Starting phenix.real_space_refine on Wed Apr 30 07:05:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ms8_48568/04_2025/9ms8_48568.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ms8_48568/04_2025/9ms8_48568.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ms8_48568/04_2025/9ms8_48568.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ms8_48568/04_2025/9ms8_48568.map" model { file = "/net/cci-nas-00/data/ceres_data/9ms8_48568/04_2025/9ms8_48568.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ms8_48568/04_2025/9ms8_48568.cif" } resolution = 3.73 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= 0.004 sd= 0.044 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 53 5.16 5 C 6020 2.51 5 N 1533 2.21 5 O 1684 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 9290 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 978, 7667 Classifications: {'peptide': 978} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 40, 'TRANS': 937} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 33 Chain: "L" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 772 Classifications: {'peptide': 102} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 95} Chain: "H" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 851 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 106} Time building chain proxies: 5.94, per 1000 atoms: 0.64 Number of scatterers: 9290 At special positions: 0 Unit cell: (83.3, 108.29, 139.111, 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 53 16.00 O 1684 8.00 N 1533 7.00 C 6020 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 203 " - pdb=" SG CYS A 226 " distance=2.03 Simple disulfide: pdb=" SG CYS A 234 " - pdb=" SG CYS A 327 " distance=2.02 Simple disulfide: pdb=" SG CYS L 42 " - pdb=" SG CYS L 108 " distance=2.03 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 115 " distance=2.03 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: 2.62 Conformation dependent library (CDL) restraints added in 1.3 seconds 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2210 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 6 sheets defined 53.5% alpha, 7.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.45 Creating SS restraints... Processing helix chain 'A' and resid 76 through 96 removed outlier: 4.294A pdb=" N ARG A 80 " --> pdb=" O PRO A 76 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS A 96 " --> pdb=" O CYS A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 116 removed outlier: 3.982A pdb=" N VAL A 103 " --> pdb=" O GLY A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 129 Processing helix chain 'A' and resid 134 through 146 removed outlier: 3.808A pdb=" N ARG A 138 " --> pdb=" O GLY A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 187 removed outlier: 3.511A pdb=" N ARG A 187 " --> pdb=" O LEU A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 224 Processing helix chain 'A' and resid 230 through 235 Processing helix chain 'A' and resid 260 through 271 removed outlier: 3.726A pdb=" N ILE A 271 " --> pdb=" O GLU A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 285 Processing helix chain 'A' and resid 338 through 342 removed outlier: 3.840A pdb=" N ILE A 342 " --> pdb=" O GLN A 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 338 through 342' Processing helix chain 'A' and resid 368 through 377 Processing helix chain 'A' and resid 388 through 411 removed outlier: 3.761A pdb=" N ALA A 392 " --> pdb=" O ASN A 388 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N VAL A 411 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 436 Processing helix chain 'A' and resid 438 through 457 Processing helix chain 'A' and resid 469 through 491 Processing helix chain 'A' and resid 502 through 528 removed outlier: 3.647A pdb=" N LEU A 508 " --> pdb=" O PRO A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 563 removed outlier: 5.554A pdb=" N ALA A 546 " --> pdb=" O LYS A 542 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N SER A 547 " --> pdb=" O ARG A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 602 Proline residue: A 593 - end of helix Processing helix chain 'A' and resid 733 through 746 Proline residue: A 742 - end of helix removed outlier: 4.603A pdb=" N LYS A 746 " --> pdb=" O PRO A 742 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 770 removed outlier: 3.655A pdb=" N LYS A 750 " --> pdb=" O LYS A 746 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ARG A 770 " --> pdb=" O TYR A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 776 through 780 Processing helix chain 'A' and resid 785 through 798 removed outlier: 3.843A pdb=" N ASP A 789 " --> pdb=" O THR A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 826 through 829 Processing helix chain 'A' and resid 843 through 866 removed outlier: 3.751A pdb=" N TYR A 847 " --> pdb=" O MET A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 871 through 875 removed outlier: 3.862A pdb=" N LYS A 874 " --> pdb=" O ASN A 871 " (cutoff:3.500A) Processing helix chain 'A' and resid 877 through 889 removed outlier: 3.677A pdb=" N GLN A 889 " --> pdb=" O LYS A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 901 removed outlier: 3.596A pdb=" N GLN A 901 " --> pdb=" O ASP A 898 " (cutoff:3.500A) Processing helix chain 'A' and resid 915 through 917 No H-bonds generated for 'chain 'A' and resid 915 through 917' Processing helix chain 'A' and resid 918 through 930 removed outlier: 3.822A pdb=" N SER A 928 " --> pdb=" O THR A 924 " (cutoff:3.500A) Processing helix chain 'A' and resid 930 through 938 Processing helix chain 'A' and resid 956 through 960 removed outlier: 4.178A pdb=" N ARG A 960 " --> pdb=" O PRO A 957 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1005 removed outlier: 3.545A pdb=" N GLU A 989 " --> pdb=" O SER A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 1012 through 1018 Processing helix chain 'A' and resid 1019 through 1022 Processing helix chain 'A' and resid 1023 through 1048 Processing helix chain 'A' and resid 1049 through 1075 Processing helix chain 'A' and resid 1079 through 1105 removed outlier: 3.796A pdb=" N VAL A1090 " --> pdb=" O LEU A1086 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N GLY A1091 " --> pdb=" O ILE A1087 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLU A1095 " --> pdb=" O GLY A1091 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N PHE A1096 " --> pdb=" O ILE A1092 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N ALA A1103 " --> pdb=" O HIS A1099 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE