Starting phenix.real_space_refine on Sat Aug 23 01:19:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f0x_28782/08_2025/8f0x_28782.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f0x_28782/08_2025/8f0x_28782.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8f0x_28782/08_2025/8f0x_28782.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f0x_28782/08_2025/8f0x_28782.map" model { file = "/net/cci-nas-00/data/ceres_data/8f0x_28782/08_2025/8f0x_28782.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f0x_28782/08_2025/8f0x_28782.cif" } resolution = 3.21 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= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 334 atoms to isotropic. 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: 4 Type Number sf(0) Gaussians S 35 5.16 5 C 5588 2.51 5 N 1441 2.21 5 O 1679 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8743 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 928, 7395 Classifications: {'peptide': 928} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 901} Chain breaks: 2 Chain: "B" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 646 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Chain: "C" Number of atoms: 702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 702 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 2, 'TRANS': 87} Time building chain proxies: 2.05, per 1000 atoms: 0.23 Number of scatterers: 8743 At special positions: 0 Unit cell: (87.897, 94.251, 114.901, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 35 16.00 O 1679 8.00 N 1441 7.00 C 5588 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: 0.65 Conformation dependent library (CDL) restraints added in 345.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2144 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 4 sheets defined 83.5% alpha, 1.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 2 through 12 Processing helix chain 'A' and resid 14 through 46 removed outlier: 3.506A pdb=" N SER A 31 " --> pdb=" O GLN A 27 " (cutoff:3.500A) removed outlier: 8.245A pdb=" N SER A 34 " --> pdb=" O ASP A 30 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N GLN A 35 " --> pdb=" O SER A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 69 removed outlier: 3.794A pdb=" N LYS A 63 " --> pdb=" O LEU A 59 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N THR A 66 " --> pdb=" O ARG A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 100 removed outlier: 3.591A pdb=" N LEU A 95 " --> pdb=" O ARG A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 123 removed outlier: 3.664A pdb=" N CYS A 114 " --> pdb=" O GLY A 110 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL A 121 " --> pdb=" O GLN A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 140 Processing helix chain 'A' and resid 143 through 158 removed outlier: 4.020A pdb=" N MET A 147 " --> pdb=" O SER A 143 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N ASP A 155 " --> pdb=" O ASN A 151 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N ASP A 156 " --> pdb=" O GLU A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 164 Processing helix chain 'A' and resid 167 through 182 Processing helix chain 'A' and resid 186 through 206 removed outlier: 3.903A pdb=" N SER A 206 " --> pdb=" O LEU A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 235 removed outlier: 3.518A pdb=" N THR A 235 " --> pdb=" O GLY A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 263 Processing helix chain 'A' and resid 265 through 269 removed outlier: 3.569A pdb=" N PHE A 269 " --> pdb=" O ARG A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 292 Processing helix chain 'A' and resid 303 through 321 removed outlier: 3.996A pdb=" N TYR A 313 " --> pdb=" O ASP A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 342 removed outlier: 3.678A pdb=" N ILE A 340 " --> pdb=" O THR A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 355 Processing helix chain 'A' and resid 355 through 364 removed outlier: 3.940A pdb=" N PHE A 359 " --> pdb=" O ASP A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 383 Processing helix chain 'A' and resid 384 through 403 removed outlier: 4.052A pdb=" N LEU A 390 " --> pdb=" O PRO A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 421 removed outlier: 4.405A pdb=" N GLU A 410 " --> pdb=" O TYR A 406 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N SER A 411 " --> pdb=" O SER A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 448 removed outlier: 4.148A pdb=" N ASP A 432 " --> pdb=" O GLY A 428 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLN A 433 " --> pdb=" O GLU A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 470 Proline residue: A 464 - end of helix