Starting phenix.real_space_refine on Tue Feb 3 18:32:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9u51_63860/02_2026/9u51_63860.cif Found real_map, /net/cci-nas-00/data/ceres_data/9u51_63860/02_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9u51_63860/02_2026/9u51_63860.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9u51_63860/02_2026/9u51_63860.map" model { file = "/net/cci-nas-00/data/ceres_data/9u51_63860/02_2026/9u51_63860.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9u51_63860/02_2026/9u51_63860.cif" } 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-2.0-5952/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 Planarities with less than four sites: {'4HH:plan-3': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 1.29, per 1000 atoms: 0.21 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: 0.46 Conformation dependent library (CDL) restraints added in 203.0 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: 0.19 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: 0.87 Time building geometry restraints manager: 0.57 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=" CQ 4HH B 41 " pdb=" NR 4HH B 41 " ideal model delta sigma weight residual 1.374 1.452 -0.078 2.00e-02 2.50e+03 1.51e+01 bond pdb=" CQ 4HH B 41 " pdb=" OR 4HH B 41 " ideal model delta sigma weight residual 1.256 1.185 0.071 2.00e-02 2.50e+03 1.27e+01 bond pdb=" CL3 4HH B 41 " pdb=" NN 4HH B 41 " ideal model delta sigma weight residual 1.386 1.453 -0.067 2.00e-02 2.50e+03 1.14e+01 bond pdb=" OG 4HH B 41 " pdb=" P 4HH B 41 " ideal model delta sigma weight residual 1.624 1.557 0.067 2.00e-02 2.50e+03 1.11e+01 bond pdb=" CL3 4HH B 41 " pdb=" ON 4HH B 41 " ideal model delta sigma weight residual 1.250 1.186 0.064 2.00e-02 2.50e+03 1.04e+01 ... (remaining 6227 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.70: 8456 3.70 - 7.39: 24 7.39 - 11.09: 2 11.09 - 14.78: 0 14.78 - 18.48: 2 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 96.91 115.39 -18.48 3.00e+00 1.11e-01 3.79e+01 angle pdb=" O1P 4HH B 41 " pdb=" P 4HH B 41 " pdb=" O2P 4HH B 41 " ideal model delta sigma weight residual 122.75 104.34 18.41 3.00e+00 1.11e-01 3.77e+01 angle pdb=" OG 4HH B 41 " pdb=" P 4HH B 41 " pdb=" O1P 4HH B 41 " ideal model delta sigma weight residual 106.46 96.17 10.29 3.00e+00 1.11e-01 1.18e+01 angle pdb=" O1P 4HH B 41 " pdb=" P 4HH B 41 " pdb=" O3P 4HH B 41 " ideal model delta sigma weight residual 106.79 114.08 -7.29 3.00e+00 1.11e-01 5.90e+00 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 ... (remaining 8479 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.86: 3482 21.86 - 43.71: 191 43.71 - 65.57: 22 65.57 - 87.43: 9 87.43 - 109.28: 1 Dihedral angle restraints: 3705 sinusoidal: 1402 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 173.45 -77.27 -109.28 1 3.00e+01 1.11e-03 1.42e+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=" CQ 4HH B 41 " pdb=" CO 4HH B 41 " pdb=" CP 4HH B 41 " pdb=" NN 4HH B 41 " ideal model delta sinusoidal sigma weight residual 156.22 -120.58 -83.20 1 3.00e+01 1.11e-03 9.40e+00 ... (remaining 3702 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 609 0.027 - 0.054: 218 0.054 - 0.081: 136 0.081 - 0.108: 42 0.108 - 0.135: 15 Chirality restraints: 1020 Sorted by residual: 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 chirality pdb=" CA ILE A 93 " pdb=" N ILE A 93 " pdb=" C ILE A 93 " pdb=" CB ILE A 93 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.85e-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: 0.830 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: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 6.520 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: 0.000 Load rotamer database and sin/cos tables:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.550 ------------------------------------------------------------------------------- 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 0.078 6232 Z= 0.161 Angle : 0.607 18.479 8484 Z= 0.282 Chirality : 0.039 0.135 1020 Planarity : 0.003 0.035 1074 Dihedral : 13.985 109.284 2227 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 covalent geometry : bond 0.00320 ( 6232) covalent geometry : angle 0.60728 ( 8484) hydrogen bonds : bond 0.12662 ( 436) hydrogen bonds : angle 4.71398 ( 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 : 0.201 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: 0.0683 time to fit residues: 7.1138 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 : 0.218 ------------------------------------------------------------------------------- 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 = 