A1104 " --> pdb=" O VAL A1100 " (cutoff:3.500A) Processing helix chain 'A' and resid 1112 through 1122 Processing helix chain 'A' and resid 1123 through 1139 removed outlier: 3.515A pdb=" N LEU A1127 " --> pdb=" O PHE A1123 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N MET A1139 " --> pdb=" O LEU A1135 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1143 Processing helix chain 'A' and resid 1145 through 1170 Processing helix chain 'A' and resid 1170 through 1176 Processing helix chain 'L' and resid 49 through 51 No H-bonds generated for 'chain 'L' and resid 49 through 51' Processing helix chain 'L' and resid 99 through 103 removed outlier: 3.650A pdb=" N ASP L 102 " --> pdb=" O GLU L 99 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ALA L 103 " --> pdb=" O ALA L 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 99 through 103' Processing sheet with id=AA1, first strand: chain 'A' and resid 343 through 344 Processing sheet with id=AA2, first strand: chain 'A' and resid 800 through 807 removed outlier: 3.531A pdb=" N ILE A 805 " --> pdb=" O PHE A 974 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 23 through 24 removed outlier: 3.678A pdb=" N SER L 90 " --> pdb=" O SER L 87 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 65 through 69 removed outlier: 6.477A pdb=" N TRP L 55 " --> pdb=" O TRP L 67 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N TYR L 69 " --> pdb=" O LEU L 53 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N LEU L 53 " --> pdb=" O TYR L 69 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 24 through 26 removed outlier: 3.504A pdb=" N LEU H 100 " --> pdb=" O LEU H 39 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU H 98 " --> pdb=" O CYS H 41 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 77 through 79 removed outlier: 3.583A pdb=" N TYR H 78 " --> pdb=" O TYR H 69 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR H 69 " --> pdb=" O TYR H 78 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N TRP H 55 " --> pdb=" O VAL H 67 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N TYR H 69 " --> pdb=" O MET H 53 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N MET H 53 " --> pdb=" O TYR H 69 " (cutoff:3.500A) 484 hydrogen bonds defined for protein. 1392 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: 3.75 Time building geometry restraints manager: 3.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2913 1.34 - 1.46: 2211 1.46 - 1.58: 4310 1.58 - 1.70: 0 1.70 - 1.82: 87 Bond restraints: 9521 Sorted by residual: bond pdb=" C SER L 26 " pdb=" N PRO L 27 " ideal model delta sigma weight residual 1.333 1.348 -0.015 1.20e-02 6.94e+03 1.48e+00 bond pdb=" CG LEU L 53 " pdb=" CD1 LEU L 53 " ideal model delta sigma weight residual 1.521 1.481 0.040 3.30e-02 9.18e+02 1.45e+00 bond pdb=" CA PHE A 153 " pdb=" CB PHE A 153 " ideal model delta sigma weight residual 1.530 1.550 -0.020 1.69e-02 3.50e+03 1.38e+00 bond pdb=" CA ILE A 897 " pdb=" CB ILE A 897 " ideal model delta sigma weight residual 1.540 1.524 0.016 1.36e-02 5.41e+03 1.35e+00 bond pdb=" C MET A 956 " pdb=" N PRO A 957 " ideal model delta sigma weight residual 1.334 1.361 -0.027 2.34e-02 1.83e+03 1.30e+00 ... (remaining 9516 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.55: 12745 2.55 - 5.09: 169 5.09 - 7.64: 19 7.64 - 10.18: 10 10.18 - 12.73: 1 Bond angle restraints: 12944 Sorted by residual: angle pdb=" N PRO A 896 " pdb=" CA PRO A 896 " pdb=" CB PRO A 896 " ideal model delta sigma weight residual 103.25 110.03 -6.78 1.05e+00 9.07e-01 4.17e+01 angle pdb=" CA GLU A 122 " pdb=" CB GLU A 122 " pdb=" CG GLU A 122 " ideal model delta sigma weight residual 114.10 124.00 -9.90 2.00e+00 2.50e-01 2.45e+01 angle pdb=" CA GLN A 839 " pdb=" CB GLN A 839 " pdb=" CG GLN A 839 " ideal model delta sigma weight residual 114.10 123.46 -9.36 2.00e+00 2.50e-01 2.19e+01 angle pdb=" CB MET A 869 " pdb=" CG MET A 869 " pdb=" SD MET A 869 " ideal model delta sigma weight residual 112.70 125.43 -12.73 3.00e+00 1.11e-01 1.80e+01 angle pdb=" C SER L 70 " pdb=" N THR L 71 " pdb=" CA THR L 71 " ideal model delta sigma weight residual 121.54 129.42 -7.88 1.91e+00 2.74e-01 1.70e+01 ... (remaining 12939 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 4845 17.95 - 35.91: 587 35.91 - 53.86: 136 53.86 - 71.81: 20 71.81 - 89.77: 9 Dihedral angle restraints: 5597 sinusoidal: 2146 harmonic: 3451 Sorted by residual: dihedral pdb=" CB CYS A 203 " pdb=" SG CYS A 203 " pdb=" SG CYS A 226 " pdb=" CB CYS A 226 " ideal model delta sinusoidal sigma weight residual -86.00 -153.08 67.08 1 1.00e+01 1.00e-02 5.86e+01 dihedral pdb=" CA TRP A 197 " pdb=" C TRP A 197 " pdb=" N LYS A 198 " pdb=" CA LYS A 198 " ideal model delta harmonic sigma weight residual -180.00 -146.91 -33.09 0 5.00e+00 4.00e-02 4.38e+01 dihedral pdb=" CA CYS A 226 " pdb=" C CYS A 226 " pdb=" N LEU A 227 " pdb=" CA LEU A 227 " ideal model delta harmonic sigma weight residual 180.00 -159.96 -20.04 0 5.00e+00 4.00e-02 1.61e+01 ... (remaining 5594 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1028 0.041 - 0.082: 319 0.082 - 0.123: 97 0.123 - 0.164: 16 0.164 - 0.206: 2 Chirality restraints: 1462 Sorted by residual: chirality pdb=" CA PRO A 896 " pdb=" N PRO A 896 " pdb=" C PRO A 896 " pdb=" CB PRO A 896 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CB ILE A 815 " pdb=" CA ILE A 815 " pdb=" CG1 ILE A 815 " pdb=" CG2 ILE A 815 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.45e-01 chirality pdb=" CG LEU A 517 " pdb=" CB LEU A 517 " pdb=" CD1 LEU A 517 " pdb=" CD2 LEU A 517 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.29e-01 ... (remaining 1459 not shown) Planarity restraints: 1628 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A1149 " -0.011 2.00e-02 2.50e+03 2.14e-02 4.58e+00 pdb=" C VAL A1149 " 0.037 2.00e-02 2.50e+03 pdb=" O VAL A1149 " -0.014 2.00e-02 2.50e+03 pdb=" N ARG A1150 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A1150 " -0.011 2.00e-02 2.50e+03 2.14e-02 4.58e+00 pdb=" C ARG A1150 " 0.037 2.00e-02 2.50e+03 pdb=" O ARG A1150 " -0.014 2.00e-02 2.50e+03 pdb=" N TYR A1151 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 308 " 0.035 5.00e-02 4.00e+02 5.35e-02 4.57e+00 pdb=" N PRO A 309 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO A 309 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 309 " 0.030 5.00e-02 4.00e+02 ... (remaining 1625 not shown) Histogram of nonbonded interaction distances: 2.52 - 3.00: 5175 3.00 - 3.47: 10019 3.47 - 3.95: 14159 3.95 - 4.42: 16363 4.42 - 4.90: 26188 