Starting phenix.real_space_refine on Wed Jun 3 13:49:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9u51_63860/06_2026/9u51_63860.cif Found real_map, /net/cci-nas-00/data/ceres_data/9u51_63860/06_2026/9u51_63860.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9u51_63860/06_2026/9u51_63860.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9u51_63860/06_2026/9u51_63860.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9u51_63860/06_2026/9u51_63860.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9u51_63860/06_2026/9u51_63860.map" } resolution = 3.05 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.016 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 30 5.16 5 C 3939 2.51 5 N 1026 2.21 5 O 1122 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6118 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 726, 5457 Classifications: {'peptide': 726} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 693} Chain breaks: 1 Chain: "B" Number of atoms: 661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 661 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'4HH:plan-3': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 1.62, per 1000 atoms: 0.26 Number of scatterers: 6118 At special positions: 0 Unit cell: (69.66, 91.16, 135.02, 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 30 16.00 P 1 15.00 O 1122 8.00 N 1026 7.00 C 3939 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.54 Conformation dependent library (CDL) restraints added in 433.3 milliseconds 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1478 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 3 sheets defined 73.5% alpha, 4.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 22 through 31 Processing helix chain 'A' and resid 31 through 50 removed outlier: 3.737A pdb=" N VAL A 50 " --> pdb=" O LEU A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 60 Processing helix chain 'A' and resid 69 through 82 Processing helix chain 'A' and resid 102 through 119 removed outlier: 3.703A pdb=" N ASP A 119 " --> pdb=" O ARG A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 139 Processing helix chain 'A' and resid 159 through 175 Processing helix chain 'A' and resid 188 through 224 Processing helix chain 'A' and resid 225 through 253 removed outlier: 3.949A pdb=" N HIS A 253 " --> pdb=" O PHE A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 290 Processing helix chain 'A' and resid 294 through 325 removed outlier: 5.776A pdb=" N HIS A 308 " --> pdb=" O GLY A 304 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N VAL A 309 " --> pdb=" O GLY A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 363 removed outlier: 4.392A pdb=" N VAL A 337 " --> pdb=" O GLN A 333 " (cutoff:3.500A) Proline residue: A 338 - end of helix Proline residue: A 355 - end of helix Processing helix chain 'A' and resid 377 through 389 Processing helix chain 'A' and resid 389 through 406 removed outlier: 4.102A pdb=" N ILE A 393 " --> pdb=" O TRP A 389 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLY A 404 " --> pdb=" O LEU A 400 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU A 405 " --> pdb=" O ALA A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 411 removed outlier: 3.689A pdb=" N GLY A 410 " --> pdb=" O THR A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 421 removed outlier: 3.838A pdb=" N LEU A 421 " --> pdb=" O ARG A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 436 Processing helix chain 'A' and resid 439 through 444 Processing helix chain 'A' and resid 458 through 475 removed outlier: 3.518A pdb=" N PHE A 462 " --> pdb=" O ASN A 458 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL A 475 " --> pdb=" O ALA A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 709 removed outlier: 4.247A pdb=" N GLY A 704 " --> pdb=" O ASP A 700 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU A 705 " --> pdb=" O PHE A 701 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU A 706 " --> pdb=" O GLN A 702 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLN A 707 " --> pdb=" O ARG A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 747 removed outlier: 3.911A pdb=" N