Starting phenix.real_space_refine on Thu Jul 2 20:12:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9x5r_66595/07_2026/9x5r_66595.cif Found real_map, /net/cci-nas-00/data/ceres_data/9x5r_66595/07_2026/9x5r_66595.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9x5r_66595/07_2026/9x5r_66595.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9x5r_66595/07_2026/9x5r_66595.map" model { file = "/net/cci-nas-00/data/ceres_data/9x5r_66595/07_2026/9x5r_66595.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9x5r_66595/07_2026/9x5r_66595.cif" } resolution = 2.7 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 ------------------------------------------------------------------------------- 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= 0.001 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 Zn 1 6.06 5 S 75 5.16 5 C 6368 2.51 5 N 1661 2.21 5 O 1835 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9940 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 9340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1186, 9340 Classifications: {'peptide': 1186} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 59, 'TRANS': 1126} Chain breaks: 3 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 49 Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 1, 'ASP:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 30 Chain: "B" Number of atoms: 341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 341 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 4, 'TRANS': 40} Chain: "A" Number of atoms: 259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 259 Unusual residues: {' ZN': 1, 'SVR': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 7707 SG CYS A 993 44.779 71.713 86.791 1.00131.86 S ATOM 9116 SG CYS A1210 41.927 73.574 87.048 1.00156.23 S ATOM 9138 SG CYS A1213 42.897 72.289 83.746 1.00136.34 S Time building chain proxies: 2.17, per 1000 atoms: 0.22 Number of scatterers: 9940 At special positions: 0 Unit cell: (88.33, 100.01, 105.85, 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) Zn 1 29.99 S 75 16.00 O 1835 8.00 N 1661 7.00 C 6368 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: 1.15 Conformation dependent library (CDL) restraints added in 428.6 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2000 " pdb="ZN ZN A2000 " - pdb=" SG CYS A1213 " pdb="ZN ZN A2000 " - pdb=" SG CYS A1210 " pdb="ZN ZN A2000 " - pdb=" SG CYS A 993 " 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2340 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 7 sheets defined 60.8% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 33 through 42 Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 65 through 70 Processing helix chain 'A' and resid 81 through 99 removed outlier: 3.523A pdb=" N TRP A 99 " --> pdb=" O ILE A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 116 removed outlier: 3.839A pdb=" N LYS A 106 " --> pdb=" O ASP A 102 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N THR A 107 " --> pdb=" O HIS A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 139 Processing helix chain 'A' and resid 176 through 202 Processing helix chain 'A' and resid 208 through 221 Processing helix chain 'A' and resid 225 through 248 removed outlier: 4.592A pdb=" N PHE A 237 " --> pdb=" O ILE A 233 " (cutoff:3.500A) Proline residue: A 238 - end of helix Processing helix chain 'A' and resid 255 through 259 removed outlier: 3.946A pdb=" N VAL A 259 " --> pdb=" O PHE A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 266 Processing helix chain 'A' and resid 266 through 280 Processing helix chain 'A' and resid 280 through 290 removed outlier: 3.942A pdb=" N VAL A 290 " --> pdb=" O MET A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 312 Processing helix chain 'A' and resid 318 through 345 Processing helix chain 'A' and resid 358 through 368 removed outlier: 3.587A pdb=" N LYS A 362 " --> pdb=" O ASP A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 377 removed outlier: 3.816A pdb=" N ASP A 375 " --> pdb=" O SER A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 382 removed outlier: 3.666A pdb=" N GLU A 382 " --> pdb=" O GLN A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 402 removed outlier: 4.043A pdb=" N VAL A 402 " --> pdb=" O PHE A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 415 removed outlier: 3.706A pdb=" N TRP A 414 " --> pdb=" O SER A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 428 Processing helix chain 'A' and resid 441 through 450 removed outlier: 3.893A pdb=" N GLY A 450 " --> pdb=" O ALA A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 465 Proline residue: A 461 - end of helix Processing helix chain 'A' and resid 468 through 471 Processing helix chain 'A' and resid 494 through 512 Processing helix chain 'A' and resid 517 through 523 removed outlier: 3.674A pdb=" N MET A 521 " --> pdb=" O LYS A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 542 Processing helix chain 'A' and resid 553 through 558 removed outlier: 3.867A pdb=" N PHE A 558 " --> pdb=" O TRP A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 575 removed outlier: 3.509A pdb=" N GLN A 563 " --> pdb=" O ARG A 559 " (cutoff:3.500A) Proline residue: A 565 - end of helix Processing helix chain 'A' and resid 578 through 586 Processing helix chain 'A' and resid 587 through 589 No H-bonds generated for 'chain 'A' and resid 587 through 589' Processing helix chain 'A' and resid 627 through 646 removed outlier: 3.881A pdb=" N ILE A 646 " --> pdb=" O ALA A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 690 Processing helix chain 'A' and resid 720 through 726 Processing helix chain 'A' and resid 738 through 756 Processing helix chain 'A' and resid 759 through 779 Processing helix chain 'A' and resid 780 through 785 Processing helix chain 'A' and resid 786 through 795 Processing helix chain 'A' and resid 797 through 801 Processing helix chain 'A' and resid 819 through 835 removed outlier: 