Starting phenix.real_space_refine on Fri Aug 22 20:07:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jhc_36262/08_2025/8jhc_36262.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jhc_36262/08_2025/8jhc_36262.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jhc_36262/08_2025/8jhc_36262.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jhc_36262/08_2025/8jhc_36262.map" model { file = "/net/cci-nas-00/data/ceres_data/8jhc_36262/08_2025/8jhc_36262.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jhc_36262/08_2025/8jhc_36262.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.025 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 37 5.16 5 C 4857 2.51 5 N 1254 2.21 5 O 1415 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7563 Number of models: 1 Model: "" Number of chains: 4 Chain: "R" Number of atoms: 3346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3346 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 16, 'TRANS': 412} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 133 Unresolved non-hydrogen dihedrals: 91 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 4, 'GLU:plan': 5, 'TYR:plan': 3, 'ASN:plan1': 1, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 76 Chain: "H" Number of atoms: 1678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1678 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 211} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "K" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 915 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 116} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "L" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1624 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 201} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Time building chain proxies: 1.93, per 1000 atoms: 0.26 Number of scatterers: 7563 At special positions: 0 Unit cell: (78.208, 99.84, 158.08, 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 37 16.00 O 1415 8.00 N 1254 7.00 C 4857 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS R 165 " - pdb=" SG CYS R 185 " distance=2.03 Simple disulfide: pdb=" SG CYS R 189 " - pdb=" SG CYS R 264 " distance=2.03 Simple disulfide: pdb=" SG CYS R 286 " - pdb=" SG CYS R 361 " distance=2.03 Simple disulfide: pdb=" SG CYS R 458 " - pdb=" SG CYS R 465 " distance=2.03 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.03 Simple disulfide: pdb=" SG CYS H 154 " - pdb=" SG CYS H 210 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.04 Simple disulfide: pdb=" SG CYS L 136 " - pdb=" SG CYS L 196 " 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: 0.45 Conformation dependent library (CDL) restraints added in 411.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1840 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 14 sheets defined 34.4% alpha, 23.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'R' and resid 195 through 227 removed outlier: 3.745A pdb=" N ILE R 212 " --> pdb=" O LEU R 208 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ASP R 227 " --> pdb=" O THR R 223 " (cutoff:3.500A) Processing helix chain 'R' and resid 236 through 259 removed outlier: 3.791A pdb=" N PHE R 240 " --> pdb=" O ARG R 236 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE R 256 " --> pdb=" O PHE R 252 " (cutoff:3.500A) Processing helix chain 'R' and resid 285 through 314 Processing helix chain 'R' and resid 327 through 336 Processing helix chain 'R' and resid 337 through 349 Processing helix chain 'R' and resid 367 through 374 removed outlier: 3.597A pdb=" N LEU R 371 " --> pdb=" O ASP R 367 " (cutoff:3.500A) Processing helix chain 'R' and resid 375 through 399 Processing helix chain 'R' and resid 1002 through 1024 removed outlier: 3.793A pdb=" N ASN R1018 " --> pdb=" O THR R1014 " (cutoff:3.500A) Processing helix chain 'R' and resid 1029 through 1049 removed outlier: 4.290A pdb=" N LYS R1037 " --> pdb=" O ASP R1033 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA R1040 " --> pdb=" O THR R1036 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA R1048 " --> pdb=" O ASP R1044 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N THR R1049 " --> pdb=" O ALA R1045 " (cutoff:3.500A) Processing helix chain 'R' and resid 1064 through 1086 removed outlier: 4.944A pdb=" N PHE R1070 " --> pdb=" O PHE R1066 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU R1083 " --> pdb=" O ASP R1079 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU R1086 " --> pdb=" O LYS R1082 " (cutoff:3.500A) Processing helix chain 'R' and resid 1088 through 1097 removed outlier: 3.885A pdb=" N ALA R1092 " --> pdb=" O LYS R1088 " (cutoff:3.500A) Processing helix chain 'R' and resid 1098 through 1107 removed outlier: 