Processing helix chain 'A' and resid 476 through 494 removed outlier: 3.537A pdb=" N LEU A 480 " --> pdb=" O ASP A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 515 removed outlier: 3.815A pdb=" N PHE A 514 " --> pdb=" O TYR A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 542 Proline residue: A 523 - end of helix removed outlier: 3.531A pdb=" N SER A 527 " --> pdb=" O PRO A 523 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER A 542 " --> pdb=" O ASN A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 562 Processing helix chain 'A' and resid 570 through 588 removed outlier: 3.946A pdb=" N ASP A 588 " --> pdb=" O ILE A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 605 Processing helix chain 'A' and resid 610 through 632 Proline residue: A 623 - end of helix Processing helix chain 'A' and resid 633 through 636 Processing helix chain 'A' and resid 640 through 656 Processing helix chain 'A' and resid 664 through 682 removed outlier: 4.036A pdb=" N ASN A 668 " --> pdb=" O PRO A 664 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N GLU A 673 " --> pdb=" O GLN A 669 " (cutoff:3.500A) Proline residue: A 674 - end of helix Processing helix chain 'A' and resid 684 through 702 Processing helix chain 'A' and resid 703 through 708 Processing helix chain 'A' and resid 710 through 723 removed outlier: 4.101A pdb=" N SER A 723 " --> pdb=" O GLU A 719 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 745 Processing helix chain 'A' and resid 745 through 750 removed outlier: 3.596A pdb=" N GLN A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 767 Processing helix chain 'A' and resid 769 through 787 removed outlier: 3.806A pdb=" N VAL A 779 " --> pdb=" O ASN A 775 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU A 780 " --> pdb=" O LEU A 776 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 798 Processing helix chain 'A' and resid 805 through 817 Processing helix chain 'A' and resid 818 through 820 No H-bonds generated for 'chain 'A' and resid 818 through 820' Processing helix chain 'A' and resid 822 through 840 Processing helix chain 'A' and resid 841 through 846 removed outlier: 3.527A pdb=" N LYS A 846 " --> pdb=" O LYS A 842 " (cutoff:3.500A) Processing helix chain 'A' and resid 863 through 867 Processing helix chain 'A' and resid 879 through 895 Processing helix chain 'A' and resid 964 through 978 Processing helix chain 'A' and resid 980 through 982 No H-bonds generated for 'chain 'A' and resid 980 through 982' Processing helix chain 'A' and resid 983 through 991 Processing helix chain 'A' and resid 992 through 1000 Processing helix chain 'B' and resid 18 through 23 Processing helix chain 'B' and resid 27 through 38 Processing helix chain 'B' and resid 46 through 74 removed outlier: 4.231A pdb=" N VAL B 50 " --> pdb=" O SER B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 91 Processing helix chain 'B' and resid 91 through 99 Processing helix chain 'C' and resid 40 through 52 removed outlier: 3.572A pdb=" N LYS C 46 " --> pdb=" O SER C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 86 Processing helix chain 'C' and resid 87 through 89 No H-bonds generated for 'chain 'C' and resid 87 through 89' Processing helix chain 'C' and resid 93 through 105 Processing helix chain 'C' and resid 107 through 124 removed outlier: 3.534A pdb=" N SER C 115 " --> pdb=" O LYS C 111 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 799 through 800 Processing sheet with id=AA2, first strand: chain 'A' and resid 848 through 854 removed outlier: 5.184A pdb=" N ASN A 850 " --> pdb=" O VAL A 877 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N VAL A 877 " --> pdb=" O ASN A 850 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ASN A 852 " --> pdb=" O VAL A 875 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N ARG A 873 " --> pdb=" O ILE A 854 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 43 through 44 removed outlier: 7.126A pdb=" N ARG B 43 " --> pdb=" O ILE C 92 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 78 through 79 637 hydrogen bonds defined for protein. 1896 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: 1.20 Time building geometry restraints manager: 0.