4.355A pdb=" N PHE A 823 " --> pdb=" O ASP A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 838 through 847 Processing helix chain 'A' and resid 855 through 862 Processing helix chain 'A' and resid 877 through 889 removed outlier: 4.043A pdb=" N TRP A 881 " --> pdb=" O GLN A 877 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N SER A 889 " --> pdb=" O ALA A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 893 through 901 Processing helix chain 'A' and resid 902 through 915 Processing helix chain 'A' and resid 921 through 932 Processing helix chain 'A' and resid 933 through 945 removed outlier: 3.657A pdb=" N GLY A 937 " --> pdb=" O ASN A 933 " (cutoff:3.500A) Processing helix chain 'A' and resid 947 through 957 removed outlier: 3.606A pdb=" N VAL A 957 " --> pdb=" O ALA A 953 " (cutoff:3.500A) Processing helix chain 'A' and resid 959 through 979 removed outlier: 4.017A pdb=" N ALA A 963 " --> pdb=" O ILE A 959 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU A 964 " --> pdb=" O GLU A 960 " (cutoff:3.500A) Processing helix chain 'A' and resid 986 through 990 Processing helix chain 'A' and resid 993 through 1007 Processing helix chain 'A' and resid 1017 through 1021 Processing helix chain 'A' and resid 1031 through 1037 removed outlier: 4.248A pdb=" N ASP A1037 " --> pdb=" O GLU A1033 " (cutoff:3.500A) Processing helix chain 'A' and resid 1049 through 1053 Processing helix chain 'A' and resid 1082 through 1100 Processing helix chain 'A' and resid 1104 through 1119 Processing helix chain 'A' and resid 1148 through 1156 Processing helix chain 'A' and resid 1178 through 1195 Processing helix chain 'A' and resid 1210 through 1214 Processing helix chain 'B' and resid 138 through 167 removed outlier: 3.673A pdb=" N THR B 151 " --> pdb=" O THR B 147 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N MET B 155 " --> pdb=" O THR B 151 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N MET B 156 " --> pdb=" O MET B 152 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS B 158 " --> pdb=" O LEU B 154 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 58 through 60 removed outlier: 4.451A pdb=" N LEU A 173 " --> pdb=" O LEU A 60 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N MET A 154 " --> pdb=" O ARG A 150 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N ARG A 150 " --> pdb=" O MET A 154 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N LEU A 156 " --> pdb=" O PRO A 148 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE A 158 " --> pdb=" O ILE A 146 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 351 through 353 Processing sheet with id=AA3, first strand: chain 'A' and resid 489 through 492 Processing sheet with id=AA4, first strand: chain 'A' and resid 650 through 654 Processing sheet with id=AA5, first strand: chain 'A' and resid 603 through 604 Processing sheet with id=AA6, first strand: chain 'A' and resid 704 through 706 Processing sheet with id=AA7, first strand: chain 'A' and resid 1022 through 1026 533 hydrogen bonds defined for protein. 1548 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.86 Time building geometry restraints manager: 1.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2369 1.33 - 1.45: 2154 1.45 - 1.58: 5555 1.58 - 1.70: 0 1.70 - 1.82: 105 Bond restraints: 10183 Sorted by residual: bond pdb=" C LEU A 586 " pdb=" N PRO A 587 " ideal model delta sigma weight residual 1.334 1.363 -0.028 1.51e-02 4.39e+03 3.53e+00 bond pdb=" C MET A 513 " pdb=" N PRO A 514 " ideal model delta sigma weight residual 1.334 1.365 -0.031 2.34e-02 1.83e+03 1.72e+00 bond pdb=" CB GLN A 320 " pdb=" CG GLN A 320 " ideal model delta sigma weight residual 1.520 1.558 -0.038 3.00e-02 1.11e+03 1.64e+00 bond pdb=" CB GLU A 971 " pdb=" CG GLU A 971 " ideal model delta sigma weight residual 1.520 1.552 -0.032 3.00e-02 1.11e+03 1.11e+00 bond pdb=" CB MET B 149 " pdb=" CG MET B 149 " ideal model delta sigma weight residual 1.520 1.551 -0.031 3.00e-02 1.11e+03 1.03e+00 ... (remaining 10178 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.28: 13727 2.28 - 4.56: 138 4.56 - 6.84: 20 6.84 - 9.12: 7 9.12 - 11.39: 7 Bond angle restraints: 13899 Sorted by residual: angle pdb=" CB MET A 301 " pdb=" CG MET A 301 " pdb=" SD MET A 301 " ideal model delta sigma weight residual 112.70 124.09 -11.39 3.00e+00 1.11e-01 1.44e+01 angle pdb=" CA GLU A 460 " pdb=" CB GLU A 460 " pdb=" CG GLU A 460 " ideal model delta sigma weight residual 114.10 121.56 -7.46 2.00e+00 2.50e-01 1.39e+01 angle pdb=" CB MET B 149 " pdb=" CG MET B 149 " pdb=" SD MET B 149 " ideal model delta sigma weight residual 112.70 123.26 -10.56 3.00e+00 1.11e-01 1.24e+01 angle pdb=" CB MET B 156 " pdb=" CG MET B 156 " pdb=" SD MET B 156 " ideal model delta sigma weight residual 112.70 123.18 -10.48 3.00e+00 1.11e-01 1.22e+01 angle pdb=" CB MET A1111 " pdb=" CG MET A1111 " pdb=" SD MET A1111 " ideal model delta sigma weight residual 112.70 123.16 -10.46 3.00e+00 1.11e-01 1.21e+01 ... (remaining 13894 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.96: 5088 16.96 - 33.92: 646 33.92 - 50.88: 201 50.88 - 67.83: 42 67.83 - 84.79: 11 Dihedral angle restraints: 5988 sinusoidal: 2376 harmonic: 3612 Sorted by residual: dihedral pdb=" CA PRO A 434 " pdb=" C PRO A 434 " pdb=" N PRO A 435 " pdb=" CA PRO A 435 " ideal model delta harmonic sigma weight residual -180.00 -154.05 -25.95 0 5.00e+00 4.00e-02 2.69e+01 dihedral pdb=" CA LEU A1147 " pdb=" C LEU A1147 " pdb=" N THR A1148 " pdb=" CA THR A1148 " ideal model delta harmonic sigma weight residual 180.00 159.74 20.26 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" CA THR A1053 " pdb=" C THR A1053 " pdb=" N THR A1054 " pdb=" CA THR A1054 " ideal model delta harmonic sigma weight residual 180.00 -161.59 -18.41 0 5.00e+00 4.00e-02 1.36e+01 ... (remaining 5985 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1110 0.036 - 0.072: 333 0.072 - 0.108: 95 0.108 - 0.144: 15 0.144 - 0.180: 2 Chirality