ILE A 735 " --> pdb=" O GLY A 731 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N ALA A 736 " --> pdb=" O ILE A 732 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS A 737 " --> pdb=" O ALA A 733 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 796 removed outlier: 3.812A pdb=" N ASP A 767 " --> pdb=" O ALA A 763 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU A 768 " --> pdb=" O MET A 764 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N THR A 773 " --> pdb=" O SER A 769 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N TYR A 774 " --> pdb=" O ASP A 770 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N SER A 782 " --> pdb=" O ILE A 778 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ALA A 783 " --> pdb=" O ALA A 779 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU A 784 " --> pdb=" O GLY A 780 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N CYS A 785 " --> pdb=" O ILE A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 797 through 824 removed outlier: 3.548A pdb=" N ALA A 801 " --> pdb=" O SER A 797 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL A 808 " --> pdb=" O ILE A 804 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N GLY A 813 " --> pdb=" O VAL A 809 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N ALA A 814 " --> pdb=" O LEU A 810 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER A 815 " --> pdb=" O SER A 811 " (cutoff:3.500A) Processing helix chain 'A' and resid 834 through 862 removed outlier: 4.077A pdb=" N MET A 838 " --> pdb=" O LEU A 834 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ILE A 841 " --> pdb=" O ALA A 837 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE A 842 " --> pdb=" O MET A 838 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ASP A 849 " --> pdb=" O ALA A 845 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N TYR A 850 " --> pdb=" O VAL A 846 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASN A 851 " --> pdb=" O GLY A 847 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 877 removed outlier: 3.604A pdb=" N ILE A 871 " --> pdb=" O ASN A 867 " (cutoff:3.500A) Processing helix chain 'A' and resid 878 through 893 removed outlier: 3.513A pdb=" N THR A 882 " --> pdb=" O GLY A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 898 removed outlier: 3.619A pdb=" N VAL A 897 " --> pdb=" O SER A 894 " (cutoff:3.500A) Processing helix chain 'A' and resid 900 through 920 Processing helix chain 'A' and resid 920 through 925 Processing helix chain 'A' and resid 925 through 934 Processing helix chain 'A' and resid 935 through 939 removed outlier: 3.522A pdb=" N TRP A 938 " --> pdb=" O LYS A 935 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TRP A 939 " --> pdb=" O TRP A 936 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 935 through 939' Processing helix chain 'B' and resid 4 through 21 Processing helix chain 'B' and resid 23 through 27 removed outlier: 3.867A pdb=" N VAL B 27 " --> pdb=" O PRO B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 55 removed outlier: 3.517A pdb=" N TYR B 55 " --> pdb=" O THR B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 65 Processing helix chain 'B' and resid 70 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 125 through 126 removed outlier: 3.620A pdb=" N SER A 125 " --> pdb=" O LYS A 152 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 413 through 414 Processing sheet with id=AA3, first strand: chain 'A' and resid 478 through 482 436 hydrogen bonds defined for protein. 1272 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: 0.83 Time building geometry restraints manager: 0.