Nonbonded interactions: 71904 Sorted by model distance: nonbonded pdb=" O GLU A 122 " pdb=" OE1 GLU A 122 " model vdw 2.522 3.040 nonbonded pdb=" OE1 GLU H 61 " pdb=" N LYS H 62 " model vdw 2.561 3.120 nonbonded pdb=" C SER A 928 " pdb=" OG SER A 928 " model vdw 2.588 2.616 nonbonded pdb=" N GLY A 244 " pdb=" N THR A 245 " model vdw 2.590 2.560 nonbonded pdb=" N ILE A 147 " pdb=" N GLY A 148 " model vdw 2.595 2.560 ... (remaining 71899 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 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: 57.540 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: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 25.220 Find NCS groups from input model: 0.100 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9525 Z= 0.154 Angle : 0.751 12.726 12952 Z= 0.382 Chirality : 0.044 0.206 1462 Planarity : 0.005 0.053 1628 Dihedral : 16.237 89.765 3375 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 1.12 % Allowed : 21.91 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.91 (0.26), residues: 1181 helix: 1.43 (0.23), residues: 548 sheet: -1.99 (0.46), residues: 137 loop : -2.64 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP H 66 HIS 0.006 0.001 HIS A 358 PHE 0.022 0.001 PHE L 91 TYR 0.012 0.001 TYR A 766 ARG 0.004 0.001 ARG A 536 Details of bonding type rmsd hydrogen bonds : bond 0.14869 ( 484) hydrogen bonds : angle 6.03260 ( 1392) SS BOND : bond 0.00424 ( 4) SS BOND : angle 1.29578 ( 8) covalent geometry : bond 0.00333 ( 9521) covalent geometry : angle 0.75041 (12944) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 170 time to evaluate : 1.186 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 280 GLU cc_start: 0.9064 (tp30) cc_final: 0.8643 (tm-30) REVERT: A 292 MET cc_start: 0.8184 (mtp) cc_final: 0.7661 (mtp) REVERT: A 372 MET cc_start: 0.9057 (ttt) cc_final: 0.8822 (ttp) REVERT: A 464 LYS cc_start: 0.7550 (mmtt) cc_final: 0.7217 (mmtt) REVERT: A 598 MET cc_start: 0.8218 (tmm) cc_final: 0.7983 (mmt) REVERT: A 748 LYS cc_start: 0.6764 (mmtm) cc_final: 0.6071 (ttpp) REVERT: A 819 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8373 (tt) REVERT: A 1066 GLU cc_start: 0.8020 (mt-10) cc_final: 0.7501 (mp0) REVERT: L 90 SER cc_start: 0.8468 (t) cc_final: 0.8087 (p) REVERT: H 25 GLU cc_start: 0.8254 (mp0) cc_final: 0.8032 (mp0) outliers start: 11 outliers final: 7 residues processed: 177 average time/residue: 0.2065 time to fit residues: 53.3398 Evaluate side-chains 155 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 147 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 819 LEU Chi-restraints excluded: chain A residue 1169 VAL Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 108 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 49 optimal weight: 0.3980 chunk 30 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 47 optimal weight: 6.9990 chunk 91 optimal weight: 8.9990 chunk 35 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 106 optimal weight: 0.7980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 25 GLN L 57 GLN ** L 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 112 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.128497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.104216 restraints weight = 19907.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.107484 restraints weight = 10787.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.109673 restraints weight = 7381.807| |-----------------------------------------------------------------------------| r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.0909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9525 Z= 0.145 Angle : 0.663 9.198 12952 Z= 0.332 Chirality : 0.042 0.175 1462 Planarity : 0.005 0.050 1628 Dihedral : 5.614 55.995 1304 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.38 % Favored : 91.62 % Rotamer: Outliers : 4.06 % Allowed : 20.99 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 (0.26), residues: 1181 helix: 1.48 (0.22), residues: 559 sheet: -1.80 (0.45), residues: 136 loop : -2.57 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 66 HIS 0.006 0.001 HIS A 944 PHE 0.024 0.002 PHE A1104 TYR 0.011 0.001 TYR A 873 ARG 0.003 0.000 ARG H 37 Details of bonding type rmsd hydrogen bonds : bond 0.04728 ( 484) hydrogen bonds : angle 4.89790 ( 1392) SS BOND : bond 0.00564 ( 4) SS BOND : angle 0.94230 ( 8) covalent geometry : bond 0.00322 ( 9521) covalent geometry : angle 0.66291 (12944) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 170 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 GLU cc_start: 0.9003 (tp30) cc_final: 0.8544 (tm-30) REVERT: A 292 MET cc_start: 0.8250 (mtp) cc_final: 0.7949 (mtp) REVERT: A 372 MET cc_start: 0.9122 (ttt) cc_final: 0.8872 (ttp) REVERT: A 464 LYS cc_start: 0.7713 (mmtt) cc_final: 0.7316 (mmtt) REVERT: A 598 MET cc_start: 0.8245 (tmm) cc_final: 0.7981 (mmt) REVERT: A 734 SER cc_start: 0.8140 (m) cc_final: 0.7847 (t) REVERT: A 748 LYS cc_start: 0.6555 (mmtm) cc_final: 0.5921 (ttpp) REVERT: A 819 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8469 (tt) REVERT: A 1066 GLU cc_start: 0.8050 (mt-10) cc_final: 0.7487 (mp0) REVERT: L 90 SER cc_start: 0.8662 (t) cc_final: 0.8055 (p) REVERT: L 99 GLU cc_start: 0.7311 (mp0) cc_final: 0.6931 (mp0) REVERT: H 62 LYS cc_start: 0.8116 (OUTLIER) cc_final: 0.7594 (mtpt) outliers start: 40 outliers final: 25 residues processed: 193 average time/residue: 0.1762 time to fit residues: 50.3753 Evaluate side-chains 179 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 152 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 525 THR Chi-restraints excluded: chain A residue 540 CYS Chi-restraints excluded: chain A residue 560 PHE Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 583 PHE Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 773 ASP Chi-restraints excluded: chain A residue 819 LEU Chi-restraints excluded: chain A residue 1131 VAL Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1139 MET Chi-restraints excluded: chain A residue 1169 VAL Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 92 SER Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 62 LYS Chi-restraints excluded: chain H residue 103 THR Chi-restraints excluded: chain H residue 121 MET Chi-restraints excluded: chain H residue 126 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 0 optimal weight: 10.0000 chunk 11 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 chunk 113 optimal weight: 8.9990 chunk 2 optimal weight: 9.9990 chunk 90 optimal weight: 0.5980 chunk 89 optimal weight: 0.7980 chunk 82 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1121 HIS ** L 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 112 HIS H 58 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.129037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.103934 restraints weight = 20123.