restraints: 1555 Sorted by residual: chirality pdb=" CA ILE A 662 " pdb=" N ILE A 662 " pdb=" C ILE A 662 " pdb=" CB ILE A 662 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 8.09e-01 chirality pdb=" CA PRO A 435 " pdb=" N PRO A 435 " pdb=" C PRO A 435 " pdb=" CB PRO A 435 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.36e-01 chirality pdb=" CA ILE A1039 " pdb=" N ILE A1039 " pdb=" C ILE A1039 " pdb=" CB ILE A1039 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.16e-01 ... (remaining 1552 not shown) Planarity restraints: 1731 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 434 " 0.028 5.00e-02 4.00e+02 4.29e-02 2.95e+00 pdb=" N PRO A 435 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 435 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 435 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A1200 " -0.007 2.00e-02 2.50e+03 1.45e-02 2.10e+00 pdb=" C ILE A1200 " 0.025 2.00e-02 2.50e+03 pdb=" O ILE A1200 " -0.009 2.00e-02 2.50e+03 pdb=" N SER A1201 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 971 " 0.007 2.00e-02 2.50e+03 1.40e-02 1.95e+00 pdb=" CD GLU A 971 " -0.024 2.00e-02 2.50e+03 pdb=" OE1 GLU A 971 " 0.009 2.00e-02 2.50e+03 pdb=" OE2 GLU A 971 " 0.008 2.00e-02 2.50e+03 ... (remaining 1728 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 70 2.56 - 3.15: 7917 3.15 - 3.73: 16540 3.73 - 4.32: 21681 4.32 - 4.90: 36299 Nonbonded interactions: 82507 Sorted by model distance: nonbonded pdb=" OE2 GLU A1020 " pdb="ZN ZN A2000 " model vdw 1.980 2.230 nonbonded pdb=" O THR A 518 " pdb=" OG1 THR A 522 " model vdw 2.223 3.040 nonbonded pdb=" NH1 ARG A 411 " pdb=" O PHE A 469 " model vdw 2.270 3.120 nonbonded pdb=" NE ARG A 815 " pdb=" O LEU A1147 " model vdw 2.274 3.120 nonbonded pdb=" OH TYR A 239 " pdb=" OD1 ASP A 270 " model vdw 2.301 3.040 ... (remaining 82502 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: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.690 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 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 : 0.002 0.038 10186 Z= 0.104 Angle : 0.594 11.394 13899 Z= 0.278 Chirality : 0.038 0.180 1555 Planarity : 0.004 0.049 1731 Dihedral : 16.917 84.792 3648 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 0.94 % Allowed : 30.15 % Favored : 68.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.25), residues: 1221 helix: 2.47 (0.21), residues: 641 sheet: 1.11 (0.71), residues: 66 loop : -1.09 (0.26), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 58 TYR 0.023 0.001 TYR A 705 PHE 0.017 0.001 PHE A 469 TRP 0.019 0.001 TRP A1157 HIS 0.004 0.001 HIS A 685 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.10 (10183) covalent geometry : angle 0.59434 / 0.28 (13899) hydrogen bonds : bond 0.13346 / 8.84 ( 533) hydrogen bonds : angle 5.17238 / 3.69 ( 1548) metal coordination : bond 0.00264 / 0.13 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 116 time to evaluate : 0.351 Fit side-chains revert: symmetry clash REVERT: A 464 ARG cc_start: 0.7782 (mtm110) cc_final: 0.7388 (mtm110) outliers start: 10 outliers final: 6 residues processed: 124 average time/residue: 0.4172 time to fit residues: 57.0572 Evaluate side-chains 119 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 113 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 584 CYS Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 916 THR Chi-restraints excluded: chain A residue 1148 THR Chi-restraints excluded: chain A residue 1194 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 108 optimal weight: 20.0000 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.0470 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 8.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 9.9990 chunk 117 optimal weight: 7.9990 overall best weight: 1.3682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 724 GLN A 738 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.126552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.086663 restraints weight = 16215.643| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 3.30 r_work: 0.3004 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 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 0.029 10186 Z= 0.138 Angle : 0.549 8.916 13899 Z= 0.267 Chirality : 0.040 0.140 1555 Planarity : 0.004 0.039 1731 Dihedral : 6.044 63.691 1376 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 3.75 % Allowed : 25.37 % Favored : 70.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.25), residues: 1221 helix: 2.23 (0.21), residues: 676 sheet: 0.65 (0.68), residues: 66 loop : -1.07 (0.28), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 58 TYR 0.023 0.001 TYR A 853 PHE 0.013 0.001 PHE A 230 TRP 0.018 0.001 TRP A 638 HIS 0.004 0.001 HIS A 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 (10183) covalent geometry : angle 0.54937 / 0.27 (13899) hydrogen bonds : bond 0.03661 / 2.39 ( 533) hydrogen bonds : angle 4.12127 / 2.98 ( 1548) metal coordination : bond 0.00762 / 0.38 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 116 time to evaluate : 0.356 Fit side-chains revert: symmetry clash REVERT: A 464 ARG cc_start: 0.7536 (mtm110) cc_final: 0.7143 (mtm110) REVERT: A 862 ASP cc_start: 0.7268 (t0) cc_final: 0.7016 (t0) REVERT: A 894 ARG cc_start: 0.5914 (pmt170) cc_final: 0.5708 (pmt170) REVERT: A 971 GLU cc_start: 0.8700 (mm-30) cc_final: 0.8128 (tp30) REVERT: A 1111 MET cc_start: 0.7396 (OUTLIER) cc_final: 0.6636 (ppp) REVERT: B 149 MET cc_start: 0.6606 (ttp) cc_final: 0.6307 (ttm) outliers start: 40 outliers final: 15 residues processed: 142 average time/residue: 0.4269 time to fit residues: 66.7246 Evaluate side-chains 122 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 106 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 414 TRP Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain A residue 871 VAL Chi-restraints excluded: chain A residue 916 THR Chi-restraints excluded: chain A residue 917 MET Chi-restraints excluded: chain A residue 1111 MET Chi-restraints excluded: chain A residue 1147 LEU Chi-restraints excluded: chain A residue 1148 THR Chi-restraints excluded: chain A residue 1194 ILE Chi-restraints excluded: chain B residue 142 ASP Chi-restraints excluded: chain B residue 151 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 71 optimal weight: 3.9990 chunk 52 optimal weight: 9.9990 chunk 60 optimal weight: 6.9990 chunk 81 optimal weight: 4.9990 chunk 114 optimal weight: 0.0070 chunk 23 optimal weight: 6.9990 chunk 120 optimal weight: 10.0000 chunk 5 optimal weight: 0.0870 chunk 79 optimal weight: 4.9990 chunk 67 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 overall best weight: 2.