Starting phenix.real_space_refine on Thu Jul 24 10:37:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8q76_18205/07_2025/8q76_18205.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q76_18205/07_2025/8q76_18205.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8q76_18205/07_2025/8q76_18205.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q76_18205/07_2025/8q76_18205.map" model { file = "/net/cci-nas-00/data/ceres_data/8q76_18205/07_2025/8q76_18205.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q76_18205/07_2025/8q76_18205.cif" } resolution = 3.29 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= -0.002 sd= 0.047 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: 7 Type Number sf(0) Gaussians Mg 1 5.21 5 S 34 5.16 5 Be 1 3.05 5 C 3760 2.51 5 N 975 2.21 5 O 1095 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 5869 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 774, 5868 Classifications: {'peptide': 774} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 738} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.70, per 1000 atoms: 0.80 Number of scatterers: 5869 At special positions: 0 Unit cell: (81.536, 83.2, 136.448, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 34 16.00 Mg 1 11.99 F 3 9.00 O 1095 8.00 N 975 7.00 C 3760 6.00 Be 1 4.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.60 Conformation dependent library (CDL) restraints added in 947.4 milliseconds 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1430 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 7 sheets defined 51.9% alpha, 8.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'A' and resid 197 through 210 removed outlier: 3.738A pdb=" N ILE A 201 " --> pdb=" O SER A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 246 removed outlier: 4.356A pdb=" N LEU A 240 " --> pdb=" O GLY A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 296 removed outlier: 4.252A pdb=" N ALA A 267 " --> pdb=" O LYS A 263 " (cutoff:3.500A) Proline residue: A 289 - end of helix Processing helix chain 'A' and resid 305 through 309 removed outlier: 3.795A pdb=" N TYR A 309 " --> pdb=" O TRP A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 332 Proline residue: A 328 - end of helix Processing helix chain 'A' and resid 334 through 344 Processing helix chain 'A' and resid 354 through 377 removed outlier: 5.943A pdb=" N THR A 360 " --> pdb=" O VAL A 356 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N ASN A 361 " --> pdb=" O ALA A 357 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA A 362 " --> pdb=" O LEU A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 407 removed outlier: 4.146A pdb=" N SER A 389 " --> pdb=" O PHE A 385 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA A 390 " --> pdb=" O PHE A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 removed outlier: 3.703A pdb=" N THR A 418 " --> pdb=" O LEU A 414 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA A 421 " --> pdb=" O LEU A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 447 No H-bonds generated for 'chain 'A' and resid 445 through 447' Processing helix chain 'A' and resid 512 through 515 Processing helix chain 'A' and resid 516 through 530 Processing helix chain 'A' and resid 537 through 545 Processing helix chain 'A' and resid 546 through 567 Processing helix chain 'A' and resid 571 through 575 Processing helix chain 'A' and resid 580 through 596 removed outlier: 3.672A pdb=" N VAL A 592 " --> pdb=" O PHE A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 620 removed outlier: 5.654A pdb=" N VAL A 611 " --> pdb=" O THR A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 632 removed outlier: 3.858A pdb=" N LEU A 629 " --> pdb=" O GLY A 625 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 676 Processing helix chain 'A' and resid 680 through 697 Processing helix chain 'A' and resid 731 through 738 removed outlier: 3.637A pdb=" N PHE A 738 " --> pdb=" O LEU A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 744 through 748 Processing helix chain 'A' and resid 782 through 793 Processing helix chain 'A' and resid 804 through 816 Processing helix chain 'A' and resid 825 through 839 Processing helix chain 'A' and resid 849 through 851 No H-bonds generated for 'chain 'A' and resid 849 through 851' Processing helix chain 'A' and resid 852 through 859 Processing helix chain 'A' and resid 869 through 876 Processing helix chain 'A' and resid 885 through 900 removed outlier: 3.870A pdb=" N ILE A 889 " --> pdb=" O LEU A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 902 through 922 removed outlier: 4.266A pdb=" N TYR A 912 " --> pdb=" O TRP A 908 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N ASN A 913 " --> pdb=" O ALA A 909 " (cutoff:3.500A) Proline