Starting phenix.real_space_refine on Thu Jun 5 10:24:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wg4_37502/06_2025/8wg4_37502.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wg4_37502/06_2025/8wg4_37502.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wg4_37502/06_2025/8wg4_37502.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wg4_37502/06_2025/8wg4_37502.map" model { file = "/net/cci-nas-00/data/ceres_data/8wg4_37502/06_2025/8wg4_37502.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wg4_37502/06_2025/8wg4_37502.cif" } resolution = 3.5 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= 0.004 sd= 0.067 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 46 5.16 5 C 3940 2.51 5 N 923 2.21 5 O 977 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 5887 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 688, 5597 Classifications: {'peptide': 688} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 26, 'TRANS': 661} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1, 'P1L:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 290 Unusual residues: {'LBN': 1, 'Y01': 7} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Time building chain proxies: 4.17, per 1000 atoms: 0.71 Number of scatterers: 5887 At special positions: 0 Unit cell: (88.7062, 88.7062, 104.269, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 46 16.00 P 1 15.00 O 977 8.00 N 923 7.00 C 3940 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 23 " - pdb=" SG CYS A 559 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.56 Conformation dependent library (CDL) restraints added in 778.9 milliseconds 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1314 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 2 sheets defined 74.6% alpha, 3.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 31 through 35 Processing helix chain 'A' and resid 36 through 39 removed outlier: 4.469A pdb=" N GLY A 39 " --> pdb=" O LEU A 36 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 36 through 39' Processing helix chain 'A' and resid 40 through 66 removed outlier: 4.003A pdb=" N ALA A 46 " --> pdb=" O PRO A 42 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N LYS A 64 " --> pdb=" O SER A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 135 removed outlier: 3.649A pdb=" N PHE A 133 " --> pdb=" O LEU A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 145 Processing helix chain 'A' and resid 145 through 172 removed outlier: 3.715A pdb=" N VAL A 149 " --> pdb=" O GLY A 145 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL A 163 " --> pdb=" O ILE A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 179 removed outlier: 3.553A pdb=" N VAL A 176 " --> pdb=" O ILE A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 198 removed outlier: 5.670A pdb=" N ILE A 195 " --> pdb=" O ARG A 192 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ALA A 196 " --> pdb=" O THR A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 231 removed outlier: 3.612A pdb=" N LEU A 207 " --> pdb=" O ASN A 203 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LEU A 216 " --> pdb=" O ALA A 212 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ARG A 231 " --> pdb=" O THR A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 240 removed outlier: 3.532A pdb=" N LYS A 239 " --> pdb=" O ASP A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 264 removed outlier: 3.708A pdb=" N ILE A 256 " --> pdb=" O GLU A 252 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N PHE A 260 " --> pdb=" O ILE A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 306 removed outlier: 3.721A pdb=" N LYS A 304 " --> pdb=" O ASN A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 320 Processing helix chain 'A' and resid 331 through 355 removed outlier: 4.313A pdb=" N ASN A 355 " --> pdb=" O LYS A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 379 Processing helix chain 'A' and resid 403 through 407 Processing helix chain 'A' and resid 421 through 426 removed outlier: 5.068A pdb=" N ARG A 426 " --> pdb=" O LEU A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 448 removed outlier: 3.560A pdb=" N TRP A 431 " --> pdb=" O GLY A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 461 removed outlier: 3.650A pdb=" N ILE A 454 " --> pdb=" O THR A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 470 removed outlier: 3.515A pdb=" N TYR A 469 " --> pdb=" O PRO A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 497 removed outlier: 3.730A pdb=" N GLN A 477 " --> pdb=" O PRO A 473 " (cutoff:3.500A) Proline residue: A 480 - end of helix Proline residue: A 492 - end of helix Processing helix chain 'A' and resid 498 through 501 Processing helix chain 'A' and resid 506 through 527 Processing helix chain 'A' and resid 527 through 533 Processing helix chain 'A' and resid 536 through 546 Processing helix chain 'A' and resid 548 through 553 Processing helix