Starting phenix.real_space_refine on Sat Dec 28 15:55:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jqg_36571/12_2024/8jqg_36571_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jqg_36571/12_2024/8jqg_36571.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jqg_36571/12_2024/8jqg_36571.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jqg_36571/12_2024/8jqg_36571.map" model { file = "/net/cci-nas-00/data/ceres_data/8jqg_36571/12_2024/8jqg_36571_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jqg_36571/12_2024/8jqg_36571_neut.cif" } resolution = 3.72 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= 0.002 sd= 0.075 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 44 5.16 5 C 5548 2.51 5 N 1494 2.21 5 O 1622 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 8708 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 8708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1061, 8708 Classifications: {'peptide': 1061} Link IDs: {'PTRANS': 47, 'TRANS': 1013} Chain breaks: 4 Time building chain proxies: 5.13, per 1000 atoms: 0.59 Number of scatterers: 8708 At special positions: 0 Unit cell: (96.8, 101.2, 121, 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 44 16.00 O 1622 8.00 N 1494 7.00 C 5548 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: 2.22 Conformation dependent library (CDL) restraints added in 925.4 milliseconds 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2034 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 13 sheets defined 33.6% alpha, 19.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'A' and resid 11 through 25 Processing helix chain 'A' and resid 66 through 68 No H-bonds generated for 'chain 'A' and resid 66 through 68' Processing helix chain 'A' and resid 115 through 136 Processing helix chain 'A' and resid 137 through 154 Processing helix chain 'A' and resid 162 through 170 Processing helix chain 'A' and resid 181 through 191 Processing helix chain 'A' and resid 198 through 221 removed outlier: 5.940A pdb=" N SER A 216 " --> pdb=" O GLU A 212 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ILE A 217 " --> pdb=" O GLN A 213 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N LEU A 218 " --> pdb=" O GLN A 214 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLU A 220 " --> pdb=" O SER A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 253 Processing helix chain 'A' and resid 257 through 260 Processing helix chain 'A' and resid 261 through 274 removed outlier: 3.620A pdb=" N VAL A 265 " --> pdb=" O ASP A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 295 Processing helix chain 'A' and resid 303 through 307 Processing helix chain 'A' and resid 310 through 315 removed outlier: 3.636A pdb=" N ASN A 315 " --> pdb=" O GLN A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 319 No H-bonds generated for 'chain 'A' and resid 317 through 319' Processing helix chain 'A' and resid 341 through 352 removed outlier: 4.035A pdb=" N TYR A 345 " --> pdb=" O SER A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 393 Processing helix chain 'A' and resid 410 through 426 Processing helix chain 'A' and resid 427 through 429 No H-bonds generated for 'chain 'A' and resid 427 through 429' Processing helix chain 'A' and resid 539 through 554 Processing helix chain 'A' and resid 609 through 620 removed outlier: 3.718A pdb=" N LEU A 613 " --> pdb=" O SER A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 644 Processing helix chain 'A' and resid 652 through 663 Processing helix chain 'A' and resid 712 through 722 removed outlier: 3.747A pdb=" N LYS A 722 " --> pdb=" O SER A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 736 through 746 removed outlier: 3.843A pdb=" N ARG A 742 " --> pdb=" O GLU A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 835 through 843 Processing helix chain 'A' and resid 845 through 849 Processing helix chain 'A' and resid 892 through 908 Processing helix chain 'A' and resid 927 through 934 Processing helix chain 'A' and resid 960 through 970 Processing helix chain 'A' and resid 970 through 979 Processing helix chain 'A' and resid 999 through 1005 Processing helix chain 'A' and resid 1018 through 1034 removed outlier: 4.195A pdb=" N LEU A1030 " --> pdb=" O ALA A1026 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N ASN A1031 " --> pdb=" O LEU A1027 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N GLY A1032 " --> pdb=" O PHE A1028 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N THR A1034 " --> pdb=" O LEU A1030 " (cutoff:3.500A) Processing helix chain 'A' and resid 1040 through 1045 removed outlier: 3.510A pdb=" N ARG A1044 " --> pdb=" O PRO A1040 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 51 through 55 removed outlier: 6.358A pdb=" N THR A 37 " --> pdb=" O SER A 32 