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.107251 restraints weight = 10974.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.109473 restraints weight = 7549.572| |-----------------------------------------------------------------------------| r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.1326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9525 Z= 0.140 Angle : 0.659 10.800 12952 Z= 0.324 Chirality : 0.042 0.197 1462 Planarity : 0.004 0.051 1628 Dihedral : 5.320 55.785 1299 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % Rotamer: Outliers : 4.87 % Allowed : 22.72 % Favored : 72.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.59 (0.26), residues: 1181 helix: 1.56 (0.22), residues: 559 sheet: -1.63 (0.44), residues: 139 loop : -2.46 (0.28), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 66 HIS 0.006 0.001 HIS A1099 PHE 0.017 0.001 PHE L 76 TYR 0.023 0.001 TYR A 766 ARG 0.003 0.000 ARG H 37 Details of bonding type rmsd hydrogen bonds : bond 0.04297 ( 484) hydrogen bonds : angle 4.62078 ( 1392) SS BOND : bond 0.00496 ( 4) SS BOND : angle 0.89556 ( 8) covalent geometry : bond 0.00314 ( 9521) covalent geometry : angle 0.65854 (12944) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 158 time to evaluate : 1.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 LEU cc_start: 0.7648 (OUTLIER) cc_final: 0.7346 (pt) REVERT: A 280 GLU cc_start: 0.9025 (tp30) cc_final: 0.8596 (tm-30) REVERT: A 292 MET cc_start: 0.8265 (mtp) cc_final: 0.7910 (mtp) REVERT: A 372 MET cc_start: 0.9136 (ttt) cc_final: 0.8924 (ttp) REVERT: A 464 LYS cc_start: 0.7758 (mmtt) cc_final: 0.7390 (mmtt) REVERT: A 598 MET cc_start: 0.8242 (tmm) cc_final: 0.7958 (mmt) REVERT: A 734 SER cc_start: 0.8160 (m) cc_final: 0.7865 (t) REVERT: A 748 LYS cc_start: 0.6606 (mmtm) cc_final: 0.5843 (ttpp) REVERT: A 1066 GLU cc_start: 0.8102 (mt-10) cc_final: 0.7512 (mp0) REVERT: A 1165 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8157 (tp) REVERT: H 62 LYS cc_start: 0.8157 (OUTLIER) cc_final: 0.7632 (mtpt) outliers start: 48 outliers final: 32 residues processed: 189 average time/residue: 0.2190 time to fit residues: 61.4898 Evaluate side-chains 182 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 147 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 525 THR Chi-restraints excluded: chain A residue 540 CYS Chi-restraints excluded: chain A residue 560 PHE Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 583 PHE Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 773 ASP Chi-restraints excluded: chain A residue 835 GLU Chi-restraints excluded: chain A residue 969 ILE Chi-restraints excluded: chain A residue 1131 VAL Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1165 LEU Chi-restraints excluded: chain A residue 1169 VAL Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 62 LYS Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 103 THR Chi-restraints excluded: chain H residue 108 GLU Chi-restraints excluded: chain H residue 121 MET Chi-restraints excluded: chain H residue 126 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 106 optimal weight: 1.9990 chunk 37 optimal weight: 0.0970 chunk 88 optimal weight: 0.9980 chunk 69 optimal weight: 9.9990 chunk 48 optimal weight: 5.9990 chunk 2 optimal weight: 0.0170 chunk 104 optimal weight: 9.9990 chunk 57 optimal weight: 5.9990 chunk 101 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 overall best weight: 1.0220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 808 GLN ** L 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 112 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.129036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.104252 restraints weight = 19869.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.107548 restraints weight = 10825.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.109579 restraints weight = 7427.933| |-----------------------------------------------------------------------------| r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9525 Z= 0.136 Angle : 0.651 9.879 12952 Z= 0.319 Chirality : 0.042 0.206 1462 Planarity : 0.004 0.049 1628 Dihedral : 4.999 44.419 1297 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer: Outliers : 5.68 % Allowed : 23.23 % Favored : 71.10 % 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: -0.44 (0.26), residues: 1181 helix: 1.64 (0.22), residues: 561 sheet: -1.63 (0.43), residues: 141 loop : -2.33 (0.29), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 197 HIS 0.004 0.001 HIS L 109 PHE 0.017 0.001 PHE L 76 TYR 0.022 0.001 TYR A 766 ARG 0.003 0.000 ARG H 37 Details of bonding type rmsd hydrogen bonds : bond 0.04030 ( 484) hydrogen bonds : angle 4.47989 ( 1392) SS BOND : bond 0.00537 ( 4) SS BOND : angle 0.83451 ( 8) covalent geometry : bond 0.00306 ( 9521) covalent geometry : angle 0.65101 (12944) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 164 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 GLU cc_start: 0.8990 (tp30) cc_final: 0.8615 (tm-30) REVERT: A 464 LYS cc_start: 0.7778 (mmtt) cc_final: 0.7420 (mmtt) REVERT: A 598 MET cc_start: 0.8283 (tmm) cc_final: 0.7956 (mmt) REVERT: A 734 SER cc_start: 0.8148 (m) cc_final: 0.7846 (t) REVERT: A 748 LYS cc_start: 0.6630 (mmtm) cc_final: 0.5810 (ttpp) REVERT: A 1066 GLU cc_start: 0.8128 (mt-10) cc_final: 0.7548 (mp0) REVERT: L 99 GLU cc_start: 0.7692 (mp0) cc_final: 0.7326 (mp0) REVERT: H 62 LYS cc_start: 0.8122 (OUTLIER) cc_final: 0.7610 (mtpt) REVERT: H 66 TRP cc_start: 0.8418 (t60) cc_final: 0.7928 (t60) outliers start: 56 outliers final: 41 residues processed: 200 average time/residue: 0.1754 time to fit residues: 51.3785 Evaluate side-chains 191 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 149 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 PHE Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 367 MET Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 525 THR Chi-restraints excluded: chain A residue 540 CYS Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 560 PHE Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 583 PHE Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 773 ASP Chi-restraints excluded: chain A residue 835 GLU Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 