chain 'A' and resid 553 through 561 removed outlier: 4.108A pdb=" N CYS A 559 " --> pdb=" O ILE A 555 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL A 560 " --> pdb=" O ARG A 556 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N PHE A 561 " --> pdb=" O PHE A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 578 Processing helix chain 'A' and resid 578 through 587 Processing helix chain 'A' and resid 587 through 600 Processing helix chain 'A' and resid 603 through 614 Processing helix chain 'A' and resid 619 through 641 removed outlier: 3.554A pdb=" N CYS A 629 " --> pdb=" O ALA A 625 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N ILE A 639 " --> pdb=" O MET A 635 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N THR A 640 " --> pdb=" O THR A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 666 removed outlier: 4.543A pdb=" N PHE A 647 " --> pdb=" O ILE A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 703 removed outlier: 3.736A pdb=" N VAL A 681 " --> pdb=" O HIS A 677 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ASN A 682 " --> pdb=" O SER A 678 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLN A 683 " --> pdb=" O GLY A 679 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL A 684 " --> pdb=" O ALA A 680 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL A 685 " --> pdb=" O VAL A 681 " (cutoff:3.500A) Proline residue: A 688 - end of helix removed outlier: 3.629A pdb=" N PHE A 698 " --> pdb=" O TRP A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 707 through 730 removed outlier: 3.506A pdb=" N THR A 713 " --> pdb=" O THR A 709 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N PHE A 714 " --> pdb=" O SER A 710 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N LEU A 717 " --> pdb=" O THR A 713 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 269 through 276 removed outlier: 5.300A pdb=" N MET A 361 " --> pdb=" O CYS A 275 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 383 through 384 349 hydrogen bonds defined for protein. 987 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.53 Time building geometry restraints manager: 1.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 884 1.32 - 1.44: 1649 1.44 - 1.57: 3456 1.57 - 1.70: 2 1.70 - 1.83: 66 Bond restraints: 6057 Sorted by residual: bond pdb=" CE1 HIS A 157 " pdb=" NE2 HIS A 157 " ideal model delta sigma weight residual 1.321 1.272 0.049 1.00e-02 1.00e+04 2.36e+01 bond pdb=" CG HIS A 157 " pdb=" CD2 HIS A 157 " ideal model delta sigma weight residual 1.354 1.322 0.032 1.10e-02 8.26e+03 8.23e+00 bond pdb=" C LEU A 36 " pdb=" N PRO A 37 " ideal model delta sigma weight residual 1.329 1.363 -0.034 1.25e-02 6.40e+03 7.34e+00 bond pdb=" C9 LBN A1201 " pdb=" O2 LBN A1201 " ideal model delta sigma weight residual 1.409 1.462 -0.053 2.00e-02 2.50e+03 6.96e+00 bond pdb=" CA SER A 699 " pdb=" CB SER A 699 " ideal model delta sigma weight residual 1.528 1.488 0.041 1.56e-02 4.11e+03 6.75e+00 ... (remaining 6052 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.30: 7432 2.30 - 4.59: 772 4.59 - 6.89: 31 6.89 - 9.19: 3 9.19 - 11.48: 1 Bond angle restraints: 8239 Sorted by residual: angle pdb=" CA ASN A 197 " pdb=" CB ASN A 197 " pdb=" CG ASN A 197 " ideal model delta sigma weight residual 112.60 118.20 -5.60 1.00e+00 1.00e+00 3.14e+01 angle pdb=" CA PHE A 479 " pdb=" CB PHE A 479 " pdb=" CG PHE A 479 " ideal model delta sigma weight residual 113.80 118.28 -4.48 1.00e+00 1.00e+00 2.01e+01 angle pdb=" CA TYR A 637 " pdb=" CB TYR A 637 " pdb=" CG TYR A 637 " ideal model delta sigma weight residual 113.90 105.89 8.01 1.80e+00 3.09e-01 1.98e+01 angle pdb=" CA HIS A 613 " pdb=" CB HIS A 613 " pdb=" CG HIS A 613 " ideal model delta sigma weight residual 113.80 109.38 4.42 1.00e+00 1.00e+00 1.95e+01 angle pdb=" C TYR A 264 " pdb=" CA TYR A 264 " pdb=" CB TYR A 264 " ideal model delta sigma weight residual 108.88 115.37 -6.49 1.50e+00 4.44e-01 1.87e+01 ... (remaining 8234 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.41: 3708 23.41 - 46.82: 171 46.82 - 70.24: 30 70.24 - 93.65: 6 93.65 - 117.06: 5 Dihedral angle restraints: 3920 sinusoidal: 1887 harmonic: 2033 Sorted by residual: dihedral pdb=" CB CYS A 23 " pdb=" SG CYS A 23 " pdb=" SG CYS A 559 " pdb=" CB CYS A 559 " ideal model delta sinusoidal sigma weight residual -86.00 -150.81 64.81 1 1.00e+01 1.00e-02 5.51e+01 dihedral pdb=" CA ILE A 28 " pdb=" C ILE A 28 " pdb=" N ARG A 29 " pdb=" CA ARG A 29 " ideal model delta harmonic sigma weight residual 180.00 -150.53 -29.47 0 5.00e+00 4.00e-02 3.47e+01 dihedral pdb=" CA ASP A 181 " pdb=" C ASP A 181 " pdb=" N LEU A 182 " pdb=" CA LEU A 182 " ideal model delta harmonic sigma weight residual -180.00 -153.61 -26.39 0 5.00e+00 4.00e-02 2.79e+01 ... (remaining 3917 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.070: 588 0.070 - 0.139: 285 0.139 - 0.209: 51 0.209 - 0.278: 7 0.278 - 0.348: 1 Chirality