Starting phenix.real_space_refine on Wed Mar 4 03:01:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pn1_13545/03_2026/7pn1_13545.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pn1_13545/03_2026/7pn1_13545.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7pn1_13545/03_2026/7pn1_13545.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pn1_13545/03_2026/7pn1_13545.map" model { file = "/net/cci-nas-00/data/ceres_data/7pn1_13545/03_2026/7pn1_13545.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pn1_13545/03_2026/7pn1_13545.cif" } resolution = 3.9 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= 1.000 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 S 32 5.16 5 C 3372 2.51 5 N 828 2.21 5 O 915 1.98 5 H 5237 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10384 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 10384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 657, 10384 Classifications: {'peptide': 657} Link IDs: {'PTRANS': 30, 'TRANS': 626} Chain breaks: 3 Time building chain proxies: 1.81, per 1000 atoms: 0.17 Number of scatterers: 10384 At special positions: 0 Unit cell: (84.15, 92.65, 121.55, 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 32 16.00 O 915 8.00 N 828 7.00 C 3372 6.00 H 5237 1.00 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: 0.74 Conformation dependent library (CDL) restraints added in 271.4 milliseconds 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1230 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 6 sheets defined 63.2% alpha, 13.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 12 through 48 removed outlier: 4.259A pdb=" N PHE A 18 " --> pdb=" O LEU A 14 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ILE A 19 " --> pdb=" O SER A 15 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ALA A 35 " --> pdb=" O TYR A 31 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N ILE A 36 " --> pdb=" O GLY A 32 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ASN A 43 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N PHE A 44 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 77 removed outlier: 3.588A pdb=" N ILE A 55 " --> pdb=" O LEU A 51 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA A 61 " --> pdb=" O HIS A 57 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU A 62 " --> pdb=" O THR A 58 " (cutoff:3.500A) Proline residue: A 67 - end of helix removed outlier: 3.853A pdb=" N ILE A 73 " --> pdb=" O LEU A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 108 removed outlier: 3.644A pdb=" N ILE A 103 " --> pdb=" O SER A 99 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ASN A 104 " --> pdb=" O VAL A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 139 removed outlier: 3.933A pdb=" N GLY A 137 " --> pdb=" O ALA A 133 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE A 139 " --> pdb=" O GLY A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 150 removed outlier: 3.608A pdb=" N SER A 144 " --> pdb=" O LYS A 140 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLN A 150 " --> pdb=" O PHE A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 185 Proline residue: A 182 - end of helix removed outlier: 4.203A pdb=" N ARG A 185 " --> pdb=" O THR A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 219 Proline residue: A 205 - end of helix removed outlier: 3.727A pdb=" N GLY A 219 " --> pdb=" O VAL A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 223 Processing helix chain 'A' and resid 231 through 249 Processing helix chain 'A' and resid 261 through 266 removed outlier: 3.808A pdb=" N LYS A 266 " --> pdb=" O LEU A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 286 removed outlier: 4.037A pdb=" N LEU A 286 " --> pdb=" O ARG A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 298 removed outlier: 3.514A pdb=" N PHE A 293 " --> pdb=" O PRO A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 310 removed outlier: 4.042A pdb=" N THR A 305 " --> pdb=" O GLY A 301 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N LEU A 306 " --> pdb=" O SER A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 325 removed outlier: 3.780A pdb=" N MET A 325 " --> pdb=" O PRO A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 343 removed outlier: 4.353A pdb=" N ALA A 330 " --> pdb=" O GLN A 326 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ILE A 335 " --> pdb=" O ILE A 331 " (cutoff:3.500A) Proline residue: A 338 - end of helix removed outlier: 3.827A pdb=" N ASP A 341 " --> pdb=" O VAL A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 