0.107684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.076464 restraints weight = 12996.624| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 2.97 r_work: 0.3020 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.0952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 6232 Z= 0.151 Angle : 0.538 8.205 8484 Z= 0.281 Chirality : 0.041 0.135 1020 Planarity : 0.004 0.049 1074 Dihedral : 5.929 84.381 869 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % 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: 3.06 (0.30), residues: 801 helix: 2.93 (0.22), residues: 510 sheet: 2.77 (0.80), residues: 46 loop : -0.15 (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 covalent geometry : bond 0.00352 ( 6232) covalent geometry : angle 0.53775 ( 8484) hydrogen bonds : bond 0.06081 ( 436) hydrogen bonds : angle 4.09492 ( 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 : 0.149 Fit side-chains REVERT: A 373 MET cc_start: 0.7946 (mpp) cc_final: 0.6577 (tmm) outliers start: 5 outliers final: 3 residues processed: 64 average time/residue: 0.0719 time to fit residues: 6.0203 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 : 0.176 ------------------------------------------------------------------------------- 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: 0.0270 chunk 27 optimal weight: 7.9990 chunk 41 optimal weight: 10.0000 chunk 71 optimal weight: 1.9990 chunk 51 optimal weight: 10.0000 chunk 18 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 10 optimal weight: 9.9990 chunk 4 optimal weight: 3.9990 chunk 45 optimal weight: 8.9990 chunk 26 optimal weight: 0.9980 overall best weight: 1.2042 ------------------------------------------------------------------------------- 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 = 0.3635 r_free = 0.3635 target = 0.108443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.077317 restraints weight = 12801.650| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 2.93 r_work: 0.3029 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.1055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 6232 Z= 0.128 Angle : 0.507 8.689 8484 Z= 0.264 Chirality : 0.040 0.136 1020 Planarity : 0.003 0.047 1074 Dihedral : 5.601 78.418 869 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.25 % Allowed : 8.14 % Favored : 90.61 % 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: 2.86 (0.22), residues: 510 sheet: 2.65 (0.79), residues: 46 loop : -0.13 (0.41), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 388 TYR 0.010 0.001 TYR B 76 PHE 0.007 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 covalent geometry : bond 0.00279 ( 6232) covalent geometry : angle 0.50739 ( 8484) hydrogen bonds : bond 0.05679 ( 436) hydrogen bonds : angle 4.00100 ( 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 : 0.226 Fit side-chains REVERT: A 373 MET cc_start: 0.7945 (mpp) cc_final: 0.6610 (tmm) REVERT: B 57 VAL cc_start: 0.8658 (t) cc_final: 0.8335 (m) outliers start: 8 outliers final: 6 residues processed: 67 average time/residue: 0.0607 time to fit residues: 5.6829 Evaluate side-chains 69 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 63 time to evaluate : 0.133 ------------------------------------------------------------------------------- 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: 2.9990 chunk 14 optimal weight: 2.9990 chunk 10 optimal weight: 10.0000 chunk 5 optimal weight: 1.9990 chunk 78 optimal weight: 0.0970 chunk 41 optimal weight: 10.0000 chunk 24 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 16 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 overall best weight: 1.1982 ------------------------------------------------------------------------------- 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 = 0.3619 r_free = 0.3619 target = 0.106103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.075836 restraints weight = 12703.704| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 2.89 r_work: 0.3004 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.1224 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= 0.126 Angle : 0.495 7.311 8484 Z= 0.258 Chirality : 0.039 0.136 1020 Planarity : 0.003 0.047 1074 Dihedral : 5.375 77.013 869 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.56 % Allowed : 9.23 % Favored : 89.20 % 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: 2.99 (0.30), residues: 801 helix: 2.91 (0.22), residues: 509 sheet: 2.53 (0.79), residues: 46 loop : -0.19 (0.40), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 388 TYR 0.006 0.001 TYR A 299 PHE 0.008 0.001 PHE A 332 TRP 0.004 0.001 TRP A 379 HIS 0.002 0.001 HIS A 832 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 