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N SER A 32 " --> pdb=" O THR A 37 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG A 41 " --> pdb=" O MET A 28 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR A 29 " --> pdb=" O ALA A 112 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N SER A 110 " --> pdb=" O PHE A 31 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU A 72 " --> pdb=" O LEU A 99 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 240 through 241 Processing sheet with id=AA3, first strand: chain 'A' and resid 938 through 939 removed outlier: 6.093A pdb=" N LYS A 938 " --> pdb=" O ILE A 955 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N SER A 957 " --> pdb=" O LYS A 938 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N GLU A 954 " --> pdb=" O LEU A 982 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N ARG A 984 " --> pdb=" O GLU A 954 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N ARG A 956 " --> pdb=" O ARG A 984 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N TYR A 986 " --> pdb=" O ARG A 956 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N PHE A 958 " --> pdb=" O TYR A 986 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N THR A 983 " --> pdb=" O MET A1009 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N ALA A1011 " --> pdb=" O THR A 983 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N VAL A 985 " --> pdb=" O ALA A1011 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N VAL A1010 " --> pdb=" O TYR A 321 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ILE A 323 " --> pdb=" O VAL A1010 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N LEU A1012 " --> pdb=" O ILE A 323 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N SER A 325 " --> pdb=" O LEU A1012 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 355 through 358 removed outlier: 6.329A pdb=" N VAL A 401 " --> pdb=" O ILE A 452 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N LYS A 454 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N LEU A 403 " --> pdb=" O LYS A 454 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 360 through 361 removed outlier: 3.606A pdb=" N VAL A 369 " --> pdb=" O TRP A 361 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE A 370 " --> pdb=" O ILE A 380 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ILE A 380 " --> pdb=" O ILE A 370 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 478 through 484 removed outlier: 7.241A pdb=" N ARG A 493 " --> pdb=" O ASP A 508 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N ASP A 508 " --> pdb=" O ARG A 493 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N TYR A 495 " --> pdb=" O SER A 506 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 561 through 565 Processing sheet with id=AA8, first strand: chain 'A' and resid 589 through 593 removed outlier: 3.954A pdb=" N LEU A 605 " --> pdb=" O LEU A 601 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 622 through 624 Processing sheet with id=AB1, first strand: chain 'A' and resid 647 through 648 removed outlier: 3.641A pdb=" N LYS A 673 " --> pdb=" O TYR A 648 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ALA A 668 " --> pdb=" O ARG A 685 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA A 708 " --> pdb=" O LEU A 704 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 647 through 648 removed outlier: 3.641A pdb=" N LYS A 673 " --> pdb=" O TYR A 648 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1120 through 1124 removed outlier: 6.780A pdb=" N LEU A1181 " --> pdb=" O LEU A1068 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ALA A1070 " --> pdb=" O SER A1179 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N SER A1179 " --> pdb=" O ALA A1070 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1097 through 1100 removed outlier: 3.812A pdb=" N ASN A1097 " --> pdb=" O ILE A1089 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA A1149 " --> pdb=" O VAL A1136 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N GLU A1138 " --> pdb=" O PHE A1147 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N PHE A1147 " --> pdb=" O GLU A1138 " (cutoff:3.500A) 338 hydrogen bonds defined for protein. 933 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: 3.11 Time building geometry restraints manager: 2.