351 Processing helix chain 'A' and resid 356 through 383 removed outlier: 3.756A pdb=" N PHE A 372 " --> pdb=" O ALA A 368 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL A 373 " --> pdb=" O SER A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 386 No H-bonds generated for 'chain 'A' and resid 384 through 386' Processing helix chain 'A' and resid 481 through 485 Processing helix chain 'A' and resid 580 through 583 removed outlier: 3.652A pdb=" N LEU A 583 " --> pdb=" O ASN A 580 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 580 through 583' Processing helix chain 'A' and resid 584 through 610 removed outlier: 4.264A pdb=" N THR A 601 " --> pdb=" O VAL A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 611 through 613 No H-bonds generated for 'chain 'A' and resid 611 through 613' Processing helix chain 'A' and resid 614 through 637 removed outlier: 3.822A pdb=" N LEU A 618 " --> pdb=" O MET A 614 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLN A 619 " --> pdb=" O LYS A 615 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL A 626 " --> pdb=" O TRP A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 654 removed outlier: 4.167A pdb=" N PHE A 652 " --> pdb=" O GLU A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 668 Processing helix chain 'A' and resid 670 through 674 removed outlier: 4.436A pdb=" N ASN A 674 " --> pdb=" O THR A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 675 through 680 removed outlier: 4.350A pdb=" N ALA A 680 " --> pdb=" O ALA A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 683 No H-bonds generated for 'chain 'A' and resid 681 through 683' Processing sheet with id=AA1, first strand: chain 'A' and resid 422 through 423 Processing sheet with id=AA2, first strand: chain 'A' and resid 422 through 423 removed outlier: 8.777A pdb=" N HIS A 460 " --> pdb=" O GLU A 394 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N GLN A 396 " --> pdb=" O HIS A 460 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N LEU A 462 " --> pdb=" O GLN A 396 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N LYS A 398 " --> pdb=" O LEU A 462 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N VAL A 464 " --> pdb=" O LYS A 398 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LEU A 400 " --> pdb=" O VAL A 464 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N ALA A 466 " --> pdb=" O LEU A 400 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TRP A 465 " --> pdb=" O HIS A 469 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N HIS A 469 " --> pdb=" O TRP A 465 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 414 through 418 Processing sheet with id=AA4, first strand: chain 'A' and resid 514 through 515 removed outlier: 3.714A pdb=" N ASN A 514 " --> pdb=" O ASN A 492 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 514 through 515 removed outlier: 3.714A pdb=" N ASN A 514 " --> pdb=" O ASN A 492 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N GLY A 487 " --> pdb=" O TYR A 554 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N TYR A 556 " --> pdb=" O GLY A 487 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ARG A 489 " --> pdb=" O TYR A 556 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N VAL A 558 " --> pdb=" O ARG A 489 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N VAL A 491 " --> pdb=" O VAL A 558 " (cutoff:3.500A) removed outlier: 8.775A pdb=" N ARG A 560 " --> pdb=" O VAL A 491 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ALA A 553 " --> pdb=" O ASP A 573 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 505 through 510 removed outlier: 6.018A pdb=" N ILE A 498 " --> pdb=" O ASN A 509 " (cutoff:3.500A) 310 hydrogen bonds defined for protein. 885 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: 2.09 Time building geometry restraints manager: 1.