residue: A 918 - end of helix Processing helix chain 'A' and resid 934 through 939 removed outlier: 4.002A pdb=" N GLY A 938 " --> pdb=" O PRO A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 940 through 948 Processing sheet with id=AA1, first strand: chain 'A' and resid 216 through 220 removed outlier: 3.625A pdb=" N ASP A 220 " --> pdb=" O THR A 225 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR A 225 " --> pdb=" O ASP A 220 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASN A 255 " --> pdb=" O GLU A 193 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 424 through 426 Processing sheet with id=AA3, first strand: chain 'A' and resid 452 through 453 removed outlier: 7.460A pdb=" N ILE A 506 " --> pdb=" O ILE A 468 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 472 through 474 Processing sheet with id=AA5, first strand: chain 'A' and resid 621 through 623 removed outlier: 6.165A pdb=" N GLY A 862 " --> pdb=" O ILE A 878 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N LEU A 880 " --> pdb=" O GLY A 862 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ALA A 864 " --> pdb=" O LEU A 880 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL A 861 " --> pdb=" O VAL A 843 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N MET A 845 " --> pdb=" O VAL A 861 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ALA A 637 " --> pdb=" O ALA A 844 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N VAL A 846 " --> pdb=" O ALA A 637 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ILE A 639 " --> pdb=" O VAL A 846 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N ILE A 638 " --> pdb=" O ILE A 798 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N VAL A 800 " --> pdb=" O ILE A 638 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N PHE A 640 " --> pdb=" O VAL A 800 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N SER A 797 " --> pdb=" O THR A 819 " (cutoff:3.500A) removed outlier: 8.886A pdb=" N PHE A 821 " --> pdb=" O SER A 797 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N MET A 799 " --> pdb=" O PHE A 821 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 652 through 654 Processing sheet with id=AA7, first strand: chain 'A' and resid 707 through 708 291 hydrogen bonds defined for protein. 834 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.04 Time building geometry restraints manager: 1.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1098 1.33 - 1.45: 1356 1.45 - 1.57: 3471 1.57 - 1.69: 1 1.69 - 1.81: 54 Bond restraints: 5980 Sorted by residual: bond pdb=" OD1 BFD A 641 " pdb="BE BFD A 641 " ideal model delta sigma weight residual 1.737 1.533 0.204 2.00e-02 2.50e+03 1.04e+02 bond pdb=" CA ALA A 637 " pdb=" C ALA A 637 " ideal model delta sigma weight residual 1.522 1.458 0.063 1.21e-02 6.83e+03 2.74e+01 bond pdb=" N ILE A 638 " pdb=" CA ILE A 638 " ideal model delta sigma weight residual 1.457 1.400 0.057 1.14e-02 7.69e+03 2.50e+01 bond pdb=" N ALA A 637 " pdb=" CA ALA A 637 " ideal model delta sigma weight residual 1.454 1.411 0.044 1.27e-02 6.20e+03 1.19e+01 bond pdb=" CA ILE A 638 " pdb=" C ILE A 638 " ideal model delta sigma weight residual 1.522 1.483 0.039 1.20e-02 6.94e+03 1.07e+01 ... (remaining 5975 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.93: 8075 3.93 - 7.87: 42 7.87 - 11.80: 5 11.80 - 15.73: 0 15.73 - 19.67: 2 Bond angle restraints: 8124 Sorted by residual: angle pdb=" O BFD A 641 " pdb=" C BFD A 641 " pdb=" N LYS A 642 " ideal model delta sigma weight residual 123.00 103.33 19.67 1.60e+00 3.91e-01 1.51e+02 angle pdb=" CA BFD A 641 " pdb=" C BFD A 641 " pdb=" N LYS A 642 " ideal model delta sigma weight residual 116.20 134.22 -18.02 2.00e+00 2.50e-01 8.12e+01 angle pdb=" C PHE A 640 " pdb=" N BFD A 641 " pdb=" CA BFD A 641 " ideal model delta sigma weight residual 121.70 111.61 10.09 1.80e+00 3.09e-01 3.15e+01 angle pdb=" N GLY A 748 " pdb=" CA GLY A 748 " pdb=" C GLY A 748 " ideal model delta sigma weight residual 113.18 123.41 -10.23 2.37e+00 1.78e-01 1.86e+01 angle pdb=" C LYS A 636 " pdb=" N ALA A 637 " pdb=" CA ALA A 637 " ideal model delta sigma weight residual 122.62 117.18 5.44 1.56e+00 4.11e-01 1.21e+01 ... (remaining 8119 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.92: 3209 15.92 - 31.85: 294 31.85 - 47.77: 72 47.77 - 63.70: 14 63.70 - 79.62: 12 Dihedral angle restraints: 3601 sinusoidal: 1380 harmonic: 2221 Sorted by residual: dihedral pdb=" CA SER A 301 " pdb=" C SER A 301 " pdb=" N PRO A 302 " pdb=" CA PRO A 302 " ideal model delta harmonic sigma weight residual -180.00 -146.83 -33.17 0 5.00e+00 4.00e-02 4.40e+01 dihedral pdb=" CA GLU A 752 " pdb=" C GLU A 752 " pdb=" N THR A 753 " pdb=" CA THR A 753 " ideal model delta harmonic sigma