restraints: 932 Sorted by residual: chirality pdb=" CA ASN A 306 " pdb=" N ASN A 306 " pdb=" C ASN A 306 " pdb=" CB ASN A 306 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.03e+00 chirality pdb=" CA ASN A 438 " pdb=" N ASN A 438 " pdb=" C ASN A 438 " pdb=" CB ASN A 438 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CB ILE A 374 " pdb=" CA ILE A 374 " pdb=" CG1 ILE A 374 " pdb=" CG2 ILE A 374 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.69e+00 ... (remaining 929 not shown) Planarity restraints: 974 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 637 " -0.100 2.00e-02 2.50e+03 5.18e-02 5.37e+01 pdb=" CG TYR A 637 " 0.076 2.00e-02 2.50e+03 pdb=" CD1 TYR A 637 " 0.030 2.00e-02 2.50e+03 pdb=" CD2 TYR A 637 " 0.027 2.00e-02 2.50e+03 pdb=" CE1 TYR A 637 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR A 637 " 0.014 2.00e-02 2.50e+03 pdb=" CZ TYR A 637 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR A 637 " -0.062 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CAM Y01 A1207 " -0.020 2.00e-02 2.50e+03 4.13e-02 1.71e+01 pdb=" CAY Y01 A1207 " 0.071 2.00e-02 2.50e+03 pdb=" OAG Y01 A1207 " -0.029 2.00e-02 2.50e+03 pdb=" OAW Y01 A1207 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 69 " 0.048 2.00e-02 2.50e+03 2.46e-02 1.21e+01 pdb=" CG TYR A 69 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 TYR A 69 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR A 69 " -0.018 2.00e-02 2.50e+03 pdb=" CE1 TYR A 69 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR A 69 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 69 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 69 " 0.021 2.00e-02 2.50e+03 ... (remaining 971 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 1775 2.86 - 3.37: 5663 3.37 - 3.88: 8983 3.88 - 4.39: 10345 4.39 - 4.90: 17873 Nonbonded interactions: 44639 Sorted by model distance: nonbonded pdb=" ND2 ASN A 682 " pdb=" OAG Y01 A1207 " model vdw 2.353 3.120 nonbonded pdb=" NH2 ARG A 512 " pdb=" OAH Y01 A1207 " model vdw 2.437 3.120 nonbonded pdb=" OH TYR A 151 " pdb=" OD2 ASP A 659 " model vdw 2.530 3.040 nonbonded pdb=" OH TYR A 264 " pdb=" OD2 ASP A 378 " model vdw 2.577 3.040 nonbonded pdb=" O LEU A 527 " pdb=" OG SER A 531 " model vdw 2.589 3.040 ... (remaining 44634 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 17.610 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6998 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.053 6058 Z= 0.566 Angle : 1.362 11.484 8241 Z= 0.899 Chirality : 0.078 0.348 932 Planarity : 0.011 0.097 974 Dihedral : 14.668 117.059 2603 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 0.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.82 % Allowed : 6.12 % Favored : 92.07 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.47 (0.29), residues: 679 helix: -1.68 (0.20), residues: 446 sheet: 0.57 (1.30), residues: 22 loop : -1.33 (0.44), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.007 TRP A 206 HIS 0.025 0.005 HIS A 226 PHE 0.035 0.007 PHE A 154 TYR 0.100 0.009 TYR A 637 ARG 0.015 0.003 ARG A 225 Details of bonding type rmsd hydrogen bonds : bond 0.21151 ( 349) hydrogen bonds : angle 8.35347 ( 987) SS BOND : bond 0.00473 ( 1) SS BOND : angle 3.97824 ( 2) covalent geometry : bond 0.00858 ( 6057) covalent geometry : angle 1.36035 ( 8239) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 99 time to evaluate : 0.631 Fit side-chains REVERT: A 69 TYR cc_start: 0.7908 (p90) cc_final: 0.7464 (p90) REVERT: A 143 LYS cc_start: 0.6429 (tptp) cc_final: 0.6045 (tptp) REVERT: A 181 ASP cc_start: 0.7692 (m-30) cc_final: 0.7461 (t0) REVERT: A 237 LEU cc_start: 0.5878 (OUTLIER) cc_final: 0.5591 (tp) REVERT: A 241 THR cc_start: 0.9239 (m) cc_final: 0.8906 (p) REVERT: A 252 GLU cc_start: 0.7348 (mt-10) cc_final: 0.6839 (mp0) REVERT: A 254 GLU cc_start: 0.7823 (mt-10) cc_final: 0.7522 (tp30) REVERT: A 310 MET cc_start: 0.6816 (mpt) cc_final: 0.6315 (mpp) REVERT: A 335 TYR cc_start: 0.7170 (t80) cc_final: 0.6755 (t80) REVERT: A 349 ARG cc_start: 0.7336 (mtm-85) cc_final: 0.6907 (mmm160) REVERT: A 445 LEU cc_start: 0.5617 (mt) cc_final: 0.5380 (mt) REVERT: A 548 LYS cc_start: 0.6310 (mtmm) cc_final: 0.6083 (pttt) REVERT: A 676 ILE cc_start: 0.7161 (OUTLIER) cc_final: 0.6934 (tp) REVERT: A 706 LEU cc_start: 0.8188 (mt) cc_final: 0.7952 (pp) REVERT: A 740 ASN cc_start: 0.6817 (t0) cc_final: 0.6609 (t0) outliers start: 11 outliers final: 2 residues processed: 107 average time/residue: 0.1910 time to fit residues: 26.6365 Evaluate side-chains 77 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 73 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain A residue 676 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 57 optimal weight: 0.3980 chunk 51 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 17 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 53 optimal weight: 8.9990 chunk 20 optimal weight: 0.9990 chunk 32 optimal weight: 20.0000 chunk 39 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 ASN A 197 ASN A 202 ASN A 516 HIS A 565 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.162440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.121843 restraints weight = 6796.