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 5227 1.03 - 1.23: 11 1.23 - 1.42: 2188 1.42 - 1.62: 3026 1.62 - 1.81: 54 Bond restraints: 10506 Sorted by residual: bond pdb=" N GLY A 602 " pdb=" CA GLY A 602 " ideal model delta sigma weight residual 1.454 1.443 0.011 1.24e-02 6.50e+03 8.33e-01 bond pdb=" N PRO A 536 " pdb=" CA PRO A 536 " ideal model delta sigma weight residual 1.457 1.467 -0.010 1.31e-02 5.83e+03 6.41e-01 bond pdb=" N ILE A 16 " pdb=" CA ILE A 16 " ideal model delta sigma weight residual 1.452 1.461 -0.009 1.18e-02 7.18e+03 6.10e-01 bond pdb=" N CYS A 197 " pdb=" CA CYS A 197 " ideal model delta sigma weight residual 1.457 1.467 -0.011 1.40e-02 5.10e+03 5.89e-01 bond pdb=" CA ILE A 585 " pdb=" CB ILE A 585 " ideal model delta sigma weight residual 1.534 1.540 -0.005 6.80e-03 2.16e+04 5.64e-01 ... (remaining 10501 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.20: 18051 1.20 - 2.40: 904 2.40 - 3.60: 42 3.60 - 4.80: 15 4.80 - 6.01: 5 Bond angle restraints: 19017 Sorted by residual: angle pdb=" C ALA A 637 " pdb=" CA ALA A 637 " pdb=" CB ALA A 637 " ideal model delta sigma weight residual 116.63 110.62 6.01 1.16e+00 7.43e-01 2.68e+01 angle pdb=" CA ALA A 637 " pdb=" C ALA A 637 " pdb=" N GLY A 638 " ideal model delta sigma weight residual 119.63 117.28 2.35 8.10e-01 1.52e+00 8.41e+00 angle pdb=" CA GLY A 79 " pdb=" C GLY A 79 " pdb=" O GLY A 79 " ideal model delta sigma weight residual 122.57 120.35 2.22 9.20e-01 1.18e+00 5.81e+00 angle pdb=" CA MET A 33 " pdb=" CB MET A 33 " pdb=" CG MET A 33 " ideal model delta sigma weight residual 114.10 118.86 -4.76 2.00e+00 2.50e-01 5.67e+00 angle pdb=" N ALA A 637 " pdb=" CA ALA A 637 " pdb=" C ALA A 637 " ideal model delta sigma weight residual 108.08 112.04 -3.96 1.69e+00 3.50e-01 5.49e+00 ... (remaining 19012 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 4559 17.98 - 35.96: 291 35.96 - 53.95: 89 53.95 - 71.93: 22 71.93 - 89.91: 10 Dihedral angle restraints: 4971 sinusoidal: 2655 harmonic: 2316 Sorted by residual: dihedral pdb=" CA GLU A 259 " pdb=" C GLU A 259 " pdb=" N HIS A 260 " pdb=" CA HIS A 260 " ideal model delta harmonic sigma weight residual -180.00 -160.13 -19.87 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA LYS A 257 " pdb=" C LYS A 257 " pdb=" N ARG A 258 " pdb=" CA ARG A 258 " ideal model delta harmonic sigma weight residual 180.00 161.68 18.32 0 5.00e+00 4.00e-02 1.34e+01 dihedral pdb=" CA LEU A 651 " pdb=" C LEU A 651 " pdb=" N PHE A 652 " pdb=" CA PHE A 652 " ideal model delta harmonic sigma weight residual 180.00 162.34 17.66 0 5.00e+00 4.00e-02 1.25e+01 ... (remaining 4968 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 503 0.027 - 0.053: 196 0.053 - 0.080: 77 0.080 - 0.106: 35 0.106 - 0.133: 16 Chirality restraints: 827 Sorted by residual: chirality pdb=" CA ILE A 535 " pdb=" N ILE A 535 " pdb=" C ILE A 535 " pdb=" CB ILE A 535 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.40e-01 chirality pdb=" CA ILE A 409 " pdb=" N ILE A 409 " pdb=" C ILE A 409 " pdb=" CB ILE A 409 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.12e-01 chirality pdb=" CA ILE A 574 " pdb=" N ILE A 574 " pdb=" C ILE A 574 " pdb=" CB ILE A 574 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.09e-01 ... (remaining 824 not shown) Planarity restraints: 1518 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 288 " 0.027 5.00e-02 4.00e+02 4.15e-02 2.76e+00 pdb=" N PRO A 289 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 289 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 289 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 337 " 0.023 5.00e-02 4.00e+02 3.54e-02 2.01e+00 pdb=" N PRO A 338 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO A 338 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 338 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 355 " -0.013 2.00e-02 2.50e+03 7.88e-03 1.86e+00 pdb=" CG PHE A 355 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 PHE A 355 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE A 355 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE A 355 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 355 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE A 355 " -0.001 2.00e-02 2.50e+03 pdb=" HD1 PHE A 355 " 0.001 2.00e-02 2.50e+03 pdb=" HD2 PHE A 355 " 0.001 2.00e-02 2.50e+03 pdb=" HE1 PHE A 355 " -0.001 2.00e-02 2.50e+03 pdb=" HE2 PHE A 355 " -0.001 2.00e-02 2.50e+03 pdb=" HZ PHE A 355 " 0.000 2.00e-02 2.50e+03 ... (remaining 1515 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.26: 1400 2.26 - 2.85: 23508 2.85 - 3.43: 26325 3.43 - 4.02: 35066 4.02 - 4.60: 53279 Nonbonded interactions: 139578 Sorted by model distance: nonbonded pdb=" HZ2 LYS A 398 " pdb=" OD1 ASP A 573 " model vdw 1.677 2.450 nonbonded pdb=" O ILE A 103 " pdb=" HG1 THR A 107 " model vdw 1.689 2.450 nonbonded pdb=" OE1 GLU A 677 " pdb=" H GLU A 677 " model vdw 1.692 2.450 nonbonded pdb=" O GLY A 94 " pdb=" HG1 THR A 98 " model vdw 1.710 2.450 nonbonded pdb=" HG1 THR A 493 " pdb=" O VAL A 558 " model vdw 1.714 2.450 ... (remaining 139573 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.040 Find NCS groups from input model: 0.030 