969 ILE Chi-restraints excluded: chain A residue 1062 LEU Chi-restraints excluded: chain A residue 1131 VAL Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1169 VAL Chi-restraints excluded: chain A residue 1170 LEU Chi-restraints excluded: chain A residue 1171 LEU Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 40 LEU Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 92 SER Chi-restraints excluded: chain L residue 95 ILE Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 62 LYS Chi-restraints excluded: chain H residue 77 ILE Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 103 THR Chi-restraints excluded: chain H residue 108 GLU Chi-restraints excluded: chain H residue 121 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 15 optimal weight: 0.0870 chunk 89 optimal weight: 0.7980 chunk 46 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 23 optimal weight: 6.9990 chunk 79 optimal weight: 0.6980 chunk 58 optimal weight: 3.9990 chunk 75 optimal weight: 5.9990 chunk 43 optimal weight: 0.9980 overall best weight: 1.1160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 57 GLN L 58 GLN ** L 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 112 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.129183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.104261 restraints weight = 20078.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.107617 restraints weight = 10939.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.109849 restraints weight = 7482.745| |-----------------------------------------------------------------------------| r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9525 Z= 0.142 Angle : 0.659 8.861 12952 Z= 0.324 Chirality : 0.042 0.161 1462 Planarity : 0.004 0.048 1628 Dihedral : 4.831 31.933 1295 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer: Outliers : 6.39 % Allowed : 24.14 % Favored : 69.47 % 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: -0.39 (0.26), residues: 1181 helix: 1.66 (0.22), residues: 560 sheet: -1.51 (0.44), residues: 140 loop : -2.30 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 197 HIS 0.005 0.001 HIS A1099 PHE 0.019 0.001 PHE L 76 TYR 0.010 0.001 TYR A 222 ARG 0.002 0.000 ARG H 117 Details of bonding type rmsd hydrogen bonds : bond 0.03995 ( 484) hydrogen bonds : angle 4.48253 ( 1392) SS BOND : bond 0.00534 ( 4) SS BOND : angle 0.86837 ( 8) covalent geometry : bond 0.00322 ( 9521) covalent geometry : angle 0.65928 (12944) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 153 time to evaluate : 1.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 GLU cc_start: 0.8980 (tp30) cc_final: 0.8619 (tm-30) REVERT: A 292 MET cc_start: 0.8302 (mtp) cc_final: 0.7703 (mtp) REVERT: A 464 LYS cc_start: 0.7755 (mmtt) cc_final: 0.7390 (mmtt) REVERT: A 598 MET cc_start: 0.8318 (tmm) cc_final: 0.7978 (mmt) REVERT: A 734 SER cc_start: 0.8126 (m) cc_final: 0.7827 (t) REVERT: A 740 TYR cc_start: 0.8064 (OUTLIER) cc_final: 0.7798 (t80) REVERT: A 748 LYS cc_start: 0.6619 (mmtm) cc_final: 0.5800 (ttpp) REVERT: A 974 PHE cc_start: 0.9068 (OUTLIER) cc_final: 0.8417 (p90) REVERT: A 1066 GLU cc_start: 0.8150 (mt-10) cc_final: 0.7565 (mp0) REVERT: H 62 LYS cc_start: 0.8089 (OUTLIER) cc_final: 0.7563 (mtpt) REVERT: H 66 TRP cc_start: 0.8461 (t60) cc_final: 0.7939 (t60) REVERT: H 117 ARG cc_start: 0.8066 (tpp-160) cc_final: 0.7767 (tpp-160) REVERT: H 126 GLN cc_start: 0.8135 (mm110) cc_final: 0.7840 (mm110) outliers start: 63 outliers final: 42 residues processed: 195 average time/residue: 0.2182 time to fit residues: 62.3063 Evaluate side-chains 191 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 146 time to evaluate : 1.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 PHE Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 525 THR Chi-restraints excluded: chain A residue 540 CYS Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 560 PHE Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 583 PHE Chi-restraints excluded: chain A residue 740 TYR Chi-restraints excluded: chain A residue 773 ASP Chi-restraints excluded: chain A residue 835 GLU Chi-restraints excluded: chain A residue 862 ASP Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 969 ILE Chi-restraints excluded: chain A residue 974 PHE Chi-restraints excluded: chain A residue 1062 LEU Chi-restraints excluded: chain A residue 1131 VAL Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1169 VAL Chi-restraints excluded: chain A residue 1170 LEU Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 40 LEU Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain L residue 95 ILE Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 62 LYS Chi-restraints excluded: chain H residue 77 ILE Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 103 THR Chi-restraints excluded: chain H residue 108 GLU Chi-restraints excluded: chain H residue 121 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 97 optimal weight: 6.9990 chunk 68 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 107 optimal weight: 9.9990 chunk 67 optimal weight: 20.0000 chunk 2 optimal weight: 0.6980 chunk 100 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 57 GLN ** L 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 112 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.128856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.103655 restraints weight = 20056.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.106935 restraints weight = 10954.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.109155 restraints weight = 7514.996| |-----------------------------------------------------------------------------| r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9525 Z= 0.151 Angle : 0.654 8.902 12952 Z= 0.324 Chirality : 0.042 0.162 1462 Planarity : 0.004 0.047 1628 Dihedral : 4.698 27.050 1293 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.38 % Favored : 91.62 % Rotamer: Outliers : 6.69 % Allowed : 24.44 % Favored : 68.86 % 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: -0.31 (0.26), residues: 1181 helix: 1.71 (0.22), residues: 564 sheet: -1.50 (0.44), residues: 140 loop : -2.25 (0.29), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 78 HIS 0.004 0.001 HIS H 54 PHE 0.020 0.001 PHE L 76 TYR 0.015 0.001 TYR H 114 ARG 0.003 0.000 ARG A 144 Details of bonding type rmsd hydrogen bonds : bond 0.04020 ( 484) hydrogen bonds : angle 4.43209 ( 1392) SS BOND : bond 0.00522 ( 4) SS BOND : angle 0.82862 ( 8) covalent geometry : bond 0.00345 ( 9521) covalent geometry : angle 0.65412 (12944) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 152 time to evaluate : 1.