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.124297 restraints weight = 4944.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.125987 restraints weight = 4063.623| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6058 Z= 0.158 Angle : 0.665 8.887 8241 Z= 0.341 Chirality : 0.042 0.152 932 Planarity : 0.004 0.035 974 Dihedral : 10.146 79.967 1313 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.98 % Allowed : 10.74 % Favored : 87.27 % 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: 0.01 (0.32), residues: 679 helix: 0.58 (0.24), residues: 446 sheet: 2.37 (1.91), residues: 10 loop : -1.16 (0.42), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 128 HIS 0.003 0.001 HIS A 259 PHE 0.021 0.002 PHE A 298 TYR 0.018 0.002 TYR A 637 ARG 0.004 0.001 ARG A 293 Details of bonding type rmsd hydrogen bonds : bond 0.05869 ( 349) hydrogen bonds : angle 4.99455 ( 987) SS BOND : bond 0.00125 ( 1) SS BOND : angle 1.70040 ( 2) covalent geometry : bond 0.00344 ( 6057) covalent geometry : angle 0.66455 ( 8239) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 83 time to evaluate : 0.624 Fit side-chains REVERT: A 205 LEU cc_start: 0.7385 (OUTLIER) cc_final: 0.6574 (tt) REVERT: A 237 LEU cc_start: 0.7448 (OUTLIER) cc_final: 0.7185 (tp) REVERT: A 292 GLU cc_start: 0.7367 (tt0) cc_final: 0.7042 (tt0) REVERT: A 445 LEU cc_start: 0.7161 (mt) cc_final: 0.6924 (mt) REVERT: A 609 ASN cc_start: 0.8208 (t0) cc_final: 0.7421 (t0) outliers start: 12 outliers final: 7 residues processed: 90 average time/residue: 0.1810 time to fit residues: 21.6929 Evaluate side-chains 77 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 650 MET Chi-restraints excluded: chain A residue 676 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 39 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.3762 r_free = 0.3762 target = 0.162144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.121336 restraints weight = 6830.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.123762 restraints weight = 4983.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.125185 restraints weight = 4098.708| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6058 Z= 0.156 Angle : 0.615 8.223 8241 Z= 0.310 Chirality : 0.041 0.151 932 Planarity : 0.004 0.039 974 Dihedral : 8.759 58.288 1311 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.14 % Allowed : 12.89 % Favored : 83.97 % 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: 0.66 (0.32), residues: 679 helix: 1.25 (0.24), residues: 447 sheet: 1.14 (1.77), residues: 10 loop : -1.26 (0.41), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 431 HIS 0.003 0.001 HIS A 516 PHE 0.017 0.002 PHE A 730 TYR 0.017 0.002 TYR A 264 ARG 0.004 0.000 ARG A 612 Details of bonding type rmsd hydrogen bonds : bond 0.05235 ( 349) hydrogen bonds : angle 4.61290 ( 987) SS BOND : bond 0.00272 ( 1) SS BOND : angle 1.18660 ( 2) covalent geometry : bond 0.00360 ( 6057) covalent geometry : angle 0.61447 ( 8239) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 68 time to evaluate : 0.500 Fit side-chains revert: symmetry clash REVERT: A 181 ASP cc_start: 0.6817 (t0) cc_final: 0.6581 (t0) REVERT: A 310 MET cc_start: 0.6693 (mpp) cc_final: 0.6469 (mmt) REVERT: A 445 LEU cc_start: 0.7094 (mt) cc_final: 0.6852 (mt) REVERT: A 628 MET cc_start: 0.7248 (mmm) cc_final: 0.6940 (mmp) outliers start: 19 outliers final: 14 residues processed: 80 average time/residue: 0.1845 time to fit residues: 20.0471 Evaluate side-chains 78 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 64 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 51 CYS Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain A residue 650 MET Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 737 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 35 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 59 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 chunk 43 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 46 optimal weight: 0.5980 chunk 11 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4025 r_free = 0.4025 target = 0.183859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.142530 restraints weight = 6991.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.145623 restraints weight = 4679.