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:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 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 : 0.002 0.023 5269 Z= 0.123 Angle : 0.568 6.005 7156 Z= 0.330 Chirality : 0.038 0.133 827 Planarity : 0.003 0.041 895 Dihedral : 12.954 89.909 1881 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.33), residues: 649 helix: 1.85 (0.29), residues: 340 sheet: 0.97 (0.70), residues: 59 loop : -0.50 (0.37), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 27 TYR 0.015 0.001 TYR A 91 PHE 0.023 0.001 PHE A 355 TRP 0.006 0.001 TRP A 646 HIS 0.006 0.001 HIS A 260 Details of bonding type rmsd covalent geometry : bond 0.00236 ( 5269) covalent geometry : angle 0.56824 ( 7156) hydrogen bonds : bond 0.14910 ( 307) hydrogen bonds : angle 5.58326 ( 885) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 421 MET cc_start: 0.8958 (mmt) cc_final: 0.8641 (mmt) REVERT: A 485 GLU cc_start: 0.7782 (mt-10) cc_final: 0.7563 (mt-10) REVERT: A 646 TRP cc_start: 0.5906 (t-100) cc_final: 0.5662 (t-100) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.0974 time to fit residues: 11.1808 Evaluate side-chains 63 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 9.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 64 optimal weight: 0.4980 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.106956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.080529 restraints weight = 41969.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.084414 restraints weight = 18544.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.086879 restraints weight = 11725.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.088254 restraints weight = 8998.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.089261 restraints weight = 7778.565| |-----------------------------------------------------------------------------| r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.0980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5269 Z= 0.166 Angle : 0.566 5.944 7156 Z= 0.306 Chirality : 0.040 0.157 827 Planarity : 0.004 0.041 895 Dihedral : 4.766 20.058 695 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.36 % Allowed : 6.04 % Favored : 93.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.33), residues: 649 helix: 1.88 (0.28), residues: 333 sheet: 0.88 (0.58), residues: 85 loop : -0.69 (0.39), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 282 TYR 0.008 0.001 TYR A 513 PHE 0.020 0.001 PHE A 355 TRP 0.005 0.001 TRP A 646 HIS 0.006 0.001 HIS A 260 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 5269) covalent geometry : angle 0.56617 ( 7156) hydrogen bonds : bond 0.05118 ( 307) hydrogen bonds : angle 4.64270 ( 885) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 63 time to evaluate : 0.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 407 MET cc_start: 0.7241 (mmt) cc_final: 0.6972 (mmt) REVERT: A 415 MET cc_start: 0.6062 (tpt) cc_final: 0.5838 (tpt) REVERT: A 421 MET cc_start: 0.8959 (mmt) cc_final: 0.8630 (mmt) REVERT: A 485 GLU cc_start: 0.7732 (mt-10) cc_final: 0.7503 (mt-10) REVERT: A 679 GLU cc_start: 0.8725 (tm-30) cc_final: 0.8499 (tm-30) outliers start: 2 outliers final: 2 residues processed: 63 average time/residue: 0.0981 time to fit residues: 9.5099 Evaluate side-chains 63 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 61 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 211 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 28 optimal weight: 2.9990 chunk 40 optimal weight: 9.9990 chunk 11 optimal weight: 3.9990 chunk 10 optimal weight: 9.9990 chunk 7 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 41 optimal weight: 9.9990 chunk 63 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 51 optimal weight: 0.5980 chunk 43 optimal weight: 6.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.107422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.080969 restraints weight = 41677.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.084857 restraints weight = 18424.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.087412 restraints weight = 11619.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.088711 restraints weight = 8855.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.089784 restraints weight = 7673.031| |-----------------------------------------------------------------------------| r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.1212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5269 Z= 0.128 Angle : 0.513 5.364 7156 Z= 0.274 Chirality : 0.039 0.146 827 Planarity : 0.004 0.040 895 Dihedral : 4.645 19.444 695 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.53 % Allowed : 6.75 % Favored : 92.