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 TYR cc_start: 0.7201 (m-80) cc_final: 0.6760 (m-80) REVERT: A 280 GLU cc_start: 0.8977 (tp30) cc_final: 0.8624 (tm-30) REVERT: A 292 MET cc_start: 0.8284 (mtp) cc_final: 0.7670 (mtp) REVERT: A 464 LYS cc_start: 0.7755 (mmtt) cc_final: 0.7404 (mmtt) REVERT: A 598 MET cc_start: 0.8320 (tmm) cc_final: 0.7981 (mmt) REVERT: A 734 SER cc_start: 0.8152 (m) cc_final: 0.7844 (t) REVERT: A 748 LYS cc_start: 0.6611 (mmtm) cc_final: 0.5778 (ttpp) REVERT: A 1051 TRP cc_start: 0.7823 (OUTLIER) cc_final: 0.6046 (t60) REVERT: A 1066 GLU cc_start: 0.8084 (mt-10) cc_final: 0.7544 (mp0) REVERT: H 62 LYS cc_start: 0.8084 (OUTLIER) cc_final: 0.7558 (mtpt) REVERT: H 66 TRP cc_start: 0.8508 (t60) cc_final: 0.8032 (t60) REVERT: H 117 ARG cc_start: 0.8148 (tpp-160) cc_final: 0.7861 (ttt180) REVERT: H 126 GLN cc_start: 0.8161 (mm110) cc_final: 0.7859 (mm110) outliers start: 66 outliers final: 46 residues processed: 196 average time/residue: 0.1899 time to fit residues: 54.1762 Evaluate side-chains 195 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 147 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 PHE Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 525 THR Chi-restraints excluded: chain A residue 540 CYS Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 560 PHE Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 583 PHE Chi-restraints excluded: chain A residue 737 GLU Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 773 ASP Chi-restraints excluded: chain A residue 835 GLU Chi-restraints excluded: chain A residue 862 ASP Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 969 ILE Chi-restraints excluded: chain A residue 974 PHE Chi-restraints excluded: chain A residue 1051 TRP Chi-restraints excluded: chain A residue 1062 LEU Chi-restraints excluded: chain A residue 1131 VAL Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1169 VAL Chi-restraints excluded: chain A residue 1170 LEU Chi-restraints excluded: chain A residue 1171 LEU Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 40 LEU Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain L residue 95 ILE Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 62 LYS Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 103 THR Chi-restraints excluded: chain H residue 108 GLU Chi-restraints excluded: chain H residue 121 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 84 optimal weight: 0.9980 chunk 49 optimal weight: 0.7980 chunk 114 optimal weight: 3.9990 chunk 78 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 12 optimal weight: 0.0470 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 112 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.131936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.109036 restraints weight = 19455.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.112429 restraints weight = 10150.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.114588 restraints weight = 6744.193| |-----------------------------------------------------------------------------| r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9525 Z= 0.122 Angle : 0.657 10.317 12952 Z= 0.318 Chirality : 0.041 0.174 1462 Planarity : 0.004 0.048 1628 Dihedral : 4.653 25.048 1293 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 4.87 % Allowed : 26.77 % Favored : 68.36 % 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: -0.23 (0.26), residues: 1181 helix: 1.73 (0.22), residues: 565 sheet: -1.46 (0.44), residues: 140 loop : -2.15 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 78 HIS 0.005 0.001 HIS H 54 PHE 0.021 0.001 PHE L 76 TYR 0.026 0.001 TYR H 114 ARG 0.004 0.000 ARG L 113 Details of bonding type rmsd hydrogen bonds : bond 0.03775 ( 484) hydrogen bonds : angle 4.36753 ( 1392) SS BOND : bond 0.00474 ( 4) SS BOND : angle 0.74207 ( 8) covalent geometry : bond 0.00270 ( 9521) covalent geometry : angle 0.65648 (12944) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 168 time to evaluate : 1.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 TRP cc_start: 0.7947 (m100) cc_final: 0.7685 (m100) REVERT: A 222 TYR cc_start: 0.7142 (m-80) cc_final: 0.6801 (m-80) REVERT: A 280 GLU cc_start: 0.8892 (tp30) cc_final: 0.8628 (tm-30) REVERT: A 292 MET cc_start: 0.8271 (mtp) cc_final: 0.7677 (mtp) REVERT: A 464 LYS cc_start: 0.7681 (mmtt) cc_final: 0.7334 (mmtt) REVERT: A 598 MET cc_start: 0.8442 (tmm) cc_final: 0.8019 (mmt) REVERT: A 734 SER cc_start: 0.8026 (m) cc_final: 0.7733 (t) REVERT: A 974 PHE cc_start: 0.8978 (OUTLIER) cc_final: 0.8267 (p90) REVERT: A 1051 TRP cc_start: 0.7755 (OUTLIER) cc_final: 0.6048 (t60) REVERT: A 1066 GLU cc_start: 0.8075 (mt-10) cc_final: 0.7565 (mp0) REVERT: H 62 LYS cc_start: 0.7952 (OUTLIER) cc_final: 0.7468 (mtpt) REVERT: H 66 TRP cc_start: 0.8495 (t60) cc_final: 0.8052 (t60) REVERT: H 117 ARG cc_start: 0.8128 (tpp-160) cc_final: 0.7499 (tpp-160) REVERT: H 126 GLN cc_start: 0.8079 (mm110) cc_final: 0.7758 (mm110) outliers start: 48 outliers final: 31 residues processed: 202 average time/residue: 0.1832 time to fit residues: 54.2192 Evaluate side-chains 190 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 156 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 540 CYS Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 560 PHE Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 583 PHE Chi-restraints excluded: chain A residue 773 ASP Chi-restraints excluded: chain A residue 835 GLU Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 974 PHE Chi-restraints excluded: chain A residue 1051 TRP Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1169 VAL Chi-restraints excluded: chain A residue 1170 LEU Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 40 LEU Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 95 ILE Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 62 LYS Chi-restraints excluded: chain H residue 77 ILE Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 103 THR Chi-restraints excluded: chain H residue 108 GLU Chi-restraints excluded: chain H residue 121 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 71 optimal weight: 5.9990 chunk 96 optimal weight: 0.7980 chunk 67 optimal weight: 10.0000 chunk 35 optimal weight: 0.8980 chunk 78 optimal weight: 3.9990 chunk 13 optimal weight: 0.0570 chunk 36 optimal weight: 0.9990 chunk 113 optimal weight: 7.9990 chunk 14 optimal weight: 6.9990 chunk 103 optimal weight: 6.9990 chunk 87 optimal weight: 3.9990 overall best weight: 1.3502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 328 HIS ** A 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 57 GLN ** L 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 112 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.128528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.103915 restraints weight = 20194.