Starting phenix.real_space_refine on Mon Jul 28 12:25:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pn1_13545/07_2025/7pn1_13545.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pn1_13545/07_2025/7pn1_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_13545/07_2025/7pn1_13545.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pn1_13545/07_2025/7pn1_13545.map" model { file = "/net/cci-nas-00/data/ceres_data/7pn1_13545/07_2025/7pn1_13545.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pn1_13545/07_2025/7pn1_13545.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 5.83, per 1000 atoms: 0.56 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: 2.77 Conformation dependent library (CDL) restraints added in 719.0 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: 1.11 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: 5.33 Time building geometry restraints manager: 3.36 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: 0.750 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: 0.190 Extract box with map and model: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 29.050 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 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:3.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.420 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.006 0.001 TRP A 646 HIS 0.006 0.001 HIS A 260 PHE 0.023 0.001 PHE A 355 TYR 0.015 0.001 TYR A 91 ARG 0.003 0.000 ARG A 27 Details of bonding type rmsd hydrogen bonds : bond 0.14910 ( 307) hydrogen bonds : angle 5.58326 ( 885) covalent geometry : bond 0.00236 ( 5269) covalent geometry : angle 0.56824 ( 7156) *********************** 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 : 1.345 Fit side-chains revert: symmetry clash 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: 0.7558 (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: 0.2682 time to fit residues: 30.4687 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 : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 54 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 26 optimal weight: 0.4980 chunk 50 optimal weight: 3.9990 chunk 19 optimal weight: 6.9990 chunk 30 optimal weight: 0.9990 chunk 37 optimal weight: 7.9990 chunk 59 optimal weight: 1.9990 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.107287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.081034 restraints weight = 41476.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.084984 restraints weight = 18332.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.087495 restraints weight = 11566.541| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.0953 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= 0.143 Angle : 0.557 5.906 7156 Z= 0.299 Chirality : 0.040 0.157 827 Planarity : 0.004 0.041 895 Dihedral : 4.723 19.461 695 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.36 % Allowed : 5.68 % Favored : 93.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.33), residues: 649 helix: 1.89 (0.28), residues: 334 sheet: 0.91 (0.58), residues: 85 loop : -0.75 (0.38), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 47 HIS 0.005 0.001 HIS A 260 PHE 0.019 0.001 PHE A 24 TYR 0.008 0.001 TYR A 513 ARG 0.001 0.000 ARG A 282 Details of bonding type rmsd hydrogen bonds : bond 0.04973 ( 307) hydrogen bonds : angle 4.57916 ( 885) covalent geometry : bond 0.00309 ( 5269) covalent geometry : angle 0.55653 ( 7156) *********************** 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 66 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 64 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 407 MET cc_start: 0.7253 (mmt) cc_final: 0.6974 (mmt) REVERT: A 415 MET cc_start: 0.6033 (tpt) cc_final: 0.5806 (tpt) REVERT: A 421 MET cc_start: 0.8972 (mmt) cc_final: 0.8642 (mmt) REVERT: A 485 GLU cc_start: 0.7708 (mt-10) cc_final: 0.7483 (mt-10) REVERT: A 679 GLU cc_start: 0.8785 (tm-30) cc_final: 0.8532 (tm-30) outliers start: 2 outliers final: 2 residues processed: 64 average time/residue: 0.2519 time to fit residues: 23.9222 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 : 0.864 ------------------------------------------------------------------------------- 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 34 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 54 optimal weight: 0.6980 chunk 23 optimal weight: 9.9990 chunk 1 optimal weight: 3.9990 chunk 41 optimal weight: 20.0000 chunk 32 optimal weight: 0.4980 chunk 44 optimal weight: 6.9990 chunk 40 optimal weight: 9.9990 chunk 24 optimal weight: 8.9990 chunk 2 optimal weight: 2.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- 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 = 0.3720 r_free = 0.3720 target = 0.106499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.079921 restraints weight = 41727.