3.977A pdb=" N THR R1102 " --> pdb=" O GLN R1098 " (cutoff:3.500A) Processing helix chain 'R' and resid 1109 through 1118 Processing helix chain 'R' and resid 413 through 445 removed outlier: 4.304A pdb=" N VAL R 430 " --> pdb=" O ILE R 426 " (cutoff:3.500A) Proline residue: R 431 - end of helix removed outlier: 3.547A pdb=" N TYR R 445 " --> pdb=" O TYR R 441 " (cutoff:3.500A) Processing helix chain 'R' and resid 445 through 457 Processing helix chain 'R' and resid 476 through 487 removed outlier: 3.761A pdb=" N PHE R 480 " --> pdb=" O ASP R 476 " (cutoff:3.500A) Processing helix chain 'R' and resid 488 through 491 Processing helix chain 'R' and resid 492 through 499 removed outlier: 4.242A pdb=" N PHE R 496 " --> pdb=" O ILE R 492 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N TRP R 497 " --> pdb=" O PRO R 493 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 94 removed outlier: 4.056A pdb=" N THR H 94 " --> pdb=" O ALA H 91 " (cutoff:3.500A) Processing helix chain 'H' and resid 107 through 112 Processing helix chain 'H' and resid 202 through 206 removed outlier: 4.132A pdb=" N GLN H 206 " --> pdb=" O LEU H 203 " (cutoff:3.500A) Processing helix chain 'L' and resid 94 through 98 removed outlier: 4.228A pdb=" N VAL L 98 " --> pdb=" O TYR L 95 " (cutoff:3.500A) Processing helix chain 'L' and resid 123 through 130 Processing sheet with id=AA1, first strand: chain 'R' and resid 178 through 179 Processing sheet with id=AA2, first strand: chain 'H' and resid 6 through 10 Processing sheet with id=AA3, first strand: chain 'H' and resid 14 through 15 removed outlier: 6.222A pdb=" N ARG H 41 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N TRP H 50 " --> pdb=" O ARG H 41 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N TYR H 53 " --> pdb=" O SER H 62 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N SER H 62 " --> pdb=" O TYR H 53 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 134 through 137 removed outlier: 6.132A pdb=" N TYR H 190 " --> pdb=" O ASP H 158 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 134 through 137 removed outlier: 6.132A pdb=" N TYR H 190 " --> pdb=" O ASP H 158 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 165 through 168 removed outlier: 3.862A pdb=" N TYR H 208 " --> pdb=" O VAL H 225 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'K' and resid 3 through 6 removed outlier: 3.762A pdb=" N THR K 69 " --> pdb=" O GLN K 82 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'K' and resid 10 through 12 removed outlier: 5.999A pdb=" N GLY K 10 " --> pdb=" O THR K 118 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'K' and resid 58 through 60 removed outlier: 6.716A pdb=" N TRP K 36 " --> pdb=" O VAL K 48 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N VAL K 50 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N MET K 34 " --> pdb=" O VAL K 50 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE K 98 " --> pdb=" O TYR K 110 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N TYR K 110 " --> pdb=" O ILE K 98 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 5 through 7 Processing sheet with id=AB2, first strand: chain 'L' and resid 11 through 13 removed outlier: 6.448A pdb=" N LEU L 12 " --> pdb=" O GLU L 107 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N TYR L 50 " --> pdb=" O VAL L 34 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 11 through 13 removed outlier: 6.448A pdb=" N LEU L 12 " --> pdb=" O GLU L 107 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N THR L 99 " --> pdb=" O GLN L 91 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 118 through 120 removed outlier: 3.731A pdb=" N VAL L 135 " --> pdb=" O PHE L 120 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 146 through 151 380 hydrogen bonds defined for protein. 1056 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.09 Time building geometry restraints manager: 0.67 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: 2372 1.34 - 1.46: 1863 1.46 - 1.58: 3457 1.58 - 1.69: 0 1.69 - 1.81: 52 Bond restraints: 7744 Sorted by residual: bond pdb=" C GLU H 162 " pdb=" N PRO H 163 " ideal model delta sigma weight residual 1.333 1.360 -0.026 1.01e-02 9.80e+03 6.74e+00 bond pdb=" CG1 ILE R 338 " pdb=" CD1 ILE R 338 " ideal model delta sigma weight residual 1.513 1.451 0.062 3.90e-02 6.57e+02 2.50e+00 bond pdb=" CA ILE R1107 " pdb=" CB ILE R1107 " ideal model delta sigma weight residual 1.540 1.558 -0.018 1.36e-02 5.41e+03 1.80e+00 bond pdb=" C VAL R 316 " pdb=" N PRO R 317 " ideal model delta sigma weight residual 1.334 1.365 -0.031 2.34e-02 1.83e+03 1.71e+00 bond pdb=" CA ILE R1107 " pdb=" C ILE R1107 " ideal model delta sigma weight residual 1.523 1.539 -0.016 