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.147480 restraints weight = 3675.841| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6058 Z= 0.132 Angle : 0.559 7.704 8241 Z= 0.279 Chirality : 0.039 0.135 932 Planarity : 0.004 0.040 974 Dihedral : 8.230 63.874 1307 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.47 % Allowed : 14.05 % Favored : 82.48 % 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: 1.02 (0.33), residues: 679 helix: 1.61 (0.25), residues: 447 sheet: 0.75 (1.66), residues: 10 loop : -1.28 (0.41), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 67 HIS 0.002 0.001 HIS A 656 PHE 0.013 0.002 PHE A 549 TYR 0.022 0.001 TYR A 496 ARG 0.007 0.000 ARG A 293 Details of bonding type rmsd hydrogen bonds : bond 0.04664 ( 349) hydrogen bonds : angle 4.35413 ( 987) SS BOND : bond 0.00210 ( 1) SS BOND : angle 1.00159 ( 2) covalent geometry : bond 0.00298 ( 6057) covalent geometry : angle 0.55871 ( 8239) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 77 time to evaluate : 0.597 Fit side-chains revert: symmetry clash REVERT: A 178 PHE cc_start: 0.8151 (OUTLIER) cc_final: 0.6902 (m-80) REVERT: A 282 MET cc_start: 0.8564 (OUTLIER) cc_final: 0.8152 (mtm) REVERT: A 335 TYR cc_start: 0.7408 (t80) cc_final: 0.6820 (t80) REVERT: A 445 LEU cc_start: 0.7072 (mt) cc_final: 0.6812 (mt) REVERT: A 482 LEU cc_start: 0.7852 (tt) cc_final: 0.7312 (mt) REVERT: A 628 MET cc_start: 0.7838 (mmm) cc_final: 0.7095 (mmp) outliers start: 21 outliers final: 15 residues processed: 89 average time/residue: 0.1925 time to fit residues: 22.9518 Evaluate side-chains 87 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 70 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 51 CYS Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 178 PHE Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain A residue 596 ILE Chi-restraints excluded: chain A residue 650 MET Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 701 MET Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 737 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 24 optimal weight: 4.9990 chunk 56 optimal weight: 0.9980 chunk 43 optimal weight: 0.4980 chunk 33 optimal weight: 6.9990 chunk 15 optimal weight: 0.9980 chunk 11 optimal weight: 0.3980 chunk 35 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 36 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3808 r_free = 0.3808 target = 0.165522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.126583 restraints weight = 6903.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.127193 restraints weight = 5377.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.128718 restraints weight = 4336.625| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.3373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 6058 Z= 0.130 Angle : 0.540 7.494 8241 Z= 0.270 Chirality : 0.039 0.135 932 Planarity : 0.004 0.041 974 Dihedral : 8.118 67.688 1307 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 4.30 % Allowed : 15.54 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 679 helix: 1.78 (0.25), residues: 447 sheet: 0.48 (1.64), residues: 10 loop : -1.19 (0.41), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 431 HIS 0.003 0.001 HIS A 157 PHE 0.015 0.001 PHE A 549 TYR 0.018 0.001 TYR A 496 ARG 0.001 0.000 ARG A 426 Details of bonding type rmsd hydrogen bonds : bond 0.04618 ( 349) hydrogen bonds : angle 4.25841 ( 987) SS BOND : bond 0.00195 ( 1) SS BOND : angle 1.07407 ( 2) covalent geometry : bond 0.00297 ( 6057) covalent geometry : angle 0.53931 ( 8239) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 77 time to evaluate : 0.653 Fit side-chains revert: symmetry clash REVERT: A 178 PHE cc_start: 0.8153 (OUTLIER) cc_final: 0.6946 (m-80) REVERT: A 282 MET cc_start: 0.8546 (OUTLIER) cc_final: 0.8171 (mtm) REVERT: A 445 LEU cc_start: 0.7089 (mt) cc_final: 0.6822 (mt) REVERT: A 606 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.7322 (mp0) outliers start: 26 outliers final: 18 residues processed: 91 average time/residue: 0.1781 time to fit residues: 21.6873 Evaluate side-chains 92 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 71 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 51 CYS Chi-restraints excluded: chain A residue 178 PHE Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 348 ARG Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 515 MET Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain A residue 596 ILE Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain A residue 650 MET Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 701 MET Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 737 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 59 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 18 optimal weight: 0.0670 chunk 67 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 overall best weight: 0.9320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 472 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.162049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.122053 restraints weight = 6818.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.124309 restraints weight = 5011.