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1007 1.31 - 1.44: 1532 1.44 - 1.56: 3635 1.56 - 1.69: 1 1.69 - 1.82: 57 Bond restraints: 6232 Sorted by residual: bond pdb=" CL3 4HH B 41 " pdb=" NN 4HH B 41 " ideal model delta sigma weight residual 1.335 1.453 -0.118 2.00e-02 2.50e+03 3.51e+01 bond pdb=" CQ 4HH B 41 " pdb=" NR 4HH B 41 " ideal model delta sigma weight residual 1.345 1.452 -0.107 2.00e-02 2.50e+03 2.84e+01 bond pdb=" OG 4HH B 41 " pdb=" P 4HH B 41 " ideal model delta sigma weight residual 1.642 1.557 0.085 2.00e-02 2.50e+03 1.79e+01 bond pdb=" CL3 4HH B 41 " pdb=" ON 4HH B 41 " ideal model delta sigma weight residual 1.226 1.186 0.040 2.00e-02 2.50e+03 4.09e+00 bond pdb=" O1P 4HH B 41 " pdb=" P 4HH B 41 " ideal model delta sigma weight residual 1.500 1.461 0.039 2.00e-02 2.50e+03 3.89e+00 ... (remaining 6227 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.49: 8470 4.49 - 8.98: 11 8.98 - 13.48: 0 13.48 - 17.97: 2 17.97 - 22.46: 1 Bond angle restraints: 8484 Sorted by residual: angle pdb=" OG 4HH B 41 " pdb=" P 4HH B 41 " pdb=" O3P 4HH B 41 " ideal model delta sigma weight residual 92.93 115.39 -22.46 3.00e+00 1.11e-01 5.60e+01 angle pdb=" O1P 4HH B 41 " pdb=" P 4HH B 41 " pdb=" O2P 4HH B 41 " ideal model delta sigma weight residual 119.62 104.34 15.28 3.00e+00 1.11e-01 2.60e+01 angle pdb=" OG 4HH B 41 " pdb=" P 4HH B 41 " pdb=" O1P 4HH B 41 " ideal model delta sigma weight residual 110.27 96.17 14.10 3.00e+00 1.11e-01 2.21e+01 angle pdb=" N GLY A 336 " pdb=" CA GLY A 336 " pdb=" C GLY A 336 " ideal model delta sigma weight residual 113.18 118.93 -5.75 2.37e+00 1.78e-01 5.89e+00 angle pdb=" CA LEU A 914 " pdb=" CB LEU A 914 " pdb=" CG LEU A 914 " ideal model delta sigma weight residual 116.30 108.31 7.99 3.50e+00 8.16e-02 5.22e+00 ... (remaining 8479 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.73: 3465 20.73 - 41.46: 216 41.46 - 62.19: 33 62.19 - 82.92: 13 82.92 - 103.65: 2 Dihedral angle restraints: 3729 sinusoidal: 1426 harmonic: 2303 Sorted by residual: dihedral pdb=" NR 4HH B 41 " pdb=" CS 4HH B 41 " pdb=" CT 4HH B 41 " pdb=" SU 4HH B 41 " ideal model delta sinusoidal sigma weight residual 179.08 -77.27 -103.65 1 3.00e+01 1.11e-03 1.32e+01 dihedral pdb=" CA GLY A 365 " pdb=" C GLY A 365 " pdb=" N LYS A 366 " pdb=" CA LYS A 366 " ideal model delta harmonic sigma weight residual -180.00 -162.79 -17.21 0 5.00e+00 4.00e-02 1.19e+01 dihedral pdb=" CB MET A 443 " pdb=" CG MET A 443 " pdb=" SD MET A 443 " pdb=" CE MET A 443 " ideal model delta sinusoidal sigma weight residual 180.00 127.68 52.32 3 1.50e+01 4.44e-03 9.10e+00 ... (remaining 3726 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 641 0.030 - 0.060: 244 0.060 - 0.090: 89 0.090 - 0.120: 41 0.120 - 0.149: 5 Chirality restraints: 1020 Sorted by residual: chirality pdb=" CM 4HH B 41 " pdb=" CK 4HH B 41 " pdb=" CL3 4HH B 41 " pdb=" OM 4HH B 41 " both_signs ideal model delta sigma weight residual False 2.34 2.49 -0.15 2.00e-01 2.50e+01 5.58e-01 chirality pdb=" CA VAL B 57 " pdb=" N VAL B 57 " pdb=" C VAL B 57 " pdb=" CB VAL B 57 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.59e-01 chirality pdb=" CA ARG B 68 " pdb=" N ARG B 68 " pdb=" C ARG B 68 " pdb=" CB ARG B 68 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 3.95e-01 ... (remaining 1017 not shown) Planarity restraints: 1074 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 21 " 0.023 5.00e-02 4.00e+02 3.47e-02 1.93e+00 pdb=" N PRO A 22 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO A 22 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 22 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 354 " 0.023 5.00e-02 4.00e+02 3.43e-02 1.88e+00 pdb=" N PRO A 355 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 355 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 355 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 725 " -0.021 5.00e-02 4.00e+02 3.17e-02 1.61e+00 pdb=" N PRO A 726 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO A 726 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 726 " -0.017 5.00e-02 4.00e+02 ... (remaining 1071 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1024 2.76 - 3.30: 5910 3.30 - 3.83: 9863 3.83 - 4.37: 10102 4.37 - 4.90: 18832 Nonbonded interactions: 45731 Sorted by model distance: nonbonded pdb=" OH TYR A 109 " pdb=" OD1 ASP A 128 " model vdw 2.229 3.040 nonbonded pdb=" O MET A 302 " pdb=" OG1 THR A 306 " model vdw 2.281 3.040 nonbonded pdb=" NE1 TRP A 130 " pdb=" OE1 GLN A 140 " model vdw 2.284 3.120 nonbonded pdb=" O LEU A 751 " pdb=" OG SER A 754 " model vdw 2.326 3.040 nonbonded pdb=" OG SER A 89 " pdb=" O GLY A 155 " model vdw 2.337 3.040 ... (remaining 45726 