1.27e-02 6.20e+03 1.67e+00 ... (remaining 7739 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.54: 10485 3.54 - 7.07: 50 7.07 - 10.61: 2 10.61 - 14.15: 0 14.15 - 17.68: 1 Bond angle restraints: 10538 Sorted by residual: angle pdb=" CG1 ILE R1107 " pdb=" CB ILE R1107 " pdb=" CG2 ILE R1107 " ideal model delta sigma weight residual 110.70 93.02 17.68 3.00e+00 1.11e-01 3.48e+01 angle pdb=" CA ILE R 338 " pdb=" CB ILE R 338 " pdb=" CG1 ILE R 338 " ideal model delta sigma weight residual 110.40 116.37 -5.97 1.70e+00 3.46e-01 1.24e+01 angle pdb=" C GLY H 204 " pdb=" N THR H 205 " pdb=" CA THR H 205 " ideal model delta sigma weight residual 121.54 127.94 -6.40 1.91e+00 2.74e-01 1.12e+01 angle pdb=" N LYS R1109 " pdb=" CA LYS R1109 " pdb=" C LYS R1109 " ideal model delta sigma weight residual 113.50 109.72 3.78 1.23e+00 6.61e-01 9.45e+00 angle pdb=" C PRO R 173 " pdb=" N ASP R 174 " pdb=" CA ASP R 174 " ideal model delta sigma weight residual 122.08 126.54 -4.46 1.47e+00 4.63e-01 9.20e+00 ... (remaining 10533 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 4108 17.94 - 35.88: 375 35.88 - 53.83: 76 53.83 - 71.77: 10 71.77 - 89.71: 4 Dihedral angle restraints: 4573 sinusoidal: 1707 harmonic: 2866 Sorted by residual: dihedral pdb=" CB CYS R 458 " pdb=" SG CYS R 458 " pdb=" SG CYS R 465 " pdb=" CB CYS R 465 " ideal model delta sinusoidal sigma weight residual -86.00 -125.99 39.99 1 1.00e+01 1.00e-02 2.24e+01 dihedral pdb=" CA GLN R1108 " pdb=" C GLN R1108 " pdb=" N LYS R1109 " pdb=" CA LYS R1109 " ideal model delta harmonic sigma weight residual 180.00 157.69 22.31 0 5.00e+00 4.00e-02 1.99e+01 dihedral pdb=" CB CYS R 286 " pdb=" SG CYS R 286 " pdb=" SG CYS R 361 " pdb=" CB CYS R 361 " ideal model delta sinusoidal sigma weight residual -86.00 -120.01 34.01 1 1.00e+01 1.00e-02 1.64e+01 ... (remaining 4570 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 933 0.054 - 0.108: 223 0.108 - 0.162: 38 0.162 - 0.216: 2 0.216 - 0.271: 1 Chirality restraints: 1197 Sorted by residual: chirality pdb=" CB ILE R1107 " pdb=" CA ILE R1107 " pdb=" CG1 ILE R1107 " pdb=" CG2 ILE R1107 " both_signs ideal model delta sigma weight residual False 2.64 2.92 -0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" CA ILE R1107 " pdb=" N ILE R1107 " pdb=" C ILE R1107 " pdb=" CB ILE R1107 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.88e-01 chirality pdb=" CA TYR R 233 " pdb=" N TYR R 233 " pdb=" C TYR R 233 " pdb=" CB TYR R 233 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.78e-01 ... (remaining 1194 not shown) Planarity restraints: 1325 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR R 233 " -0.050 5.00e-02 4.00e+02 7.53e-02 9.06e+00 pdb=" N PRO R 234 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO R 234 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO R 234 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE R1107 " -0.009 2.00e-02 2.50e+03 1.81e-02 3.28e+00 pdb=" C ILE R1107 " 0.031 2.00e-02 2.50e+03 pdb=" O ILE R1107 " -0.012 2.00e-02 2.50e+03 pdb=" N GLN R1108 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU H 108 " 0.030 5.00e-02 4.00e+02 4.50e-02 3.24e+00 pdb=" N PRO H 109 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO H 109 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO H 109 " 0.025 5.00e-02 4.00e+02 ... (remaining 1322 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1230 2.76 - 3.30: 7178 3.30 - 3.83: 12464 3.83 - 4.37: 14426 4.37 - 4.90: 24844 Nonbonded interactions: 60142 Sorted by model distance: nonbonded pdb=" O TYR L 188 " pdb=" OH TYR L 194 " model vdw 2.227 3.040 nonbonded pdb=" OG SER L 64 " pdb=" OG1 THR L 75 " model vdw 2.260 3.040 nonbonded pdb=" O ILE R 206 " pdb=" OG SER R 210 " model vdw 2.265 3.040 nonbonded pdb=" OG SER H 200 " pdb=" N SER H 201 " model vdw 2.273 3.120 nonbonded pdb=" OH TYR R 241 " pdb=" O VAL R 490 " model vdw 2.286 3.040 ... (remaining 60137 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.030 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 7753 Z= 0.181 Angle : 0.701 17.685 10556 Z= 0.365 Chirality : 0.046 0.271 1197 Planarity : 0.005 0.075 1325 Dihedral : 14.173 89.710 2706 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.38 (0.27), residues: 972 helix: -0.81 (0.28), residues: 319 sheet: 0.05 (0.33), residues: 255 loop : -1.55 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 27 TYR 0.023 0.002 TYR R 241 PHE 0.013 0.002 PHE R 362 TRP 0.011 0.001 TRP K 111 HIS 0.003 0.001 HIS L 191 Details of bonding type rmsd covalent geometry : bond 0.00400 ( 7744) covalent geometry : angle 0.70162 (10538) SS BOND : bond 0.00317 ( 9) SS BOND : angle 0.55211 ( 18) hydrogen bonds : bond 0.15807 ( 365) hydrogen bonds : angle 6.15867 ( 1056) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 205 time to evaluate : 0.