weight residual 180.00 146.90 33.10 0 5.00e+00 4.00e-02 4.38e+01 dihedral pdb=" CA LEU A 910 " pdb=" C LEU A 910 " pdb=" N GLY A 911 " pdb=" CA GLY A 911 " ideal model delta harmonic sigma weight residual 180.00 150.21 29.79 0 5.00e+00 4.00e-02 3.55e+01 ... (remaining 3598 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 778 0.059 - 0.118: 171 0.118 - 0.177: 12 0.177 - 0.236: 1 0.236 - 0.295: 1 Chirality restraints: 963 Sorted by residual: chirality pdb=" CA BFD A 641 " pdb=" N BFD A 641 " pdb=" C BFD A 641 " pdb=" CB BFD A 641 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" CA VAL A 311 " pdb=" N VAL A 311 " pdb=" C VAL A 311 " pdb=" CB VAL A 311 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 7.90e-01 chirality pdb=" CA PRO A 302 " pdb=" N PRO A 302 " pdb=" C PRO A 302 " pdb=" CB PRO A 302 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 7.80e-01 ... (remaining 960 not shown) Planarity restraints: 1027 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 640 " 0.019 2.00e-02 2.50e+03 4.03e-02 1.62e+01 pdb=" C PHE A 640 " -0.070 2.00e-02 2.50e+03 pdb=" O PHE A 640 " 0.027 2.00e-02 2.50e+03 pdb=" N BFD A 641 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 236 " -0.041 5.00e-02 4.00e+02 6.27e-02 6.30e+00 pdb=" N PRO A 237 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO A 237 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 237 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 297 " -0.041 5.00e-02 4.00e+02 6.25e-02 6.26e+00 pdb=" N PRO A 298 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO A 298 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 298 " -0.035 5.00e-02 4.00e+02 ... (remaining 1024 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.54: 63 2.54 - 3.13: 5041 3.13 - 3.72: 9719 3.72 - 4.31: 12835 4.31 - 4.90: 20738 Nonbonded interactions: 48396 Sorted by model distance: nonbonded pdb=" OD2 BFD A 641 " pdb="MG MG A1001 " model vdw 1.945 2.170 nonbonded pdb=" OD2 ASP A 848 " pdb="MG MG A1001 " model vdw 2.048 2.170 nonbonded pdb=" NH1 ARG A 269 " pdb=" O GLY A 408 " model vdw 2.192 3.120 nonbonded pdb=" NZ LYS A 488 " pdb=" O LYS A 493 " model vdw 2.220 3.120 nonbonded pdb=" O ALA A 267 " pdb=" ND1 HIS A 271 " model vdw 2.275 3.120 ... (remaining 48391 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.550 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: 0.020 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 20.340 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 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 : 0.005 0.204 5980 Z= 0.249 Angle : 0.849 19.668 8124 Z= 0.452 Chirality : 0.048 0.295 963 Planarity : 0.007 0.063 1027 Dihedral : 14.275 79.622 2171 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 17.61 Ramachandran Plot: Outliers : 0.52 % Allowed : 12.22 % Favored : 87.26 % Rotamer: Outliers : 0.16 % Allowed : 0.16 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.31), residues: 769 helix: 1.22 (0.28), residues: 369 sheet: -2.19 (0.56), residues: 81 loop : -3.10 (0.31), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 935 HIS 0.006 0.001 HIS A 270 PHE 0.013 0.001 PHE A 337 TYR 0.012 0.001 TYR A 338 ARG 0.004 0.001 ARG A 347 Details of bonding type rmsd hydrogen bonds : bond 0.12936 ( 291) hydrogen bonds : angle 5.86357 ( 834) covalent geometry : bond 0.00460 ( 5980) covalent geometry : angle 0.84949 ( 8124) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 111 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 385 PHE cc_start: 0.9086 (m-10) cc_final: 0.8883 (m-10) REVERT: A 387 GLU cc_start: 0.8275 (mp0) cc_final: 0.8031 (mp0) REVERT: A 403 GLU cc_start: 0.8946 (tp30) cc_final: 0.8649 (tp30) REVERT: A 526 GLU cc_start: 0.8796 (pm20) cc_final: 0.8555 (pm20) REVERT: A 630 GLU cc_start: 0.8610 (mp0) cc_final: 0.8247 (mp0) REVERT: A 647 THR cc_start: 0.7809 (p) cc_final: 0.7269 (p) REVERT: A 659 PHE cc_start: 0.9502 (p90) cc_final: 0.9236 (p90) REVERT: A 881 MET cc_start: 0.9033 (tpp) cc_final: 0.8789 (mmm) REVERT: A 887 ASP cc_start: 0.8728 (m-30) cc_final: 0.8449 (m-30) REVERT: A 915 LEU cc_start: 0.9216 (mt) cc_final: 0.9009 (tp) outliers start: 1 outliers final: 0 residues processed: 111 average time/residue: 0.1578 time to fit residues: 23.6234 Evaluate side-chains 64 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 65 optimal weight: 0.8980 chunk 58 optimal weight: 8.9990 chunk 32 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 chunk 31 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 chunk 69 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.126480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.084551 restraints weight = 16993.017| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 4.76 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 5980 Z= 0.156 Angle : 0.754 10.637 8124 Z= 0.382 Chirality : 0.048 0.216 963 Planarity : 0.006 0.050 1027 Dihedral : 5.638 28.422 818 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.39 % Allowed : 12.35 % Favored : 87.26 % Rotamer: Outliers : 2.03 % Allowed : 10.64 % Favored : 87.