Starting phenix.real_space_refine on Fri Oct 10 13:21:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wg4_37502/10_2025/8wg4_37502.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wg4_37502/10_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 { model { file = "/net/cci-nas-00/data/ceres_data/8wg4_37502/10_2025/8wg4_37502.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wg4_37502/10_2025/8wg4_37502.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wg4_37502/10_2025/8wg4_37502.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wg4_37502/10_2025/8wg4_37502.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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: 1.47, per 1000 atoms: 0.25 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: 0.53 Conformation dependent library (CDL) restraints added in 309.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.14 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: 0.84 Time building geometry restraints manager: 0.70 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: 0.330 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: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.020 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.740 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.015 0.003 ARG A 225 TYR 0.100 0.009 TYR A 637 PHE 0.035 0.007 PHE A 154 TRP 0.030 0.007 TRP A 206 HIS 0.025 0.005 HIS A 226 Details of bonding type rmsd covalent geometry : bond 0.00858 ( 6057) covalent geometry : angle 1.36035 ( 8239) SS BOND : bond 0.00473 ( 1) SS BOND : angle 3.97824 ( 2) hydrogen bonds : bond 0.21151 ( 349) hydrogen bonds : angle 8.35347 ( 987) *********************** 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 : 0.234 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: 0.0782 time to fit residues: 10.9944 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 : 0.186 ------------------------------------------------------------------------------- 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 49 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 0.0870 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 27 optimal weight: 6.9990 overall best weight: 0.6960 ------------------------------------------------------------------------------- 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 = 0.3770 r_free = 0.3770 target = 0.163043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.122490 restraints weight = 6877.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.124976 restraints weight = 4982.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.126621 restraints weight = 4075.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.127559 restraints weight = 3597.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.127688 restraints weight = 3355.025| |-----------------------------------------------------------------------------| r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.2149 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= 0.153 Angle : 0.661 8.853 8241 Z= 0.338 Chirality : 0.041 0.143 932 Planarity : 0.004 0.035 974 Dihedral : 10.033 80.279 1313 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.98 % Allowed : 10.41 % Favored : 87.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.08 (0.32), residues: 679 helix: 0.64 (0.24), residues: 446 sheet: 2.38 (1.91), residues: 10 loop : -1.15 (0.42), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 293 TYR 0.017 0.002 TYR A 637 PHE 0.022 0.002 PHE A 298 TRP 0.010 0.001 TRP A 128 HIS 0.003 0.001 HIS A 226 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 6057) covalent geometry : angle 0.66014 ( 8239) SS BOND : bond 0.00038 ( 1) SS BOND : angle 1.64319 ( 2) hydrogen bonds : bond 0.05596 ( 349) hydrogen bonds : angle 4.91959 ( 987) *********************** 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 97 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 85 time to evaluate : 0.202 Fit side-chains REVERT: A 205 LEU cc_start: 0.7331 (OUTLIER) cc_final: 0.6497 (tt) REVERT: A 237 LEU cc_start: 0.7441 (OUTLIER) cc_final: 0.7178 (tp) REVERT: A 292 GLU cc_start: 0.7342 (tt0) cc_final: 0.7031 (tt0) REVERT: A 445 LEU cc_start: 0.7184 (mt) cc_final: 0.6960 (mt) REVERT: A 609 ASN cc_start: 0.8179 (t0) cc_final: 0.7386 (t0) outliers start: 12 outliers final: 7 residues processed: 92 average time/residue: 0.0737 time to fit residues: 9.0658 Evaluate side-chains 80 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 0.220 ------------------------------------------------------------------------------- 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 33 optimal weight: 8.9990 chunk 57 optimal weight: 0.6980 chunk 23 optimal weight: 7.9990 chunk 50 optimal weight: 1.9990 chunk 53 optimal weight: 7.9990 chunk 46 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 40 optimal weight: 7.9990 chunk 19 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 = 0.3968 r_free = 0.3968 target = 0.177535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.135270 restraints weight = 6913.