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2304 1.33 - 1.45: 1673 1.45 - 1.58: 4863 1.58 - 1.70: 0 1.70 - 1.82: 70 Bond restraints: 8910 Sorted by residual: bond pdb=" N VAL A 635 " pdb=" CA VAL A 635 " ideal model delta sigma weight residual 1.456 1.495 -0.039 8.70e-03 1.32e+04 1.99e+01 bond pdb=" CE1 HIS A 641 " pdb=" NE2 HIS A 641 " ideal model delta sigma weight residual 1.321 1.361 -0.040 1.00e-02 1.00e+04 1.61e+01 bond pdb=" N ASP A 224 " pdb=" CA ASP A 224 " ideal model delta sigma weight residual 1.456 1.496 -0.040 1.23e-02 6.61e+03 1.05e+01 bond pdb=" CA LEU A 562 " pdb=" C LEU A 562 " ideal model delta sigma weight residual 1.523 1.563 -0.040 1.34e-02 5.57e+03 8.85e+00 bond pdb=" N TYR A1036 " pdb=" CA TYR A1036 " ideal model delta sigma weight residual 1.458 1.422 0.035 1.22e-02 6.72e+03 8.29e+00 ... (remaining 8905 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.87: 11850 2.87 - 5.73: 145 5.73 - 8.60: 25 8.60 - 11.46: 4 11.46 - 14.33: 1 Bond angle restraints: 12025 Sorted by residual: angle pdb=" N PHE A 221 " pdb=" CA PHE A 221 " pdb=" C PHE A 221 " ideal model delta sigma weight residual 112.87 105.56 7.31 1.20e+00 6.94e-01 3.71e+01 angle pdb=" N LEU A 218 " pdb=" CA LEU A 218 " pdb=" C LEU A 218 " ideal model delta sigma weight residual 112.38 105.16 7.22 1.22e+00 6.72e-01 3.50e+01 angle pdb=" N ARG A 540 " pdb=" CA ARG A 540 " pdb=" C ARG A 540 " ideal model delta sigma weight residual 111.28 105.07 6.21 1.09e+00 8.42e-01 3.25e+01 angle pdb=" N PHE A 577 " pdb=" CA PHE A 577 " pdb=" C PHE A 577 " ideal model delta sigma weight residual 108.41 117.50 -9.09 1.63e+00 3.76e-01 3.11e+01 angle pdb=" N PHE A 182 " pdb=" CA PHE A 182 " pdb=" C PHE A 182 " ideal model delta sigma weight residual 111.82 105.76 6.06 1.16e+00 7.43e-01 2.73e+01 ... (remaining 12020 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 4588 17.92 - 35.84: 645 35.84 - 53.76: 145 53.76 - 71.68: 25 71.68 - 89.61: 10 Dihedral angle restraints: 5413 sinusoidal: 2281 harmonic: 3132 Sorted by residual: dihedral pdb=" CA THR A 632 " pdb=" C THR A 632 " pdb=" N ASP A 633 " pdb=" CA ASP A 633 " ideal model delta harmonic sigma weight residual -180.00 -154.76 -25.24 0 5.00e+00 4.00e-02 2.55e+01 dihedral pdb=" CA THR A 560 " pdb=" C THR A 560 " pdb=" N PHE A 561 " pdb=" CA PHE A 561 " ideal model delta harmonic sigma weight residual -180.00 -158.13 -21.87 0 5.00e+00 4.00e-02 1.91e+01 dihedral pdb=" CA TYR A 321 " pdb=" C TYR A 321 " pdb=" N TRP A 322 " pdb=" CA TRP A 322 " ideal model delta harmonic sigma weight residual 180.00 162.06 17.94 0 5.00e+00 4.00e-02 1.29e+01 ... (remaining 5410 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 896 0.040 - 0.081: 260 0.081 - 0.121: 109 0.121 - 0.161: 22 0.161 - 0.201: 4 Chirality restraints: 1291 Sorted by residual: chirality pdb=" CA MET A 210 " pdb=" N MET A 210 " pdb=" C MET A 210 " pdb=" CB MET A 210 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CA LEU A 601 " pdb=" N LEU A 601 " pdb=" C LEU A 601 " pdb=" CB LEU A 601 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.20e-01 chirality pdb=" CA HIS A 527 " pdb=" N HIS A 527 " pdb=" C HIS A 527 " pdb=" CB HIS A 527 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.95e-01 ... (remaining 1288 not shown) Planarity restraints: 1546 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 647 " -0.016 2.00e-02 2.50e+03 1.78e-02 6.32e+00 pdb=" CG TYR A 647 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 TYR A 647 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR A 647 " -0.016 2.00e-02 2.50e+03 pdb=" CE1 TYR A 647 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR A 647 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR A 647 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 647 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 561 " -0.012 2.00e-02 2.50e+03 2.39e-02 5.70e+00 pdb=" C PHE A 561 " 0.041 2.00e-02 2.50e+03 pdb=" O PHE A 561 " -0.016 2.00e-02 2.50e+03 pdb=" N LEU A 562 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 37 " -0.039 5.00e-02 4.00e+02 5.84e-02 5.47e+00 pdb=" N PRO A 38 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO A 38 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 38 " -0.032 5.00e-02 4.00e+02 ... (remaining 1543 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1222 2.75 - 3.29: 9082 3.29 - 3.83: 14998 3.83 - 4.36: 17376 4.36 - 4.90: 29274 Nonbonded interactions: 71952 Sorted by model distance: nonbonded pdb=" O PRO A 400 " pdb=" OH TYR A1036 " model vdw 2.217 3.040 nonbonded pdb=" OG1 THR A 632 " pdb=" OD2 ASP A 633 " model vdw 2.225 3.040 nonbonded pdb=" O SER A 580 " pdb=" OG SER A 580 " model vdw 2.226 3.040 nonbonded pdb=" O SER A 296 " pdb=" OG SER A1164 " model vdw 2.237 3.040 nonbonded pdb=" O ILE A 749 " pdb=" OH TYR A 753 " model vdw 2.238 3.040 ... (remaining 71947 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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=0.01 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 22.100 Find NCS groups from input model: 0.090 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: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 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 0.041 8910 Z= 0.256 Angle : 0.823 14.328 12025 Z= 0.470 Chirality : 0.046 0.201 1291 Planarity : 0.005 0.058 1546 Dihedral : 17.222 89.606 3379 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 22.