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -1.06 (0.31), residues: 769 helix: 1.20 (0.28), residues: 374 sheet: -1.71 (0.66), residues: 54 loop : -2.87 (0.31), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 935 HIS 0.002 0.001 HIS A 473 PHE 0.015 0.001 PHE A 337 TYR 0.013 0.001 TYR A 689 ARG 0.004 0.000 ARG A 896 Details of bonding type rmsd hydrogen bonds : bond 0.03821 ( 291) hydrogen bonds : angle 5.29165 ( 834) covalent geometry : bond 0.00357 ( 5980) covalent geometry : angle 0.75421 ( 8124) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 0.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 361 ASN cc_start: 0.8547 (t0) cc_final: 0.8243 (m-40) REVERT: A 403 GLU cc_start: 0.8940 (tp30) cc_final: 0.8666 (tp30) REVERT: A 659 PHE cc_start: 0.9488 (p90) cc_final: 0.9177 (p90) REVERT: A 887 ASP cc_start: 0.8704 (m-30) cc_final: 0.8392 (m-30) REVERT: A 924 LEU cc_start: 0.9398 (mt) cc_final: 0.9035 (tt) outliers start: 13 outliers final: 7 residues processed: 83 average time/residue: 0.1622 time to fit residues: 18.3992 Evaluate side-chains 72 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 65 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 CYS Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 804 ASN Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 899 LEU Chi-restraints excluded: chain A residue 907 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 35 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 61 optimal weight: 5.9990 chunk 30 optimal weight: 6.9990 chunk 27 optimal weight: 0.0970 chunk 52 optimal weight: 0.8980 chunk 29 optimal weight: 0.3980 chunk 50 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 72 optimal weight: 0.6980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.126921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.085254 restraints weight = 17325.055| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 4.89 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 5980 Z= 0.137 Angle : 0.722 10.425 8124 Z= 0.364 Chirality : 0.047 0.220 963 Planarity : 0.005 0.052 1027 Dihedral : 5.534 28.422 818 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 15.00 Ramachandran Plot: Outliers : 0.39 % Allowed : 12.09 % Favored : 87.52 % Rotamer: Outliers : 2.66 % Allowed : 12.36 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.92 (0.31), residues: 769 helix: 1.31 (0.28), residues: 375 sheet: -1.50 (0.64), residues: 66 loop : -2.88 (0.31), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 935 HIS 0.003 0.001 HIS A 271 PHE 0.012 0.001 PHE A 337 TYR 0.007 0.001 TYR A 697 ARG 0.003 0.000 ARG A 274 Details of bonding type rmsd hydrogen bonds : bond 0.03530 ( 291) hydrogen bonds : angle 5.10491 ( 834) covalent geometry : bond 0.00298 ( 5980) covalent geometry : angle 0.72206 ( 8124) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 67 time to evaluate : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 ARG cc_start: 0.9164 (mmm160) cc_final: 0.8549 (mmm160) REVERT: A 361 ASN cc_start: 0.8564 (t0) cc_final: 0.8248 (m-40) REVERT: A 387 GLU cc_start: 0.8149 (mp0) cc_final: 0.7825 (mp0) REVERT: A 403 GLU cc_start: 0.8934 (tp30) cc_final: 0.8684 (tp30) REVERT: A 659 PHE cc_start: 0.9495 (p90) cc_final: 0.9179 (p90) REVERT: A 887 ASP cc_start: 0.8743 (m-30) cc_final: 0.8373 (m-30) REVERT: A 924 LEU cc_start: 0.9428 (mt) cc_final: 0.9071 (tt) outliers start: 17 outliers final: 11 residues processed: 80 average time/residue: 0.1670 time to fit residues: 18.1300 Evaluate side-chains 75 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 HIS Chi-restraints excluded: chain A residue 284 CYS Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 804 ASN Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 899 LEU Chi-restraints excluded: chain A residue 907 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 23 optimal weight: 0.8980 chunk 72 optimal weight: 0.5980 chunk 61 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 25 optimal weight: 20.0000 chunk 30 optimal weight: 8.9990 chunk 6 optimal weight: 40.0000 chunk 13 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 52 optimal weight: 9.