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 1.150 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.530 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 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 : 0.003 0.118 6232 Z= 0.171 Angle : 0.612 22.459 8484 Z= 0.283 Chirality : 0.040 0.149 1020 Planarity : 0.003 0.035 1074 Dihedral : 14.351 103.654 2251 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.15 (0.30), residues: 801 helix: 2.98 (0.22), residues: 508 sheet: 2.85 (0.81), residues: 46 loop : -0.05 (0.41), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 412 TYR 0.006 0.001 TYR A 299 PHE 0.007 0.001 PHE A 888 TRP 0.005 0.001 TRP A 389 HIS 0.002 0.000 HIS A 832 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.17 ( 6232) covalent geometry : angle 0.61237 / 0.28 ( 8484) hydrogen bonds : bond 0.12662 / 9.38 ( 436) hydrogen bonds : angle 4.71398 / 3.51 ( 1272) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.155 Fit side-chains REVERT: A 373 MET cc_start: 0.7645 (mpp) cc_final: 0.6524 (tmm) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.0776 time to fit residues: 8.0193 Evaluate side-chains 60 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 74 optimal weight: 8.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN B 78 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.107711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.076453 restraints weight = 12990.323| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 2.97 r_work: 0.3018 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.0950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 6232 Z= 0.154 Angle : 0.536 8.408 8484 Z= 0.281 Chirality : 0.040 0.138 1020 Planarity : 0.004 0.048 1074 Dihedral : 7.724 72.449 893 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.78 % Allowed : 6.26 % Favored : 92.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.07 (0.30), residues: 801 helix: 2.94 (0.22), residues: 510 sheet: 2.77 (0.80), residues: 46 loop : -0.14 (0.41), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 412 TYR 0.008 0.001 TYR B 76 PHE 0.013 0.001 PHE A 462 TRP 0.004 0.001 TRP A 379 HIS 0.003 0.001 HIS A 832 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 ( 6232) covalent geometry : angle 0.53622 / 0.28 ( 8484) hydrogen bonds : bond 0.06153 / 4.44 ( 436) hydrogen bonds : angle 4.09824 / 3.03 ( 1272) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 61 time to evaluate : 0.196 Fit side-chains REVERT: A 373 MET cc_start: 0.7948 (mpp) cc_final: 0.6574 (tmm) outliers start: 5 outliers final: 3 residues processed: 64 average time/residue: 0.0874 time to fit residues: 7.3186 Evaluate side-chains 59 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 56 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 302 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 24 optimal weight: 0.9990 chunk 27 optimal weight: 7.9990 chunk 41 optimal weight: 10.0000 chunk 71 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 10 optimal weight: 9.9990 chunk 4 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- 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 = 0.3645 r_free = 0.3645 target = 0.109009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.078009 restraints weight = 12724.949| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 2.92 r_work: 0.3049 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.1030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 6232 Z= 0.123 Angle : 0.502 8.535 8484 Z= 0.261 Chirality : 0.040 0.136 1020 Planarity : 0.003 0.047 1074 Dihedral : 7.470 68.895 893 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.25 % Allowed : 7.82 % Favored : 90.