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.138352 restraints weight = 4673.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.140107 restraints weight = 3713.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.140942 restraints weight = 3250.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.140942 restraints weight = 3044.131| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 6058 Z= 0.191 Angle : 0.655 8.478 8241 Z= 0.330 Chirality : 0.042 0.139 932 Planarity : 0.004 0.038 974 Dihedral : 8.953 59.781 1311 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.31 % Allowed : 13.72 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.47 (0.32), residues: 679 helix: 1.13 (0.24), residues: 445 sheet: 1.20 (1.79), residues: 10 loop : -1.39 (0.40), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 231 TYR 0.016 0.002 TYR A 264 PHE 0.015 0.002 PHE A 243 TRP 0.008 0.001 TRP A 431 HIS 0.004 0.001 HIS A 157 Details of bonding type rmsd covalent geometry : bond 0.00454 ( 6057) covalent geometry : angle 0.65464 ( 8239) SS BOND : bond 0.00369 ( 1) SS BOND : angle 1.24373 ( 2) hydrogen bonds : bond 0.05625 ( 349) hydrogen bonds : angle 4.71572 ( 987) *********************** 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 90 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 70 time to evaluate : 0.244 Fit side-chains revert: symmetry clash REVERT: A 181 ASP cc_start: 0.6834 (t0) cc_final: 0.6602 (t0) REVERT: A 310 MET cc_start: 0.6629 (mpp) cc_final: 0.6389 (mmt) REVERT: A 445 LEU cc_start: 0.7139 (mt) cc_final: 0.6883 (mt) REVERT: A 628 MET cc_start: 0.7353 (mmm) cc_final: 0.7023 (mmp) outliers start: 20 outliers final: 14 residues processed: 83 average time/residue: 0.0799 time to fit residues: 8.8447 Evaluate side-chains 77 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 63 time to evaluate : 0.259 ------------------------------------------------------------------------------- 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 281 LEU Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 535 SER 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 12 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 66 optimal weight: 10.0000 chunk 46 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 2 optimal weight: 0.0570 chunk 20 optimal weight: 1.9990 chunk 67 optimal weight: 0.4980 chunk 22 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 26 optimal weight: 9.9990 overall best weight: 1.0702 ------------------------------------------------------------------------------- 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 = 0.3761 r_free = 0.3761 target = 0.161742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.121368 restraints weight = 6910.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.123650 restraints weight = 5080.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.124892 restraints weight = 4207.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.125947 restraints weight = 3782.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.126414 restraints weight = 3528.470| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.3083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6058 Z= 0.162 Angle : 0.600 8.178 8241 Z= 0.299 Chirality : 0.040 0.137 932 Planarity : 0.004 0.039 974 Dihedral : 8.516 64.236 1307 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 4.46 % Allowed : 13.72 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.71 (0.32), residues: 679 helix: 1.35 (0.24), residues: 451 sheet: 0.86 (1.71), residues: 10 loop : -1.43 (0.41), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 293 TYR 0.022 0.002 TYR A 496 PHE 0.014 0.002 PHE A 154 TRP 0.007 0.001 TRP A 67 HIS 0.003 0.001 HIS A 157 Details of bonding type rmsd covalent geometry : bond 0.00383 ( 6057) covalent geometry : angle 0.60028 ( 8239) SS BOND : bond 0.00277 ( 1) SS BOND : angle 1.09362 ( 2) hydrogen bonds : bond 0.05077 ( 349) hydrogen bonds : angle 4.48474 ( 987) *********************** 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 97 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 70 time to evaluate : 0.205 Fit side-chains revert: symmetry clash REVERT: A 178 PHE cc_start: 0.8140 (OUTLIER) cc_final: 0.6919 (m-80) REVERT: A 335 TYR cc_start: 0.7433 (t80) cc_final: 0.7036 (t80) REVERT: A 351 LYS cc_start: 0.7251 (tttt) cc_final: 0.7020 (tptt) REVERT: A 445 LEU cc_start: 0.7119 (mt) cc_final: 0.6843 (mt) REVERT: A 606 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.7142 (mp0) REVERT: A 628 MET cc_start: 0.7910 (mmm) cc_final: 0.7314 (mmp) outliers start: 27 outliers final: 19 residues processed: 85 average time/residue: 0.0712 time to fit residues: 8.1760 Evaluate side-chains 88 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 67 time to evaluate : 0.206 ------------------------------------------------------------------------------- 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 178 PHE Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 195 ILE 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 66 optimal weight: 9.9990 chunk 1 optimal weight: 0.0670 chunk 50 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 46 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- 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 = 0.3820 r_free = 0.3820 target = 0.166344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.125150 restraints weight = 7007.