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.124868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.083193 restraints weight = 17703.377| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 4.88 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 5980 Z= 0.174 Angle : 0.736 11.295 8124 Z= 0.371 Chirality : 0.047 0.216 963 Planarity : 0.005 0.049 1027 Dihedral : 5.483 28.835 818 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.39 % Allowed : 12.09 % Favored : 87.52 % Rotamer: Outliers : 2.66 % Allowed : 14.40 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.80 (0.32), residues: 769 helix: 1.39 (0.28), residues: 375 sheet: -1.47 (0.67), residues: 58 loop : -2.74 (0.32), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 935 HIS 0.014 0.001 HIS A 270 PHE 0.012 0.001 PHE A 337 TYR 0.007 0.001 TYR A 570 ARG 0.005 0.000 ARG A 274 Details of bonding type rmsd hydrogen bonds : bond 0.03523 ( 291) hydrogen bonds : angle 5.11504 ( 834) covalent geometry : bond 0.00388 ( 5980) covalent geometry : angle 0.73641 ( 8124) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 66 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 315 MET cc_start: 0.8731 (ttm) cc_final: 0.8153 (mtp) REVERT: A 375 LEU cc_start: 0.9636 (tp) cc_final: 0.9417 (tp) REVERT: A 403 GLU cc_start: 0.8962 (tp30) cc_final: 0.8711 (tp30) REVERT: A 630 GLU cc_start: 0.8631 (mt-10) cc_final: 0.8185 (mp0) REVERT: A 659 PHE cc_start: 0.9470 (p90) cc_final: 0.9155 (p90) REVERT: A 750 MET cc_start: 0.9077 (tpt) cc_final: 0.8767 (tpt) REVERT: A 780 LYS cc_start: 0.7507 (ptmm) cc_final: 0.7300 (ptmm) REVERT: A 887 ASP cc_start: 0.8732 (m-30) cc_final: 0.8353 (m-30) REVERT: A 924 LEU cc_start: 0.9445 (mt) cc_final: 0.9093 (tt) outliers start: 17 outliers final: 15 residues processed: 79 average time/residue: 0.1673 time to fit residues: 18.2335 Evaluate side-chains 79 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 64 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 CYS Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 804 ASN Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 899 LEU Chi-restraints excluded: chain A residue 907 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 76 optimal weight: 0.3980 chunk 38 optimal weight: 2.9990 chunk 28 optimal weight: 0.0970 chunk 65 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 0 optimal weight: 20.0000 chunk 37 optimal weight: 0.9980 chunk 41 optimal weight: 0.3980 chunk 5 optimal weight: 30.0000 overall best weight: 0.5178 ------------------------------------------------------------------------------- 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 = 0.4093 r_free = 0.4093 target = 0.126072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.085210 restraints weight = 17233.281| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 4.85 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 5980 Z= 0.128 Angle : 0.713 12.627 8124 Z= 0.356 Chirality : 0.046 0.214 963 Planarity : 0.005 0.050 1027 Dihedral : 5.387 29.186 818 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.39 % Allowed : 11.31 % Favored : 88.30 % Rotamer: Outliers : 2.97 % Allowed : 15.81 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.68 (0.32), residues: 769 helix: 1.54 (0.28), residues: 375 sheet: -1.66 (0.56), residues: 87 loop : -2.75 (0.33), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 935 HIS 0.004 0.001 HIS A 189 PHE 0.011 0.001 PHE A 337 TYR 0.011 0.001 TYR A 338 ARG 0.002 0.000 ARG A 274 Details of bonding type rmsd hydrogen bonds : bond 0.03267 ( 291) hydrogen bonds : angle 4.97514 ( 834) covalent geometry : bond 0.00279 ( 5980) covalent geometry : angle 0.71258 ( 8124) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 75 time to evaluate : 0.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 387 GLU cc_start: 0.8085 (mp0) cc_final: 0.7786 (mp0) REVERT: A 489 LYS cc_start: 0.9488 (ptmm) cc_final: 0.9287 (pptt) REVERT: A 630 GLU cc_start: 0.8609 (mt-10) cc_final: 0.8154 (mp0) REVERT: A 659 PHE cc_start: 0.9508 (p90) cc_final: 0.9105 (p90) REVERT: A 688 GLU cc_start: 0.9507 (mp0) cc_final: 0.9215 (mp0) REVERT: A 750 MET cc_start: 0.9138 (tpt) cc_final: 0.8851 (tpt) REVERT: A 887 ASP cc_start: 0.8695 (m-30) cc_final: 0.8306 (m-30) REVERT: A 924 LEU cc_start: 0.9408 (mt) cc_final: 0.9059 (tt) outliers start: 19 outliers final: 11 residues processed: 88 average time/residue: 0.1713 time to fit residues: 21.4537 Evaluate side-chains 77 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 CYS Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 804 ASN Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 899 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 67 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 28 optimal weight: 8.9990 chunk 2 optimal weight: 8.9990 chunk 51 optimal weight: 9.9990 chunk 66 optimal weight: 0.9980 chunk 56 optimal weight: 20.0000 chunk 57 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 587 GLN A 680 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.124397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.082651 