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.125947 restraints weight = 4131.185| |-----------------------------------------------------------------------------| r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.3453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6058 Z= 0.147 Angle : 0.566 7.588 8241 Z= 0.279 Chirality : 0.039 0.135 932 Planarity : 0.004 0.041 974 Dihedral : 8.175 70.697 1307 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 4.46 % Allowed : 16.53 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.22 (0.33), residues: 679 helix: 1.75 (0.25), residues: 450 sheet: 0.34 (1.65), residues: 10 loop : -1.21 (0.42), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 431 HIS 0.003 0.001 HIS A 516 PHE 0.018 0.001 PHE A 549 TYR 0.017 0.001 TYR A 496 ARG 0.002 0.000 ARG A 71 Details of bonding type rmsd hydrogen bonds : bond 0.04749 ( 349) hydrogen bonds : angle 4.27089 ( 987) SS BOND : bond 0.00258 ( 1) SS BOND : angle 0.79033 ( 2) covalent geometry : bond 0.00346 ( 6057) covalent geometry : angle 0.56560 ( 8239) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 73 time to evaluate : 0.657 Fit side-chains revert: symmetry clash REVERT: A 282 MET cc_start: 0.8526 (mtm) cc_final: 0.8182 (mtm) REVERT: A 383 LYS cc_start: 0.7428 (ptpt) cc_final: 0.6564 (mttp) REVERT: A 445 LEU cc_start: 0.7107 (mt) cc_final: 0.6824 (mt) outliers start: 27 outliers final: 23 residues processed: 88 average time/residue: 0.1689 time to fit residues: 20.2424 Evaluate side-chains 97 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 74 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 51 CYS Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 348 ARG Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 411 TYR Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 515 MET Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain A residue 593 MET Chi-restraints excluded: chain A residue 596 ILE Chi-restraints excluded: chain A residue 650 MET Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 701 MET Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 737 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 57 optimal weight: 0.7980 chunk 41 optimal weight: 0.3980 chunk 27 optimal weight: 6.9990 chunk 60 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 32 optimal weight: 4.9990 chunk 10 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3770 r_free = 0.3770 target = 0.163035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.125518 restraints weight = 6891.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.127441 restraints weight = 5063.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.127601 restraints weight = 3907.613| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.3605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6058 Z= 0.124 Angle : 0.540 8.064 8241 Z= 0.265 Chirality : 0.038 0.133 932 Planarity : 0.003 0.041 974 Dihedral : 8.033 72.300 1307 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 4.46 % Allowed : 16.86 % Favored : 78.68 % 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: 1.41 (0.33), residues: 679 helix: 1.89 (0.25), residues: 450 sheet: 0.18 (1.61), residues: 10 loop : -1.07 (0.42), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 420 HIS 0.002 0.001 HIS A 656 PHE 0.015 0.001 PHE A 549 TYR 0.017 0.001 TYR A 496 ARG 0.001 0.000 ARG A 556 Details of bonding type rmsd hydrogen bonds : bond 0.04459 ( 349) hydrogen bonds : angle 4.17282 ( 987) SS BOND : bond 0.00204 ( 1) SS BOND : angle 0.76274 ( 2) covalent geometry : bond 0.00280 ( 6057) covalent geometry : angle 0.54000 ( 8239) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 76 time to evaluate : 0.614 Fit side-chains revert: symmetry clash REVERT: A 178 PHE cc_start: 0.8112 (OUTLIER) cc_final: 0.6964 (m-80) REVERT: A 383 LYS cc_start: 0.7246 (ptpt) cc_final: 0.6414 (mttp) REVERT: A 445 LEU cc_start: 0.7087 (mt) cc_final: 0.6815 (mt) REVERT: A 583 MET cc_start: 0.7615 (mmm) cc_final: 0.7335 (mmt) REVERT: A 606 GLU cc_start: 0.7534 (mp0) cc_final: 0.7267 (mp0) outliers start: 27 outliers final: 22 residues processed: 93 average time/residue: 0.1646 time to fit residues: 20.8769 Evaluate side-chains 96 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 73 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 51 CYS Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 178 PHE Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 348 ARG Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 411 TYR Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 515 MET Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain A residue 596 ILE Chi-restraints excluded: chain A residue 650 MET Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 701 MET Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 737 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 31 optimal weight: 0.0370 chunk 4 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 41 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 39 optimal weight: 5.9990 overall best weight: 0.7260 ------------------------------------------------------------------------------- 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 = 0.3775 r_free = 0.3775 target = 0.163272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.123378 restraints weight = 6832.