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.127842 restraints weight = 4889.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.129407 restraints weight = 3929.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.130095 restraints weight = 3461.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.131057 restraints weight = 3247.746| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.3380 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= 0.125 Angle : 0.544 7.775 8241 Z= 0.270 Chirality : 0.038 0.135 932 Planarity : 0.004 0.041 974 Dihedral : 8.180 67.120 1307 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 4.63 % Allowed : 14.71 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.08 (0.33), residues: 679 helix: 1.68 (0.25), residues: 450 sheet: 0.48 (1.65), residues: 10 loop : -1.35 (0.41), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 556 TYR 0.019 0.001 TYR A 496 PHE 0.014 0.001 PHE A 549 TRP 0.004 0.001 TRP A 128 HIS 0.002 0.001 HIS A 157 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 6057) covalent geometry : angle 0.54357 ( 8239) SS BOND : bond 0.00199 ( 1) SS BOND : angle 1.17825 ( 2) hydrogen bonds : bond 0.04561 ( 349) hydrogen bonds : angle 4.28390 ( 987) *********************** 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 108 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 80 time to evaluate : 0.155 Fit side-chains REVERT: A 178 PHE cc_start: 0.8138 (OUTLIER) cc_final: 0.6929 (m-80) REVERT: A 181 ASP cc_start: 0.6728 (t0) cc_final: 0.6517 (t70) REVERT: A 292 GLU cc_start: 0.7289 (tt0) cc_final: 0.6557 (tt0) REVERT: A 335 TYR cc_start: 0.7386 (t80) cc_final: 0.7127 (t80) REVERT: A 351 LYS cc_start: 0.7199 (tttt) cc_final: 0.6949 (tptt) REVERT: A 445 LEU cc_start: 0.7034 (mt) cc_final: 0.6777 (mt) REVERT: A 606 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.7165 (mp0) outliers start: 28 outliers final: 19 residues processed: 97 average time/residue: 0.0704 time to fit residues: 9.1343 Evaluate side-chains 94 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 73 time to evaluate : 0.216 ------------------------------------------------------------------------------- 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 311 ILE Chi-restraints excluded: chain A residue 348 ARG Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 513 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 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 38 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 24 optimal weight: 8.9990 chunk 15 optimal weight: 0.9990 chunk 26 optimal weight: 10.0000 chunk 2 optimal weight: 0.0050 chunk 32 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 overall best weight: 1.1800 ------------------------------------------------------------------------------- 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 = 0.3775 r_free = 0.3775 target = 0.162399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.121669 restraints weight = 6934.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.124117 restraints weight = 4974.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.125553 restraints weight = 4054.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.126626 restraints weight = 3601.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.127157 restraints weight = 3352.024| |-----------------------------------------------------------------------------| r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.3423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 6058 Z= 0.170 Angle : 0.590 7.324 8241 Z= 0.293 Chirality : 0.040 0.136 932 Planarity : 0.004 0.040 974 Dihedral : 8.301 69.959 1307 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 5.62 % Allowed : 15.54 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.03 (0.33), residues: 679 helix: 1.64 (0.25), residues: 450 sheet: 0.48 (1.68), residues: 10 loop : -1.37 (0.41), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 556 TYR 0.016 0.001 TYR A 496 PHE 0.014 0.002 PHE A 243 TRP 0.007 0.001 TRP A 431 HIS 0.004 0.001 HIS A 157 Details of bonding type rmsd covalent geometry : bond 0.00409 ( 6057) covalent geometry : angle 0.59035 ( 8239) SS BOND : bond 0.00311 ( 1) SS BOND : angle 0.89042 ( 2) hydrogen bonds : bond 0.05063 ( 349) hydrogen bonds : angle 4.35560 ( 987) *********************** 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 107 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 73 time to evaluate : 0.152 Fit side-chains revert: symmetry clash REVERT: A 178 PHE cc_start: 0.8109 (OUTLIER) cc_final: 0.6967 (m-80) REVERT: A 351 LYS cc_start: 0.7197 (tttt) cc_final: 0.6974 (tptt) REVERT: A 383 LYS cc_start: 0.7438 (ptpt) cc_final: 0.6571 (mttp) REVERT: A 445 LEU cc_start: 0.7094 (mt) cc_final: 0.6810 (mt) REVERT: A 606 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.7352 (mp0) REVERT: A 628 MET cc_start: 0.7530 (mmp) cc_final: 0.7312 (mmp) outliers start: 34 outliers final: 23 residues processed: 94 average time/residue: 0.0666 time to fit residues: 8.5550 Evaluate side-chains 97 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 72 time to evaluate : 0.201 ------------------------------------------------------------------------------- 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 179 SER 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 482 LEU 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 33 optimal weight: 6.9990 chunk 42 optimal weight: 0.7980 chunk 47 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 40 optimal weight: 10.0000 chunk 35 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 66 optimal weight: 10.0000 chunk 55 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 5 optimal weight: 4.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 = 0.3758 r_free = 0.3758 target = 0.161473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.123505 restraints weight = 6973.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.124011 restraints weight = 5796.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.124130 restraints weight = 4750.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.124366 restraints weight = 4804.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.124911 restraints weight = 4392.670| |-----------------------------------------------------------------------------| r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.3546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 6058 Z= 0.156 Angle : 0.579 7.628 8241 Z= 0.285 Chirality : 0.040 0.135 932 Planarity : 0.004 0.040 974 Dihedral : 8.202 73.425 1307 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 5.62 % Allowed : 15.70 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.13 (0.33), residues: 679 helix: 1.70 (0.25), residues: 450 sheet: 0.33 (1.65), residues: 10 loop : -1.29 (0.41), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 556 TYR 0.016 0.001 TYR A 496 PHE 0.015 0.001 PHE A 154 TRP 0.006 0.001 TRP A 431 HIS 0.003 0.001 HIS A 157 Details of bonding type rmsd covalent geometry : bond 0.00372 ( 6057) covalent geometry : angle 0.57886 ( 8239) SS BOND : bond 0.00283 ( 1) SS BOND : angle 0.81183 ( 2) hydrogen bonds : bond 0.04895 ( 349) hydrogen bonds : angle 4.29744 ( 987) *********************** 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 106 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 72 time to evaluate : 0.213 Fit side-chains revert: symmetry clash REVERT: A 178 PHE cc_start: 0.8085 (OUTLIER) cc_final: 0.6964 (m-80) REVERT: A 351 LYS cc_start: 0.7169 (tttt) cc_final: 0.6932 (tptt) REVERT: A 383 LYS cc_start: 0.7261 (ptpt) cc_final: 0.6411 (mttp) REVERT: A 445 LEU cc_start: 0.7132 (mt) cc_final: 0.6849 (mt) REVERT: A 583 MET cc_start: 0.7618 (mmm) cc_final: 0.7246 (mmt) REVERT: A 606 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.7166 (mp0) outliers start: 34 outliers final: 29 residues processed: 95 average time/residue: 0.0663 time to fit residues: 8.7518 Evaluate side-chains 101 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 70 time to evaluate : 0.205 ------------------------------------------------------------------------------- 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 158 ILE Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 178 PHE Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 210 SER 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 482 LEU 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 576 SER Chi-restraints excluded: chain A residue 596 ILE Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain A residue 617 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 727 HIS 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 3 optimal weight: 1.9990 chunk 25 optimal weight: 0.0270 chunk 36 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 27 optimal weight: 6.9990 chunk 66 optimal weight: 9.9990 chunk 65 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 52 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 1 optimal weight: 4.9990 overall best weight: 1.1442 ------------------------------------------------------------------------------- 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 = 0.3755 r_free = 0.3755 target = 0.161028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.120398 restraints weight = 6951.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.122724 restraints weight = 5097.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.124209 restraints weight = 4216.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.125154 restraints weight = 3751.