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 47 HIS A 241 GLN A 724 GLN A 738 ASN ** A1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.120834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.080952 restraints weight = 16280.240| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 3.20 r_work: 0.2853 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10186 Z= 0.187 Angle : 0.590 9.376 13899 Z= 0.287 Chirality : 0.041 0.149 1555 Planarity : 0.004 0.050 1731 Dihedral : 6.093 64.337 1372 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 4.31 % Allowed : 25.19 % Favored : 70.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.25), residues: 1221 helix: 2.04 (0.21), residues: 674 sheet: 0.17 (0.65), residues: 68 loop : -1.03 (0.28), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 58 TYR 0.022 0.002 TYR A 853 PHE 0.018 0.001 PHE A 230 TRP 0.020 0.002 TRP A 638 HIS 0.005 0.001 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.19 (10183) covalent geometry : angle 0.58972 / 0.29 (13899) hydrogen bonds : bond 0.04005 / 2.61 ( 533) hydrogen bonds : angle 4.10888 / 2.93 ( 1548) metal coordination : bond 0.01003 / 0.50 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 108 time to evaluate : 0.372 Fit side-chains revert: symmetry clash REVERT: A 142 ARG cc_start: 0.8688 (mtp85) cc_final: 0.7934 (mmm160) REVERT: A 320 GLN cc_start: 0.8933 (mm-40) cc_final: 0.8706 (mp10) REVERT: A 454 ASN cc_start: 0.8389 (t0) cc_final: 0.8117 (t0) REVERT: A 471 ASP cc_start: 0.8768 (OUTLIER) cc_final: 0.8465 (t0) REVERT: A 505 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.8424 (mp0) REVERT: A 515 TYR cc_start: 0.7639 (OUTLIER) cc_final: 0.5993 (p90) REVERT: A 568 ARG cc_start: 0.7689 (OUTLIER) cc_final: 0.7311 (ttm-80) REVERT: A 862 ASP cc_start: 0.7358 (t0) cc_final: 0.6961 (OUTLIER) REVERT: A 971 GLU cc_start: 0.8733 (mm-30) cc_final: 0.8181 (tp30) REVERT: A 1111 MET cc_start: 0.7460 (ptm) cc_final: 0.6711 (ppp) REVERT: A 1147 LEU cc_start: 0.6079 (OUTLIER) cc_final: 0.5541 (pp) REVERT: B 154 LEU cc_start: 0.6920 (OUTLIER) cc_final: 0.6581 (tm) REVERT: B 162 LEU cc_start: 0.6425 (OUTLIER) cc_final: 0.6223 (tm) outliers start: 46 outliers final: 19 residues processed: 143 average time/residue: 0.3991 time to fit residues: 62.6536 Evaluate side-chains 127 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 102 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 414 TRP Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 505 GLU Chi-restraints excluded: chain A residue 515 TYR Chi-restraints excluded: chain A residue 521 MET Chi-restraints excluded: chain A residue 568 ARG Chi-restraints excluded: chain A residue 638 TRP Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain A residue 871 VAL Chi-restraints excluded: chain A residue 916 THR Chi-restraints excluded: chain A residue 917 MET Chi-restraints excluded: chain A residue 957 VAL Chi-restraints excluded: chain A residue 1147 LEU Chi-restraints excluded: chain A residue 1148 THR Chi-restraints excluded: chain A residue 1196 SER Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 142 ASP Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 166 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 48 optimal weight: 6.9990 chunk 103 optimal weight: 7.9990 chunk 45 optimal weight: 1.9990 chunk 72 optimal weight: 0.4980 chunk 43 optimal weight: 1.9990 chunk 65 optimal weight: 0.0970 chunk 20 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 84 optimal weight: 0.2980 chunk 64 optimal weight: 6.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 724 GLN A 738 ASN A1145 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.123863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.084155 restraints weight = 16356.768| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 3.26 r_work: 0.2922 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10186 Z= 0.106 Angle : 0.563 9.564 13899 Z= 0.268 Chirality : 0.039 0.144 1555 Planarity : 0.004 0.047 1731 Dihedral : 6.017 63.624 1370 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.18 % Allowed : 26.12 % Favored : 70.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.25), residues: 1221 helix: 2.08 (0.20), residues: 674 sheet: 0.49 (0.67), residues: 67 loop : -1.05 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 58 TYR 0.023 0.001 TYR A1150 PHE 0.017 0.001 PHE A 230 TRP 0.019 0.001 TRP A 638 HIS 0.005 0.001 HIS A 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.11 (10183) covalent geometry : angle 0.56293 / 0.27 (13899) hydrogen bonds : bond 0.03394 / 2.21 ( 533) hydrogen bonds : angle 3.99082 / 2.88 ( 1548) metal coordination : bond 0.00498 / 0.25 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 106 time to evaluate : 0.446 Fit side-chains revert: symmetry clash REVERT: A 142 ARG cc_start: 0.8671 (mtp85) cc_final: 0.7932 (mmm160) REVERT: A 320 GLN cc_start: 0.8930 (mm-40) cc_final: 0.8730 (mp10) REVERT: A 454 ASN cc_start: 0.8393 (t0) cc_final: 0.8080 (t0) REVERT: A 471 ASP cc_start: 0.8703 (OUTLIER) cc_final: 0.8369 (t0) REVERT: A 515 TYR cc_start: 0.7451 (OUTLIER) cc_final: 0.5827 (p90) REVERT: A 568 ARG cc_start: 0.7733 (OUTLIER) cc_final: 0.7444 (ttm-80) REVERT: A 862 ASP cc_start: 0.7390 (t0) cc_final: 0.6946 (t0) REVERT: A 971 GLU cc_start: 0.8740 (mm-30) cc_final: 0.8173 (tp30) REVERT: A 1111 MET cc_start: 0.7470 (OUTLIER) cc_final: 0.6705 (ppp) REVERT: A 1147 LEU cc_start: 0.6031 (OUTLIER) cc_final: 0.5774 (pp) REVERT: B 154 LEU cc_start: 0.6811 (OUTLIER) cc_final: 0.6483 (tm) outliers start: 34 outliers final: 15 residues processed: 133 average time/residue: 0.4569 time to fit residues: 66.4082 Evaluate side-chains 121 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 100 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 414 TRP Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 505 GLU Chi-restraints excluded: chain A residue 515 TYR Chi-restraints excluded: chain A residue 568 ARG Chi-restraints excluded: chain A residue 638 TRP Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 871 VAL Chi-restraints excluded: chain A residue 916 THR Chi-restraints excluded: chain A residue 917 MET Chi-restraints excluded: chain A residue 1111 MET Chi-restraints excluded: chain A residue 1147 LEU Chi-restraints excluded: chain A residue 1148 THR Chi-restraints excluded: chain A residue 1196 SER Chi-restraints excluded: chain B residue 142 ASP Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 166 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 46 optimal weight: 4.9990 chunk 77 optimal weight: 0.2980 chunk 48 optimal weight: 5.9990 chunk 119 optimal weight: 6.9990 chunk 54 optimal weight: 7.9990 chunk 3 optimal weight: 0.0030 chunk 116 optimal weight: 6.9990 chunk 21 optimal weight: 5.9990 chunk 20 optimal weight: 0.4980 chunk 58 optimal weight: 3.9990 chunk 51 optimal weight: 9.9990 overall best weight: 1.9594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 724 GLN A 738 ASN A1044 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.119781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.079837 restraints weight = 16456.920| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 3.25 r_work: 0.2880 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10186 Z= 0.172 Angle : 0.589 9.146 13899 Z= 0.283 Chirality : 0.041 0.140 1555 Planarity : 0.004 0.048 1731 Dihedral : 6.104 63.056 1370 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.93 % Allowed : 25.84 % Favored : 70.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.25), residues: 1221 helix: 2.11 (0.21), residues: 663 sheet: -0.13 (0.61), residues: 78 loop : -1.08 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 58 TYR 0.025 0.002 TYR A 853 PHE 0.017 0.001 PHE A 230 TRP 0.020 0.001 TRP A 638 HIS 0.005 0.001 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.17 (10183) covalent geometry : angle 0.58896 / 0.28 (13899) hydrogen bonds : bond 0.03760 / 2.43 ( 533) hydrogen bonds : angle 3.99008 / 2.86 ( 1548) metal coordination : bond 0.00885 / 0.44 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 103 time to evaluate : 0.382 Fit side-chains revert: symmetry clash REVERT: A 140 TYR cc_start: 0.8826 (OUTLIER) cc_final: 0.8302 (m-80) REVERT: A 142 ARG cc_start: 0.8671 (mtp85) cc_final: 0.7881 (mmm160) REVERT: A 320 GLN cc_start: 0.8936 (mm-40) cc_final: 0.8732 (mp10) REVERT: A 454 ASN cc_start: 0.8412 (t0) cc_final: 0.8120 (t0) REVERT: A 471 ASP cc_start: 0.8789 (OUTLIER) cc_final: 0.8469 (t0) REVERT: A 515 TYR cc_start: 0.7756 (OUTLIER) cc_final: 0.6094 (p90) REVERT: A 568 ARG cc_start: 0.7719 (OUTLIER) cc_final: 0.7370 (ttm-80) REVERT: A 610 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.7249 (tp30) REVERT: A 862 ASP cc_start: 0.7476 (t0) cc_final: 0.7006 (t0) REVERT: A 971 GLU cc_start: 0.8740 (mm-30) cc_final: 0.8152 (tp30) REVERT: A 1111 MET cc_start: 0.7510 (OUTLIER) cc_final: 0.6761 (ppp) REVERT: B 154 LEU cc_start: 0.6841 (OUTLIER) cc_final: 0.6477 (tm) outliers start: 42 outliers final: 19 residues processed: 135 average time/residue: 0.4602 time to fit residues: 67.9648 Evaluate side-chains 125 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 99 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 140 TYR Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 414 TRP Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 505 GLU Chi-restraints excluded: chain A residue 515 TYR Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 568 ARG Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 638 TRP Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain A residue 871 VAL Chi-restraints excluded: chain A residue 916 THR Chi-restraints excluded: chain A residue 917 MET Chi-restraints excluded: chain A residue 1111 MET Chi-restraints excluded: chain A residue 1148 THR Chi-restraints excluded: chain A residue 1196 SER Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 166 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 43 optimal weight: 10.0000 chunk 98 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 chunk 38 optimal weight: 0.8980 chunk 117 optimal weight: 7.9990 chunk 102 optimal weight: 9.9990 chunk 16 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 79 optimal weight: 0.0170 chunk 84 optimal weight: 6.9990 overall best weight: 2.3824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 241 GLN A 724 GLN A 738 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.118439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.078516 restraints weight = 16468.132| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 3.21 r_work: 0.2834 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 10186 Z= 0.193 Angle : 0.596 9.059 13899 Z= 0.289 Chirality : 0.041 0.149 1555 Planarity : 0.004 0.048 1731 Dihedral : 6.229 62.886 1370 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 4.03 % Allowed : 25.56 % Favored : 70.