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.33), residues: 649 helix: 1.88 (0.28), residues: 335 sheet: 0.70 (0.57), residues: 85 loop : -0.93 (0.38), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 249 TYR 0.010 0.001 TYR A 507 PHE 0.018 0.001 PHE A 355 TRP 0.005 0.001 TRP A 264 HIS 0.006 0.001 HIS A 260 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 5269) covalent geometry : angle 0.51261 ( 7156) hydrogen bonds : bond 0.04633 ( 307) hydrogen bonds : angle 4.38315 ( 885) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 60 time to evaluate : 0.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 MET cc_start: 0.7986 (tmm) cc_final: 0.7768 (tmm) REVERT: A 407 MET cc_start: 0.7172 (mmt) cc_final: 0.6870 (mmt) REVERT: A 415 MET cc_start: 0.6176 (tpt) cc_final: 0.5964 (tpt) REVERT: A 421 MET cc_start: 0.8947 (mmt) cc_final: 0.8606 (mmt) REVERT: A 485 GLU cc_start: 0.7741 (mt-10) cc_final: 0.7462 (mt-10) outliers start: 3 outliers final: 2 residues processed: 61 average time/residue: 0.1019 time to fit residues: 9.4944 Evaluate side-chains 62 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 60 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 380 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 16 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 20 optimal weight: 6.9990 chunk 43 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 9.9990 chunk 60 optimal weight: 0.8980 chunk 58 optimal weight: 4.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.107831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.082187 restraints weight = 40776.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.085870 restraints weight = 18996.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.088290 restraints weight = 12212.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.089667 restraints weight = 9412.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.090270 restraints weight = 8115.661| |-----------------------------------------------------------------------------| r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 5269 Z= 0.116 Angle : 0.506 5.321 7156 Z= 0.268 Chirality : 0.039 0.143 827 Planarity : 0.004 0.040 895 Dihedral : 4.546 18.648 695 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.71 % Allowed : 7.28 % Favored : 92.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.33), residues: 649 helix: 1.96 (0.28), residues: 341 sheet: 0.64 (0.58), residues: 85 loop : -0.92 (0.38), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 249 TYR 0.009 0.001 TYR A 507 PHE 0.018 0.001 PHE A 24 TRP 0.004 0.001 TRP A 264 HIS 0.005 0.001 HIS A 260 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 5269) covalent geometry : angle 0.50579 ( 7156) hydrogen bonds : bond 0.04250 ( 307) hydrogen bonds : angle 4.20549 ( 885) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 61 time to evaluate : 0.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 MET cc_start: 0.7977 (tmm) cc_final: 0.7765 (tmm) REVERT: A 407 MET cc_start: 0.7218 (mmt) cc_final: 0.6908 (mmt) REVERT: A 421 MET cc_start: 0.8903 (mmt) cc_final: 0.8559 (mmt) REVERT: A 485 GLU cc_start: 0.7669 (mt-10) cc_final: 0.7366 (mt-10) outliers start: 4 outliers final: 3 residues processed: 63 average time/residue: 0.0916 time to fit residues: 8.8133 Evaluate side-chains 64 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 61 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 380 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 18 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 10 optimal weight: 10.0000 chunk 63 optimal weight: 0.9990 chunk 9 optimal weight: 9.9990 chunk 56 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.107436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.081093 restraints weight = 40425.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.084924 restraints weight = 17799.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.087402 restraints weight = 11195.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.088927 restraints weight = 8558.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.089607 restraints weight = 7294.510| |-----------------------------------------------------------------------------| r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5269 Z= 0.126 Angle : 0.505 5.260 7156 Z= 0.268 Chirality : 0.039 0.142 827 Planarity : 0.004 0.041 895 Dihedral : 4.519 18.654 695 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.71 % Allowed : 7.99 % Favored : 91.