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.083718 restraints weight = 18589.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.086205 restraints weight = 11798.217| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5269 Z= 0.165 Angle : 0.538 5.363 7156 Z= 0.291 Chirality : 0.039 0.145 827 Planarity : 0.004 0.040 895 Dihedral : 4.709 20.108 695 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.71 % Allowed : 6.75 % Favored : 92.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.33), residues: 649 helix: 1.89 (0.28), residues: 334 sheet: 0.58 (0.57), residues: 85 loop : -0.81 (0.39), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 264 HIS 0.007 0.001 HIS A 260 PHE 0.019 0.001 PHE A 355 TYR 0.011 0.001 TYR A 40 ARG 0.001 0.000 ARG A 161 Details of bonding type rmsd hydrogen bonds : bond 0.04785 ( 307) hydrogen bonds : angle 4.47400 ( 885) covalent geometry : bond 0.00362 ( 5269) covalent geometry : angle 0.53797 ( 7156) *********************** 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 64 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 60 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 MET cc_start: 0.7972 (tmm) cc_final: 0.7759 (tmm) REVERT: A 407 MET cc_start: 0.7303 (mmt) cc_final: 0.6975 (mmt) REVERT: A 415 MET cc_start: 0.6208 (tpt) cc_final: 0.6006 (tpt) REVERT: A 421 MET cc_start: 0.8939 (mmt) cc_final: 0.8600 (mmt) REVERT: A 485 GLU cc_start: 0.7831 (mt-10) cc_final: 0.7573 (mt-10) outliers start: 4 outliers final: 2 residues processed: 61 average time/residue: 0.2885 time to fit residues: 26.5052 Evaluate side-chains 61 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 59 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 VAL 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 38 optimal weight: 5.9990 chunk 9 optimal weight: 0.6980 chunk 39 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 22 optimal weight: 8.9990 chunk 0 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 overall best weight: 1.7184 ------------------------------------------------------------------------------- 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 = 0.3728 r_free = 0.3728 target = 0.106935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.080566 restraints weight = 40805.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.084416 restraints weight = 18071.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.086917 restraints weight = 11393.295| |-----------------------------------------------------------------------------| r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.1523 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= 0.133 Angle : 0.514 5.308 7156 Z= 0.275 Chirality : 0.039 0.142 827 Planarity : 0.004 0.041 895 Dihedral : 4.622 19.349 695 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.89 % Allowed : 7.46 % Favored : 91.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.33), residues: 649 helix: 1.96 (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 TRP 0.005 0.001 TRP A 47 HIS 0.006 0.001 HIS A 260 PHE 0.018 0.001 PHE A 24 TYR 0.009 0.001 TYR A 507 ARG 0.001 0.000 ARG A 272 Details of bonding type rmsd hydrogen bonds : bond 0.04473 ( 307) hydrogen bonds : angle 4.27592 ( 885) covalent geometry : bond 0.00294 ( 5269) covalent geometry : angle 0.51395 ( 7156) *********************** 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 66 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 61 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 MET cc_start: 0.8076 (tmm) cc_final: 0.7837 (tmm) REVERT: A 407 MET cc_start: 0.7418 (mmt) cc_final: 0.7052 (mmt) REVERT: A 421 MET cc_start: 0.8947 (mmt) cc_final: 0.8584 (mmt) REVERT: A 485 GLU cc_start: 0.7772 (mt-10) cc_final: 0.7470 (mt-10) REVERT: A 679 GLU cc_start: 0.8759 (tm-30) cc_final: 0.8525 (tm-30) outliers start: 5 outliers final: 3 residues processed: 63 average time/residue: 0.4297 time to fit residues: 40.3469 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 : 0.919 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 32 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 10 optimal weight: 10.0000 chunk 33 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 2 optimal weight: 5.9990 chunk 39 optimal weight: 7.9990 chunk 40 optimal weight: 8.9990 chunk 47 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 = 0.3709 r_free = 0.3709 target = 0.105825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.079407 restraints weight = 40777.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.083101 restraints weight = 18068.