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 265 ASN cc_start: 0.8071 (m110) cc_final: 0.7477 (m110) REVERT: R 292 ILE cc_start: 0.8351 (tt) cc_final: 0.7986 (pt) REVERT: R 382 TYR cc_start: 0.7851 (m-10) cc_final: 0.7536 (m-10) REVERT: R 1002 ARG cc_start: 0.7487 (ttm170) cc_final: 0.7172 (ttm170) REVERT: R 1004 GLN cc_start: 0.7049 (pp30) cc_final: 0.6801 (pp30) REVERT: R 1019 LEU cc_start: 0.8410 (tp) cc_final: 0.8203 (tp) REVERT: R 1072 ILE cc_start: 0.8836 (tp) cc_final: 0.8613 (pt) REVERT: H 185 GLN cc_start: 0.7978 (mm-40) cc_final: 0.7706 (mm-40) REVERT: K 104 TYR cc_start: 0.8164 (m-10) cc_final: 0.7958 (m-10) REVERT: L 5 MET cc_start: 0.8332 (mmm) cc_final: 0.7821 (mmt) REVERT: L 55 LEU cc_start: 0.8714 (mm) cc_final: 0.8513 (mp) REVERT: L 109 LYS cc_start: 0.8922 (ttmm) cc_final: 0.8678 (tttp) REVERT: L 149 GLN cc_start: 0.8088 (mt0) cc_final: 0.7650 (mt0) REVERT: L 158 SER cc_start: 0.8714 (m) cc_final: 0.8314 (t) outliers start: 0 outliers final: 0 residues processed: 205 average time/residue: 0.0838 time to fit residues: 22.9586 Evaluate side-chains 191 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 191 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 0.0980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 8.9990 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 0.5980 chunk 74 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 85 GLN ** L 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 162 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.147941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.125921 restraints weight = 12278.649| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 2.77 r_work: 0.3489 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.1233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7753 Z= 0.161 Angle : 0.627 8.976 10556 Z= 0.321 Chirality : 0.043 0.179 1197 Planarity : 0.005 0.067 1325 Dihedral : 4.711 21.433 1065 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 2.60 % Allowed : 14.11 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.83 (0.27), residues: 972 helix: -0.03 (0.28), residues: 331 sheet: 0.19 (0.33), residues: 253 loop : -1.43 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R1113 TYR 0.026 0.002 TYR R 241 PHE 0.018 0.002 PHE R 290 TRP 0.010 0.001 TRP R 311 HIS 0.004 0.001 HIS L 191 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 7744) covalent geometry : angle 0.62661 (10538) SS BOND : bond 0.00307 ( 9) SS BOND : angle 0.93913 ( 18) hydrogen bonds : bond 0.03872 ( 365) hydrogen bonds : angle 4.64781 ( 1056) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 193 time to evaluate : 0.288 Fit side-chains revert: symmetry clash REVERT: R 265 ASN cc_start: 0.7946 (m110) cc_final: 0.7540 (m110) REVERT: R 1003 ARG cc_start: 0.7644 (OUTLIER) cc_final: 0.7437 (ptt90) REVERT: R 1019 LEU cc_start: 0.8232 (tp) cc_final: 0.7996 (tp) REVERT: R 1033 ASP cc_start: 0.7995 (t0) cc_final: 0.7607 (t0) REVERT: R 1072 ILE cc_start: 0.8491 (tp) cc_final: 0.8283 (pt) REVERT: R 1097 GLU cc_start: 0.7828 (pp20) cc_final: 0.7226 (pp20) REVERT: H 86 MET cc_start: 0.7483 (mtm) cc_final: 0.6648 (mtm) REVERT: H 121 THR cc_start: 0.8201 (t) cc_final: 0.7933 (m) REVERT: H 185 GLN cc_start: 0.7985 (mm-40) cc_final: 0.7731 (mm-40) REVERT: K 77 ASN cc_start: 0.5133 (t0) cc_final: 0.4784 (t0) REVERT: L 5 MET cc_start: 0.8197 (mmm) cc_final: 0.7745 (mmt) REVERT: L 23 THR cc_start: 0.8617 (t) cc_final: 0.8400 (m) REVERT: L 109 LYS cc_start: 0.8917 (ttmm) cc_final: 0.8690 (ttmt) REVERT: L 147 LYS cc_start: 0.8588 (OUTLIER) cc_final: 0.8279 (pttp) REVERT: L 158 SER cc_start: 0.8618 (m) cc_final: 0.8249 (t) REVERT: L 188 TYR cc_start: 0.7408 (t80) cc_final: 0.7114 (t80) REVERT: L 211 PHE cc_start: 0.8567 (p90) cc_final: 0.8194 (p90) outliers start: 21 outliers final: 9 residues processed: 199 average time/residue: 0.0764 time to fit residues: 20.4969 Evaluate side-chains 198 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 187 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 171 ILE Chi-restraints excluded: chain R residue 246 MET Chi-restraints excluded: chain R residue 387 VAL Chi-restraints excluded: chain R residue 1003 ARG Chi-restraints excluded: chain R residue 1031 VAL Chi-restraints excluded: chain R residue 445 TYR Chi-restraints excluded: chain R residue 477 LEU Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 219 THR Chi-restraints excluded: chain L residue 147 LYS Chi-restraints excluded: chain L residue 198 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 83 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 chunk 85 optimal weight: 0.3980 chunk 