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.04 (0.30), residues: 801 helix: 2.90 (0.22), residues: 509 sheet: 2.66 (0.79), residues: 46 loop : -0.09 (0.41), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 388 TYR 0.010 0.001 TYR B 76 PHE 0.008 0.001 PHE A 82 TRP 0.004 0.001 TRP A 379 HIS 0.002 0.001 HIS A 832 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 ( 6232) covalent geometry : angle 0.50162 / 0.26 ( 8484) hydrogen bonds : bond 0.05491 / 3.98 ( 436) hydrogen bonds : angle 3.98117 / 2.94 ( 1272) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.233 Fit side-chains REVERT: A 373 MET cc_start: 0.7939 (mpp) cc_final: 0.6602 (tmm) REVERT: B 57 VAL cc_start: 0.8628 (t) cc_final: 0.8296 (m) outliers start: 8 outliers final: 6 residues processed: 67 average time/residue: 0.0773 time to fit residues: 7.0479 Evaluate side-chains 68 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 62 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 417 ASP Chi-restraints excluded: chain A residue 791 MET Chi-restraints excluded: chain A residue 925 MET Chi-restraints excluded: chain B residue 25 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 3 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 10 optimal weight: 10.0000 chunk 5 optimal weight: 3.9990 chunk 78 optimal weight: 0.8980 chunk 41 optimal weight: 9.9990 chunk 24 optimal weight: 1.9990 chunk 46 optimal weight: 9.9990 chunk 40 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 28 optimal weight: 0.9980 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 78 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.102608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.071943 restraints weight = 12844.971| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 2.87 r_work: 0.2935 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.1466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 6232 Z= 0.175 Angle : 0.546 7.553 8484 Z= 0.287 Chirality : 0.041 0.132 1020 Planarity : 0.004 0.048 1074 Dihedral : 7.033 71.191 893 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.41 % Allowed : 9.23 % Favored : 89.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.89 (0.30), residues: 801 helix: 2.73 (0.22), residues: 515 sheet: 2.46 (0.78), residues: 46 loop : -0.03 (0.41), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 388 TYR 0.008 0.001 TYR A 431 PHE 0.011 0.001 PHE A 332 TRP 0.004 0.001 TRP A 379 HIS 0.003 0.001 HIS A 832 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.17 ( 6232) covalent geometry : angle 0.54558 / 0.29 ( 8484) hydrogen bonds : bond 0.06875 / 4.94 ( 436) hydrogen bonds : angle 4.15038 / 3.07 ( 1272) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 65 time to evaluate : 0.223 Fit side-chains revert: symmetry clash REVERT: A 373 MET cc_start: 0.7905 (mpp) cc_final: 0.6705 (tmm) REVERT: B 31 LYS cc_start: 0.8807 (mttp) cc_final: 0.8586 (mttp) REVERT: B 57 VAL cc_start: 0.8870 (t) cc_final: 0.8617 (m) REVERT: B 76 TYR cc_start: 0.9159 (t80) cc_final: 0.8813 (t80) outliers start: 9 outliers final: 6 residues processed: 68 average time/residue: 0.0798 time to fit residues: 7.3822 Evaluate side-chains 70 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 64 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 791 MET Chi-restraints excluded: chain A residue 925 MET Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 78 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 6 optimal weight: 10.0000 chunk 71 optimal weight: 0.0170 chunk 45 optimal weight: 0.0570 chunk 55 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 46 optimal weight: 6.9990 chunk 54 optimal weight: 9.9990 chunk 1 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 41 optimal weight: 9.9990 overall best weight: 1.1740 ------------------------------------------------------------------------------- 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 = 0.3599 r_free = 0.3599 target = 0.104682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.074178 restraints weight = 12836.657| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 2.89 r_work: 0.2974 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.1450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 6232 Z= 0.131 Angle : 0.506 7.480 8484 Z= 0.266 Chirality : 0.040 0.140 1020 Planarity : 0.003 0.047 1074 Dihedral : 6.712 72.600 893 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.72 % Allowed : 10.02 % Favored : 88.