Starting phenix.real_space_refine on Sat Jun 7 19:03:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f0x_28782/06_2025/8f0x_28782.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f0x_28782/06_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_28782/06_2025/8f0x_28782.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f0x_28782/06_2025/8f0x_28782.map" model { file = "/net/cci-nas-00/data/ceres_data/8f0x_28782/06_2025/8f0x_28782.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f0x_28782/06_2025/8f0x_28782.cif" } resolution = 3.21 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 6.70, per 1000 atoms: 0.77 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: 2.32 Conformation dependent library (CDL) restraints added in 993.1 milliseconds 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: 1.04 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: 3.09 Time building geometry restraints manager: 2.74 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: 4.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.000 Extract box with map and model: 0.450 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 25.570 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.570 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (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 TRP 0.004 0.001 TRP A 127 HIS 0.003 0.001 HIS C 52 PHE 0.012 0.001 PHE C 68 TYR 0.010 0.001 TYR C 86 ARG 0.011 0.000 ARG A 755 Details of bonding type rmsd hydrogen bonds : bond 0.22314 ( 637) hydrogen bonds : angle 7.48568 ( 1896) covalent geometry : bond 0.00411 ( 8880) covalent geometry : angle 0.64677 (12025) *********************** 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 : 1.044 Fit side-chains 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: 0.7244 (ttmt) outliers start: 5 outliers final: 0 residues processed: 105 average time/residue: 0.2623 time to fit residues: 37.1542 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 : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 45 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 chunk 55 optimal weight: 0.0980 chunk 44 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 chunk 98 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 599 GLN A 774 GLN A 840 ASN A 967 GLN C 59 GLN C 87 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.182785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.139912 restraints weight = 8228.564| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 1.94 r_work: 0.3081 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8880 Z= 0.140 Angle : 0.503 8.468 12025 Z= 0.272 Chirality : 0.037 0.124 1443 Planarity : 0.004 0.045 1522 Dihedral : 3.848 18.293 1171 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.50 % Allowed : 4.81 % Favored : 94.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.25), residues: 1091 helix: 1.48 (0.17), residues: 882 sheet: None (None), residues: 0 loop : 0.31 (0.42), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 69 HIS 0.003 0.001 HIS A 207 PHE 0.025 0.002 PHE A 837 TYR 0.020 0.002 TYR C 86 ARG 0.006 0.000 ARG A 755 Details of bonding type rmsd hydrogen bonds : bond 0.04589 ( 637) hydrogen bonds : angle 4.23331 ( 1896) covalent geometry : bond 0.00318 ( 8880) covalent geometry : angle 0.50284 (12025) *********************** 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 118 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 113 time to evaluate : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 188 ILE cc_start: 0.7174 (OUTLIER) cc_final: 0.6963 (mm) REVERT: A 309 ASP cc_start: 0.7580 (m-30) cc_final: 0.7192 (m-30) REVERT: A 627 ASN cc_start: 0.6320 (m110) cc_final: 0.5594 (m110) REVERT: A 702 THR cc_start: 0.8410 (t) cc_final: 0.8170 (t) REVERT: A 859 ASP cc_start: 0.7733 (t0) cc_final: 0.7329 (t0) outliers start: 5 outliers final: 1 residues processed: 114 average time/residue: 0.2644 time to fit residues: 40.1320 Evaluate side-chains 96 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 94 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 188 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 48 optimal weight: 2.9990 chunk 54 optimal weight: 0.3980 