74 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 36 optimal weight: 0.3980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R1018 ASN R 443 GLN K 77 ASN L 149 GLN L 162 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.146380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.124111 restraints weight = 12114.489| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 2.74 r_work: 0.3463 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7753 Z= 0.177 Angle : 0.624 7.524 10556 Z= 0.319 Chirality : 0.043 0.145 1197 Planarity : 0.005 0.067 1325 Dihedral : 4.686 21.164 1065 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 3.09 % Allowed : 15.72 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.65 (0.28), residues: 972 helix: 0.27 (0.29), residues: 332 sheet: 0.15 (0.34), residues: 252 loop : -1.38 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 27 TYR 0.027 0.002 TYR R 241 PHE 0.022 0.002 PHE H 160 TRP 0.011 0.001 TRP H 50 HIS 0.006 0.001 HIS L 191 Details of bonding type rmsd covalent geometry : bond 0.00398 ( 7744) covalent geometry : angle 0.62362 (10538) SS BOND : bond 0.00266 ( 9) SS BOND : angle 0.81548 ( 18) hydrogen bonds : bond 0.03737 ( 365) hydrogen bonds : angle 4.56472 ( 1056) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 197 time to evaluate : 0.185 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 174 ASP cc_start: 0.7412 (t0) cc_final: 0.7126 (t0) REVERT: R 265 ASN cc_start: 0.7950 (m110) cc_final: 0.7607 (m110) REVERT: R 291 MET cc_start: 0.7579 (mmm) cc_final: 0.7132 (mmm) REVERT: R 292 ILE cc_start: 0.8183 (tt) cc_final: 0.7853 (pt) REVERT: R 382 TYR cc_start: 0.7543 (m-10) cc_final: 0.6341 (m-10) REVERT: R 1003 ARG cc_start: 0.7637 (OUTLIER) cc_final: 0.7421 (ptt90) REVERT: R 1019 LEU cc_start: 0.8261 (tp) cc_final: 0.8032 (tp) REVERT: R 1033 ASP cc_start: 0.8036 (t0) cc_final: 0.7653 (t0) REVERT: H 21 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7957 (tt) REVERT: H 86 MET cc_start: 0.7516 (mtm) cc_final: 0.6819 (mtm) REVERT: H 124 THR cc_start: 0.7911 (p) cc_final: 0.7400 (t) REVERT: H 185 GLN cc_start: 0.8028 (mm-40) cc_final: 0.7795 (mm-40) REVERT: K 34 MET cc_start: 0.7764 (mtt) cc_final: 0.7432 (mtt) REVERT: L 5 MET cc_start: 0.8255 (mmm) cc_final: 0.7732 (mmt) REVERT: L 95 TYR cc_start: 0.8201 (m-10) cc_final: 0.7952 (m-10) REVERT: L 109 LYS cc_start: 0.8932 (ttmm) cc_final: 0.8701 (ttmt) REVERT: L 158 SER cc_start: 0.8633 (m) cc_final: 0.8278 (t) REVERT: L 188 TYR cc_start: 0.7386 (t80) cc_final: 0.7163 (t80) REVERT: L 211 PHE cc_start: 0.8605 (p90) cc_final: 0.8297 (p90) outliers start: 25 outliers final: 14 residues processed: 207 average time/residue: 0.0743 time to fit residues: 20.8234 Evaluate side-chains 209 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 193 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 171 ILE Chi-restraints excluded: chain R residue 246 MET Chi-restraints excluded: chain R residue 387 VAL Chi-restraints excluded: chain R residue 1003 ARG Chi-restraints excluded: chain R residue 1031 VAL Chi-restraints excluded: chain R residue 1081 LEU Chi-restraints excluded: chain R residue 445 TYR Chi-restraints excluded: chain R residue 477 LEU Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain H residue 209 ILE Chi-restraints excluded: chain H residue 219 THR Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain L residue 198 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 73 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 70 optimal weight: 0.2980 chunk 59 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 55 optimal weight: 3.9990 chunk 85 optimal weight: 0.9990 chunk 33 optimal weight: 0.2980 chunk 93 optimal weight: 0.8980 chunk 89 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R1018 ASN R 443 GLN K 77 ASN ** L 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 162 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.147564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.125627 restraints weight = 12241.126| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 2.75 r_work: 0.3482 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7753 Z= 0.142 Angle : 0.595 7.740 10556 Z= 0.303 Chirality : 0.042 0.145 1197 Planarity : 0.005 0.066 1325 Dihedral : 4.577 20.710 1065 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 3.09 % Allowed : 16.34 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.45 (0.28), residues: 972 helix: 0.51 (0.29), residues: 326 sheet: 0.24 (0.34), residues: 248 loop : -1.29 (0.32), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 27 TYR 0.031 0.002 TYR L 50 PHE 0.023 0.002 PHE R 224 TRP 0.009 0.001 TRP H 50 HIS 0.004 0.001 HIS L 191 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 