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1583 1.33 - 1.45: 2076 1.45 - 1.57: 5168 1.57 - 1.69: 0 1.69 - 1.81: 53 Bond restraints: 8880 Sorted by residual: bond pdb=" N VAL A 965 " pdb=" CA VAL A 965 " ideal model delta sigma weight residual 1.462 1.499 -0.037 1.18e-02 7.18e+03 9.89e+00 bond pdb=" CA SER A 251 " pdb=" CB SER A 251 " ideal model delta sigma weight residual 1.530 1.483 0.047 1.56e-02 4.11e+03 9.01e+00 bond pdb=" N ILE A 884 " pdb=" CA ILE A 884 " ideal model delta sigma weight residual 1.460 1.495 -0.035 1.19e-02 7.06e+03 8.66e+00 bond pdb=" N VAL A 82 " pdb=" CA VAL A 82 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.66e+00 bond pdb=" N ILE A 252 " pdb=" CA ILE A 252 " ideal model delta sigma weight residual 1.460 1.495 -0.036 1.21e-02 6.83e+03 8.64e+00 ... (remaining 8875 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.19: 11269 1.19 - 2.39: 549 2.39 - 3.58: 166 3.58 - 4.77: 38 4.77 - 5.96: 3 Bond angle restraints: 12025 Sorted by residual: angle pdb=" N VAL A 258 " pdb=" CA VAL A 258 " pdb=" C VAL A 258 " ideal model delta sigma weight residual 112.35 106.73 5.62 1.41e+00 5.03e-01 1.59e+01 angle pdb=" N SER C 115 " pdb=" CA SER C 115 " pdb=" C SER C 115 " ideal model delta sigma weight residual 111.07 106.87 4.20 1.07e+00 8.73e-01 1.54e+01 angle pdb=" CA ILE C 97 " pdb=" C ILE C 97 " pdb=" O ILE C 97 " ideal model delta sigma weight residual 121.17 117.02 4.15 1.06e+00 8.90e-01 1.54e+01 angle pdb=" N VAL A 966 " pdb=" CA VAL A 966 " pdb=" C VAL A 966 " ideal model delta sigma weight residual 110.42 106.66 3.76 9.60e-01 1.09e+00 1.53e+01 angle pdb=" CA VAL C 69 " pdb=" C VAL C 69 " pdb=" O VAL C 69 " ideal model delta sigma weight residual 121.27 117.26 4.01 1.04e+00 9.25e-01 1.48e+01 ... (remaining 12020 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 5006 17.99 - 35.98: 364 35.98 - 53.97: 63 53.97 - 71.96: 16 71.96 - 89.95: 5 Dihedral angle restraints: 5454 sinusoidal: 2181 harmonic: 3273 Sorted by residual: dihedral pdb=" CA ALA C 85 " pdb=" C ALA C 85 " pdb=" N TYR C 86 " pdb=" CA TYR C 86 " ideal model delta harmonic sigma weight residual 180.00 163.16 16.84 0 5.00e+00 4.00e-02 1.13e+01 dihedral pdb=" CA ASP A 476 " pdb=" CB ASP A 476 " pdb=" CG ASP A 476 " pdb=" OD1 ASP A 476 " ideal model delta sinusoidal sigma weight residual -30.00 -87.77 57.77 1 2.00e+01 2.50e-03 1.12e+01 dihedral pdb=" CA MET A 1 " pdb=" C MET A 1 " pdb=" N ASP A 2 " pdb=" CA ASP A 2 " ideal model delta harmonic sigma weight residual 180.00 -163.31 -16.69 0 5.00e+00 4.00e-02 1.11e+01 ... (remaining 5451 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1116 0.042 - 0.085: 230 0.085 - 0.127: 69 0.127 - 0.169: 21 0.169 - 0.212: 7 Chirality restraints: 1443 Sorted by residual: chirality pdb=" CA ILE C 72 " pdb=" N ILE C 72 " pdb=" C ILE C 72 " pdb=" CB ILE C 72 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA VAL A 258 " pdb=" N VAL A 258 " pdb=" C VAL A 258 " pdb=" CB VAL A 258 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 9.66e-01 chirality pdb=" CA ILE C 76 " pdb=" N ILE C 76 " pdb=" C ILE C 76 " pdb=" CB ILE C 76 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.19 2.00e-01 2.50e+01 9.36e-01 ... (remaining 1440 not shown) Planarity restraints: 1522 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 373 " 0.016 2.00e-02 2.50e+03 3.11e-02 9.64e+00 pdb=" C ARG A 373 " -0.054 2.00e-02 2.50e+03 pdb=" O ARG A 373 " 0.020 2.00e-02 2.50e+03 pdb=" N ASP A 374 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 114 " -0.015 2.00e-02 2.50e+03 3.10e-02 9.61e+00 pdb=" C VAL C 114 " 0.054 2.00e-02 2.50e+03 pdb=" O VAL C 114 " -0.020 2.00e-02 2.50e+03 pdb=" N SER C 115 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU C 105 " -0.025 5.00e-02 4.00e+02 3.72e-02 2.21e+00 pdb=" N PRO C 106 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO C 106 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 106 " -0.021 5.00e-02 4.00e+02 ... (remaining 1519 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1428 2.76 - 3.29: 9391 3.29 - 3.83: 14030 3.83 - 4.36: 17806 4.36 - 4.90: 30711 Nonbonded interactions: 73366 Sorted by model distance: nonbonded pdb=" OG SER B 19 " pdb=" O PHE B 26 " model vdw 2.221 3.040 nonbonded pdb=" O ASN A 422 " pdb=" NZ LYS A 469 " model vdw 2.226 3.120 nonbonded pdb=" OD1 ASP A 14 " pdb=" OG1 THR A 17 " model vdw 2.250 3.040 nonbonded pdb=" NZ LYS A 657 " pdb=" O GLY A 661 " model vdw 2.291 3.120 nonbonded pdb=" OD2 ASP A 841 " pdb=" NH2 ARG A 843 " model vdw 2.301 3.120 ... (remaining 73361 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: 4.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.340 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 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 : 0.004 0.047 8880 Z= 0.294 Angle : 0.647 5.965 12025 Z= 0.470 Chirality : 0.043 0.212 1443 Planarity : 0.004 0.052 1522 Dihedral : 13.349 89.950 3310 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.50 % Allowed : 0.40 % Favored : 99.