restraints weight = 17421.564| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 4.80 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 5980 Z= 0.162 Angle : 0.738 13.196 8124 Z= 0.369 Chirality : 0.047 0.206 963 Planarity : 0.005 0.048 1027 Dihedral : 5.332 28.921 818 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.26 % Allowed : 11.96 % Favored : 87.78 % Rotamer: Outliers : 3.13 % Allowed : 18.00 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.63 (0.32), residues: 769 helix: 1.65 (0.28), residues: 374 sheet: -1.71 (0.61), residues: 72 loop : -2.76 (0.32), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 935 HIS 0.003 0.001 HIS A 189 PHE 0.019 0.001 PHE A 562 TYR 0.008 0.001 TYR A 689 ARG 0.002 0.000 ARG A 694 Details of bonding type rmsd hydrogen bonds : bond 0.03429 ( 291) hydrogen bonds : angle 5.00004 ( 834) covalent geometry : bond 0.00368 ( 5980) covalent geometry : angle 0.73832 ( 8124) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 67 time to evaluate : 0.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 MET cc_start: 0.8594 (ttm) cc_final: 0.8177 (mtp) REVERT: A 319 MET cc_start: 0.8738 (mtm) cc_final: 0.8538 (mtm) REVERT: A 375 LEU cc_start: 0.9549 (tp) cc_final: 0.9346 (tp) REVERT: A 489 LYS cc_start: 0.9544 (ptmm) cc_final: 0.9340 (pptt) REVERT: A 630 GLU cc_start: 0.8606 (mt-10) cc_final: 0.8142 (mp0) REVERT: A 659 PHE cc_start: 0.9554 (p90) cc_final: 0.9112 (p90) REVERT: A 688 GLU cc_start: 0.9519 (mp0) cc_final: 0.9235 (mp0) REVERT: A 735 MET cc_start: 0.9216 (ptp) cc_final: 0.8999 (ptp) REVERT: A 750 MET cc_start: 0.9140 (OUTLIER) cc_final: 0.8836 (tpt) REVERT: A 780 LYS cc_start: 0.7429 (ptmm) cc_final: 0.6812 (ptmt) REVERT: A 881 MET cc_start: 0.9123 (mmm) cc_final: 0.8750 (mmm) REVERT: A 887 ASP cc_start: 0.8687 (m-30) cc_final: 0.8312 (m-30) REVERT: A 924 LEU cc_start: 0.9418 (mt) cc_final: 0.9080 (tt) outliers start: 20 outliers final: 15 residues processed: 79 average time/residue: 0.1622 time to fit residues: 17.7105 Evaluate side-chains 82 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 66 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 CYS Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 750 MET Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 804 ASN Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 899 LEU Chi-restraints excluded: chain A residue 907 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 25 optimal weight: 8.9990 chunk 46 optimal weight: 0.7980 chunk 56 optimal weight: 7.9990 chunk 44 optimal weight: 0.0870 chunk 5 optimal weight: 20.0000 chunk 33 optimal weight: 3.9990 chunk 45 optimal weight: 0.6980 chunk 2 optimal weight: 4.9990 chunk 22 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 overall best weight: 0.8960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 361 ASN ** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 680 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.123855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.081859 restraints weight = 17235.869| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 5.22 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 5980 Z= 0.146 Angle : 0.748 14.311 8124 Z= 0.366 Chirality : 0.047 0.201 963 Planarity : 0.005 0.047 1027 Dihedral : 5.367 28.857 818 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.13 % Allowed : 11.31 % Favored : 88.56 % Rotamer: Outliers : 2.66 % Allowed : 18.94 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.60 (0.31), residues: 769 helix: 1.65 (0.27), residues: 375 sheet: -1.34 (0.64), residues: 65 loop : -2.81 (0.32), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 935 HIS 0.004 0.001 HIS A 189 PHE 0.012 0.001 PHE A 337 TYR 0.010 0.001 TYR A 689 ARG 0.002 0.000 ARG A 694 Details of bonding type rmsd hydrogen bonds : bond 0.03314 ( 291) hydrogen bonds : angle 4.91065 ( 834) covalent geometry : bond 0.00329 ( 5980) covalent geometry : angle 0.74781 ( 8124) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 69 time to evaluate : 0.