7744) covalent geometry : angle 0.59500 (10538) SS BOND : bond 0.00256 ( 9) SS BOND : angle 0.71530 ( 18) hydrogen bonds : bond 0.03436 ( 365) hydrogen bonds : angle 4.45895 ( 1056) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 195 time to evaluate : 0.232 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 174 ASP cc_start: 0.7355 (t0) cc_final: 0.7048 (t0) REVERT: R 265 ASN cc_start: 0.7948 (m110) cc_final: 0.7618 (m110) REVERT: R 291 MET cc_start: 0.7497 (mmm) cc_final: 0.7088 (mmm) REVERT: R 292 ILE cc_start: 0.8127 (tt) cc_final: 0.7783 (pt) REVERT: R 321 SER cc_start: 0.8343 (p) cc_final: 0.8019 (p) REVERT: R 1003 ARG cc_start: 0.7663 (OUTLIER) cc_final: 0.7437 (ptm160) REVERT: R 1019 LEU cc_start: 0.8263 (tp) cc_final: 0.8042 (tp) REVERT: R 1033 ASP cc_start: 0.8003 (t0) cc_final: 0.7606 (t0) REVERT: R 1097 GLU cc_start: 0.7993 (pp20) cc_final: 0.7354 (pp20) REVERT: R 1112 GLU cc_start: 0.7184 (pm20) cc_final: 0.6830 (pm20) REVERT: H 21 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7865 (tt) REVERT: H 86 MET cc_start: 0.7518 (mtm) cc_final: 0.6874 (mtm) REVERT: H 124 THR cc_start: 0.7996 (p) cc_final: 0.7577 (t) REVERT: H 185 GLN cc_start: 0.7969 (mm-40) cc_final: 0.7738 (mm-40) REVERT: K 34 MET cc_start: 0.7775 (mtt) cc_final: 0.7471 (mtt) REVERT: L 5 MET cc_start: 0.8189 (mmm) cc_final: 0.7743 (mmt) REVERT: L 95 TYR cc_start: 0.8175 (m-10) cc_final: 0.7928 (m-10) REVERT: L 109 LYS cc_start: 0.8937 (ttmm) cc_final: 0.8702 (ttmt) REVERT: L 158 SER cc_start: 0.8578 (m) cc_final: 0.8216 (t) REVERT: L 188 TYR cc_start: 0.7305 (t80) cc_final: 0.7060 (t80) REVERT: L 211 PHE cc_start: 0.8583 (p90) cc_final: 0.8269 (p90) outliers start: 25 outliers final: 15 residues processed: 210 average time/residue: 0.0791 time to fit residues: 22.3957 Evaluate side-chains 210 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 193 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 171 ILE Chi-restraints excluded: chain R residue 246 MET Chi-restraints excluded: chain R residue 306 ILE Chi-restraints excluded: chain R residue 1003 ARG Chi-restraints excluded: chain R residue 1031 VAL Chi-restraints excluded: chain R residue 1081 LEU Chi-restraints excluded: chain R residue 445 TYR Chi-restraints excluded: chain R residue 477 LEU Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 209 ILE Chi-restraints excluded: chain H residue 219 THR Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain L residue 198 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 21 optimal weight: 0.6980 chunk 71 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 9 optimal weight: 0.0670 chunk 34 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 chunk 86 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 89 optimal weight: 0.7980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 443 GLN K 77 ASN L 162 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.147483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.125477 restraints weight = 12182.233| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 2.73 r_work: 0.3485 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7753 Z= 0.142 Angle : 0.602 10.715 10556 Z= 0.304 Chirality : 0.042 0.144 1197 Planarity : 0.005 0.071 1325 Dihedral : 4.522 21.949 1065 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 3.59 % Allowed : 16.34 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.37 (0.28), residues: 972 helix: 0.62 (0.29), residues: 326 sheet: 0.21 (0.33), residues: 261 loop : -1.27 (0.33), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 27 TYR 0.025 0.002 TYR L 50 PHE 0.025 0.002 PHE R 224 TRP 0.009 0.001 TRP H 50 HIS 0.005 0.001 HIS L 191 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 7744) covalent geometry : angle 0.60213 (10538) SS BOND : bond 0.00248 ( 9) SS BOND : angle 0.66967 ( 18) hydrogen bonds : bond 0.03361 ( 365) hydrogen bonds : angle 4.41274 ( 1056) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 193 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 174 ASP cc_start: 0.7455 (t0) cc_final: 0.7178 (t0) REVERT: R 265 ASN cc_start: 0.7930 (m110) cc_final: 0.7610 (m110) REVERT: R 291 MET cc_start: 0.7490 (mmm) cc_final: 0.7098 (mmm) REVERT: R 325 GLU cc_start: 0.7031 (mm-30) cc_final: 0.6558 (tm-30) REVERT: R 1003 ARG cc_start: 0.7697 (OUTLIER) cc_final: 0.7476 (ptm160) REVERT: R 1019 LEU cc_start: 0.8302 (tp) cc_final: 0.8073 (tp) REVERT: R 1033 ASP cc_start: 0.7986 (t0) cc_final: 0.7618 (t0) REVERT: R 1076 GLN cc_start: 0.8132 (OUTLIER) cc_final: 0.7735 (mp10) REVERT: R 1097 GLU cc_start: 0.8014 (pp20) cc_final: 0.7378 (pp20) REVERT: H 21 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7890 (tt) REVERT: H 86 MET