6232) covalent geometry : angle 0.49465 ( 8484) hydrogen bonds : bond 0.05581 ( 436) hydrogen bonds : angle 3.96204 ( 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 76 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 0.135 Fit side-chains revert: symmetry clash REVERT: A 373 MET cc_start: 0.7853 (mpp) cc_final: 0.6629 (tmm) REVERT: B 57 VAL cc_start: 0.8742 (t) cc_final: 0.8461 (m) REVERT: B 76 TYR cc_start: 0.9110 (t80) cc_final: 0.8807 (t80) outliers start: 10 outliers final: 8 residues processed: 70 average time/residue: 0.0722 time to fit residues: 6.7464 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 : 0.171 ------------------------------------------------------------------------------- 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 16 ILE 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: 5.9990 chunk 71 optimal weight: 2.9990 chunk 45 optimal weight: 0.0030 chunk 55 optimal weight: 0.9980 chunk 8 optimal weight: 5.9990 chunk 46 optimal weight: 6.9990 chunk 54 optimal weight: 9.9990 chunk 1 optimal weight: 0.9990 chunk 52 optimal weight: 10.0000 chunk 44 optimal weight: 10.0000 chunk 41 optimal weight: 5.9990 overall best weight: 2.1996 ------------------------------------------------------------------------------- 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 = 0.3581 r_free = 0.3581 target = 0.103299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.072827 restraints weight = 12835.342| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 2.88 r_work: 0.2943 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6232 Z= 0.173 Angle : 0.535 7.568 8484 Z= 0.282 Chirality : 0.041 0.136 1020 Planarity : 0.004 0.048 1074 Dihedral : 5.362 76.148 869 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.72 % Allowed : 10.64 % Favored : 87.64 % 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: 2.92 (0.30), residues: 801 helix: 2.77 (0.22), residues: 513 sheet: 2.48 (0.79), residues: 46 loop : -0.05 (0.41), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 99 TYR 0.007 0.001 TYR A 431 PHE 0.011 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 covalent geometry : bond 0.00413 ( 6232) covalent geometry : angle 0.53469 ( 8484) hydrogen bonds : bond 0.06563 ( 436) hydrogen bonds : angle 4.10641 ( 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 : 0.142 Fit side-chains revert: symmetry clash REVERT: A 373 MET cc_start: 0.7897 (mpp) cc_final: 0.6670 (tmm) REVERT: B 31 LYS cc_start: 0.8711 (mttp) cc_final: 0.8509 (mttp) REVERT: B 57 VAL cc_start: 0.8801 (t) cc_final: 0.8524 (m) REVERT: B 67 LEU cc_start: 0.8564 (tp) cc_final: 0.8342 (tp) REVERT: B 76 TYR cc_start: 0.9193 (t80) cc_final: 0.8872 (t80) outliers start: 11 outliers final: 6 residues processed: 67 average time/residue: 0.0618 time to fit residues: 5.7410 Evaluate side-chains 67 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 61 time to evaluate : 0.211 ------------------------------------------------------------------------------- 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 403 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 71 optimal weight: 0.6980 chunk 13 optimal weight: 3.9990 chunk 52 optimal weight: 10.0000 chunk 3 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 6 optimal weight: 9.9990 chunk 4 optimal weight: 0.9990 chunk 44 optimal weight: 6.9990 chunk 53 optimal weight: 4.9990 chunk 35 optimal weight: 0.3980 chunk 75 optimal weight: 7.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- 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 = 0.3604 r_free = 0.3604 target = 0.104771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.074382 restraints weight = 12723.147| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 2.87 r_work: 0.2973 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.1505 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= 0.136 Angle : 0.506 8.144 8484 Z= 0.263 Chirality : 0.040 0.141 1020 Planarity : 0.003 0.048 1074 Dihedral : 5.297 75.354 869 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.88 % Allowed : 11.11 % Favored : 87.01 % 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: 2.80 (0.22), residues: 515 sheet: 2.44 (0.77), residues: 46 loop : -0.12 (0.41), residues: 240 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 0.016 0.001 PHE A 462 TRP 0.005 0.001 TRP A 379 HIS 0.002 0.001 HIS A 832 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 6232) covalent geometry : angle 0.50581 ( 8484) hydrogen bonds : bond 0.06090 ( 436) hydrogen bonds : angle 4.03394 ( 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 72 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 0.213 Fit