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 0.00 % Allowed : 27.15 % Favored : 72.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.73 (0.25), residues: 1051 helix: 0.49 (0.29), residues: 320 sheet: -0.96 (0.38), residues: 175 loop : -0.85 (0.25), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 578 HIS 0.005 0.001 HIS A 494 PHE 0.020 0.002 PHE A 221 TYR 0.043 0.002 TYR A 647 ARG 0.008 0.001 ARG A 850 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 330 TYR cc_start: 0.6614 (p90) cc_final: 0.6227 (p90) REVERT: A 562 LEU cc_start: 0.7931 (tt) cc_final: 0.7709 (pp) outliers start: 0 outliers final: 0 residues processed: 166 average time/residue: 0.2147 time to fit residues: 49.5248 Evaluate side-chains 139 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 chunk 44 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 54 optimal weight: 10.0000 chunk 42 optimal weight: 0.0980 chunk 83 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 50 optimal weight: 5.9990 chunk 61 optimal weight: 6.9990 chunk 96 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 263 ASN ** A 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 408 HIS A 637 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8910 Z= 0.184 Angle : 0.621 7.462 12025 Z= 0.319 Chirality : 0.042 0.140 1291 Planarity : 0.004 0.046 1546 Dihedral : 4.662 22.191 1166 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.38 % Allowed : 26.11 % Favored : 71.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.42 (0.25), residues: 1051 helix: 0.91 (0.28), residues: 332 sheet: -0.70 (0.36), residues: 196 loop : -0.84 (0.26), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 578 HIS 0.004 0.001 HIS A 494 PHE 0.039 0.002 PHE A1000 TYR 0.013 0.001 TYR A 617 ARG 0.005 0.000 ARG A 347 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 164 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 311 MET cc_start: 0.8521 (mmt) cc_final: 0.8196 (mmt) REVERT: A 330 TYR cc_start: 0.6587 (p90) cc_final: 0.5935 (p90) REVERT: A 1013 ASN cc_start: 0.8670 (m-40) cc_final: 0.7957 (m-40) REVERT: A 1015 GLN cc_start: 0.8664 (pm20) cc_final: 0.8415 (pm20) REVERT: A 1022 GLN cc_start: 0.8422 (mt0) cc_final: 0.7984 (mt0) outliers start: 23 outliers final: 11 residues processed: 180 average time/residue: 0.2074 time to fit residues: 52.2867 Evaluate side-chains 148 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 137 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain A residue 578 TRP Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 933 LEU Chi-restraints excluded: chain A residue 1071 ARG Chi-restraints excluded: chain A residue 1103 VAL Chi-restraints excluded: chain A residue 1112 ILE Chi-restraints excluded: chain A residue 1180 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 53 optimal weight: 0.0770 chunk 29 optimal weight: 1.9990 chunk 80 optimal weight: 6.9990 chunk 65 optimal weight: 5.9990 chunk 26 optimal weight: 0.0870 chunk 96 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 chunk 95 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 GLN ** A 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8910 Z= 0.178 Angle : 0.601 7.287 12025 Z= 0.304 Chirality : 0.043 0.202 1291 Planarity : 0.004 0.050 1546 Dihedral : 4.564 21.439 1166 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.21 % Allowed : 25.18 % Favored : 71.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.20 (0.26), residues: 1051 helix: 1.16 (0.29), residues: 328 sheet: -0.69 (0.37), residues: 196 loop : -0.69 (0.26), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 578 HIS 0.005 0.001 HIS A 408 PHE 0.024 0.001 PHE A 888 TYR 0.010 0.001 TYR A1036 ARG 0.006 0.000 ARG A 850 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 157 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 GLU cc_start: 0.8400 (pp20) cc_final: 0.8140 (tm-30) REVERT: A 311 MET cc_start: 0.8825 (mmt) cc_final: 0.8557 (mmt) REVERT: A 330 TYR cc_start: 0.6448 (p90) cc_final: 0.5673 (p90) REVERT: A 561 PHE cc_start: 0.7324 (p90) cc_final: 0.7076 (p90) REVERT: A 562 LEU cc_start: 0.7516 (pp) cc_final: 0.7311 (pp) REVERT: A 1013 ASN cc_start: 0.8657 (m-40) cc_final: 0.7868 (m-40) REVERT: A 1015 GLN cc_start: 0.8640 (pm20) cc_final: 0.8414 (pm20) REVERT: A 1022 GLN cc_start: 0.8297 (mt0) cc_final: 0.7858 (mt0) REVERT: A 1025 HIS cc_start: 0.7711 (OUTLIER) cc_final: 0.6632 (t-90) REVERT: A 1066 LYS cc_start: 0.8421 (tttt) cc_final: 0.8064 (tttt) outliers start: 31 outliers final: 20 residues processed: 179 average time/residue: 0.1969 time to fit residues: 49.7438 Evaluate side-chains 169 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 148 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 305 