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.085510 restraints weight = 11450.292| |-----------------------------------------------------------------------------| r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 5269 Z= 0.171 Angle : 0.536 5.377 7156 Z= 0.288 Chirality : 0.039 0.137 827 Planarity : 0.004 0.041 895 Dihedral : 4.650 19.914 695 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.89 % Allowed : 8.35 % Favored : 90.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.33), residues: 649 helix: 1.96 (0.28), residues: 339 sheet: 0.23 (0.58), residues: 85 loop : -0.81 (0.39), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 264 HIS 0.006 0.001 HIS A 260 PHE 0.020 0.001 PHE A 24 TYR 0.007 0.001 TYR A 40 ARG 0.001 0.000 ARG A 303 Details of bonding type rmsd hydrogen bonds : bond 0.04620 ( 307) hydrogen bonds : angle 4.34134 ( 885) covalent geometry : bond 0.00383 ( 5269) covalent geometry : angle 0.53579 ( 7156) *********************** 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 65 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 60 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 MET cc_start: 0.8080 (tmm) cc_final: 0.7861 (tmm) REVERT: A 415 MET cc_start: 0.6152 (tpt) cc_final: 0.5884 (tpt) REVERT: A 485 GLU cc_start: 0.7832 (mt-10) cc_final: 0.7629 (mt-10) outliers start: 5 outliers final: 4 residues processed: 62 average time/residue: 0.2617 time to fit residues: 24.1074 Evaluate side-chains 63 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 59 time to evaluate : 0.867 ------------------------------------------------------------------------------- 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 211 VAL 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 34 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 19 optimal weight: 7.9990 chunk 51 optimal weight: 0.0060 chunk 12 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 40 optimal weight: 10.0000 chunk 20 optimal weight: 4.9990 overall best weight: 1.1398 ------------------------------------------------------------------------------- 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 = 0.3733 r_free = 0.3733 target = 0.107214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.080780 restraints weight = 40632.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.084612 restraints weight = 17895.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.087106 restraints weight = 11239.095| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 5269 Z= 0.112 Angle : 0.508 5.560 7156 Z= 0.268 Chirality : 0.039 0.134 827 Planarity : 0.004 0.041 895 Dihedral : 4.518 18.676 695 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.33), residues: 649 helix: 2.04 (0.28), residues: 341 sheet: 0.28 (0.58), residues: 85 loop : -0.90 (0.38), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 47 HIS 0.004 0.001 HIS A 260 PHE 0.013 0.001 PHE A 44 TYR 0.008 0.001 TYR A 507 ARG 0.001 0.000 ARG A 272 Details of bonding type rmsd hydrogen bonds : bond 0.04255 ( 307) hydrogen bonds : angle 4.10631 ( 885) covalent geometry : bond 0.00248 ( 5269) covalent geometry : angle 0.50847 ( 7156) *********************** 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 64 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 61 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 407 MET cc_start: 0.7329 (mmt) cc_final: 0.7060 (mmt) REVERT: A 415 MET cc_start: 0.6222 (tpt) cc_final: 0.5945 (tpt) REVERT: A 485 GLU cc_start: 0.7711 (mt-10) cc_final: 0.7476 (mt-10) REVERT: A 679 GLU cc_start: 0.8679 (tm-30) cc_final: 0.8451 (tm-30) outliers start: 3 outliers final: 3 residues processed: 62 average time/residue: 0.2379 time to fit residues: 22.0340 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 : 0.841 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 60 optimal weight: 0.9980 chunk 17 optimal weight: 4.9990 chunk 29 optimal weight: 0.6980 chunk 48 optimal weight: 6.9990 chunk 50 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 12 optimal weight: 0.4980 chunk 18 optimal weight: 1.9990 chunk 23 optimal weight: 8.9990 chunk 2 optimal weight: 7.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.106801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.080238 restraints weight = 41728.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.084008 restraints weight = 18438.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.086471 restraints weight = 11641.394| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.1920 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= 0.131 Angle : 0.518 6.523 7156 Z= 0.273 Chirality : 0.039 0.130 827 Planarity : 0.004 0.042 895 Dihedral : 4.496 18.716 695 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.71 % Allowed : 9.06 % Favored : 90.