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.01 (0.30), residues: 801 helix: 2.84 (0.22), residues: 514 sheet: 2.48 (0.78), residues: 46 loop : -0.04 (0.42), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 99 TYR 0.007 0.001 TYR A 299 PHE 0.017 0.001 PHE A 462 TRP 0.005 0.001 TRP A 379 HIS 0.002 0.001 HIS A 722 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 ( 6232) covalent geometry : angle 0.50641 / 0.27 ( 8484) hydrogen bonds : bond 0.06017 / 4.35 ( 436) hydrogen bonds : angle 4.01961 / 2.98 ( 1272) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 63 time to evaluate : 0.230 Fit side-chains revert: symmetry clash REVERT: A 373 MET cc_start: 0.7865 (mpp) cc_final: 0.6632 (tmm) REVERT: B 31 LYS cc_start: 0.8767 (mttp) cc_final: 0.8548 (mttp) REVERT: B 57 VAL cc_start: 0.8764 (t) cc_final: 0.8494 (m) REVERT: B 76 TYR cc_start: 0.9149 (t80) cc_final: 0.8883 (t80) outliers start: 11 outliers final: 8 residues processed: 68 average time/residue: 0.0712 time to fit residues: 6.7800 Evaluate side-chains 70 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 62 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 417 ASP Chi-restraints excluded: chain A residue 791 MET Chi-restraints excluded: chain A residue 925 MET Chi-restraints excluded: chain B residue 25 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 71 optimal weight: 0.2980 chunk 13 optimal weight: 0.0050 chunk 52 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 2 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 44 optimal weight: 6.9990 chunk 53 optimal weight: 4.9990 chunk 35 optimal weight: 0.0870 chunk 75 optimal weight: 7.9990 overall best weight: 0.7974 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 78 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.107199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.076933 restraints weight = 12726.001| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 2.90 r_work: 0.3016 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 6232 Z= 0.115 Angle : 0.483 6.542 8484 Z= 0.251 Chirality : 0.039 0.140 1020 Planarity : 0.003 0.047 1074 Dihedral : 6.429 72.584 893 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.35 % Allowed : 10.33 % Favored : 87.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.98 (0.30), residues: 801 helix: 2.88 (0.22), residues: 513 sheet: 2.44 (0.77), residues: 46 loop : -0.17 (0.41), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 99 TYR 0.007 0.001 TYR A 299 PHE 0.015 0.001 PHE A 462 TRP 0.005 0.001 TRP A 833 HIS 0.002 0.001 HIS A 832 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 ( 6232) covalent geometry : angle 0.48252 / 0.25 ( 8484) hydrogen bonds : bond 0.05202 / 3.78 ( 436) hydrogen bonds : angle 3.93015 / 2.91 ( 1272) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 62 time to evaluate : 0.224 Fit side-chains revert: symmetry clash REVERT: A 373 MET cc_start: 0.7896 (mpp) cc_final: 0.6668 (tmm) outliers start: 15 outliers final: 11 residues processed: 71 average time/residue: 0.0741 time to fit residues: 7.2184 Evaluate side-chains 71 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 60 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 417 ASP Chi-restraints excluded: chain A residue 791 MET Chi-restraints excluded: chain A residue 899 GLU Chi-restraints excluded: chain A residue 925 MET Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 78 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 53 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 9 optimal weight: 0.9980 chunk 7 optimal weight: 10.0000 chunk 68 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 43 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 78 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.104310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.073978 restraints weight = 12759.190| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 2.86 r_work: 0.2963 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6232 Z= 0.163 Angle : 0.524 7.855 8484 Z= 0.274 Chirality : 0.040 0.137 1020 Planarity : 0.004 0.048 1074 Dihedral : 6.429 72.860 893 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.72 % Allowed : 12.68 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.95 (0.30), residues: 801 helix: 2.81 (0.22), residues: 515 sheet: 2.41 (0.76), residues: 46 loop : -0.09 (0.42), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 