 0.9276 (mm-40) cc_final: 0.8947 (mm-40) REVERT: A 329 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.6513 (mp0) REVERT: A 367 MET cc_start: 0.8978 (tmm) cc_final: 0.8730 (tpp) REVERT: A 392 MET cc_start: 0.8896 (OUTLIER) cc_final: 0.8579 (mtm) REVERT: A 578 MET cc_start: 0.8679 (OUTLIER) cc_final: 0.8413 (tmm) REVERT: A 586 LYS cc_start: 0.7698 (tttm) cc_final: 0.7360 (tttt) REVERT: A 694 GLU cc_start: 0.9375 (tp30) cc_final: 0.8984 (tp30) REVERT: A 698 TYR cc_start: 0.9309 (m-80) cc_final: 0.8437 (m-80) outliers start: 16 outliers final: 11 residues processed: 81 average time/residue: 0.0536 time to fit residues: 6.0096 Evaluate side-chains 88 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 74 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 157 ASN Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 299 GLN Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 392 MET Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 422 PHE Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 583 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 33 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 chunk 59 optimal weight: 20.0000 chunk 20 optimal weight: 0.7980 chunk 46 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 54 optimal weight: 5.9990 chunk 42 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 416 HIS ** 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 = 0.3799 r_free = 0.3799 target = 0.095322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.074535 restraints weight = 17886.356| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 4.65 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.3290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5630 Z= 0.123 Angle : 0.618 12.612 7832 Z= 0.295 Chirality : 0.042 0.156 910 Planarity : 0.004 0.046 858 Dihedral : 17.269 89.090 1268 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.83 % Allowed : 20.81 % Favored : 76.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.36), residues: 573 helix: 0.90 (0.41), residues: 182 sheet: -1.25 (0.53), residues: 90 loop : -0.14 (0.38), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 79 TYR 0.011 0.001 TYR A 83 PHE 0.025 0.001 PHE A 148 TRP 0.009 0.001 TRP A 127 HIS 0.002 0.001 HIS A 697 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.12 ( 5630) covalent geometry : angle 0.61811 / 0.30 ( 7832) hydrogen bonds : bond 0.03460 / 2.13 ( 189) hydrogen bonds : angle 4.96457 / 3.60 ( 479) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 73 time to evaluate : 0.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 GLU cc_start: 0.8794 (tm-30) cc_final: 0.8363 (mm-30) REVERT: A 277 MET cc_start: 0.9086 (mtp) cc_final: 0.8788 (mmm) REVERT: A 294 GLN cc_start: 0.9318 (mm-40) cc_final: 0.8988 (mm-40) REVERT: A 328 ASP cc_start: 0.7298 (t0) cc_final: 0.6474 (t0) REVERT: A 329 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.6379 (mp0) REVERT: A 367 MET cc_start: 0.9064 (tmm) cc_final: 0.8779 (tpp) REVERT: A 392 MET cc_start: 0.8906 (OUTLIER) cc_final: 0.8585 (mtm) REVERT: A 578 MET cc_start: 0.8663 (OUTLIER) cc_final: 0.8365 (tmm) REVERT: A 586 LYS cc_start: 0.7667 (tttm) cc_final: 0.7340 (tttt) REVERT: A 694 GLU cc_start: 0.9398 (tp30) cc_final: 0.9111 (tp30) REVERT: A 698 TYR cc_start: 0.9314 (m-80) cc_final: 0.8517 (m-80) outliers start: 14 outliers final: 10 residues processed: 79 average time/residue: 0.0486 time to fit residues: 5.2786 Evaluate side-chains 86 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 73 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 157 ASN Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 299 GLN Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 392 MET Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 422 PHE Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 583 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 26 optimal weight: 2.9990 chunk 57 optimal weight: 20.0000 chunk 34 optimal weight: 5.9990 chunk 48 optimal weight: 0.0050 chunk 6 optimal weight: 7.9990 chunk 14 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 10 optimal weight: 0.7980 chunk 35 optimal weight: 0.0040 chunk 1 optimal weight: 1.9990 chunk 30 optimal weight: 0.0980 overall best weight: 0.5808 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 573 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.098921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.078361 restraints weight = 17669.688| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 4.72 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.3363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5630 Z= 0.109 Angle : 0.615 13.320 7832 Z= 0.293 Chirality : 0.041 0.149 910 Planarity : 0.004 0.046 858 Dihedral : 17.257 89.024 1268 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.83 % Allowed : 21.01 % Favored : 76.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.36), residues: 573 helix: 0.85 (0.41), residues: 183 sheet: -1.16 (0.53), residues: 90 loop : -0.09 (0.37), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 175 TYR 0.010 0.001 TYR A 83 PHE 0.026 0.001 PHE A 148 TRP 0.008 0.001 TRP A 127 HIS 0.002 0.001 HIS A 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.11 ( 5630) covalent geometry : angle 0.61499 / 0.29 ( 7832) hydrogen bonds : bond 0.03330 / 2.04 ( 189) hydrogen bonds : angle 4.89394 / 3.53 ( 479) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1165.66 seconds wall clock time: 20 minutes 45.89 seconds (1245.89 seconds total)