side-chains REVERT: A 373 MET cc_start: 0.7844 (mpp) cc_final: 0.6631 (tmm) REVERT: A 899 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7570 (pm20) REVERT: B 57 VAL cc_start: 0.8782 (t) cc_final: 0.8500 (m) REVERT: B 76 TYR cc_start: 0.9149 (t80) cc_final: 0.8782 (t80) outliers start: 12 outliers final: 8 residues processed: 65 average time/residue: 0.0619 time to fit residues: 5.5761 Evaluate side-chains 69 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.188 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 53 optimal weight: 2.9990 chunk 47 optimal weight: 10.0000 chunk 59 optimal weight: 5.9990 chunk 9 optimal weight: 0.9990 chunk 7 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 43 optimal weight: 8.9990 chunk 50 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 = 0.3594 r_free = 0.3594 target = 0.106049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.074434 restraints weight = 13134.218| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 2.98 r_work: 0.2974 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.1576 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= 0.153 Angle : 0.531 8.183 8484 Z= 0.277 Chirality : 0.040 0.139 1020 Planarity : 0.004 0.048 1074 Dihedral : 5.302 74.952 869 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.88 % Allowed : 11.42 % Favored : 86.70 % 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: 2.84 (0.30), residues: 801 helix: 2.76 (0.22), residues: 515 sheet: 2.17 (0.74), residues: 46 loop : -0.18 (0.41), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 99 TYR 0.007 0.001 TYR A 285 PHE 0.020 0.001 PHE A 462 TRP 0.004 0.001 TRP A 379 HIS 0.002 0.001 HIS A 308 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 6232) covalent geometry : angle 0.53131 ( 8484) hydrogen bonds : bond 0.06317 ( 436) hydrogen bonds : angle 4.06822 ( 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: 12 poor density : 58 time to evaluate : 0.155 Fit side-chains REVERT: A 373 MET cc_start: 0.7925 (mpp) cc_final: 0.6632 (tmm) REVERT: B 57 VAL cc_start: 0.8707 (t) cc_final: 0.8417 (m) outliers start: 12 outliers final: 9 residues processed: 63 average time/residue: 0.0539 time to fit residues: 4.8806 Evaluate side-chains 65 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.223 ------------------------------------------------------------------------------- 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: 0.8980 chunk 40 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 7 optimal weight: 8.9990 chunk 74 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 = 0.3603 r_free = 0.3603 target = 0.106714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.075133 restraints weight = 13122.981| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 3.01 r_work: 0.2981 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.1573 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= 0.137 Angle : 0.527 8.179 8484 Z= 0.275 Chirality : 0.040 0.142 1020 Planarity : 0.004 0.048 1074 Dihedral : 5.269 74.482 869 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.88 % Allowed : 11.89 % Favored : 86.23 % 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: 2.80 (0.22), residues: 515 sheet: 2.09 (0.72), residues: 46 loop : -0.16 (0.41), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 99 TYR 0.017 0.001 TYR B 76 PHE 0.008 0.001 PHE A 332 TRP 0.005 0.001 TRP A 379 HIS 0.002 0.001 HIS A 308 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 6232) covalent geometry : angle 0.52687 ( 8484) hydrogen bonds : bond 0.06041 ( 436) hydrogen bonds : angle 4.02077 ( 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 70 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 0.211 Fit side-chains REVERT: A 373 MET cc_start: 0.7933 (mpp) cc_final: 0.6643 (tmm) outliers start: 12 outliers final: 8 residues processed: 64 average time/residue: 0.0474 time to fit residues: 4.4590 Evaluate side-chains 64 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 0.205 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 62 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 58 optimal weight: 0.4980 chunk 8 optimal weight: 0.9990 chunk 43 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 4 optimal weight: 0.0000 chunk 0 optimal weight: 4.9990 overall best weight: 0.6988 ------------------------------------------------------------------------------- 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 = 0.3636 r_free = 0.3636 target = 0.109003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.077643 restraints weight = 13002.253| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 3.01 r_work: 0.3028 