99 TYR 0.016 0.001 TYR B 76 PHE 0.010 0.001 PHE A 332 TRP 0.004 0.001 TRP A 379 HIS 0.002 0.001 HIS A 308 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.16 ( 6232) covalent geometry : angle 0.52432 / 0.27 ( 8484) hydrogen bonds : bond 0.06207 / 4.47 ( 436) hydrogen bonds : angle 4.05808 / 3.01 ( 1272) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 0.215 Fit side-chains revert: symmetry clash REVERT: A 373 MET cc_start: 0.7901 (mpp) cc_final: 0.6710 (tmm) REVERT: A 899 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7569 (pm20) REVERT: B 57 VAL cc_start: 0.8801 (t) cc_final: 0.8512 (m) outliers start: 11 outliers final: 8 residues processed: 64 average time/residue: 0.0654 time to fit residues: 5.9043 Evaluate side-chains 67 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 58 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 417 ASP Chi-restraints excluded: chain A residue 899 GLU Chi-restraints excluded: chain A residue 925 MET Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 78 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 52 optimal weight: 5.9990 chunk 40 optimal weight: 4.9990 chunk 70 optimal weight: 0.9990 chunk 73 optimal weight: 4.9990 chunk 7 optimal weight: 10.0000 chunk 74 optimal weight: 5.9990 chunk 61 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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 = 0.3593 r_free = 0.3593 target = 0.104067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.073704 restraints weight = 12783.495| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 2.86 r_work: 0.2961 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 6232 Z= 0.152 Angle : 0.521 7.749 8484 Z= 0.273 Chirality : 0.040 0.140 1020 Planarity : 0.003 0.048 1074 Dihedral : 6.438 73.440 893 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.72 % Allowed : 12.52 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.89 (0.30), residues: 801 helix: 2.76 (0.22), residues: 515 sheet: 2.39 (0.76), residues: 46 loop : -0.13 (0.41), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 99 TYR 0.008 0.001 TYR B 76 PHE 0.018 0.001 PHE A 462 TRP 0.005 0.001 TRP A 379 HIS 0.002 0.001 HIS A 308 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 ( 6232) covalent geometry : angle 0.52150 / 0.27 ( 8484) hydrogen bonds : bond 0.06247 / 4.51 ( 436) hydrogen bonds : angle 4.06771 / 3.02 ( 1272) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 0.235 Fit side-chains revert: symmetry clash REVERT: A 373 MET cc_start: 0.7911 (mpp) cc_final: 0.6703 (tmm) REVERT: B 57 VAL cc_start: 0.8801 (t) cc_final: 0.8512 (m) outliers start: 11 outliers final: 8 residues processed: 65 average time/residue: 0.0669 time to fit residues: 6.1308 Evaluate side-chains 66 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 417 ASP Chi-restraints excluded: chain A residue 899 GLU Chi-restraints excluded: chain A residue 925 MET Chi-restraints excluded: chain B residue 25 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 62 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 chunk 51 optimal weight: 0.7980 chunk 4 optimal weight: 0.0060 chunk 0 optimal weight: 4.9990 overall best weight: 0.9600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 78 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.106713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.076473 restraints weight = 12741.401| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 2.89 r_work: 0.3011 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 6232 Z= 0.121 Angle : 0.495 7.744 8484 Z= 0.259 Chirality : 0.039 0.141 1020 Planarity : 0.003 0.047 1074 Dihedral : 6.374 74.057 893 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.56 % Allowed : 12.52 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.01 (0.30), residues: 801 helix: 2.89 (0.22), residues: 515 sheet: 2.42 (0.76), residues: 46 loop : -0.16 (0.41), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 388 TYR 0.007 0.001 TYR A 299 PHE 0.007 0.001 PHE A 332 TRP 0.006 0.001 TRP A 833 HIS 0.002 0.000 HIS A 308 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 ( 6232) covalent geometry : angle 0.49505 / 0.26 ( 