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.47 (0.25), residues: 1091 helix: 0.49 (0.18), residues: 864 sheet: None (None), residues: 0 loop : 0.13 (0.40), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 755 TYR 0.010 0.001 TYR C 86 PHE 0.012 0.001 PHE C 68 TRP 0.004 0.001 TRP A 127 HIS 0.003 0.001 HIS C 52 Details of bonding type rmsd covalent geometry : bond 0.00411 ( 8880) covalent geometry : angle 0.64677 (12025) hydrogen bonds : bond 0.22314 ( 637) hydrogen bonds : angle 7.48568 ( 1896) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 102 time to evaluate : 0.365 Fit side-chains revert: symmetry clash REVERT: A 309 ASP cc_start: 0.7675 (m-30) cc_final: 0.7212 (m-30) REVERT: A 425 GLU cc_start: 0.7194 (tp30) cc_final: 0.6950 (mm-30) REVERT: A 579 HIS cc_start: 0.8401 (t-90) cc_final: 0.8014 (t-170) REVERT: A 766 LYS cc_start: 0.7691 (mtpp) cc_final: 0.7243 (ttmt) outliers start: 5 outliers final: 0 residues processed: 105 average time/residue: 0.1133 time to fit residues: 15.9263 Evaluate side-chains 87 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 0.3980 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 overall best weight: 1.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 ASN A 375 GLN A 563 ASN A 599 GLN A 774 GLN A 840 ASN A 967 GLN B 74 ASN C 59 GLN C 87 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.178677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.135287 restraints weight = 8371.180| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 1.91 r_work: 0.3032 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 8880 Z= 0.204 Angle : 0.557 9.096 12025 Z= 0.298 Chirality : 0.040 0.122 1443 Planarity : 0.004 0.047 1522 Dihedral : 4.013 20.585 1171 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.00 % Allowed : 5.11 % Favored : 93.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.45 (0.24), residues: 1091 helix: 1.24 (0.17), residues: 879 sheet: None (None), residues: 0 loop : 0.13 (0.41), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 755 TYR 0.021 0.002 TYR C 86 PHE 0.024 0.002 PHE A 837 TRP 0.006 0.001 TRP A 69 HIS 0.004 0.001 HIS C 112 Details of bonding type rmsd covalent geometry : bond 0.00514 ( 8880) covalent geometry : angle 0.55677 (12025) hydrogen bonds : bond 0.05122 ( 637) hydrogen bonds : angle 4.36639 ( 1896) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 113 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 ASP cc_start: 0.7781 (m-30) cc_final: 0.7346 (m-30) REVERT: A 425 GLU cc_start: 0.7542 (tp30) cc_final: 0.7334 (mm-30) REVERT: A 440 LYS cc_start: 0.6780 (mtpt) cc_final: 0.6557 (mtpp) REVERT: A 574 LEU cc_start: 0.6543 (mt) cc_final: 0.6325 (mm) REVERT: A 702 THR cc_start: 0.8400 (t) cc_final: 0.8168 (t) REVERT: A 859 ASP cc_start: 0.7775 (t0) cc_final: 0.7350 (t0) REVERT: B 74 ASN cc_start: 0.6954 (OUTLIER) cc_final: 0.6745 (m-40) outliers start: 10 outliers final: 4 residues processed: 118 average time/residue: 0.1012 time to fit residues: 15.9719 Evaluate side-chains 106 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 101 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 472 ASP Chi-restraints excluded: chain A residue 653 PHE Chi-restraints excluded: chain B residue 74 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 53 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 25 optimal weight: 0.2980 chunk 15 optimal weight: 2.9990 chunk 94 optimal weight: 0.6980 chunk 46 optimal weight: 0.7980 chunk 104 optimal weight: 0.8980 chunk 80 optimal weight: 0.5980 chunk 83 optimal weight: 6.9990 chunk 72 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 563 ASN A 579 HIS A 613 ASN B 74 ASN C 87 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.182134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.139327 restraints weight = 8221.692| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 1.93 r_work: 0.3077 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8880 Z= 0.127 Angle : 0.465 9.238 12025 Z= 0.249 Chirality : 0.036 0.124 1443 Planarity : 0.004 0.046 1522 Dihedral : 3.808 19.082 1171 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.70 % Allowed : 5.91 % Favored : 93.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.18 (0.25), residues: 1091 helix: 1.77 (0.17), residues: 882 sheet: None (None), residues: 0 loop : 0.24 (0.41), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 755 TYR 0.024 0.001 TYR A 68 PHE 0.022 0.001 PHE A 837 TRP 0.005 0.001 TRP A 69 HIS 0.003 0.001 HIS C 52 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 8880) covalent geometry : angle 0.46520 (12025) hydrogen bonds : bond 0.03884 ( 637) hydrogen bonds : angle 3.93475 ( 1896) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 112 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 ASP cc_start: 0.7627 (m-30) cc_final: 0.7260 (m-30) REVERT: A 611 MET cc_start: 0.7061 (mmm) cc_final: 0.6430 (mmm) REVERT: A 702 THR cc_start: 0.8483 (t) cc_final: 0.8213 (t) REVERT: A 