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.33), residues: 649 helix: 2.05 (0.28), residues: 340 sheet: 0.50 (0.58), residues: 85 loop : -0.82 (0.39), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 161 TYR 0.008 0.001 TYR A 507 PHE 0.018 0.001 PHE A 24 TRP 0.005 0.001 TRP A 264 HIS 0.005 0.001 HIS A 260 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 5269) covalent geometry : angle 0.50541 ( 7156) hydrogen bonds : bond 0.04223 ( 307) hydrogen bonds : angle 4.17972 ( 885) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 62 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 MET cc_start: 0.8047 (tmm) cc_final: 0.7844 (tmm) REVERT: A 407 MET cc_start: 0.7358 (mmt) cc_final: 0.6983 (mmt) REVERT: A 415 MET cc_start: 0.6132 (tpt) cc_final: 0.5843 (tpt) REVERT: A 421 MET cc_start: 0.8930 (mmt) cc_final: 0.8551 (mmt) REVERT: A 485 GLU cc_start: 0.7718 (mt-10) cc_final: 0.7504 (mt-10) REVERT: A 679 GLU cc_start: 0.8705 (tm-30) cc_final: 0.8478 (tm-30) outliers start: 4 outliers final: 2 residues processed: 64 average time/residue: 0.1041 time to fit residues: 10.2117 Evaluate side-chains 64 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 62 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 380 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 46 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 38 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.106761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.081276 restraints weight = 40840.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.084821 restraints weight = 19147.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.087110 restraints weight = 12380.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.088397 restraints weight = 9609.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.088968 restraints weight = 8334.623| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5269 Z= 0.144 Angle : 0.513 5.268 7156 Z= 0.275 Chirality : 0.039 0.131 827 Planarity : 0.004 0.041 895 Dihedral : 4.532 18.894 695 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.53 % Allowed : 8.53 % Favored : 90.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.33), residues: 649 helix: 1.99 (0.28), residues: 345 sheet: 0.36 (0.57), residues: 85 loop : -0.77 (0.40), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 303 TYR 0.013 0.001 TYR A 198 PHE 0.014 0.001 PHE A 355 TRP 0.005 0.001 TRP A 264 HIS 0.005 0.001 HIS A 260 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 5269) covalent geometry : angle 0.51301 ( 7156) hydrogen bonds : bond 0.04319 ( 307) hydrogen bonds : angle 4.20263 ( 885) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 63 time to evaluate : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 407 MET cc_start: 0.7380 (mmt) cc_final: 0.7033 (mmt) REVERT: A 415 MET cc_start: 0.6135 (tpt) cc_final: 0.5855 (tpt) REVERT: A 485 GLU cc_start: 0.7713 (mt-10) cc_final: 0.7480 (mt-10) outliers start: 3 outliers final: 3 residues processed: 63 average time/residue: 0.1028 time to fit residues: 9.8766 Evaluate side-chains 62 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 59 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 380 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 6 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 25 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 42 optimal weight: 10.0000 chunk 54 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.105585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.078959 restraints weight = 41591.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.082638 restraints weight = 18575.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.085001 restraints weight = 11842.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.086411 restraints weight = 9129.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.086793 restraints weight = 7878.441| |-----------------------------------------------------------------------------| r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5269 Z= 0.176 Angle : 0.537 5.310 7156 Z= 0.290 Chirality : 0.039 0.131 827 Planarity : 0.004 0.041 895 Dihedral : 4.617 21.090 695 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.89 % Allowed : 9.24 % Favored : 89.