chunk 1 optimal weight: 20.0000 chunk 13 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 5 optimal weight: 0.5980 chunk 27 optimal weight: 0.6980 chunk 4 optimal weight: 3.9990 chunk 41 optimal weight: 0.0970 chunk 21 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 GLN A 549 ASN 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 = 0.4497 r_free = 0.4497 target = 0.220499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.182717 restraints weight = 8622.686| |-----------------------------------------------------------------------------| r_work (start): 0.4285 rms_B_bonded: 2.00 r_work: 0.4007 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.4007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.2237 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= 0.118 Angle : 0.458 8.730 12025 Z= 0.243 Chirality : 0.036 0.125 1443 Planarity : 0.004 0.045 1522 Dihedral : 3.711 18.027 1171 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.70 % Allowed : 6.21 % Favored : 93.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.42 (0.25), residues: 1091 helix: 1.92 (0.17), residues: 886 sheet: None (None), residues: 0 loop : 0.38 (0.42), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 69 HIS 0.002 0.001 HIS C 52 PHE 0.022 0.001 PHE A 837 TYR 0.022 0.001 TYR A 68 ARG 0.004 0.000 ARG A 755 Details of bonding type rmsd hydrogen bonds : bond 0.03675 ( 637) hydrogen bonds : angle 3.83532 ( 1896) covalent geometry : bond 0.00273 ( 8880) covalent geometry : angle 0.45754 (12025) *********************** 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 115 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 108 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 309 ASP cc_start: 0.7750 (m-30) cc_final: 0.7438 (m-30) REVERT: A 611 MET cc_start: 0.6869 (mmm) cc_final: 0.6329 (mmm) REVERT: A 843 ARG cc_start: 0.7744 (mtm-85) cc_final: 0.7434 (mtm-85) REVERT: A 859 ASP cc_start: 0.7507 (t0) cc_final: 0.7189 (t0) REVERT: B 74 ASN cc_start: 0.7345 (OUTLIER) cc_final: 0.6253 (t0) outliers start: 7 outliers final: 3 residues processed: 112 average time/residue: 0.2337 time to fit residues: 35.7832 Evaluate side-chains 100 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 96 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 653 PHE Chi-restraints excluded: chain B residue 74 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 82 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 chunk 102 optimal weight: 0.6980 chunk 23 optimal weight: 0.3980 chunk 99 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 88 optimal weight: 5.9990 chunk 22 optimal weight: 0.5980 chunk 52 optimal weight: 0.5980 chunk 29 optimal weight: 4.9990 chunk 69 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.4491 r_free = 0.4491 target = 0.219992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.182232 restraints weight = 8555.478| |-----------------------------------------------------------------------------| r_work (start): 0.4283 rms_B_bonded: 2.01 r_work: 0.3997 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.2460 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= 0.119 Angle : 0.457 9.552 12025 Z= 0.243 Chirality : 0.036 0.142 1443 Planarity : 0.004 0.044 1522 Dihedral : 3.629 17.895 1171 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 0.50 % Allowed : 8.02 % Favored : 91.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.71 (0.25), residues: 1091 helix: 2.16 (0.17), residues: 875 sheet: None (None), residues: 0 loop : 0.39 (0.40), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 127 HIS 0.003 0.001 HIS C 52 PHE 0.018 0.001 PHE A 837 TYR 0.019 0.001 TYR A 68 ARG 0.003 0.000 ARG A 755 Details of bonding type rmsd hydrogen bonds : bond 0.03482 ( 637) hydrogen bonds : angle 3.74832 ( 1896) covalent geometry : bond 0.00278 ( 8880) covalent geometry : angle 0.45743 (12025) *********************** 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 107 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 102 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 GLN cc_start: 0.7572 (tp40) cc_final: 0.6800 (tt0) REVERT: A 309 ASP cc_start: 0.7728 (m-30) cc_final: 0.7420 (m-30) REVERT: A 496 