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.33), residues: 649 helix: 2.08 (0.28), residues: 340 sheet: 0.25 (0.58), residues: 85 loop : -0.83 (0.39), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 264 HIS 0.004 0.001 HIS A 260 PHE 0.012 0.001 PHE A 355 TYR 0.008 0.001 TYR A 40 ARG 0.001 0.000 ARG A 34 Details of bonding type rmsd hydrogen bonds : bond 0.04271 ( 307) hydrogen bonds : angle 4.12212 ( 885) covalent geometry : bond 0.00291 ( 5269) covalent geometry : angle 0.51785 ( 7156) *********************** 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 66 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 62 time to evaluate : 0.823 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 407 MET cc_start: 0.7370 (mmt) cc_final: 0.7120 (mmt) REVERT: A 415 MET cc_start: 0.6200 (tpt) cc_final: 0.5933 (tpt) REVERT: A 485 GLU cc_start: 0.7727 (mt-10) cc_final: 0.7487 (mt-10) outliers start: 4 outliers final: 4 residues processed: 63 average time/residue: 0.2593 time to fit residues: 24.7914 Evaluate side-chains 63 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 59 time to evaluate : 0.928 ------------------------------------------------------------------------------- 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 380 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 63 optimal weight: 0.9980 chunk 54 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 31 optimal weight: 0.6980 chunk 46 optimal weight: 0.8980 chunk 12 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- 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 = 0.3735 r_free = 0.3735 target = 0.107106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.080616 restraints weight = 41108.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.084432 restraints weight = 18141.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.086918 restraints weight = 11393.415| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 5269 Z= 0.116 Angle : 0.515 6.556 7156 Z= 0.269 Chirality : 0.039 0.134 827 Planarity : 0.004 0.041 895 Dihedral : 4.461 18.978 695 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.71 % Allowed : 9.59 % Favored : 89.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.33), residues: 649 helix: 2.06 (0.28), residues: 347 sheet: 0.29 (0.58), residues: 85 loop : -0.84 (0.40), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 264 HIS 0.004 0.001 HIS A 260 PHE 0.016 0.001 PHE A 44 TYR 0.008 0.001 TYR A 40 ARG 0.001 0.000 ARG A 272 Details of bonding type rmsd hydrogen bonds : bond 0.04170 ( 307) hydrogen bonds : angle 4.04365 ( 885) covalent geometry : bond 0.00258 ( 5269) covalent geometry : angle 0.51501 ( 7156) *********************** 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 64 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 60 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 407 MET cc_start: 0.7493 (mmt) cc_final: 0.7194 (mmt) REVERT: A 415 MET cc_start: 0.6255 (tpt) cc_final: 0.5911 (tpt) REVERT: A 485 GLU cc_start: 0.7692 (mt-10) cc_final: 0.7438 (mt-10) outliers start: 4 outliers final: 4 residues processed: 61 average time/residue: 0.2579 time to fit residues: 23.6323 Evaluate side-chains 63 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 59 time to evaluate : 0.834 ------------------------------------------------------------------------------- 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 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 9 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 30 optimal weight: 0.0870 chunk 50 optimal weight: 7.9990 chunk 39 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 chunk 42 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 overall best weight: 0.9962 ------------------------------------------------------------------------------- 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 = 0.3740 r_free = 0.3740 target = 0.107447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.081189 restraints weight = 40757.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.085016 restraints weight = 17828.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.087517 restraints weight = 11168.771| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 5269 Z= 0.107 Angle : 0.517 6.850 7156 Z= 0.268 Chirality : 0.039 0.137 827 Planarity : 0.004 0.042 895 Dihedral : 4.393 18.335 695 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.89 % Allowed : 9.59 % Favored : 89.