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.33), residues: 649 helix: 1.94 (0.28), residues: 345 sheet: 0.19 (0.57), residues: 85 loop : -0.77 (0.40), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 303 TYR 0.006 0.001 TYR A 12 PHE 0.014 0.001 PHE A 355 TRP 0.006 0.001 TRP A 264 HIS 0.006 0.001 HIS A 260 Details of bonding type rmsd covalent geometry : bond 0.00392 ( 5269) covalent geometry : angle 0.53671 ( 7156) hydrogen bonds : bond 0.04617 ( 307) hydrogen bonds : angle 4.30565 ( 885) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 62 time to evaluate : 0.268 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 298 ASP cc_start: 0.8743 (t0) cc_final: 0.8425 (t0) REVERT: A 415 MET cc_start: 0.6215 (tpt) cc_final: 0.5941 (tpt) REVERT: A 485 GLU cc_start: 0.7789 (mt-10) cc_final: 0.7548 (mt-10) outliers start: 5 outliers final: 5 residues processed: 64 average time/residue: 0.1015 time to fit residues: 9.9584 Evaluate side-chains 65 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 60 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 197 CYS Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 380 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 40 optimal weight: 0.1980 chunk 62 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.106597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.079968 restraints weight = 41596.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.083737 restraints weight = 18429.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.086182 restraints weight = 11687.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.087412 restraints weight = 8985.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.088512 restraints weight = 7817.770| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 5269 Z= 0.119 Angle : 0.516 5.181 7156 Z= 0.272 Chirality : 0.039 0.135 827 Planarity : 0.004 0.041 895 Dihedral : 4.535 19.983 695 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.07 % Allowed : 8.88 % Favored : 90.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.33), residues: 649 helix: 1.95 (0.28), residues: 352 sheet: 0.21 (0.57), residues: 85 loop : -0.76 (0.40), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 272 TYR 0.007 0.001 TYR A 507 PHE 0.012 0.001 PHE A 355 TRP 0.005 0.001 TRP A 264 HIS 0.005 0.001 HIS A 260 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 5269) covalent geometry : angle 0.51648 ( 7156) hydrogen bonds : bond 0.04343 ( 307) hydrogen bonds : angle 4.11838 ( 885) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 63 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 415 MET cc_start: 0.6245 (tpt) cc_final: 0.5909 (tpt) REVERT: A 485 GLU cc_start: 0.7708 (mt-10) cc_final: 0.7448 (mt-10) outliers start: 6 outliers final: 6 residues processed: 65 average time/residue: 0.1105 time to fit residues: 10.8981 Evaluate side-chains 66 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 60 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLU Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 197 CYS Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 652 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 5 optimal weight: 0.8980 chunk 45 optimal weight: 0.2980 chunk 62 optimal weight: 0.4980 chunk 35 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 chunk 9 optimal weight: 5.9990 chunk 53 optimal weight: 6.9990 chunk 29 optimal weight: 0.7980 chunk 2 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.107927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.082341 restraints weight = 40373.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.085920 restraints weight = 18701.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.088346 restraints weight = 12095.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.089639 restraints weight = 9314.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.090643 restraints weight = 8055.717| |-----------------------------------------------------------------------------| r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 5269 Z= 0.102 Angle : 0.508 5.272 7156 Z= 0.265 Chirality : 0.039 0.135 827 Planarity : 0.004 0.042 895 Dihedral : 4.417 17.830 695 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.89 % Allowed : 9.06 % Favored : 90.