LYS Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 578 TRP Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 933 LEU Chi-restraints excluded: chain A residue 1025 HIS Chi-restraints excluded: chain A residue 1071 ARG Chi-restraints excluded: chain A residue 1103 VAL Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain A residue 1112 ILE Chi-restraints excluded: chain A residue 1175 ILE Chi-restraints excluded: chain A residue 1176 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 0.9990 chunk 72 optimal weight: 0.9990 chunk 50 optimal weight: 7.9990 chunk 10 optimal weight: 9.9990 chunk 46 optimal weight: 9.9990 chunk 64 optimal weight: 1.9990 chunk 96 optimal weight: 0.4980 chunk 102 optimal weight: 0.1980 chunk 91 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 856 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8910 Z= 0.170 Angle : 0.589 9.337 12025 Z= 0.297 Chirality : 0.042 0.137 1291 Planarity : 0.004 0.051 1546 Dihedral : 4.424 20.811 1166 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 3.11 % Allowed : 26.53 % Favored : 70.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.10 (0.26), residues: 1051 helix: 1.28 (0.29), residues: 329 sheet: -0.63 (0.37), residues: 196 loop : -0.67 (0.26), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 578 HIS 0.008 0.001 HIS A 621 PHE 0.021 0.001 PHE A 221 TYR 0.010 0.001 TYR A1036 ARG 0.007 0.000 ARG A 850 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 158 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 GLU cc_start: 0.8475 (pp20) cc_final: 0.8229 (tm-30) REVERT: A 726 TYR cc_start: 0.8134 (t80) cc_final: 0.7313 (t80) REVERT: A 886 VAL cc_start: 0.8058 (t) cc_final: 0.7689 (t) REVERT: A 1013 ASN cc_start: 0.8652 (m-40) cc_final: 0.7990 (m-40) REVERT: A 1025 HIS cc_start: 0.7788 (OUTLIER) cc_final: 0.6783 (t-90) REVERT: A 1066 LYS cc_start: 0.8380 (tttt) cc_final: 0.8065 (tttt) outliers start: 30 outliers final: 22 residues processed: 180 average time/residue: 0.1996 time to fit residues: 50.5155 Evaluate side-chains 168 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 145 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 305 LYS Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 348 CYS Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 578 TRP Chi-restraints excluded: chain A residue 691 LYS Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 933 LEU Chi-restraints excluded: chain A residue 1025 HIS Chi-restraints excluded: chain A residue 1071 ARG Chi-restraints excluded: chain A residue 1103 VAL Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain A residue 1112 ILE Chi-restraints excluded: chain A residue 1175 ILE Chi-restraints excluded: chain A residue 1176 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 58 optimal weight: 6.9990 chunk 1 optimal weight: 7.9990 chunk 76 optimal weight: 6.9990 chunk 42 optimal weight: 0.8980 chunk 87 optimal weight: 0.8980 chunk 70 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 52 optimal weight: 10.0000 chunk 91 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 34 optimal weight: 4.9990 overall best weight: 1.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 GLN ** A 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8910 Z= 0.270 Angle : 0.646 11.500 12025 Z= 0.325 Chirality : 0.043 0.154 1291 Planarity : 0.004 0.049 1546 Dihedral : 4.622 21.275 1166 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 4.35 % Allowed : 27.05 % Favored : 68.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.22 (0.26), residues: 1051 helix: 1.28 (0.29), residues: 327 sheet: -0.80 (0.38), residues: 195 loop : -0.74 (0.26), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 578 HIS 0.006 0.001 HIS A 621 PHE 0.021 0.002 PHE A 221 TYR 0.017 0.002 TYR A 720 ARG 0.007 0.000 ARG A 727 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 150 time to evaluate : 1.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 GLU cc_start: 0.8495 (OUTLIER) cc_final: 0.8226 (tm-30) REVERT: A 269 MET cc_start: 0.7930 (mmm) cc_final: 0.7627 (mtt) REVERT: A 330 TYR cc_start: 0.6721 (p90) cc_final: 0.5950 (p90) REVERT: A 574 THR cc_start: 0.5836 (OUTLIER) cc_final: 0.5281 (p) REVERT: A 588 ILE cc_start: 0.7631 (mt) cc_final: 0.7379 (tp) REVERT: A 622 LEU cc_start: 0.6565 (OUTLIER) cc_final: 0.6326 (pp) REVERT: A 726 TYR cc_start: 0.8194 (t80) cc_final: 0.7910 (t80) REVERT: A 1009 MET cc_start: 0.6937 (mtt) cc_final: 0.6615 (mtt) REVERT: A 1022 GLN cc_start: 0.8452 (mt0) cc_final: 0.7829 (mt0) REVERT: A 1066 LYS cc_start: 0.8446 (tttt) cc_final: 0.8139 (tttt) outliers start: 42 outliers final: 20 residues processed: 178 average time/residue: 0.2130 time to fit residues: 53.7695 Evaluate side-chains 161 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 138 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 