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.125682 restraints weight = 4945.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.127275 restraints weight = 4070.406| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.3669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6058 Z= 0.128 Angle : 0.543 7.105 8241 Z= 0.266 Chirality : 0.038 0.137 932 Planarity : 0.004 0.041 974 Dihedral : 7.965 72.467 1307 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 4.46 % Allowed : 17.36 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.43 (0.33), residues: 679 helix: 1.91 (0.25), residues: 451 sheet: 0.07 (1.59), residues: 10 loop : -1.10 (0.42), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 420 HIS 0.003 0.001 HIS A 516 PHE 0.014 0.001 PHE A 549 TYR 0.016 0.001 TYR A 496 ARG 0.002 0.000 ARG A 556 Details of bonding type rmsd hydrogen bonds : bond 0.04502 ( 349) hydrogen bonds : angle 4.15620 ( 987) SS BOND : bond 0.00200 ( 1) SS BOND : angle 0.68729 ( 2) covalent geometry : bond 0.00294 ( 6057) covalent geometry : angle 0.54261 ( 8239) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 74 time to evaluate : 0.635 Fit side-chains revert: symmetry clash REVERT: A 178 PHE cc_start: 0.8113 (OUTLIER) cc_final: 0.6988 (m-80) REVERT: A 348 ARG cc_start: 0.7620 (OUTLIER) cc_final: 0.6881 (ttm110) REVERT: A 383 LYS cc_start: 0.7079 (ptpt) cc_final: 0.6434 (mttp) REVERT: A 445 LEU cc_start: 0.7088 (mt) cc_final: 0.6803 (mt) REVERT: A 583 MET cc_start: 0.7588 (mmm) cc_final: 0.7305 (mmt) REVERT: A 628 MET cc_start: 0.7558 (mmp) cc_final: 0.7351 (mmp) outliers start: 27 outliers final: 21 residues processed: 90 average time/residue: 0.1583 time to fit residues: 19.6208 Evaluate side-chains 97 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 74 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 51 CYS Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 178 PHE Chi-restraints excluded: chain A residue 348 ARG Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 411 TYR Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 515 MET Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain A residue 593 MET Chi-restraints excluded: chain A residue 596 ILE Chi-restraints excluded: chain A residue 650 MET Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 701 MET Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 737 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 28 optimal weight: 6.9990 chunk 7 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 29 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 58 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3801 r_free = 0.3801 target = 0.164753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.123811 restraints weight = 6962.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.126402 restraints weight = 4903.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.128095 restraints weight = 3963.024| |-----------------------------------------------------------------------------| r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.3749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6058 Z= 0.134 Angle : 0.548 7.250 8241 Z= 0.268 Chirality : 0.038 0.136 932 Planarity : 0.003 0.041 974 Dihedral : 7.964 73.304 1307 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 4.63 % Allowed : 17.02 % Favored : 78.35 % 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: 1.40 (0.33), residues: 679 helix: 1.87 (0.25), residues: 451 sheet: 0.04 (1.59), residues: 10 loop : -1.07 (0.42), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 420 HIS 0.003 0.001 HIS A 516 PHE 0.014 0.001 PHE A 549 TYR 0.016 0.001 TYR A 496 ARG 0.002 0.000 ARG A 556 Details of bonding type rmsd hydrogen bonds : bond 0.04551 ( 349) hydrogen bonds : angle 4.15474 ( 987) SS BOND : bond 0.00213 ( 1) SS BOND : angle 0.69771 ( 2) covalent geometry : bond 0.00312 ( 6057) covalent geometry : angle 0.54788 ( 8239) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 73 time to evaluate : 0.623 Fit side-chains revert: symmetry clash REVERT: A 178 PHE cc_start: 0.8110 (OUTLIER) cc_final: 0.6991 (m-80) REVERT: A 348 ARG cc_start: 0.7621 (OUTLIER) cc_final: 0.6923 (ttm110) REVERT: A 383 LYS cc_start: 0.7059 (ptpt) cc_final: 0.6450 (mttp) REVERT: A 445 LEU cc_start: 0.7072 (mt) cc_final: 0.6777 (mt) REVERT: A 583 MET cc_start: 0.7556 (mmm) cc_final: 0.7269 (mmt) REVERT: A 628 MET cc_start: 0.7581 (mmp) cc_final: 0.7374 (mmp) outliers start: 28 outliers final: 21 residues processed: 91 average time/residue: 0.1459 time to fit residues: 18.5595 Evaluate side-chains 96 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 73 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 