859 ASP cc_start: 0.7695 (t0) cc_final: 0.7277 (t0) REVERT: B 74 ASN cc_start: 0.6977 (OUTLIER) cc_final: 0.6715 (m-40) outliers start: 7 outliers final: 5 residues processed: 116 average time/residue: 0.1064 time to fit residues: 16.5711 Evaluate side-chains 110 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 104 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 563 ASN Chi-restraints excluded: chain B residue 74 ASN Chi-restraints excluded: chain C residue 126 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 17 optimal weight: 0.5980 chunk 60 optimal weight: 10.0000 chunk 64 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 3 optimal weight: 6.9990 chunk 19 optimal weight: 0.9980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 579 HIS C 87 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.183202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.145841 restraints weight = 8264.763| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 1.86 r_work: 0.3099 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8880 Z= 0.160 Angle : 0.487 9.917 12025 Z= 0.258 Chirality : 0.038 0.121 1443 Planarity : 0.004 0.048 1522 Dihedral : 3.826 19.856 1171 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 0.70 % Allowed : 7.52 % Favored : 91.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.25 (0.25), residues: 1091 helix: 1.83 (0.17), residues: 876 sheet: None (None), residues: 0 loop : 0.22 (0.39), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 755 TYR 0.016 0.002 TYR A 68 PHE 0.019 0.002 PHE A 837 TRP 0.002 0.001 TRP A 127 HIS 0.003 0.001 HIS C 52 Details of bonding type rmsd covalent geometry : bond 0.00400 ( 8880) covalent geometry : angle 0.48738 (12025) hydrogen bonds : bond 0.03927 ( 637) hydrogen bonds : angle 3.89074 ( 1896) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 102 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 GLN cc_start: 0.7322 (tp40) cc_final: 0.6460 (tt0) REVERT: A 309 ASP cc_start: 0.7936 (m-30) cc_final: 0.7566 (m-30) REVERT: A 516 GLU cc_start: 0.7846 (mt-10) cc_final: 0.7324 (mm-30) REVERT: A 611 MET cc_start: 0.7010 (mmm) cc_final: 0.6164 (mmm) REVERT: A 859 ASP cc_start: 0.7623 (t0) cc_final: 0.7233 (t0) REVERT: C 42 SER cc_start: 0.8133 (t) cc_final: 0.7770 (p) outliers start: 7 outliers final: 5 residues processed: 108 average time/residue: 0.0906 time to fit residues: 13.7594 Evaluate side-chains 103 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 98 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 653 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 22 optimal weight: 0.5980 chunk 96 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 62 optimal weight: 6.9990 chunk 28 optimal weight: 0.7980 chunk 34 optimal weight: 0.1980 chunk 50 optimal weight: 0.9980 chunk 81 optimal weight: 4.9990 chunk 88 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 104 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 237 ASN A 579 HIS B 39 ASN B 74 ASN C 87 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.185854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.148517 restraints weight = 8237.623| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 1.72 r_work: 0.3521 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3351 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8880 Z= 0.122 Angle : 0.451 10.439 12025 Z= 0.239 Chirality : 0.036 0.124 1443 Planarity : 0.004 0.045 1522 Dihedral : 3.675 18.552 1171 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 1.10 % Allowed : 8.42 % Favored : 90.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.51 (0.25), residues: 1091 helix: 2.04 (0.17), residues: 876 sheet: None (None), residues: 0 loop : 0.16 (0.39), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 755 TYR 0.018 0.001 TYR A 68 PHE 0.015 0.001 PHE A 249 TRP 0.002 0.001 TRP A 69 HIS 0.002 0.001 HIS C 52 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 8880) covalent geometry : angle 0.45082 (12025) hydrogen bonds : bond 0.03478 ( 637) hydrogen bonds : angle 3.75315 ( 1896) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 106 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 GLN cc_start: 0.7405 (tp40) cc_final: 0.6581 (tt0) REVERT: A 59 LEU cc_start: 0.7890 (tp) cc_final: 0.7493 (mp) REVERT: A 309 ASP cc_start: 0.7890 (m-30) cc_final: 0.7545 (m-30) REVERT: A 516 GLU cc_start: 0.7878 (mt-10) cc_final: 0.7428 (mm-30) REVERT: A 859 ASP cc_start: 0.7571 (t0) cc_final: 0.7201 (t0) REVERT: B 74 ASN cc_start: 0.7287 (OUTLIER) cc_final: 0.6209 (t0) REVERT: C 42 SER cc_start: 0.8160 (t) cc_final: 0.7816 (p) outliers start: 11 outliers final: 7 residues processed: 114 average time/residue: 0.0935 time to fit residues: 14.9516 Evaluate