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 489 LYS cc_start: 0.9547 (ptmm) cc_final: 0.9344 (pptt) REVERT: A 630 GLU cc_start: 0.8651 (mt-10) cc_final: 0.8218 (mp0) REVERT: A 659 PHE cc_start: 0.9517 (p90) cc_final: 0.9073 (p90) REVERT: A 750 MET cc_start: 0.9231 (OUTLIER) cc_final: 0.8952 (tpt) REVERT: A 887 ASP cc_start: 0.8686 (m-30) cc_final: 0.8305 (m-30) REVERT: A 924 LEU cc_start: 0.9438 (mt) cc_final: 0.9120 (pt) outliers start: 17 outliers final: 14 residues processed: 79 average time/residue: 0.1822 time to fit residues: 19.6771 Evaluate side-chains 81 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 66 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 CYS Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 750 MET Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 804 ASN Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 899 LEU Chi-restraints excluded: chain A residue 907 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 6 optimal weight: 30.0000 chunk 12 optimal weight: 3.9990 chunk 74 optimal weight: 0.5980 chunk 35 optimal weight: 4.9990 chunk 59 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 30 optimal weight: 0.9980 chunk 7 optimal weight: 0.0570 chunk 28 optimal weight: 4.9990 chunk 52 optimal weight: 6.9990 overall best weight: 0.8900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 680 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.124966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.083141 restraints weight = 17248.974| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 4.81 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.3029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 5980 Z= 0.147 Angle : 0.754 13.901 8124 Z= 0.367 Chirality : 0.047 0.195 963 Planarity : 0.005 0.047 1027 Dihedral : 5.342 28.801 818 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.13 % Allowed : 11.83 % Favored : 88.04 % Rotamer: Outliers : 2.50 % Allowed : 19.09 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.59 (0.31), residues: 769 helix: 1.68 (0.27), residues: 375 sheet: -1.26 (0.65), residues: 64 loop : -2.84 (0.31), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 935 HIS 0.004 0.001 HIS A 189 PHE 0.012 0.001 PHE A 337 TYR 0.009 0.001 TYR A 689 ARG 0.002 0.000 ARG A 694 Details of bonding type rmsd hydrogen bonds : bond 0.03332 ( 291) hydrogen bonds : angle 4.93341 ( 834) covalent geometry : bond 0.00328 ( 5980) covalent geometry : angle 0.75420 ( 8124) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 73 time to evaluate : 0.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 489 LYS cc_start: 0.9531 (ptmm) cc_final: 0.9326 (pptt) REVERT: A 630 GLU cc_start: 0.8627 (mt-10) cc_final: 0.8178 (mp0) REVERT: A 659 PHE cc_start: 0.9577 (p90) cc_final: 0.9116 (p90) REVERT: A 750 MET cc_start: 0.9233 (OUTLIER) cc_final: 0.8945 (tpt) REVERT: A 887 ASP cc_start: 0.8678 (m-30) cc_final: 0.8296 (m-30) REVERT: A 924 LEU cc_start: 0.9411 (mt) cc_final: 0.9077 (pt) outliers start: 16 outliers final: 14 residues processed: 81 average time/residue: 0.1833 time to fit residues: 20.1175 Evaluate side-chains 83 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 68 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 CYS Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 750 MET Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 804 ASN Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 899 LEU Chi-restraints excluded: chain A residue 907 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 69 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 66 optimal weight: 0.0980 chunk 71 optimal weight: 1.9990 chunk 25 optimal weight: 0.0970 chunk 73 optimal weight: 0.7980 chunk 14 optimal weight: 0.4980 chunk 0 optimal weight: 20.0000 chunk 1 optimal weight: 4.9990 chunk 42 optimal weight: 0.5980 chunk 63 optimal weight: 0.4980 overall best weight: 0.3578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 471 GLN A 502 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.125679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.083942 restraints weight = 17197.967| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 5.23 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.3195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 5980 Z= 0.126 Angle : 0.766 14.353 8124 Z= 0.371 Chirality : 0.047 0.203 963 Planarity : 0.005 0.047 1027 Dihedral : 5.311 28.190 818 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.26 % Allowed : 11.44 % Favored : 88.30 % Rotamer: Outliers : 2.03 % Allowed : 20.19 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.51 (0.32), residues: 769 helix: 1.72 (0.28), residues: 374 sheet: -1.12 (0.62), residues: 75 loop : -2.83 (0.32), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 908 HIS 0.004 0.001 HIS A 189 PHE 0.022 0.001 PHE A 562 TYR 0.016 0.001 TYR A 689 ARG 0.002 0.000 ARG A 694 Details of bonding type rmsd hydrogen bonds : bond 0.03193 ( 291) hydrogen bonds : angle 4.86557 ( 834) covalent geometry : bond 0.00273 ( 5980) covalent geometry : angle 0.76585 ( 8124) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 1.