51 CYS Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 178 PHE Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 348 ARG Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 411 TYR Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 496 TYR Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 515 MET Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain A residue 650 MET Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 701 MET Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 737 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 0 optimal weight: 5.9990 chunk 64 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 30 optimal weight: 0.3980 chunk 33 optimal weight: 8.9990 chunk 43 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.3778 r_free = 0.3778 target = 0.163467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.123283 restraints weight = 6939.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.125677 restraints weight = 5001.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.127163 restraints weight = 4116.141| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.3817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6058 Z= 0.130 Angle : 0.548 7.462 8241 Z= 0.268 Chirality : 0.038 0.130 932 Planarity : 0.003 0.041 974 Dihedral : 7.897 73.298 1307 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.80 % Allowed : 18.02 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.45 (0.33), residues: 679 helix: 1.93 (0.25), residues: 451 sheet: 0.01 (1.58), residues: 10 loop : -1.10 (0.41), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 420 HIS 0.002 0.001 HIS A 516 PHE 0.014 0.001 PHE A 549 TYR 0.015 0.001 TYR A 496 ARG 0.002 0.000 ARG A 556 Details of bonding type rmsd hydrogen bonds : bond 0.04491 ( 349) hydrogen bonds : angle 4.12733 ( 987) SS BOND : bond 0.00207 ( 1) SS BOND : angle 0.66017 ( 2) covalent geometry : bond 0.00300 ( 6057) covalent geometry : angle 0.54758 ( 8239) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 73 time to evaluate : 0.553 Fit side-chains revert: symmetry clash REVERT: A 178 PHE cc_start: 0.8110 (OUTLIER) cc_final: 0.6997 (m-80) REVERT: A 348 ARG cc_start: 0.7590 (OUTLIER) cc_final: 0.6888 (ttm110) REVERT: A 383 LYS cc_start: 0.7007 (ptpt) cc_final: 0.6340 (mttp) REVERT: A 445 LEU cc_start: 0.7064 (mt) cc_final: 0.6780 (mt) REVERT: A 583 MET cc_start: 0.7560 (mmm) cc_final: 0.7282 (mmt) outliers start: 23 outliers final: 19 residues processed: 88 average time/residue: 0.1561 time to fit residues: 18.9347 Evaluate side-chains 92 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 71 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 51 CYS Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 178 PHE Chi-restraints excluded: chain A residue 348 ARG Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 411 TYR Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 515 MET Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain A residue 650 MET Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 701 MET Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 737 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 28 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 20 optimal weight: 0.0040 chunk 43 optimal weight: 2.9990 chunk 54 optimal weight: 7.9990 chunk 51 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 17 optimal weight: 0.3980 chunk 42 optimal weight: 0.8980 overall best weight: 0.5992 ------------------------------------------------------------------------------- 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 = 0.3783 r_free = 0.3783 target = 0.164209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.124529 restraints weight = 6953.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.126885 restraints weight = 5057.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.128522 restraints weight = 4135.405| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.3992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6058 Z= 0.118 Angle : 0.532 7.614 8241 Z= 0.261 Chirality : 0.038 0.134 932 Planarity : 0.003 0.041 974 Dihedral : 7.679 74.439 1307 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.47 % Allowed : 18.35 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.53 (0.33), residues: 679 helix: 2.00 (0.25), residues: 451 sheet: -0.06 (1.57), residues: 10 loop : -1.08 (0.41), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 420 HIS 0.002 0.001 HIS A 259 PHE 0.013 0.001 PHE A 549 TYR 0.015 0.001 TYR A 496 ARG 0.002 0.000 ARG A 556 Details of bonding type rmsd hydrogen bonds : bond 0.04269 ( 349) hydrogen bonds : angle 4.06027 ( 987) SS BOND : bond 0.00162 ( 1) SS BOND : angle 0.58465 ( 2) covalent geometry : bond 0.00267 ( 6057) covalent geometry : angle 0.53197 ( 8239) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2134.08 seconds wall clock time: 38 minutes 19.67 seconds (2299.67 seconds total)