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.25), residues: 1221 helix: 2.05 (0.21), residues: 667 sheet: -0.09 (0.66), residues: 68 loop : -1.11 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 58 TYR 0.021 0.001 TYR A1150 PHE 0.019 0.001 PHE A 230 TRP 0.019 0.002 TRP A 638 HIS 0.004 0.001 HIS A 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.19 (10183) covalent geometry : angle 0.59579 / 0.29 (13899) hydrogen bonds : bond 0.03867 / 2.49 ( 533) hydrogen bonds : angle 4.09531 / 2.94 ( 1548) metal coordination : bond 0.00918 / 0.45 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 102 time to evaluate : 0.420 Fit side-chains revert: symmetry clash REVERT: A 140 TYR cc_start: 0.8864 (OUTLIER) cc_final: 0.8331 (m-80) REVERT: A 142 ARG cc_start: 0.8671 (mtp85) cc_final: 0.7888 (mmm160) REVERT: A 294 TRP cc_start: 0.8841 (OUTLIER) cc_final: 0.8510 (m100) REVERT: A 320 GLN cc_start: 0.8938 (mm-40) cc_final: 0.8725 (mp10) REVERT: A 454 ASN cc_start: 0.8491 (t0) cc_final: 0.8225 (t0) REVERT: A 471 ASP cc_start: 0.8803 (OUTLIER) cc_final: 0.8455 (t0) REVERT: A 515 TYR cc_start: 0.7942 (OUTLIER) cc_final: 0.6326 (p90) REVERT: A 568 ARG cc_start: 0.7787 (OUTLIER) cc_final: 0.7422 (ttm-80) REVERT: A 862 ASP cc_start: 0.7518 (t0) cc_final: 0.7022 (t0) REVERT: A 971 GLU cc_start: 0.8754 (mm-30) cc_final: 0.8216 (tp30) REVERT: A 1111 MET cc_start: 0.7559 (OUTLIER) cc_final: 0.6802 (ppp) REVERT: A 1147 LEU cc_start: 0.6138 (OUTLIER) cc_final: 0.5741 (pt) REVERT: B 154 LEU cc_start: 0.6897 (OUTLIER) cc_final: 0.6544 (tm) outliers start: 43 outliers final: 23 residues processed: 134 average time/residue: 0.4522 time to fit residues: 66.3836 Evaluate side-chains 128 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 97 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 140 TYR Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 294 TRP Chi-restraints excluded: chain A residue 414 TRP Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 505 GLU Chi-restraints excluded: chain A residue 515 TYR Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 568 ARG Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 638 TRP Chi-restraints excluded: chain A residue 661 ILE Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain A residue 871 VAL Chi-restraints excluded: chain A residue 916 THR Chi-restraints excluded: chain A residue 917 MET Chi-restraints excluded: chain A residue 1111 MET Chi-restraints excluded: chain A residue 1147 LEU Chi-restraints excluded: chain A residue 1148 THR Chi-restraints excluded: chain A residue 1196 SER Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 142 ASP Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 166 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 47 optimal weight: 0.9980 chunk 78 optimal weight: 0.6980 chunk 36 optimal weight: 5.9990 chunk 87 optimal weight: 8.9990 chunk 72 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 38 optimal weight: 6.9990 chunk 79 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 101 optimal weight: 0.4980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 249 ASN A 724 GLN A 738 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.120925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.081025 restraints weight = 16290.659| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 3.26 r_work: 0.2906 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10186 Z= 0.121 Angle : 0.573 9.510 13899 Z= 0.276 Chirality : 0.040 0.140 1555 Planarity : 0.004 0.048 1731 Dihedral : 6.206 62.988 1370 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 3.18 % Allowed : 26.97 % Favored : 69.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.25), residues: 1221 helix: 2.07 (0.21), residues: 667 sheet: 0.06 (0.67), residues: 68 loop : -1.14 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 58 TYR 0.021 0.001 TYR A1150 PHE 0.018 0.001 PHE A 230 TRP 0.021 0.001 TRP A 638 HIS 0.005 0.001 HIS A 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (10183) covalent geometry : angle 0.57304 / 0.28 (13899) hydrogen bonds : bond 0.03450 / 2.23 ( 533) hydrogen bonds : angle 4.03418 / 2.92 ( 1548) metal coordination : bond 0.00541 / 0.27 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 103 time to evaluate : 0.344 Fit side-chains revert: symmetry clash REVERT: A 142 ARG cc_start: 0.8641 (mtp85) cc_final: 0.7895 (mmm160) REVERT: A 294 TRP cc_start: 0.8697 (OUTLIER) cc_final: 0.8241 (m100) REVERT: A 454 ASN cc_start: 0.8489 (t0) cc_final: 0.8218 (t0) REVERT: A 471 ASP cc_start: 0.8750 (OUTLIER) cc_final: 0.8392 (t0) REVERT: A 515 TYR cc_start: 0.7751 (OUTLIER) cc_final: 0.6084 (p90) REVERT: A 568 ARG cc_start: 0.7651 (OUTLIER) cc_final: 0.7295 (ttm-80) REVERT: A 862 ASP cc_start: 0.7459 (t0) cc_final: 0.6971 (t0) REVERT: A 971 GLU cc_start: 0.8746 (mm-30) cc_final: 0.8181 (tp30) REVERT: A 1111 MET cc_start: 0.7545 (OUTLIER) cc_final: 0.6799 (ppp) REVERT: A 1147 LEU cc_start: 0.6157 (OUTLIER) cc_final: 0.5537 (pp) REVERT: B 154 LEU cc_start: 0.6818 (OUTLIER) cc_final: 0.6457 (tm) outliers start: 34 outliers final: 17 residues processed: 128 average time/residue: 0.4253 time to fit residues: 59.7750 Evaluate side-chains 125 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 101 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 294 TRP Chi-restraints excluded: chain A residue 414 TRP Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 505 GLU Chi-restraints excluded: chain A residue 515 TYR Chi-restraints excluded: chain A residue 521 MET Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 568 ARG Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 638 TRP Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain A residue 871 VAL Chi-restraints excluded: chain A residue 916 THR Chi-restraints excluded: chain A residue 917 MET Chi-restraints excluded: chain A residue 1111 MET Chi-restraints excluded: chain A residue 1147 LEU Chi-restraints excluded: chain A residue 1148 THR Chi-restraints excluded: chain A residue 1196 SER Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 166 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 86 optimal weight: 3.9990 chunk 95 optimal weight: 10.0000 chunk 62 optimal weight: 0.9990 chunk 110 optimal weight: 0.5980 chunk 33 optimal weight: 0.0010 chunk 29 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 59 optimal weight: 6.9990 chunk 5 optimal weight: 0.9980 chunk 80 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 overall best weight: 1.1190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 249 ASN A 724 GLN A 738 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.120980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.081143 restraints weight = 16174.328| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 3.23 r_work: 0.2876 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10186 Z= 0.126 Angle : 0.586 10.447 13899 Z= 0.282 Chirality : 0.040 0.172 1555 Planarity : 0.004 0.049 1731 Dihedral : 6.209 62.830 1370 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 3.00 % Allowed : 27.25 % Favored : 69.