348 CYS Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 578 TRP Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 691 LYS Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 933 LEU Chi-restraints excluded: chain A residue 1080 ILE Chi-restraints excluded: chain A residue 1103 VAL Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain A residue 1112 ILE Chi-restraints excluded: chain A residue 1175 ILE Chi-restraints excluded: chain A residue 1182 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 92 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 102 optimal weight: 0.2980 chunk 85 optimal weight: 0.8980 chunk 47 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 chunk 33 optimal weight: 0.5980 chunk 53 optimal weight: 9.9990 chunk 98 optimal weight: 0.9980 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 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8910 Z= 0.177 Angle : 0.631 13.544 12025 Z= 0.316 Chirality : 0.042 0.178 1291 Planarity : 0.004 0.050 1546 Dihedral : 4.484 20.604 1166 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.90 % Allowed : 28.29 % Favored : 68.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.20 (0.26), residues: 1051 helix: 1.41 (0.30), residues: 327 sheet: -0.90 (0.37), residues: 200 loop : -0.77 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 361 HIS 0.005 0.001 HIS A 621 PHE 0.022 0.001 PHE A 221 TYR 0.009 0.001 TYR A1036 ARG 0.007 0.000 ARG A 850 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 157 time to evaluate : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 574 THR cc_start: 0.5786 (OUTLIER) cc_final: 0.5166 (p) REVERT: A 588 ILE cc_start: 0.7518 (mt) cc_final: 0.7278 (tp) REVERT: A 619 GLU cc_start: 0.6785 (OUTLIER) cc_final: 0.4990 (tm-30) REVERT: A 622 LEU cc_start: 0.6664 (OUTLIER) cc_final: 0.6417 (pp) REVERT: A 721 GLU cc_start: 0.7769 (tm-30) cc_final: 0.7553 (tm-30) REVERT: A 729 MET cc_start: 0.8003 (ppp) cc_final: 0.7751 (tmm) REVERT: A 1013 ASN cc_start: 0.8730 (m-40) cc_final: 0.8045 (m-40) REVERT: A 1025 HIS cc_start: 0.7858 (OUTLIER) cc_final: 0.6718 (t-90) REVERT: A 1066 LYS cc_start: 0.8463 (tttt) cc_final: 0.8109 (tttt) outliers start: 28 outliers final: 18 residues processed: 178 average time/residue: 0.1903 time to fit residues: 48.5274 Evaluate side-chains 163 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 141 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 305 LYS Chi-restraints excluded: chain A residue 348 CYS Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 578 TRP Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 691 LYS Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 933 LEU Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 1025 HIS Chi-restraints excluded: chain A residue 1103 VAL Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain A residue 1112 ILE Chi-restraints excluded: chain A residue 1182 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 11 optimal weight: 0.8980 chunk 58 optimal weight: 5.9990 chunk 74 optimal weight: 0.6980 chunk 86 optimal weight: 5.9990 chunk 57 optimal weight: 6.9990 chunk 102 optimal weight: 0.8980 chunk 63 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 47 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.2764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8910 Z= 0.271 Angle : 0.657 8.583 12025 Z= 0.335 Chirality : 0.044 0.174 1291 Planarity : 0.004 0.048 1546 Dihedral : 4.647 20.917 1166 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 3.52 % Allowed : 29.12 % Favored : 67.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.28 (0.26), residues: 1051 helix: 1.34 (0.29), residues: 327 sheet: -0.94 (0.37), residues: 198 loop : -0.83 (0.26), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 145 HIS 0.005 0.001 HIS A 621 PHE 0.022 0.002 PHE A 221 TYR 0.029 0.002 TYR A 206 ARG 0.007 0.000 ARG A 850 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 141 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.8265 (tm-30) REVERT: A 330 TYR cc_start: 0.6708 (p90) cc_final: 0.5865 (p90) REVERT: A 574 THR cc_start: 0.5713 (OUTLIER) cc_final: 0.5159 (p) REVERT: A 588 ILE cc_start: 0.7662 (mt) cc_final: 0.7448 (tp) REVERT: A 619 GLU cc_start: 0.6829 (OUTLIER) cc_final: 0.4988 (tm-30) REVERT: A 622 LEU cc_start: 0.6472 (OUTLIER) cc_final: 0.6235 (pp) REVERT: A 902 SER cc_start: 0.8333 (OUTLIER) cc_final: 0.8098 (p) REVERT: A 1009 MET cc_start: 0.6983 (mtt) cc_final: 0.6512 (mtt) REVERT: A 1025 HIS cc_start: 0.8158 (OUTLIER) cc_final: 0.7144 (t-90) REVERT: A 1066 LYS cc_start: 0.8481 (tttt) cc_final: 0.8113 (tttt) outliers start: 34 outliers final: 20 residues processed: 165 average time/residue: 0.1992 time to fit residues: 46.9365 Evaluate side-chains 154 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 128 