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.33), residues: 649 helix: 2.07 (0.28), residues: 352 sheet: 0.30 (0.57), residues: 85 loop : -0.77 (0.41), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 47 HIS 0.004 0.001 HIS A 260 PHE 0.016 0.001 PHE A 216 TYR 0.009 0.001 TYR A 40 ARG 0.001 0.000 ARG A 272 Details of bonding type rmsd hydrogen bonds : bond 0.03989 ( 307) hydrogen bonds : angle 3.95720 ( 885) covalent geometry : bond 0.00240 ( 5269) covalent geometry : angle 0.51694 ( 7156) *********************** 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 67 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 62 time to evaluate : 0.933 Fit side-chains revert: symmetry clash REVERT: A 407 MET cc_start: 0.7449 (mmt) cc_final: 0.7172 (mmt) REVERT: A 415 MET cc_start: 0.6300 (tpt) cc_final: 0.5956 (tpt) REVERT: A 485 GLU cc_start: 0.7677 (mt-10) cc_final: 0.7453 (mt-10) outliers start: 5 outliers final: 5 residues processed: 63 average time/residue: 0.3472 time to fit residues: 32.3130 Evaluate side-chains 62 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 57 time to evaluate : 0.905 ------------------------------------------------------------------------------- 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 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 56 optimal weight: 2.9990 chunk 55 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 17 optimal weight: 0.3980 chunk 19 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 22 optimal weight: 0.0870 chunk 54 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 41 optimal weight: 20.0000 chunk 39 optimal weight: 0.9990 overall best weight: 0.5960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.108328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.082045 restraints weight = 41387.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.085932 restraints weight = 18221.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.088481 restraints weight = 11448.825| |-----------------------------------------------------------------------------| r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 5269 Z= 0.103 Angle : 0.526 6.504 7156 Z= 0.270 Chirality : 0.039 0.140 827 Planarity : 0.004 0.041 895 Dihedral : 4.327 18.730 695 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.89 % Allowed : 10.12 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.33), residues: 649 helix: 2.12 (0.28), residues: 352 sheet: 0.32 (0.56), residues: 85 loop : -0.67 (0.41), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 47 HIS 0.003 0.001 HIS A 260 PHE 0.021 0.001 PHE A 44 TYR 0.008 0.001 TYR A 40 ARG 0.001 0.000 ARG A 258 Details of bonding type rmsd hydrogen bonds : bond 0.03741 ( 307) hydrogen bonds : angle 3.83918 ( 885) covalent geometry : bond 0.00233 ( 5269) covalent geometry : angle 0.52627 ( 7156) ********************** 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 65 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 60 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 407 MET cc_start: 0.7441 (mmt) cc_final: 0.7179 (mmt) REVERT: A 415 MET cc_start: 0.6217 (tpt) cc_final: 0.5876 (tpt) outliers start: 5 outliers final: 5 residues processed: 61 average time/residue: 0.3051 time to fit residues: 27.7123 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 : 0.912 ------------------------------------------------------------------------------- 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 134 LEU 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 45 optimal weight: 0.9980 chunk 44 optimal weight: 7.9990 chunk 28 optimal weight: 2.9990 chunk 31 optimal weight: 0.3980 chunk 20 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 chunk 62 optimal weight: 0.7980 chunk 8 optimal weight: 5.9990 chunk 49 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 = 0.3742 r_free = 0.3742 target = 0.107793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.082094 restraints weight = 41134.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.085733 restraints weight = 19294.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.087979 restraints weight = 12481.771| |-----------------------------------------------------------------------------| r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 5269 Z= 0.105 Angle : 0.520 6.261 7156 Z= 0.268 Chirality : 0.039 0.135 827 Planarity : 0.003 0.042 895 Dihedral : 4.288 18.672 695 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.71 % Allowed : 11.01 % Favored : 88.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.33), residues: 649 helix: 2.21 (0.28), residues: 352 sheet: 0.33 (0.56), residues: 85 loop : -0.69 (0.41), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 261 HIS 0.005 0.001 HIS A 260 PHE 0.015 0.001 PHE A 216 TYR 0.008 0.001 TYR A 40 ARG 0.001 0.000 ARG A 251 Details of bonding type rmsd hydrogen bonds : bond 0.03756 ( 307) hydrogen bonds : angle 3.84709 ( 885) covalent geometry : bond 0.00236 ( 5269) covalent geometry : angle 0.52009 ( 7156) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4182.52 seconds wall clock time: 75 minutes 31.82 seconds (4531.82 seconds total)