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.107174 restraints weight = 11003.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.109328 restraints weight = 7505.855| |-----------------------------------------------------------------------------| r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9525 Z= 0.156 Angle : 0.691 10.739 12952 Z= 0.334 Chirality : 0.043 0.290 1462 Planarity : 0.004 0.047 1628 Dihedral : 4.766 25.330 1293 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer: Outliers : 5.07 % Allowed : 27.79 % Favored : 67.14 % 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: -0.23 (0.26), residues: 1181 helix: 1.74 (0.22), residues: 567 sheet: -1.50 (0.45), residues: 135 loop : -2.17 (0.29), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 78 HIS 0.005 0.001 HIS H 54 PHE 0.022 0.002 PHE L 76 TYR 0.020 0.001 TYR H 114 ARG 0.005 0.000 ARG H 117 Details of bonding type rmsd hydrogen bonds : bond 0.03890 ( 484) hydrogen bonds : angle 4.38405 ( 1392) SS BOND : bond 0.00646 ( 4) SS BOND : angle 2.69758 ( 8) covalent geometry : bond 0.00361 ( 9521) covalent geometry : angle 0.68773 (12944) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 152 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 TYR cc_start: 0.7283 (m-80) cc_final: 0.6881 (m-80) REVERT: A 280 GLU cc_start: 0.8949 (tp30) cc_final: 0.8654 (tm-30) REVERT: A 292 MET cc_start: 0.8303 (mtp) cc_final: 0.7653 (mtp) REVERT: A 598 MET cc_start: 0.8448 (tmm) cc_final: 0.7993 (mmt) REVERT: A 1051 TRP cc_start: 0.7788 (OUTLIER) cc_final: 0.6097 (t60) REVERT: A 1066 GLU cc_start: 0.8111 (mt-10) cc_final: 0.7558 (mp0) REVERT: H 62 LYS cc_start: 0.8030 (OUTLIER) cc_final: 0.7524 (mtpt) REVERT: H 66 TRP cc_start: 0.8545 (t60) cc_final: 0.8055 (t60) REVERT: H 126 GLN cc_start: 0.8199 (mm110) cc_final: 0.7864 (mm110) outliers start: 50 outliers final: 39 residues processed: 188 average time/residue: 0.1807 time to fit residues: 49.7663 Evaluate side-chains 188 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 147 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 PHE Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 525 THR Chi-restraints excluded: chain A residue 540 CYS Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 560 PHE Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 583 PHE Chi-restraints excluded: chain A residue 737 GLU Chi-restraints excluded: chain A residue 773 ASP Chi-restraints excluded: chain A residue 835 GLU Chi-restraints excluded: chain A residue 862 ASP Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 974 PHE Chi-restraints excluded: chain A residue 1051 TRP Chi-restraints excluded: chain A residue 1131 VAL Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1169 VAL Chi-restraints excluded: chain A residue 1170 LEU Chi-restraints excluded: chain A residue 1171 LEU Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 40 LEU Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 95 ILE Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 62 LYS Chi-restraints excluded: chain H residue 77 ILE Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 103 THR Chi-restraints excluded: chain H residue 108 GLU Chi-restraints excluded: chain H residue 121 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 86 optimal weight: 0.7980 chunk 103 optimal weight: 9.9990 chunk 99 optimal weight: 10.0000 chunk 49 optimal weight: 0.4980 chunk 71 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 21 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 27 optimal weight: 0.0070 chunk 60 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 57 GLN ** L 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 112 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.136374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.112002 restraints weight = 19744.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.115382 restraints weight = 10629.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.117672 restraints weight = 7229.561| |-----------------------------------------------------------------------------| r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9525 Z= 0.123 Angle : 0.687 11.015 12952 Z= 0.329 Chirality : 0.042 0.233 1462 Planarity : 0.004 0.047 1628 Dihedral : 4.715 25.042 1293 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 4.16 % Allowed : 28.70 % Favored : 67.14 % 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: -0.19 (0.26), residues: 1181 helix: 1.77 (0.22), residues: 565 sheet: -1.41 (0.45), residues: 135 loop : -2.16 (0.29), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 78 HIS 0.005 0.001 HIS H 54 PHE 0.023 0.001 PHE L 76 TYR 0.020 0.001 TYR H 114 ARG 0.008 0.000 ARG H 117 Details of bonding type rmsd hydrogen bonds : bond 0.03626 ( 484) hydrogen bonds : angle 4.37149 ( 1392) SS BOND : bond 0.00475 ( 4) SS BOND : angle 1.81862 ( 8) covalent geometry : bond 0.00273 ( 9521) covalent geometry : angle 0.68555 (12944) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 160 time to evaluate : 1.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 TRP cc_start: 0.7888 (m100) cc_final: 0.7591 (m100) REVERT: A 222 TYR cc_start: 0.7294 (m-80) cc_final: 0.6912 (m-80) REVERT: A 280 GLU cc_start: 0.8940 (tp30) cc_final: 0.8656 (tm-30) REVERT: A 292 MET cc_start: 0.8269 (mtp) cc_final: 0.7679 (mtp) REVERT: A 598 MET cc_start: 0.8396 (tmm) cc_final: 0.7945 (mmt) REVERT: A 974 PHE cc_start: 0.8976 (OUTLIER) cc_final: 0.8220 (p90) REVERT: A 1051 TRP cc_start: 0.7708 (OUTLIER) cc_final: 0.6031 (t60) REVERT: A 1063 MET cc_start: 0.8659 (ttp) cc_final: 0.8166 (ttp) REVERT: A 1066 GLU cc_start: 0.8079 (mt-10) cc_final: 0.7662 (mp0) REVERT: L 30 MET cc_start: 0.7825 (ppp) cc_final: 0.7491 (ppp) REVERT: H 62 LYS cc_start: 0.7954 (OUTLIER) cc_final: 0.7457 (mtpt) REVERT: H 66 TRP cc_start: 0.8510 (t60) cc_final: 0.7988 (t60) REVERT: H 126 GLN cc_start: 0.8159 (mm110) cc_final: 0.7764 (mm110) outliers start: 41 outliers final: 32 residues processed: 192 average time/residue: 0.2000 time to fit residues: 56.0835 Evaluate side-chains 189 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 154 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 328 