ASP cc_start: 0.8058 (m-30) cc_final: 0.7801 (m-30) REVERT: A 516 GLU cc_start: 0.8054 (mt-10) cc_final: 0.7609 (mm-30) REVERT: A 611 MET cc_start: 0.6870 (mmm) cc_final: 0.6369 (mmm) REVERT: A 859 ASP cc_start: 0.7328 (t0) cc_final: 0.7110 (t0) REVERT: B 74 ASN cc_start: 0.7473 (OUTLIER) cc_final: 0.6101 (t0) outliers start: 5 outliers final: 4 residues processed: 106 average time/residue: 0.2141 time to fit residues: 32.1236 Evaluate side-chains 102 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 97 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 653 PHE Chi-restraints excluded: chain B residue 74 ASN Chi-restraints excluded: chain C residue 126 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 38 optimal weight: 0.8980 chunk 95 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.4481 r_free = 0.4481 target = 0.218974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.180492 restraints weight = 8540.716| |-----------------------------------------------------------------------------| r_work (start): 0.4261 rms_B_bonded: 1.92 r_work: 0.3973 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8880 Z= 0.134 Angle : 0.471 10.263 12025 Z= 0.247 Chirality : 0.037 0.124 1443 Planarity : 0.004 0.045 1522 Dihedral : 3.635 18.626 1171 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 0.90 % Allowed : 8.72 % Favored : 90.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.67 (0.25), residues: 1091 helix: 2.13 (0.17), residues: 879 sheet: None (None), residues: 0 loop : 0.30 (0.40), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 127 HIS 0.003 0.001 HIS C 112 PHE 0.015 0.001 PHE A 249 TYR 0.019 0.001 TYR A 68 ARG 0.003 0.000 ARG A 755 Details of bonding type rmsd hydrogen bonds : bond 0.03561 ( 637) hydrogen bonds : angle 3.75699 ( 1896) covalent geometry : bond 0.00327 ( 8880) covalent geometry : angle 0.47101 (12025) *********************** 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 107 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 98 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 GLN cc_start: 0.7577 (tp40) cc_final: 0.6819 (tt0) REVERT: A 309 ASP cc_start: 0.7814 (m-30) cc_final: 0.7501 (m-30) REVERT: A 496 ASP cc_start: 0.8080 (m-30) cc_final: 0.7845 (m-30) REVERT: A 516 GLU cc_start: 0.8033 (mt-10) cc_final: 0.7612 (mm-30) REVERT: A 719 GLU cc_start: 0.6664 (mt-10) cc_final: 0.6454 (mt-10) REVERT: B 74 ASN cc_start: 0.7566 (OUTLIER) cc_final: 0.7125 (m-40) REVERT: C 42 SER cc_start: 0.8236 (t) cc_final: 0.7910 (p) outliers start: 9 outliers final: 3 residues processed: 103 average time/residue: 0.2079 time to fit residues: 30.1096 Evaluate side-chains 99 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 95 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 653 PHE Chi-restraints excluded: chain B residue 74 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 28 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 1 optimal weight: 10.0000 chunk 91 optimal weight: 8.9990 chunk 103 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 chunk 74 optimal weight: 7.9990 chunk 5 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 67 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 549 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 = 0.4083 r_free = 0.4083 target = 0.187906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.150393 restraints weight = 8212.737| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 1.74 r_work: 0.3519 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3350 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.2620 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 : 0.465 10.759 12025 Z= 0.245 Chirality : 0.036 0.134 1443 Planarity : 0.004 0.045 1522 Dihedral : 3.587 17.894 1171 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.30 % Allowed : 8.72 % Favored : 89.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.71 (0.25), residues: 1091 helix: 2.18 (0.17), residues: 879 sheet: None (None), residues: 0 loop : 0.23 (0.40), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 28 HIS 0.002 0.001 HIS A 568 PHE 0.014 0.001 PHE A 249 TYR 0.019 0.001 TYR A 68 ARG 0.002 0.000 ARG A 755 Details of bonding type rmsd hydrogen bonds : bond 0.03450 ( 637) hydrogen bonds : angle 3.72481 ( 1896) covalent geometry : bond 0.00302 ( 8880) covalent geometry : angle 0.46482 (12025) *********************** 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 109 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 96 time to evaluate : 1.