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 489 LYS cc_start: 0.9482 (ptmm) cc_final: 0.9257 (pptt) REVERT: A 630 GLU cc_start: 0.8643 (mt-10) cc_final: 0.8219 (mp0) REVERT: A 659 PHE cc_start: 0.9562 (p90) cc_final: 0.9102 (p90) REVERT: A 750 MET cc_start: 0.9232 (OUTLIER) cc_final: 0.8989 (tpt) REVERT: A 887 ASP cc_start: 0.8656 (m-30) cc_final: 0.8269 (m-30) outliers start: 13 outliers final: 10 residues processed: 82 average time/residue: 0.1922 time to fit residues: 22.4948 Evaluate side-chains 80 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 69 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 CYS Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 750 MET Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 804 ASN Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 899 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 63 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 34 optimal weight: 6.9990 chunk 43 optimal weight: 0.5980 chunk 7 optimal weight: 40.0000 chunk 36 optimal weight: 0.6980 chunk 56 optimal weight: 9.9990 chunk 59 optimal weight: 0.0170 chunk 55 optimal weight: 1.9990 chunk 32 optimal weight: 10.0000 chunk 35 optimal weight: 0.0670 overall best weight: 0.6758 ------------------------------------------------------------------------------- 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 = 0.4096 r_free = 0.4096 target = 0.125031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.083461 restraints weight = 17325.928| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 5.09 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.3305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 5980 Z= 0.138 Angle : 0.776 14.402 8124 Z= 0.379 Chirality : 0.048 0.203 963 Planarity : 0.005 0.047 1027 Dihedral : 5.316 27.700 818 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.26 % Allowed : 11.05 % Favored : 88.69 % Rotamer: Outliers : 2.03 % Allowed : 19.87 % Favored : 78.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.49 (0.32), residues: 769 helix: 1.74 (0.28), residues: 375 sheet: -1.20 (0.62), residues: 74 loop : -2.81 (0.32), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 935 HIS 0.004 0.001 HIS A 189 PHE 0.011 0.001 PHE A 337 TYR 0.014 0.001 TYR A 689 ARG 0.002 0.000 ARG A 274 Details of bonding type rmsd hydrogen bonds : bond 0.03435 ( 291) hydrogen bonds : angle 4.91316 ( 834) covalent geometry : bond 0.00308 ( 5980) covalent geometry : angle 0.77615 ( 8124) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 70 time to evaluate : 1.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 489 LYS cc_start: 0.9481 (ptmm) cc_final: 0.9261 (pptt) REVERT: A 540 ASP cc_start: 0.8837 (m-30) cc_final: 0.8485 (t0) REVERT: A 630 GLU cc_start: 0.8646 (mt-10) cc_final: 0.8211 (mp0) REVERT: A 659 PHE cc_start: 0.9564 (p90) cc_final: 0.9090 (p90) REVERT: A 750 MET cc_start: 0.9230 (OUTLIER) cc_final: 0.9000 (tpt) REVERT: A 887 ASP cc_start: 0.8674 (m-30) cc_final: 0.8293 (m-30) outliers start: 13 outliers final: 12 residues processed: 77 average time/residue: 0.1793 time to fit residues: 20.7308 Evaluate side-chains 83 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 70 time to evaluate : 1.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 CYS Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 750 MET Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 804 ASN Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 899 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 56 optimal weight: 20.0000 chunk 8 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 51 optimal weight: 10.0000 chunk 55 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 39 optimal weight: 0.8980 chunk 25 optimal weight: 9.9990 chunk 15 optimal weight: 0.9980 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 = 0.4056 r_free = 0.4056 target = 0.123404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.081932 restraints weight = 17069.075| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 4.94 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.3427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 5980 Z= 0.180 Angle : 0.793 14.423 8124 Z= 0.388 Chirality : 0.048 0.201 963 Planarity : 0.005 0.046 1027 Dihedral : 5.421 28.984 818 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.26 % Allowed : 11.83 % Favored : 87.91 % Rotamer: Outliers : 2.35 % Allowed : 20.34 % Favored : 77.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.51 (0.32), residues: 769 helix: 1.66 (0.28), residues: 375 sheet: -0.80 (0.80), residues: 36 loop : -2.67 (0.31), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 935 HIS 0.003 0.001 HIS A 189 PHE 0.026 0.001 PHE A 562 TYR 0.014 0.001 TYR A 689 ARG 0.005 0.000 ARG A 785 Details of bonding type rmsd hydrogen bonds : bond 0.03596 ( 291) hydrogen bonds : angle 5.06324 ( 834) covalent geometry : bond 0.00405 ( 5980) covalent geometry : angle 0.79252 ( 8124) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3356.46 seconds wall clock time: 60 minutes 35.09 seconds (3635.09 seconds total)