cc_start: 0.7514 (mtm) cc_final: 0.6860 (mtm) REVERT: H 124 THR cc_start: 0.8006 (p) cc_final: 0.7587 (t) REVERT: H 185 GLN cc_start: 0.7967 (mm-40) cc_final: 0.7761 (mm-40) REVERT: K 27 ARG cc_start: 0.8417 (ttm-80) cc_final: 0.8197 (ttm110) REVERT: K 34 MET cc_start: 0.7771 (mtt) cc_final: 0.7426 (mtt) REVERT: L 5 MET cc_start: 0.8227 (mmm) cc_final: 0.7739 (mmm) REVERT: L 95 TYR cc_start: 0.8148 (m-10) cc_final: 0.7919 (m-10) REVERT: L 109 LYS cc_start: 0.8937 (ttmm) cc_final: 0.8709 (ttmt) REVERT: L 158 SER cc_start: 0.8600 (m) cc_final: 0.8240 (t) REVERT: L 211 PHE cc_start: 0.8591 (p90) cc_final: 0.8279 (p90) outliers start: 29 outliers final: 17 residues processed: 210 average time/residue: 0.0804 time to fit residues: 22.9460 Evaluate side-chains 212 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 192 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 171 ILE Chi-restraints excluded: chain R residue 246 MET Chi-restraints excluded: chain R residue 306 ILE Chi-restraints excluded: chain R residue 358 SER Chi-restraints excluded: chain R residue 1003 ARG Chi-restraints excluded: chain R residue 1031 VAL Chi-restraints excluded: chain R residue 1076 GLN Chi-restraints excluded: chain R residue 445 TYR Chi-restraints excluded: chain R residue 477 LEU Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 123 VAL Chi-restraints excluded: chain H residue 219 THR Chi-restraints excluded: chain K residue 98 ILE Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain L residue 198 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 32 optimal weight: 0.5980 chunk 38 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 67 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 chunk 76 optimal weight: 0.0270 chunk 3 optimal weight: 0.9990 chunk 72 optimal weight: 0.9990 overall best weight: 0.7042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 443 GLN K 77 ASN L 162 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.147545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.125718 restraints weight = 12153.799| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 2.71 r_work: 0.3484 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7753 Z= 0.160 Angle : 0.632 10.307 10556 Z= 0.316 Chirality : 0.043 0.166 1197 Planarity : 0.005 0.075 1325 Dihedral : 4.551 22.505 1065 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 3.59 % Allowed : 18.19 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.31 (0.28), residues: 972 helix: 0.63 (0.29), residues: 326 sheet: 0.37 (0.33), residues: 262 loop : -1.31 (0.34), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 27 TYR 0.025 0.002 TYR R 241 PHE 0.029 0.002 PHE R 224 TRP 0.010 0.001 TRP H 50 HIS 0.005 0.001 HIS L 191 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 7744) covalent geometry : angle 0.63144 (10538) SS BOND : bond 0.00298 ( 9) SS BOND : angle 0.70106 ( 18) hydrogen bonds : bond 0.03459 ( 365) hydrogen bonds : angle 4.42689 ( 1056) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 194 time to evaluate : 0.209 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 174 ASP cc_start: 0.7434 (t0) cc_final: 0.7156 (t0) REVERT: R 265 ASN cc_start: 0.7957 (m110) cc_final: 0.7680 (m110) REVERT: R 291 MET cc_start: 0.7484 (mmm) cc_final: 0.7089 (mmm) REVERT: R 292 ILE cc_start: 0.8119 (tt) cc_final: 0.7816 (pt) REVERT: R 298 MET cc_start: 0.7545 (mmm) cc_final: 0.7239 (mmm) REVERT: R 325 GLU cc_start: 0.7083 (mm-30) cc_final: 0.6709 (tm-30) REVERT: R 1003 ARG cc_start: 0.7677 (OUTLIER) cc_final: 0.7468 (ptm160) REVERT: R 1009 GLU cc_start: 0.7763 (tp30) cc_final: 0.7415 (tp30) REVERT: R 1019 LEU cc_start: 0.8322 (tp) cc_final: 0.8105 (tp) REVERT: R 1033 ASP cc_start: 0.7993 (t0) cc_final: 0.7632 (t0) REVERT: R 1076 GLN cc_start: 0.8174 (OUTLIER) cc_final: 0.7778 (mp10) REVERT: R 1097 GLU cc_start: 0.8069 (pp20) cc_final: 0.7449 (pp20) REVERT: H 21 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7918 (tt) REVERT: H 86 MET cc_start: 0.7510 (mtm) cc_final: 0.6834 (mtm) REVERT: H 124 THR cc_start: 0.8021 (p) cc_final: 0.7590 (t) REVERT: H 185 GLN cc_start: 0.7989 (mm-40) cc_final: 0.7783 (mm-40) REVERT: K 34 MET cc_start: 0.7769 (mtt) cc_final: 0.7534 (mtt) REVERT: L 2 ASP cc_start: 0.7953 (t0) cc_final: 0.7713 (t0) REVERT: L 5 MET cc_start: 0.8194 (mmm) cc_final: 0.7740 (mmt) REVERT: L 95 TYR cc_start: 0.8156 (m-10) cc_final: 0.7943 (m-10) REVERT: L 109 LYS cc_start: 0.8951 (ttmm) cc_final: 0.8720 (ttmt) REVERT: L 149 GLN cc_start: 0.8000 (mm-40) cc_final: 0.7720 (mt0) REVERT: L 158 SER cc_start: 0.8611 (m) cc_final: 0.8255 (t) REVERT: L 211 PHE cc_start: 0.8620 (p90) cc_final: 0.8299 (p90) outliers start: 29 outliers final: 20 residues processed: 212 average