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 GLN cc_start: 0.7457 (tp40) cc_final: 0.6681 (tt0) REVERT: A 309 ASP cc_start: 0.7917 (m-30) cc_final: 0.7584 (m-30) REVERT: A 496 ASP cc_start: 0.8261 (m-30) cc_final: 0.8053 (m-30) REVERT: A 516 GLU cc_start: 0.7890 (mt-10) cc_final: 0.7452 (mm-30) REVERT: A 611 MET cc_start: 0.6855 (mmm) cc_final: 0.6062 (mmm) REVERT: A 719 GLU cc_start: 0.6547 (mt-10) cc_final: 0.6265 (mt-10) REVERT: B 74 ASN cc_start: 0.7499 (OUTLIER) cc_final: 0.7076 (t160) REVERT: C 42 SER cc_start: 0.8185 (t) cc_final: 0.7851 (p) outliers start: 13 outliers final: 8 residues processed: 106 average time/residue: 0.2215 time to fit residues: 33.2359 Evaluate side-chains 103 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 94 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 683 THR Chi-restraints excluded: chain A residue 711 LEU 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 39 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 104 optimal weight: 0.6980 chunk 24 optimal weight: 0.2980 chunk 0 optimal weight: 20.0000 chunk 2 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 chunk 72 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4088 r_free = 0.4088 target = 0.188313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.150236 restraints weight = 8299.988| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 1.84 r_work: 0.3522 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3350 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.2696 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= 0.120 Angle : 0.456 10.980 12025 Z= 0.239 Chirality : 0.036 0.124 1443 Planarity : 0.004 0.044 1522 Dihedral : 3.548 18.016 1171 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.10 % Allowed : 9.32 % Favored : 89.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.81 (0.25), residues: 1091 helix: 2.25 (0.17), residues: 879 sheet: None (None), residues: 0 loop : 0.26 (0.40), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 28 HIS 0.002 0.001 HIS A 568 PHE 0.014 0.001 PHE A 249 TYR 0.019 0.001 TYR A 68 ARG 0.002 0.000 ARG A 755 Details of bonding type rmsd hydrogen bonds : bond 0.03378 ( 637) hydrogen bonds : angle 3.69846 ( 1896) covalent geometry : bond 0.00286 ( 8880) covalent geometry : angle 0.45585 (12025) *********************** 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 111 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 100 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 GLN cc_start: 0.7439 (tp40) cc_final: 0.6657 (tt0) REVERT: A 309 ASP cc_start: 0.7905 (m-30) cc_final: 0.7578 (m-30) REVERT: A 516 GLU cc_start: 0.7843 (mt-10) cc_final: 0.7411 (mm-30) REVERT: A 611 MET cc_start: 0.6872 (mmm) cc_final: 0.6096 (mmm) REVERT: A 719 GLU cc_start: 0.6507 (mt-10) cc_final: 0.6207 (mt-10) REVERT: B 74 ASN cc_start: 0.7472 (OUTLIER) cc_final: 0.7073 (t160) REVERT: C 42 SER cc_start: 0.8196 (t) cc_final: 0.7870 (p) outliers start: 11 outliers final: 8 residues processed: 108 average time/residue: 0.2365 time to fit residues: 35.1172 Evaluate side-chains 103 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 94 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 683 THR Chi-restraints excluded: chain A residue 711 LEU 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 27 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 chunk 50 optimal weight: 0.0060 chunk 0 optimal weight: 20.0000 chunk 76 optimal weight: 0.7980 chunk 108 optimal weight: 0.5980 chunk 13 optimal weight: 0.7980 chunk 26 optimal weight: 0.7980 chunk 75 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 overall best weight: 0.5596 ------------------------------------------------------------------------------- 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 = 0.4087 r_free = 0.4087 target = 0.188799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.150561 restraints weight = 8276.629| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 1.86 r_work: 0.3528 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3355 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8880 Z= 0.113 Angle : 0.458 11.178 12025 Z= 0.242 Chirality : 0.036 0.167 1443 Planarity : 0.004 0.044 1522 Dihedral : 3.509 17.606 1171 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.20 % Allowed : 9.22 % Favored : 89.