side-chains 109 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 101 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 237 ASN Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 653 PHE Chi-restraints excluded: chain A residue 774 GLN Chi-restraints excluded: chain B residue 74 ASN Chi-restraints excluded: chain C residue 126 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 27 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 3 optimal weight: 7.9990 chunk 51 optimal weight: 0.9980 chunk 70 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 83 optimal weight: 8.9990 chunk 54 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 237 ASN A 579 HIS A 835 ASN B 74 ASN C 87 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.186622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.148692 restraints weight = 8266.836| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 1.84 r_work: 0.3115 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8880 Z= 0.142 Angle : 0.475 10.845 12025 Z= 0.249 Chirality : 0.037 0.130 1443 Planarity : 0.004 0.046 1522 Dihedral : 3.678 18.918 1171 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.60 % Allowed : 8.72 % Favored : 89.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.48 (0.25), residues: 1091 helix: 2.03 (0.17), residues: 877 sheet: None (None), residues: 0 loop : 0.10 (0.39), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 755 TYR 0.018 0.002 TYR A 68 PHE 0.015 0.001 PHE A 249 TRP 0.002 0.001 TRP A 127 HIS 0.003 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 8880) covalent geometry : angle 0.47455 (12025) hydrogen bonds : bond 0.03599 ( 637) hydrogen bonds : angle 3.76750 ( 1896) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 100 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 GLN cc_start: 0.7355 (tp40) cc_final: 0.6532 (tt0) REVERT: A 59 LEU cc_start: 0.7831 (tp) cc_final: 0.7439 (mp) REVERT: A 309 ASP cc_start: 0.7923 (m-30) cc_final: 0.7575 (m-30) REVERT: A 516 GLU cc_start: 0.7837 (mt-10) cc_final: 0.7402 (mm-30) REVERT: A 611 MET cc_start: 0.7062 (mmm) cc_final: 0.6233 (mmm) REVERT: A 859 ASP cc_start: 0.7532 (t0) cc_final: 0.7177 (t0) REVERT: B 74 ASN cc_start: 0.7291 (OUTLIER) cc_final: 0.6232 (t0) REVERT: C 42 SER cc_start: 0.8171 (t) cc_final: 0.7837 (p) outliers start: 16 outliers final: 10 residues processed: 111 average time/residue: 0.0955 time to fit residues: 14.7929 Evaluate side-chains 107 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 96 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 237 ASN Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 494 LYS Chi-restraints excluded: chain A residue 653 PHE Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 774 GLN Chi-restraints excluded: chain B residue 74 ASN Chi-restraints excluded: chain C residue 126 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 71 optimal weight: 4.9990 chunk 73 optimal weight: 0.8980 chunk 29 optimal weight: 0.3980 chunk 33 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 26 optimal weight: 0.0970 chunk 28 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 92 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 237 ASN A 579 HIS B 74 ASN C 87 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.188177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.150365 restraints weight = 8317.280| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 1.83 r_work: 0.3132 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8880 Z= 0.115 Angle : 0.452 10.849 12025 Z= 0.238 Chirality : 0.036 0.126 1443 Planarity : 0.004 0.045 1522 Dihedral : 3.615 18.700 1171 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.20 % Allowed : 9.72 % Favored : 89.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.67 (0.25), residues: 1091 helix: 2.18 (0.17), residues: 877 sheet: None (None), residues: 0 loop : 0.12 (0.39), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 77 TYR 0.020 0.001 TYR A 68 PHE 0.014 0.001 PHE A 249 TRP 0.002 0.001 TRP A 69 HIS 0.002 0.001 HIS A 568 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 8880) covalent geometry : angle 0.45218 (12025) hydrogen bonds : bond 0.03384 ( 637) hydrogen bonds : angle 3.71530 ( 1896) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 101 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 GLN cc_start: 0.7361 (tp40) cc_final: 0.6565 (tt0) REVERT: A 59 LEU cc_start: 0.7796 (tp) cc_final: 0.7421 (mp) REVERT: A 309 ASP cc_start: 0.7868 (m-30) cc_final: 0.7542 (m-30) REVERT: A 516 GLU cc_start: 0.7791 (mt-10) cc_final: 0.7362 (mm-30) REVERT: A 611 MET cc_start: 0.6992 (mmm) cc_final: 0.6212 (mmm) REVERT: A 859 ASP cc_start: 0.7503 (t0) cc_final: 0.7153 (t0) REVERT: B 74 ASN cc_start: 