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.25), residues: 1221 helix: 2.08 (0.21), residues: 667 sheet: 0.12 (0.68), residues: 68 loop : -1.13 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A 58 TYR 0.028 0.001 TYR A 853 PHE 0.017 0.001 PHE A 230 TRP 0.020 0.001 TRP A 638 HIS 0.005 0.001 HIS A 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (10183) covalent geometry : angle 0.58580 / 0.28 (13899) hydrogen bonds : bond 0.03434 / 2.23 ( 533) hydrogen bonds : angle 4.08285 / 2.96 ( 1548) metal coordination : bond 0.00549 / 0.27 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 101 time to evaluate : 0.386 Fit side-chains revert: symmetry clash REVERT: A 142 ARG cc_start: 0.8647 (mtp85) cc_final: 0.7888 (mmm160) REVERT: A 294 TRP cc_start: 0.8667 (OUTLIER) cc_final: 0.8172 (m100) REVERT: A 454 ASN cc_start: 0.8472 (t0) cc_final: 0.8204 (t0) REVERT: A 471 ASP cc_start: 0.8746 (OUTLIER) cc_final: 0.8346 (t0) REVERT: A 515 TYR cc_start: 0.7705 (OUTLIER) cc_final: 0.6087 (p90) REVERT: A 568 ARG cc_start: 0.7657 (OUTLIER) cc_final: 0.7285 (ttm-80) REVERT: A 815 ARG cc_start: 0.7887 (mtm110) cc_final: 0.7526 (ptm-80) REVERT: A 862 ASP cc_start: 0.7453 (t0) cc_final: 0.6968 (t0) REVERT: A 971 GLU cc_start: 0.8750 (mm-30) cc_final: 0.8182 (tp30) REVERT: A 1111 MET cc_start: 0.7549 (OUTLIER) cc_final: 0.6800 (ppp) REVERT: A 1147 LEU cc_start: 0.6107 (OUTLIER) cc_final: 0.5339 (pp) REVERT: B 154 LEU cc_start: 0.6788 (OUTLIER) cc_final: 0.6440 (tm) outliers start: 32 outliers final: 17 residues processed: 126 average time/residue: 0.4550 time to fit residues: 62.7386 Evaluate side-chains 124 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 100 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 294 TRP Chi-restraints excluded: chain A residue 414 TRP Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 505 GLU Chi-restraints excluded: chain A residue 515 TYR Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 568 ARG Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 638 TRP Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain A residue 871 VAL Chi-restraints excluded: chain A residue 916 THR Chi-restraints excluded: chain A residue 917 MET Chi-restraints excluded: chain A residue 1111 MET Chi-restraints excluded: chain A residue 1147 LEU Chi-restraints excluded: chain A residue 1148 THR Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 142 ASP Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 166 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 7 optimal weight: 3.9990 chunk 45 optimal weight: 0.5980 chunk 61 optimal weight: 0.5980 chunk 8 optimal weight: 3.9990 chunk 69 optimal weight: 5.9990 chunk 96 optimal weight: 0.0970 chunk 20 optimal weight: 0.6980 chunk 98 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 724 GLN A 738 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.123032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.083281 restraints weight = 16127.417| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 3.26 r_work: 0.2948 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 10186 Z= 0.108 Angle : 0.589 10.437 13899 Z= 0.282 Chirality : 0.040 0.183 1555 Planarity : 0.004 0.051 1731 Dihedral : 6.202 62.824 1370 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.62 % Allowed : 28.00 % Favored : 69.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.25), residues: 1221 helix: 2.04 (0.20), residues: 675 sheet: 0.26 (0.69), residues: 68 loop : -1.11 (0.28), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A 58 TYR 0.027 0.001 TYR A1150 PHE 0.016 0.001 PHE A 230 TRP 0.021 0.001 TRP A 638 HIS 0.005 0.001 HIS A 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (10183) covalent geometry : angle 0.58931 / 0.28 (13899) hydrogen bonds : bond 0.03206 / 2.07 ( 533) hydrogen bonds : angle 4.06504 / 2.95 ( 1548) metal coordination : bond 0.00379 / 0.19 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 104 time to evaluate : 0.385 Fit side-chains revert: symmetry clash REVERT: A 142 ARG cc_start: 0.8626 (mtp85) cc_final: 0.7860 (mmm160) REVERT: A 294 TRP cc_start: 0.8594 (OUTLIER) cc_final: 0.8119 (m100) REVERT: A 454 ASN cc_start: 0.8425 (t0) cc_final: 0.8140 (t0) REVERT: A 471 ASP cc_start: 0.8671 (OUTLIER) cc_final: 0.8257 (t0) REVERT: A 505 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.8269 (mp0) REVERT: A 515 TYR cc_start: 0.7576 (OUTLIER) cc_final: 0.5922 (p90) REVERT: A 568 ARG cc_start: 0.7613 (OUTLIER) cc_final: 0.7225 (ttm-80) REVERT: A 815 ARG cc_start: 0.7817 (mtm110) cc_final: 0.7490 (ptm-80) REVERT: A 862 ASP cc_start: 0.7441 (t0) cc_final: 0.6958 (t0) REVERT: A 971 GLU cc_start: 0.8739 (mm-30) cc_final: 0.8148 (tp30) REVERT: A 1111 MET cc_start: 0.7539 (OUTLIER) cc_final: 0.6794 (ppp) REVERT: A 1147 LEU cc_start: 0.5981 (OUTLIER) cc_final: 0.5155 (pp) REVERT: B 154 LEU cc_start: 0.6747 (OUTLIER) cc_final: 0.6420 (tm) outliers start: 28 outliers final: 15 residues processed: 125 average time/residue: 0.4495 time to fit residues: 61.6405 Evaluate side-chains 128 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 105 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 