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 348 CYS Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 578 TRP Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 659 MET Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 902 SER Chi-restraints excluded: chain A residue 933 LEU Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 1025 HIS Chi-restraints excluded: chain A residue 1080 ILE Chi-restraints excluded: chain A residue 1103 VAL Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain A residue 1112 ILE Chi-restraints excluded: chain A residue 1175 ILE Chi-restraints excluded: chain A residue 1182 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 30 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 64 optimal weight: 5.9990 chunk 69 optimal weight: 3.9990 chunk 50 optimal weight: 7.9990 chunk 9 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 89 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8910 Z= 0.216 Angle : 0.648 8.117 12025 Z= 0.330 Chirality : 0.043 0.245 1291 Planarity : 0.004 0.049 1546 Dihedral : 4.608 21.334 1166 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 3.01 % Allowed : 29.64 % Favored : 67.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.25 (0.26), residues: 1051 helix: 1.40 (0.29), residues: 326 sheet: -0.88 (0.37), residues: 201 loop : -0.85 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP A 361 HIS 0.005 0.001 HIS A 621 PHE 0.023 0.002 PHE A 221 TYR 0.025 0.002 TYR A 321 ARG 0.006 0.000 ARG A 665 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 142 time to evaluate : 1.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 574 THR cc_start: 0.5646 (OUTLIER) cc_final: 0.5067 (p) REVERT: A 588 ILE cc_start: 0.7648 (mt) cc_final: 0.7424 (tp) REVERT: A 619 GLU cc_start: 0.6814 (OUTLIER) cc_final: 0.4999 (tm-30) REVERT: A 622 LEU cc_start: 0.6337 (OUTLIER) cc_final: 0.6127 (pp) REVERT: A 902 SER cc_start: 0.8408 (OUTLIER) cc_final: 0.8190 (p) REVERT: A 1013 ASN cc_start: 0.8725 (m-40) cc_final: 0.8105 (m-40) REVERT: A 1025 HIS cc_start: 0.7984 (OUTLIER) cc_final: 0.6845 (t-90) outliers start: 29 outliers final: 19 residues processed: 162 average time/residue: 0.1933 time to fit residues: 44.5204 Evaluate side-chains 159 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 135 time to evaluate : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 348 CYS Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 578 TRP Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 902 SER Chi-restraints excluded: chain A residue 933 LEU Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 1025 HIS Chi-restraints excluded: chain A residue 1103 VAL Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain A residue 1112 ILE Chi-restraints excluded: chain A residue 1158 VAL Chi-restraints excluded: chain A residue 1175 ILE Chi-restraints excluded: chain A residue 1182 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 chunk 41 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 chunk 86 optimal weight: 3.9990 chunk 90 optimal weight: 0.7980 chunk 94 optimal weight: 0.9980 chunk 62 optimal weight: 6.9990 chunk 100 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8910 Z= 0.196 Angle : 0.654 8.180 12025 Z= 0.331 Chirality : 0.043 0.275 1291 Planarity : 0.004 0.048 1546 Dihedral : 4.575 26.895 1166 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 3.01 % Allowed : 29.84 % Favored : 67.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.13 (0.26), residues: 1051 helix: 1.62 (0.29), residues: 317 sheet: -0.86 (0.37), residues: 202 loop : -0.79 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 361 HIS 0.005 0.001 HIS A 621 PHE 0.024 0.001 PHE A 221 TYR 0.034 0.002 TYR A 321 ARG 0.009 0.000 ARG A 850 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 145 time to evaluate : 1.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 574 THR cc_start: 0.5598 (OUTLIER) cc_final: 0.5054 (p) REVERT: A 588 ILE cc_start: 0.7684 (mt) cc_final: 0.7469 (tp) REVERT: A 619 GLU cc_start: 0.6907 (OUTLIER) cc_final: 0.5153 (tm-30) REVERT: A 622 LEU cc_start: 0.6347 (OUTLIER) cc_final: 0.6137 (pp) REVERT: A 673 LYS cc_start: 0.8625 (tmtt) cc_final: 0.8379 (tmtt) REVERT: A 902 SER cc_start: 0.8410 (OUTLIER) cc_final: 0.7715 (p) REVERT: A 1013 ASN cc_start: 0.8655 (m-40) cc_final: 0.7985 (m-40) REVERT: A 1025 HIS cc_start: 0.7873 (OUTLIER) cc_final: 0.6658 (t-90) outliers start: 29 outliers final: 19 residues processed: 165 average time/residue: 0.2061 time to fit residues: 48.6813 Evaluate side-chains 161 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 137 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 305 LYS Chi-restraints excluded: chain A residue 348 CYS Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 578 TRP Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 902 SER