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.94 (0.25), residues: 1091 helix: 2.35 (0.17), residues: 879 sheet: None (None), residues: 0 loop : 0.29 (0.40), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 28 HIS 0.003 0.001 HIS C 52 PHE 0.013 0.001 PHE A 249 TYR 0.019 0.001 TYR A 68 ARG 0.007 0.000 ARG A 77 Details of bonding type rmsd hydrogen bonds : bond 0.03258 ( 637) hydrogen bonds : angle 3.65755 ( 1896) covalent geometry : bond 0.00261 ( 8880) covalent geometry : angle 0.45809 (12025) *********************** 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 113 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 101 time to evaluate : 1.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 GLN cc_start: 0.7401 (tp40) cc_final: 0.6634 (tt0) REVERT: A 309 ASP cc_start: 0.7872 (m-30) cc_final: 0.7543 (m-30) REVERT: A 516 GLU cc_start: 0.7804 (mt-10) cc_final: 0.7379 (mm-30) REVERT: A 611 MET cc_start: 0.6856 (mmm) cc_final: 0.6078 (mmm) REVERT: A 719 GLU cc_start: 0.6438 (mt-10) cc_final: 0.6144 (mt-10) REVERT: B 74 ASN cc_start: 0.7435 (OUTLIER) cc_final: 0.7038 (t160) REVERT: C 42 SER cc_start: 0.8155 (t) cc_final: 0.7826 (p) outliers start: 12 outliers final: 9 residues processed: 110 average time/residue: 0.2265 time to fit residues: 35.6557 Evaluate side-chains 105 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 95 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 683 THR Chi-restraints excluded: chain A residue 711 LEU 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 86 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 68 optimal weight: 2.9990 chunk 58 optimal weight: 0.0970 chunk 94 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 4 optimal weight: 7.9990 chunk 22 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 overall best weight: 1.0780 ------------------------------------------------------------------------------- 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 = 0.4071 r_free = 0.4071 target = 0.186633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.149210 restraints weight = 8323.277| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 1.68 r_work: 0.3126 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.2767 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= 0.151 Angle : 0.489 11.512 12025 Z= 0.257 Chirality : 0.037 0.186 1443 Planarity : 0.004 0.046 1522 Dihedral : 3.604 18.843 1171 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.10 % Allowed : 9.82 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.64 (0.24), residues: 1091 helix: 2.17 (0.17), residues: 885 sheet: None (None), residues: 0 loop : -0.04 (0.38), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 813 HIS 0.003 0.001 HIS C 112 PHE 0.015 0.001 PHE A 249 TYR 0.018 0.001 TYR A 68 ARG 0.006 0.000 ARG A 77 Details of bonding type rmsd hydrogen bonds : bond 0.03567 ( 637) hydrogen bonds : angle 3.72821 ( 1896) covalent geometry : bond 0.00374 ( 8880) covalent geometry : angle 0.48914 (12025) *********************** 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 107 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 96 time to evaluate : 1.627 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 GLN cc_start: 0.7376 (tp40) cc_final: 0.6601 (tt0) REVERT: A 309 ASP cc_start: 0.7925 (m-30) cc_final: 0.7586 (m-30) REVERT: A 516 GLU cc_start: 0.7776 (mt-10) cc_final: 0.7353 (mm-30) REVERT: A 611 MET cc_start: 0.6897 (mmm) cc_final: 0.6124 (mmm) REVERT: A 719 GLU cc_start: 0.6438 (mt-10) cc_final: 0.6100 (mt-10) REVERT: B 74 ASN cc_start: 0.7435 (OUTLIER) cc_final: 0.7075 (t160) REVERT: C 42 SER cc_start: 0.8189 (t) cc_final: 0.7859 (p) outliers start: 11 outliers final: 8 residues processed: 105 average time/residue: 