HIS Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 540 CYS Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 560 PHE Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 583 PHE Chi-restraints excluded: chain A residue 773 ASP Chi-restraints excluded: chain A residue 835 GLU Chi-restraints excluded: chain A residue 862 ASP Chi-restraints excluded: chain A residue 932 VAL Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 974 PHE Chi-restraints excluded: chain A residue 1051 TRP Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1169 VAL Chi-restraints excluded: chain L residue 40 LEU Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 95 ILE Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 62 LYS Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 103 THR Chi-restraints excluded: chain H residue 121 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 24 optimal weight: 0.0370 chunk 49 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 40 optimal weight: 6.9990 chunk 112 optimal weight: 0.0470 chunk 103 optimal weight: 6.9990 chunk 71 optimal weight: 0.0870 chunk 62 optimal weight: 0.5980 chunk 84 optimal weight: 2.9990 chunk 23 optimal weight: 9.9990 chunk 6 optimal weight: 0.9990 overall best weight: 0.3134 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 112 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.138403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.114159 restraints weight = 19984.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.117671 restraints weight = 10627.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.120007 restraints weight = 7101.356| |-----------------------------------------------------------------------------| r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.2697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9525 Z= 0.118 Angle : 0.697 11.536 12952 Z= 0.330 Chirality : 0.042 0.230 1462 Planarity : 0.004 0.047 1628 Dihedral : 4.657 26.199 1293 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 3.75 % Allowed : 29.31 % Favored : 66.94 % 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: -0.11 (0.26), residues: 1181 helix: 1.80 (0.22), residues: 564 sheet: -1.30 (0.46), residues: 135 loop : -2.08 (0.29), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 78 HIS 0.006 0.001 HIS H 54 PHE 0.025 0.001 PHE L 76 TYR 0.019 0.001 TYR L 56 ARG 0.003 0.000 ARG A 85 Details of bonding type rmsd hydrogen bonds : bond 0.03460 ( 484) hydrogen bonds : angle 4.34167 ( 1392) SS BOND : bond 0.00460 ( 4) SS BOND : angle 1.45614 ( 8) covalent geometry : bond 0.00258 ( 9521) covalent geometry : angle 0.69598 (12944) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 172 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 TYR cc_start: 0.7281 (m-80) cc_final: 0.6923 (m-80) REVERT: A 280 GLU cc_start: 0.8931 (tp30) cc_final: 0.8681 (tm-30) REVERT: A 292 MET cc_start: 0.8239 (mtp) cc_final: 0.7649 (mtp) REVERT: A 598 MET cc_start: 0.8398 (tmm) cc_final: 0.7930 (mmt) REVERT: A 869 MET cc_start: 0.7691 (mmm) cc_final: 0.6879 (mmm) REVERT: A 974 PHE cc_start: 0.8927 (OUTLIER) cc_final: 0.8582 (p90) REVERT: A 1051 TRP cc_start: 0.7708 (OUTLIER) cc_final: 0.6030 (t60) REVERT: A 1063 MET cc_start: 0.8615 (ttp) cc_final: 0.8174 (ttp) REVERT: A 1066 GLU cc_start: 0.8070 (mt-10) cc_final: 0.7680 (mp0) REVERT: A 1166 ASN cc_start: 0.8289 (m-40) cc_final: 0.8035 (t0) REVERT: L 30 MET cc_start: 0.7736 (ppp) cc_final: 0.7435 (ppp) REVERT: H 25 GLU cc_start: 0.8512 (mp0) cc_final: 0.8090 (mp0) REVERT: H 62 LYS cc_start: 0.7938 (OUTLIER) cc_final: 0.7424 (mtpt) REVERT: H 102 MET cc_start: 0.7396 (tmm) cc_final: 0.7192 (tmm) outliers start: 37 outliers final: 29 residues processed: 201 average time/residue: 0.1833 time to fit residues: 53.2908 Evaluate side-chains 191 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 159 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 525 THR Chi-restraints excluded: chain A residue 540 CYS Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 560 PHE Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 583 PHE Chi-restraints excluded: chain A residue 773 ASP Chi-restraints excluded: chain A residue 835 GLU Chi-restraints excluded: chain A residue 862 ASP Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 974 PHE Chi-restraints excluded: chain A residue 1051 TRP Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1169 VAL Chi-restraints excluded: chain L residue 40 LEU Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 95 ILE Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 62 LYS Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 121 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 68 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 115 optimal weight: 0.8980 chunk 66 optimal weight: 6.9990 chunk 96 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 86 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 GLN ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 365 GLN ** L 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 58 GLN ** L 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 112 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.133693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.109653 restraints weight = 19619.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.113074 restraints weight = 10546.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.115353 restraints weight = 7180.643| |-----------------------------------------------------------------------------| r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.2800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9525 Z= 0.133 Angle : 0.709 13.846 12952 Z= 0.339 Chirality : 0.042 0.222 1462 Planarity : 0.004 0.046 1628 Dihedral : 4.668 26.846 1293 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 3.85 % Allowed : 29.11 % Favored : 67.04 % 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: -0.11 (0.26), residues: 1181 helix: 1.76 (0.22), residues: 565 sheet: -1.34 (0.45), residues: 133 loop : -2.02 (0.29), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 197 HIS 0.005 0.001 HIS H 54 PHE 0.024 0.001 PHE L 76 TYR 0.031 0.001 TYR A1001 ARG 0.004 0.000 ARG L 81 Details of bonding type rmsd hydrogen bonds : bond 0.03551 ( 484) hydrogen bonds : angle 4.33698 ( 1392) SS BOND : bond 0.00441 ( 4) SS BOND : angle 1.41868 ( 8) covalent geometry : bond 0.00303 ( 9521) covalent geometry : angle 0.70853 (12944) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3526.00 seconds wall clock time: 63 minutes 55.97 seconds (3835.97 seconds total)