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.33), residues: 649 helix: 2.06 (0.28), residues: 352 sheet: 0.33 (0.57), residues: 85 loop : -0.72 (0.40), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 27 TYR 0.007 0.001 TYR A 507 PHE 0.011 0.001 PHE A 528 TRP 0.004 0.001 TRP A 264 HIS 0.004 0.001 HIS A 260 Details of bonding type rmsd covalent geometry : bond 0.00226 ( 5269) covalent geometry : angle 0.50834 ( 7156) hydrogen bonds : bond 0.03916 ( 307) hydrogen bonds : angle 3.92612 ( 885) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 64 time to evaluate : 0.274 Fit side-chains revert: symmetry clash REVERT: A 415 MET cc_start: 0.6287 (tpt) cc_final: 0.5941 (tpt) REVERT: A 485 GLU cc_start: 0.7598 (mt-10) cc_final: 0.7384 (mt-10) outliers start: 5 outliers final: 5 residues processed: 66 average time/residue: 0.1111 time to fit residues: 10.7713 Evaluate side-chains 63 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 58 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLU Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 197 CYS Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 652 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 33 optimal weight: 3.9990 chunk 41 optimal weight: 20.0000 chunk 12 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 42 optimal weight: 0.0980 chunk 2 optimal weight: 8.9990 chunk 11 optimal weight: 0.9990 chunk 62 optimal weight: 0.0170 overall best weight: 1.4224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.106936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.081247 restraints weight = 40990.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.084848 restraints weight = 19190.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.087041 restraints weight = 12425.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.088538 restraints weight = 9705.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.089042 restraints weight = 8346.986| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5269 Z= 0.124 Angle : 0.531 5.409 7156 Z= 0.277 Chirality : 0.039 0.131 827 Planarity : 0.004 0.042 895 Dihedral : 4.403 20.063 695 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.07 % Allowed : 9.95 % Favored : 88.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.33), residues: 649 helix: 2.09 (0.28), residues: 352 sheet: 0.27 (0.57), residues: 85 loop : -0.71 (0.41), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 258 TYR 0.006 0.001 TYR A 670 PHE 0.012 0.001 PHE A 355 TRP 0.005 0.001 TRP A 264 HIS 0.005 0.001 HIS A 260 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 5269) covalent geometry : angle 0.53065 ( 7156) hydrogen bonds : bond 0.04009 ( 307) hydrogen bonds : angle 3.97637 ( 885) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 60 time to evaluate : 0.272 Fit side-chains revert: symmetry clash REVERT: A 415 MET cc_start: 0.6322 (tpt) cc_final: 0.5987 (tpt) outliers start: 6 outliers final: 5 residues processed: 63 average time/residue: 0.1091 time to fit residues: 10.4302 Evaluate side-chains 65 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 60 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 197 CYS Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 652 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 7.9990 chunk 46 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 22 optimal weight: 0.0980 chunk 7 optimal weight: 0.9980 chunk 39 optimal weight: 6.9990 chunk 10 optimal weight: 6.9990 chunk 60 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.107934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.082314 restraints weight = 41234.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.085931 restraints weight = 19163.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.088354 restraints weight = 12352.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.089808 restraints weight = 9524.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.090484 restraints weight = 8163.268| |-----------------------------------------------------------------------------| r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 5269 Z= 0.100 Angle : 0.516 5.169 7156 Z= 0.266 Chirality : 0.039 0.135 827 Planarity : 0.004 0.042 895 Dihedral : 4.310 18.603 695 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.89 % Allowed : 9.95 % Favored : 89.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.33), residues: 649 helix: 2.20 (0.28), residues: 352 sheet: 0.36 (0.57), residues: 85 loop : -0.67 (0.41), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 272 TYR 0.008 0.001 TYR A 507 PHE 0.011 0.001 PHE A 528 TRP 0.004 0.001 TRP A 264 HIS 0.004 0.001 HIS A 260 Details of bonding type rmsd covalent geometry : bond 0.00225 ( 5269) covalent geometry : angle 0.51636 ( 7156) hydrogen bonds : bond 0.03747 ( 307) hydrogen bonds : angle 3.84509 ( 885) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1922.06 seconds wall clock time: 33 minutes 23.61 seconds (2003.61 seconds total)