0.2165 time to fit residues: 32.2798 Evaluate side-chains 105 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 96 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 711 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 99 optimal weight: 0.6980 chunk 65 optimal weight: 7.9990 chunk 66 optimal weight: 0.6980 chunk 37 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 95 optimal weight: 1.9990 chunk 91 optimal weight: 7.9990 chunk 1 optimal weight: 0.0970 chunk 48 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 overall best weight: 0.5778 ------------------------------------------------------------------------------- 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 = 0.4098 r_free = 0.4098 target = 0.189384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.151733 restraints weight = 8264.245| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 1.83 r_work: 0.3540 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3371 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8880 Z= 0.116 Angle : 0.471 11.476 12025 Z= 0.249 Chirality : 0.036 0.231 1443 Planarity : 0.004 0.044 1522 Dihedral : 3.537 17.851 1171 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.00 % Allowed : 9.82 % Favored : 89.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.85 (0.25), residues: 1091 helix: 2.33 (0.17), residues: 885 sheet: None (None), residues: 0 loop : -0.05 (0.38), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 28 HIS 0.002 0.001 HIS C 52 PHE 0.013 0.001 PHE A 249 TYR 0.019 0.001 TYR A 68 ARG 0.009 0.000 ARG A 843 Details of bonding type rmsd hydrogen bonds : bond 0.03292 ( 637) hydrogen bonds : angle 3.65554 ( 1896) covalent geometry : bond 0.00271 ( 8880) covalent geometry : angle 0.47088 (12025) ********************** 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 106 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 96 time to evaluate : 1.003 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 GLN cc_start: 0.7407 (tp40) cc_final: 0.6674 (tt0) REVERT: A 516 GLU cc_start: 0.7826 (mt-10) cc_final: 0.7408 (mm-30) REVERT: A 611 MET cc_start: 0.6840 (mmm) cc_final: 0.6089 (mmm) REVERT: A 719 GLU cc_start: 0.6460 (mt-10) cc_final: 0.6158 (mt-10) REVERT: B 74 ASN cc_start: 0.7409 (OUTLIER) cc_final: 0.7054 (t160) REVERT: C 42 SER cc_start: 0.8180 (t) cc_final: 0.7874 (p) outliers start: 10 outliers final: 8 residues processed: 104 average time/residue: 0.2442 time to fit residues: 36.0023 Evaluate side-chains 103 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 94 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 711 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 22 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 47 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 48 optimal weight: 0.6980 chunk 78 optimal weight: 0.9990 chunk 90 optimal weight: 0.0980 chunk 54 optimal weight: 0.8980 chunk 83 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.4099 r_free = 0.4099 target = 0.189618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.151802 restraints weight = 8226.663| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 1.82 r_work: 0.3540 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3367 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.2925 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= 0.117 Angle : 0.472 11.453 12025 Z= 0.249 Chirality : 0.036 0.240 1443 Planarity : 0.004 0.044 1522 Dihedral : 3.516 17.331 1171 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.20 % Allowed : 9.52 % Favored : 89.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.89 (0.25), residues: 1091 helix: 2.36 (0.17), residues: 885 sheet: None (None), residues: 0 loop : -0.05 (0.38), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 28 HIS 0.002 0.001 HIS A 568 PHE 0.013 0.001 PHE A 249 TYR 0.019 0.001 TYR A 68 ARG 0.007 0.000 ARG A 843 Details of bonding type rmsd hydrogen bonds : bond 0.03258 ( 637) hydrogen bonds : angle 3.64094 ( 1896) covalent geometry : bond 0.00273 ( 8880) covalent geometry : angle 0.47205 (12025) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5144.87 seconds wall clock time: 89 minutes 46.77 seconds (5386.77 seconds total)