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 14)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.125445 restraints weight = 3519.710| |-----------------------------------------------------------------------------| r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.3582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6058 Z= 0.165 Angle : 0.585 7.450 8241 Z= 0.289 Chirality : 0.040 0.133 932 Planarity : 0.004 0.040 974 Dihedral : 8.074 72.541 1307 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 5.79 % Allowed : 15.70 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.10 (0.33), residues: 679 helix: 1.70 (0.25), residues: 449 sheet: 0.37 (1.64), residues: 10 loop : -1.33 (0.41), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 556 TYR 0.015 0.001 TYR A 496 PHE 0.016 0.002 PHE A 549 TRP 0.006 0.001 TRP A 431 HIS 0.004 0.001 HIS A 157 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 6057) covalent geometry : angle 0.58526 ( 8239) SS BOND : bond 0.00261 ( 1) SS BOND : angle 0.79250 ( 2) hydrogen bonds : bond 0.05022 ( 349) hydrogen bonds : angle 4.33200 ( 987) *********************** 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 108 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 73 time to evaluate : 0.271 Fit side-chains revert: symmetry clash REVERT: A 178 PHE cc_start: 0.8077 (OUTLIER) cc_final: 0.6979 (m-80) REVERT: A 351 LYS cc_start: 0.7212 (tttt) cc_final: 0.6993 (tptt) REVERT: A 383 LYS cc_start: 0.7331 (ptpt) cc_final: 0.6542 (mttp) REVERT: A 445 LEU cc_start: 0.7108 (mt) cc_final: 0.6820 (mt) REVERT: A 583 MET cc_start: 0.7565 (mmm) cc_final: 0.7282 (mmt) REVERT: A 606 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.7186 (mp0) outliers start: 35 outliers final: 27 residues processed: 95 average time/residue: 0.0664 time to fit residues: 8.7347 Evaluate side-chains 101 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 72 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 31 THR 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 158 ILE Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 178 PHE Chi-restraints excluded: chain A residue 210 SER 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 482 LEU 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 523 ILE Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain A residue 576 SER Chi-restraints excluded: chain A residue 593 MET 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 20 optimal weight: 0.0670 chunk 67 optimal weight: 0.0030 chunk 54 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 55 optimal weight: 0.0470 chunk 52 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 7 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 overall best weight: 0.3626 ------------------------------------------------------------------------------- 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 = 0.3817 r_free = 0.3817 target = 0.166433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.126088 restraints weight = 6977.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.128651 restraints weight = 4848.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.130374 restraints weight = 3919.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.131330 restraints weight = 3464.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.132009 restraints weight = 3209.751| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.3894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6058 Z= 0.110 Angle : 0.523 7.939 8241 Z= 0.257 Chirality : 0.037 0.135 932 Planarity : 0.003 0.039 974 Dihedral : 7.574 74.691 1307 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.64 % Allowed : 18.02 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.44 (0.33), residues: 679 helix: 1.98 (0.25), residues: 451 sheet: 0.05 (1.57), residues: 10 loop : -1.24 (0.41), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 71 TYR 0.016 0.001 TYR A 496 PHE 0.014 0.001 PHE A 549 TRP 0.004 0.001 TRP A 128 HIS 0.002 0.001 HIS A 422 Details of bonding type rmsd covalent geometry : bond 0.00235 ( 6057) covalent geometry : angle 0.52288 ( 8239) SS BOND : bond 0.00128 ( 1) SS BOND : angle 0.72082 ( 2) hydrogen bonds : bond 0.04141 ( 349) hydrogen bonds : angle 4.10282 ( 987) *********************** 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 94 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 72 time to evaluate : 0.215 Fit side-chains revert: symmetry clash REVERT: A 348 ARG cc_start: 0.7232 (OUTLIER) cc_final: 0.6557 (ttm110) REVERT: A 383 LYS cc_start: 0.7080 (ptpt) cc_final: 0.6472 (mttp) REVERT: A 445 LEU cc_start: 0.7062 (mt) cc_final: 0.6774 (mt) REVERT: A 583 MET cc_start: 0.7577 (mmm) cc_final: 0.7313 (mmt) REVERT: A 606 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.7100 (mp0) REVERT: A 628 MET cc_start: 0.7530 (mmp) cc_final: 0.7255 (mmp) outliers start: 22 outliers final: 13 residues processed: 86 average time/residue: 0.0634 time to fit residues: 7.6337 Evaluate side-chains 84 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 69 time to evaluate : 0.201 ------------------------------------------------------------------------------- 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 158 ILE Chi-restraints excluded: chain A residue 348 ARG Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 411 TYR Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 496 TYR 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 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 38 optimal weight: 5.9990 chunk 19 optimal weight: 0.1980 chunk 13 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 66 optimal weight: 9.9990 chunk 63 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 chunk 53 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3788 r_free = 0.3788 target = 0.163854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.124052 restraints weight = 6945.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.126337 restraints weight = 5071.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.127550 restraints weight = 4176.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.128547 restraints weight = 3753.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.129302 restraints weight = 3492.414| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.3851 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 : 0.540 7.555 8241 Z= 0.265 Chirality : 0.038 0.132 932 Planarity : 0.004 0.039 974 Dihedral : 7.643 73.768 1307 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.64 % Allowed : 18.02 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.43 (0.33), residues: 679 helix: 1.98 (0.25), residues: 450 sheet: 0.01 (1.58), residues: 10 loop : -1.26 (0.41), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 556 TYR 0.015 0.001 TYR A 336 PHE 0.014 0.001 PHE A 549 TRP 0.005 0.001 TRP A 420 HIS 0.003 0.001 HIS A 157 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 6057) covalent geometry : angle 0.53959 ( 8239) SS BOND : bond 0.00167 ( 1) SS BOND : angle 0.66377 ( 2) hydrogen bonds : bond 0.04463 ( 349) hydrogen bonds : angle 4.08380 ( 987) ********************** 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 92 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 70 time to evaluate : 0.211 Fit side-chains revert: symmetry clash REVERT: A 348 ARG cc_start: 0.7300 (OUTLIER) cc_final: 0.6613 (ttm110) REVERT: A 383 LYS cc_start: 0.7064 (ptpt) cc_final: 0.6395 (mttp) REVERT: A 445 LEU cc_start: 0.7088 (mt) cc_final: 0.6805 (mt) REVERT: A 583 MET cc_start: 0.7567 (mmm) cc_final: 0.7293 (mmt) REVERT: A 606 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.7094 (mp0) outliers start: 22 outliers final: 16 residues processed: 84 average time/residue: 0.0648 time to fit residues: 7.6421 Evaluate side-chains 88 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 70 time to evaluate : 0.288 ------------------------------------------------------------------------------- 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 158 ILE Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 348 ARG Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 411 TYR Chi-restraints excluded: chain A residue 482 LEU 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 532 LEU 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 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 1 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 23 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 35 optimal weight: 0.4980 chunk 64 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 739 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.161306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.123652 restraints weight = 6942.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.123909 restraints weight = 5764.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.123844 restraints weight = 4717.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.124132 restraints weight = 4633.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.124413 restraints weight = 4315.579| |-----------------------------------------------------------------------------| r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.3839 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= 0.150 Angle : 0.562 7.565 8241 Z= 0.277 Chirality : 0.039 0.138 932 Planarity : 0.004 0.039 974 Dihedral : 7.794 73.479 1307 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.97 % Allowed : 17.52 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.31 (0.33), residues: 679 helix: 1.90 (0.25), residues: 450 sheet: 0.00 (1.57), residues: 10 loop : -1.33 (0.40), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 556 TYR 0.016 0.001 TYR A 335 PHE 0.014 0.001 PHE A 549 TRP 0.006 0.001 TRP A 431 HIS 0.003 0.001 HIS A 157 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 6057) covalent geometry : angle 0.56186 ( 8239) SS BOND : bond 0.00225 ( 1) SS BOND : angle 0.70248 ( 2) hydrogen bonds : bond 0.04793 ( 349) hydrogen bonds : angle 4.17389 ( 987) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1049.97 seconds wall clock time: 18 minutes 51.87 seconds (1131.87 seconds total)