8484) hydrogen bonds : bond 0.05345 / 3.90 ( 436) hydrogen bonds : angle 3.97091 / 2.94 ( 1272) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 0.207 Fit side-chains revert: symmetry clash REVERT: A 373 MET cc_start: 0.7835 (mpp) cc_final: 0.6671 (tmm) REVERT: B 57 VAL cc_start: 0.8733 (t) cc_final: 0.8440 (m) outliers start: 10 outliers final: 9 residues processed: 71 average time/residue: 0.0709 time to fit residues: 6.8787 Evaluate side-chains 71 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 62 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 417 ASP Chi-restraints excluded: chain A residue 899 GLU Chi-restraints excluded: chain A residue 925 MET Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 78 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 40 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 73 optimal weight: 6.9990 chunk 58 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 77 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 chunk 52 optimal weight: 0.0070 chunk 71 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 overall best weight: 0.9202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 78 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.106487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.076339 restraints weight = 12813.053| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 2.90 r_work: 0.3009 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 6232 Z= 0.127 Angle : 0.543 8.358 8484 Z= 0.278 Chirality : 0.040 0.140 1020 Planarity : 0.003 0.047 1074 Dihedral : 6.357 74.149 893 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.56 % Allowed : 12.99 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.94 (0.30), residues: 801 helix: 2.83 (0.22), residues: 516 sheet: 2.47 (0.76), residues: 46 loop : -0.19 (0.41), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 99 TYR 0.007 0.001 TYR A 299 PHE 0.019 0.001 PHE A 462 TRP 0.005 0.001 TRP A 379 HIS 0.002 0.000 HIS A 308 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 ( 6232) covalent geometry : angle 0.54253 / 0.28 ( 8484) hydrogen bonds : bond 0.05330 / 3.86 ( 436) hydrogen bonds : angle 3.96936 / 2.94 ( 1272) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 59 time to evaluate : 0.223 Fit side-chains REVERT: A 373 MET cc_start: 0.7858 (mpp) cc_final: 0.6637 (tmm) REVERT: B 57 VAL cc_start: 0.8774 (t) cc_final: 0.8499 (m) outliers start: 10 outliers final: 8 residues processed: 64 average time/residue: 0.0701 time to fit residues: 6.2828 Evaluate side-chains 65 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 417 ASP Chi-restraints excluded: chain A residue 925 MET Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 78 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 24 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 6 optimal weight: 10.0000 chunk 5 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 3 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 55 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 78 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.106742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.076683 restraints weight = 12653.206| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 2.90 r_work: 0.3003 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 6232 Z= 0.124 Angle : 0.526 8.172 8484 Z= 0.271 Chirality : 0.040 0.144 1020 Planarity : 0.003 0.047 1074 Dihedral : 6.329 74.143 893 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.72 % Allowed : 12.83 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.95 (0.30), residues: 801 helix: 2.84 (0.22), residues: 516 sheet: 2.45 (0.76), residues: 46 loop : -0.22 (0.40), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 99 TYR 0.007 0.001 TYR A 299 PHE 0.007 0.001 PHE A 332 TRP 0.005 0.001 TRP A 379 HIS 0.002 0.000 HIS A 308 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 ( 6232) covalent geometry : angle 0.52605 / 0.27 ( 8484) hydrogen bonds : bond 0.05236 / 3.79 ( 436) hydrogen bonds : angle 3.96004 / 2.93 ( 1272) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1540.92 seconds wall clock time: 27 minutes 4.27 seconds (1624.27 seconds total)