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 6232 Z= 0.120 Angle : 0.506 8.779 8484 Z= 0.262 Chirality : 0.039 0.141 1020 Planarity : 0.003 0.048 1074 Dihedral : 5.192 73.716 869 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % 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: 2.95 (0.30), residues: 801 helix: 2.91 (0.22), residues: 513 sheet: 2.15 (0.73), residues: 46 loop : -0.26 (0.41), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 99 TYR 0.023 0.001 TYR B 76 PHE 0.017 0.001 PHE A 462 TRP 0.006 0.001 TRP A 379 HIS 0.002 0.000 HIS A 308 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 6232) covalent geometry : angle 0.50610 ( 8484) hydrogen bonds : bond 0.05366 ( 436) hydrogen bonds : angle 3.94749 ( 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 69 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 59 time to evaluate : 0.133 Fit side-chains REVERT: A 232 MET cc_start: 0.8465 (mmm) cc_final: 0.8248 (mmm) REVERT: A 373 MET cc_start: 0.7902 (mpp) cc_final: 0.6660 (tmm) REVERT: B 57 VAL cc_start: 0.8636 (t) cc_final: 0.8323 (m) outliers start: 10 outliers final: 8 residues processed: 64 average time/residue: 0.0487 time to fit residues: 4.4756 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 : 0.129 ------------------------------------------------------------------------------- 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 40 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 73 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 71 optimal weight: 0.3980 chunk 0 optimal weight: 4.9990 chunk 75 optimal weight: 0.7980 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 = 0.3642 r_free = 0.3642 target = 0.109198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.077884 restraints weight = 12979.068| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 2.97 r_work: 0.3037 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.1542 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= 0.122 Angle : 0.521 8.463 8484 Z= 0.268 Chirality : 0.040 0.146 1020 Planarity : 0.003 0.048 1074 Dihedral : 5.164 73.188 869 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.41 % Allowed : 12.21 % Favored : 86.38 % 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: 2.90 (0.30), residues: 801 helix: 2.86 (0.22), residues: 513 sheet: 2.15 (0.73), residues: 46 loop : -0.26 (0.40), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 99 TYR 0.018 0.001 TYR B 76 PHE 0.008 0.001 PHE A 473 TRP 0.005 0.001 TRP A 379 HIS 0.002 0.000 HIS A 308 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 6232) covalent geometry : angle 0.52059 ( 8484) hydrogen bonds : bond 0.05269 ( 436) hydrogen bonds : angle 3.93908 ( 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 65 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.151 Fit side-chains REVERT: A 373 MET cc_start: 0.7932 (mpp) cc_final: 0.6604 (tmm) REVERT: B 57 VAL cc_start: 0.8620 (t) cc_final: 0.8356 (m) outliers start: 9 outliers final: 7 residues processed: 60 average time/residue: 0.0491 time to fit residues: 4.2513 Evaluate side-chains 62 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 55 time to evaluate : 0.159 ------------------------------------------------------------------------------- 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 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: 0.7980 chunk 9 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 6 optimal weight: 10.0000 chunk 5 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 chunk 55 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 = 0.3618 r_free = 0.3618 target = 0.107549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.076251 restraints weight = 12943.123| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 2.98 r_work: 0.3002 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 6232 Z= 0.143 Angle : 0.550 9.432 8484 Z= 0.280 Chirality : 0.040 0.140 1020 Planarity : 0.004 0.048 1074 Dihedral : 5.160 72.944 869 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.41 % Allowed : 12.68 % 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: 2.85 (0.30), residues: 801 helix: 2.78 (0.22), residues: 516 sheet: 2.15 (0.73), residues: 46 loop : -0.23 (0.40), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 99 TYR 0.014 0.001 TYR B 76 PHE 0.018 0.001 PHE A 462 TRP 0.005 0.001 TRP A 379 HIS 0.002 0.000 HIS A 308 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 6232) covalent geometry : angle 0.54963 ( 8484) hydrogen bonds : bond 0.05743 ( 436) hydrogen bonds : angle 4.02359 ( 1272) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1206.39 seconds wall clock time: 21 minutes 14.24 seconds (1274.24 seconds total)