294 TRP Chi-restraints excluded: chain A residue 414 TRP Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 505 GLU Chi-restraints excluded: chain A residue 515 TYR Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 568 ARG Chi-restraints excluded: chain A residue 638 TRP Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain A residue 871 VAL Chi-restraints excluded: chain A residue 916 THR Chi-restraints excluded: chain A residue 917 MET Chi-restraints excluded: chain A residue 1111 MET Chi-restraints excluded: chain A residue 1147 LEU Chi-restraints excluded: chain A residue 1148 THR Chi-restraints excluded: chain B residue 142 ASP Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 166 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 18 optimal weight: 4.9990 chunk 69 optimal weight: 5.9990 chunk 103 optimal weight: 0.4980 chunk 56 optimal weight: 5.9990 chunk 104 optimal weight: 5.9990 chunk 79 optimal weight: 0.0870 chunk 120 optimal weight: 6.9990 chunk 98 optimal weight: 5.9990 chunk 16 optimal weight: 0.8980 chunk 35 optimal weight: 9.9990 chunk 21 optimal weight: 2.9990 overall best weight: 1.8962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 738 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.119681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.079590 restraints weight = 16106.631| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 3.21 r_work: 0.2854 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10186 Z= 0.169 Angle : 0.625 10.121 13899 Z= 0.300 Chirality : 0.042 0.244 1555 Planarity : 0.004 0.056 1731 Dihedral : 6.281 62.414 1370 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.72 % Allowed : 28.09 % Favored : 69.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.25), residues: 1221 helix: 2.01 (0.20), residues: 674 sheet: 0.10 (0.69), residues: 68 loop : -1.12 (0.28), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG A 58 TYR 0.033 0.001 TYR A1150 PHE 0.017 0.001 PHE A 230 TRP 0.018 0.002 TRP A 638 HIS 0.005 0.001 HIS A 685 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.17 (10183) covalent geometry : angle 0.62501 / 0.30 (13899) hydrogen bonds : bond 0.03636 / 2.37 ( 533) hydrogen bonds : angle 4.13716 / 2.99 ( 1548) metal coordination : bond 0.00656 / 0.32 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 97 time to evaluate : 0.434 Fit side-chains revert: symmetry clash REVERT: A 142 ARG cc_start: 0.8653 (mtp85) cc_final: 0.8271 (mtp85) REVERT: A 294 TRP cc_start: 0.8741 (OUTLIER) cc_final: 0.8277 (m100) REVERT: A 454 ASN cc_start: 0.8481 (t0) cc_final: 0.8192 (t0) REVERT: A 471 ASP cc_start: 0.8772 (OUTLIER) cc_final: 0.8377 (t0) REVERT: A 505 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.8314 (mp0) REVERT: A 515 TYR cc_start: 0.7748 (OUTLIER) cc_final: 0.6104 (p90) REVERT: A 568 ARG cc_start: 0.7686 (OUTLIER) cc_final: 0.7326 (ttm-80) REVERT: A 610 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.7264 (tp30) REVERT: A 815 ARG cc_start: 0.7971 (mtm110) cc_final: 0.7420 (ptm-80) REVERT: A 862 ASP cc_start: 0.7523 (t0) cc_final: 0.7048 (t0) REVERT: A 971 GLU cc_start: 0.8773 (mm-30) cc_final: 0.8192 (tp30) REVERT: A 1111 MET cc_start: 0.7558 (OUTLIER) cc_final: 0.6812 (ppp) REVERT: A 1147 LEU cc_start: 0.6125 (OUTLIER) cc_final: 0.5169 (pp) REVERT: B 154 LEU cc_start: 0.6779 (OUTLIER) cc_final: 0.6403 (tm) outliers start: 29 outliers final: 17 residues processed: 120 average time/residue: 0.4905 time to fit residues: 64.1930 Evaluate side-chains 122 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 96 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 294 TRP Chi-restraints excluded: chain A residue 414 TRP Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 505 GLU Chi-restraints excluded: chain A residue 515 TYR Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 568 ARG Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain A residue 638 TRP Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain A residue 871 VAL Chi-restraints excluded: chain A residue 916 THR Chi-restraints excluded: chain A residue 917 MET Chi-restraints excluded: chain A residue 1111 MET Chi-restraints excluded: chain A residue 1147 LEU Chi-restraints excluded: chain A residue 1148 THR Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 142 ASP Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 166 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 100 optimal weight: 0.9980 chunk 97 optimal weight: 0.0370 chunk 4 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 74 optimal weight: 0.6980 chunk 110 optimal weight: 0.8980 chunk 101 optimal weight: 0.4980 chunk 23 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 738 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.122629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.082879 restraints weight = 16217.503| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 3.25 r_work: 0.2936 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10186 Z= 0.111 Angle : 0.614 10.875 13899 Z= 0.293 Chirality : 0.040 0.241 1555 Planarity : 0.004 0.048 1731 Dihedral : 6.235 62.653 1370 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 2.43 % Allowed : 28.75 % Favored : 68.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.25), residues: 1221 helix: 1.97 (0.20), residues: 680 sheet: 0.26 (0.69), residues: 68 loop : -1.04 (0.29), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG A 58 TYR 0.021 0.001 TYR A1150 PHE 0.017 0.001 PHE A 230 TRP 0.019 0.001 TRP A 638 HIS 0.005 0.001 HIS A 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (10183) covalent geometry : angle 0.61436 / 0.29 (13899) hydrogen bonds : bond 0.03170 / 2.06 ( 533) hydrogen bonds : angle 4.11267 / 2.99 ( 1548) metal coordination : bond 0.00341 / 0.17 ( 3) =============================================================================== Job complete usr+sys time: 3050.79 seconds wall clock time: 52 minutes 59.24 seconds (3179.24 seconds total)