Chi-restraints excluded: chain A residue 933 LEU Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 1025 HIS Chi-restraints excluded: chain A residue 1103 VAL Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain A residue 1112 ILE Chi-restraints excluded: chain A residue 1182 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 61 optimal weight: 0.7980 chunk 47 optimal weight: 8.9990 chunk 69 optimal weight: 0.7980 chunk 105 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 8 optimal weight: 7.9990 chunk 64 optimal weight: 2.9990 chunk 51 optimal weight: 7.9990 chunk 66 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 8910 Z= 0.238 Angle : 0.687 9.069 12025 Z= 0.349 Chirality : 0.044 0.191 1291 Planarity : 0.004 0.047 1546 Dihedral : 4.662 27.171 1166 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 15.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 3.11 % Allowed : 30.26 % Favored : 66.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.16 (0.26), residues: 1051 helix: 1.54 (0.29), residues: 319 sheet: -0.83 (0.37), residues: 199 loop : -0.81 (0.27), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 361 HIS 0.007 0.001 HIS A1025 PHE 0.025 0.002 PHE A 221 TYR 0.030 0.002 TYR A 321 ARG 0.007 0.000 ARG A 850 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 141 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 TYR cc_start: 0.8322 (t80) cc_final: 0.8099 (t80) REVERT: A 210 MET cc_start: 0.8393 (mpp) cc_final: 0.8069 (mtt) REVERT: A 574 THR cc_start: 0.5541 (OUTLIER) cc_final: 0.4980 (p) REVERT: A 619 GLU cc_start: 0.6917 (OUTLIER) cc_final: 0.5189 (tm-30) REVERT: A 622 LEU cc_start: 0.6276 (OUTLIER) cc_final: 0.6072 (pp) REVERT: A 673 LYS cc_start: 0.8650 (tmtt) cc_final: 0.8379 (tmtt) REVERT: A 747 ARG cc_start: 0.7433 (OUTLIER) cc_final: 0.7129 (mtm-85) REVERT: A 902 SER cc_start: 0.8605 (OUTLIER) cc_final: 0.8373 (p) REVERT: A 1009 MET cc_start: 0.6892 (mtt) cc_final: 0.6386 (mtt) REVERT: A 1013 ASN cc_start: 0.8639 (m-40) cc_final: 0.8022 (m-40) outliers start: 30 outliers final: 20 residues processed: 160 average time/residue: 0.2106 time to fit residues: 47.1328 Evaluate side-chains 161 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 136 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 305 LYS Chi-restraints excluded: chain A residue 348 CYS Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 578 TRP Chi-restraints excluded: chain A residue 585 HIS Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 747 ARG Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 902 SER Chi-restraints excluded: chain A residue 933 LEU Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1103 VAL Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain A residue 1112 ILE Chi-restraints excluded: chain A residue 1158 VAL Chi-restraints excluded: chain A residue 1182 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 25 optimal weight: 0.7980 chunk 77 optimal weight: 6.9990 chunk 12 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 86 optimal weight: 0.0870 chunk 10 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 73 optimal weight: 0.7980 chunk 4 optimal weight: 6.9990 overall best weight: 0.9360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 ASN A1025 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.134707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.106869 restraints weight = 16855.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.110713 restraints weight = 8632.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.113200 restraints weight = 5583.798| |-----------------------------------------------------------------------------| r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3719 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3719 r_free = 0.3719 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3698 r_free = 0.3698 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 44 | |-----------------------------------------------------------------------------| r_final: 0.3698 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.3315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8910 Z= 0.206 Angle : 0.671 8.532 12025 Z= 0.340 Chirality : 0.044 0.193 1291 Planarity : 0.004 0.048 1546 Dihedral : 4.592 26.675 1166 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.69 % Allowed : 30.78 % Favored : 66.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.17 (0.26), residues: 1051 helix: 1.53 (0.29), residues: 319 sheet: -0.84 (0.37), residues: 202 loop : -0.81 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 361 HIS 0.008 0.001 HIS A1025 PHE 0.026 0.002 PHE A 221 TYR 0.029 0.002 TYR A 321 ARG 0.007 0.000 ARG A 850 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1931.49 seconds wall clock time: 36 minutes 2.69 seconds (2162.69 seconds total)