0.7380 (OUTLIER) cc_final: 0.6189 (t0) REVERT: C 42 SER cc_start: 0.8156 (t) cc_final: 0.7837 (p) outliers start: 12 outliers final: 8 residues processed: 110 average time/residue: 0.0897 time to fit residues: 13.8049 Evaluate side-chains 108 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 99 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 237 ASN Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 653 PHE Chi-restraints excluded: chain A residue 774 GLN Chi-restraints excluded: chain B residue 74 ASN Chi-restraints excluded: chain C residue 126 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 56 optimal weight: 4.9990 chunk 99 optimal weight: 0.5980 chunk 90 optimal weight: 0.4980 chunk 40 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 105 optimal weight: 2.9990 chunk 70 optimal weight: 6.9990 chunk 62 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 GLN A 237 ASN A 375 GLN B 74 ASN C 87 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.186921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.149002 restraints weight = 8280.396| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 1.83 r_work: 0.3123 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.2647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8880 Z= 0.140 Angle : 0.473 11.256 12025 Z= 0.247 Chirality : 0.037 0.148 1443 Planarity : 0.004 0.046 1522 Dihedral : 3.634 19.158 1171 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.30 % Allowed : 10.12 % Favored : 88.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.60 (0.25), residues: 1091 helix: 2.13 (0.17), residues: 877 sheet: None (None), residues: 0 loop : 0.08 (0.39), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 77 TYR 0.019 0.001 TYR A 68 PHE 0.014 0.001 PHE A 249 TRP 0.002 0.001 TRP A 813 HIS 0.003 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 8880) covalent geometry : angle 0.47306 (12025) hydrogen bonds : bond 0.03522 ( 637) hydrogen bonds : angle 3.73438 ( 1896) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 99 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 GLN cc_start: 0.7375 (tp40) cc_final: 0.6589 (tt0) REVERT: A 59 LEU cc_start: 0.7851 (tp) cc_final: 0.7472 (mp) REVERT: A 309 ASP cc_start: 0.7929 (m-30) cc_final: 0.7594 (m-30) REVERT: A 516 GLU cc_start: 0.7815 (mt-10) cc_final: 0.7393 (mm-30) REVERT: A 611 MET cc_start: 0.6973 (mmm) cc_final: 0.6198 (mmm) REVERT: A 859 ASP cc_start: 0.7512 (t0) cc_final: 0.7141 (t0) REVERT: B 74 ASN cc_start: 0.7312 (OUTLIER) cc_final: 0.5928 (t0) REVERT: C 42 SER cc_start: 0.8180 (t) cc_final: 0.7863 (p) outliers start: 13 outliers final: 8 residues processed: 108 average time/residue: 0.0950 time to fit residues: 14.2080 Evaluate side-chains 106 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 97 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 494 LYS Chi-restraints excluded: chain A residue 653 PHE Chi-restraints excluded: chain A residue 774 GLN Chi-restraints excluded: chain B residue 74 ASN Chi-restraints excluded: chain C residue 126 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 68 optimal weight: 0.9990 chunk 81 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 7 optimal weight: 4.9990 chunk 75 optimal weight: 0.7980 chunk 95 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 74 ASN C 87 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.186560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.148593 restraints weight = 8177.040| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 1.78 r_work: 0.3124 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8880 Z= 0.128 Angle : 0.468 11.449 12025 Z= 0.243 Chirality : 0.037 0.126 1443 Planarity : 0.004 0.045 1522 Dihedral : 3.594 18.883 1171 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.30 % Allowed : 10.42 % Favored : 88.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.70 (0.25), residues: 1091 helix: 2.20 (0.17), residues: 877 sheet: None (None), residues: 0 loop : 0.10 (0.39), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 77 TYR 0.019 0.001 TYR A 68 PHE 0.014 0.001 PHE A 249 TRP 0.002 0.001 TRP A 69 HIS 0.002 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 8880) covalent geometry : angle 0.46786 (12025) hydrogen bonds : bond 0.03432 ( 637) hydrogen bonds : angle 3.70931 ( 1896) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 GLN cc_start: 0.7285 (tp40) cc_final: 0.6500 (tt0) REVERT: A 59 LEU cc_start: 0.7696 (tp) cc_final: 0.7320 (mp) REVERT: A 516 GLU cc_start: 0.7737 (mt-10) cc_final: 0.7301 (mm-30) REVERT: A 611 MET cc_start: 0.7002 (mmm) cc_final: 0.6222 (mmm) REVERT: A 635 ASN cc_start: 0.8074 (t0) cc_final: 0.7819 (t0) REVERT: A 853 LEU cc_start: 0.7280 (OUTLIER) cc_final: 0.6918 (tt) REVERT: A 859 ASP cc_start: 0.7381 (t0) cc_final: 0.7102 (t0) REVERT: B 74 ASN cc_start: 0.7099 (OUTLIER) cc_final: 0.6100 (t0) REVERT: C 42 SER cc_start: 0.8105 (t) cc_final: 0.7786 (p) outliers start: 13 outliers final: 9 residues processed: 108 average time/residue: 0.1007 time to fit residues: 15.0559 Evaluate side-chains 108 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 97 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 494 LYS Chi-restraints excluded: chain A residue 653 PHE Chi-restraints excluded: chain A residue 774 GLN Chi-restraints excluded: chain A residue 853 LEU Chi-restraints excluded: chain B residue 74 ASN Chi-restraints excluded: chain C residue 126 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 76 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 90 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 36 optimal weight: 0.8980 chunk 16 optimal weight: 0.2980 chunk 58 optimal weight: 2.9990 chunk 95 optimal weight: 0.5980 chunk 91 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 74 ASN C 87 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.187646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.150028 restraints weight = 8199.056| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 1.77 r_work: 0.3130 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8880 Z= 0.126 Angle : 0.472 11.447 12025 Z= 0.245 Chirality : 0.036 0.137 1443 Planarity : 0.004 0.045 1522 Dihedral : 3.574 18.419 1171 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.20 % Allowed : 10.52 % Favored : 88.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.75 (0.25), residues: 1091 helix: 2.24 (0.17), residues: 877 sheet: None (None), residues: 0 loop : 0.12 (0.39), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 843 TYR 0.020 0.001 TYR A 68 PHE 0.014 0.001 PHE A 249 TRP 0.003 0.001 TRP A 69 HIS 0.002 0.001 HIS A 568 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 8880) covalent geometry : angle 0.47246 (12025) hydrogen bonds : bond 0.03405 ( 637) hydrogen bonds : angle 3.70346 ( 1896) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 97 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 GLN cc_start: 0.7351 (tp40) cc_final: 0.6586 (tt0) REVERT: A 59 LEU cc_start: 0.7815 (tp) cc_final: 0.7441 (mp) REVERT: A 516 GLU cc_start: 0.7768 (mt-10) cc_final: 0.7342 (mm-30) REVERT: A 611 MET cc_start: 0.6984 (mmm) cc_final: 0.6235 (mmm) REVERT: A 853 LEU cc_start: 0.7399 (OUTLIER) cc_final: 0.7057 (tt) REVERT: A 859 ASP cc_start: 0.7217 (t0) cc_final: 0.7014 (t70) REVERT: B 74 ASN cc_start: 0.7428 (OUTLIER) cc_final: 0.6278 (t0) REVERT: C 42 SER cc_start: 0.8179 (t) cc_final: 0.7872 (p) outliers start: 12 outliers final: 8 residues processed: 107 average time/residue: 0.0994 time to fit residues: 14.7851 Evaluate side-chains 108 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 98 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 653 PHE Chi-restraints excluded: chain A residue 774 GLN Chi-restraints excluded: chain A residue 853 LEU Chi-restraints excluded: chain B residue 74 ASN Chi-restraints excluded: chain C residue 126 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 20 optimal weight: 4.9990 chunk 50 optimal weight: 0.7980 chunk 102 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 57 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 60 optimal weight: 0.4980 chunk 55 optimal weight: 0.6980 chunk 0 optimal weight: 20.0000 chunk 22 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 74 ASN C 87 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.188128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.150622 restraints weight = 8179.443| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 1.72 r_work: 0.3131 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.2812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8880 Z= 0.123 Angle : 0.470 11.526 12025 Z= 0.246 Chirality : 0.036 0.226 1443 Planarity : 0.004 0.045 1522 Dihedral : 3.552 18.368 1171 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 1.30 % Allowed : 10.52 % Favored : 88.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.82 (0.25), residues: 1091 helix: 2.28 (0.17), residues: 877 sheet: None (None), residues: 0 loop : 0.13 (0.39), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 843 TYR 0.020 0.001 TYR A 68 PHE 0.014 0.001 PHE A 249 TRP 0.003 0.001 TRP A 69 HIS 0.002 0.001 HIS A 568 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 8880) covalent geometry : angle 0.47043 (12025) hydrogen bonds : bond 0.03360 ( 637) hydrogen bonds : angle 3.68564 ( 1896) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2579.54 seconds wall clock time: 44 minutes 50.63 seconds (2690.63 seconds total)