time/residue: 0.0794 time to fit residues: 22.9419 Evaluate side-chains 216 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 193 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 171 ILE Chi-restraints excluded: chain R residue 246 MET Chi-restraints excluded: chain R residue 306 ILE Chi-restraints excluded: chain R residue 358 SER Chi-restraints excluded: chain R residue 1003 ARG Chi-restraints excluded: chain R residue 1031 VAL Chi-restraints excluded: chain R residue 1044 ASP Chi-restraints excluded: chain R residue 1076 GLN Chi-restraints excluded: chain R residue 445 TYR Chi-restraints excluded: chain R residue 477 LEU Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 123 VAL Chi-restraints excluded: chain H residue 219 THR Chi-restraints excluded: chain K residue 83 MET Chi-restraints excluded: chain K residue 98 ILE Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain L residue 165 VAL Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain L residue 198 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 54 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 79 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 95 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 69 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 70 optimal weight: 0.5980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 443 GLN ** H 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 162 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.147107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.125496 restraints weight = 12048.860| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 2.67 r_work: 0.3486 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7753 Z= 0.168 Angle : 0.636 9.264 10556 Z= 0.320 Chirality : 0.043 0.164 1197 Planarity : 0.005 0.083 1325 Dihedral : 4.586 22.556 1065 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 3.84 % Allowed : 18.81 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.30 (0.28), residues: 972 helix: 0.69 (0.30), residues: 324 sheet: 0.26 (0.32), residues: 272 loop : -1.27 (0.35), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 27 TYR 0.025 0.002 TYR R 428 PHE 0.033 0.002 PHE R 224 TRP 0.010 0.001 TRP H 50 HIS 0.006 0.001 HIS L 191 Details of bonding type rmsd covalent geometry : bond 0.00384 ( 7744) covalent geometry : angle 0.63639 (10538) SS BOND : bond 0.00282 ( 9) SS BOND : angle 0.67000 ( 18) hydrogen bonds : bond 0.03495 ( 365) hydrogen bonds : angle 4.45152 ( 1056) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 188 time to evaluate : 0.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 174 ASP cc_start: 0.7349 (t0) cc_final: 0.7083 (t0) REVERT: R 265 ASN cc_start: 0.7962 (m110) cc_final: 0.7697 (m110) REVERT: R 291 MET cc_start: 0.7489 (mmm) cc_final: 0.7091 (mmm) REVERT: R 292 ILE cc_start: 0.8155 (tt) cc_final: 0.7808 (pt) REVERT: R 325 GLU cc_start: 0.7156 (mm-30) cc_final: 0.6787 (tm-30) REVERT: R 1003 ARG cc_start: 0.7732 (OUTLIER) cc_final: 0.7526 (ptt90) REVERT: R 1009 GLU cc_start: 0.7759 (tp30) cc_final: 0.7442 (tp30) REVERT: R 1019 LEU cc_start: 0.8297 (tp) cc_final: 0.8078 (tp) REVERT: R 1033 ASP cc_start: 0.8021 (t0) cc_final: 0.7658 (t0) REVERT: R 1076 GLN cc_start: 0.8187 (OUTLIER) cc_final: 0.7778 (mp10) REVERT: R 1097 GLU cc_start: 0.8075 (pp20) cc_final: 0.7459 (pp20) REVERT: H 21 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7909 (tt) REVERT: H 86 MET cc_start: 0.7539 (mtm) cc_final: 0.6855 (mtm) REVERT: H 124 THR cc_start: 0.8000 (p) cc_final: 0.7648 (t) REVERT: H 185 GLN cc_start: 0.8015 (mm-40) cc_final: 0.7803 (mm-40) REVERT: K 34 MET cc_start: 0.7704 (mtt) cc_final: 0.7465 (mtt) REVERT: L 2 ASP cc_start: 0.7962 (t0) cc_final: 0.7727 (t0) REVERT: L 5 MET cc_start: 0.8201 (mmm) cc_final: 0.7748 (mmt) REVERT: L 109 LYS cc_start: 0.8951 (ttmm) cc_final: 0.8720 (ttmt) REVERT: L 149 GLN cc_start: 0.8024 (mm-40) cc_final: 0.7766 (mt0) REVERT: L 158 SER cc_start: 0.8613 (m) cc_final: 0.8259 (t) REVERT: L 211 PHE cc_start: 0.8620 (p90) cc_final: 0.8288 (p90) outliers start: 31 outliers final: 23 residues processed: 205 average time/residue: 0.0760 time to fit residues: 21.3175 Evaluate side-chains 214 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 188 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 171 ILE Chi-restraints excluded: chain R residue 246 MET Chi-restraints excluded: chain R residue 306 ILE Chi-restraints excluded: chain R residue 309 ILE Chi-restraints excluded: chain R residue 347 LEU Chi-restraints excluded: chain R residue 358 SER Chi-restraints excluded: chain R residue 387 VAL Chi-restraints excluded: chain R residue 1003 ARG Chi-restraints excluded: chain R residue 1031 VAL Chi-restraints excluded: chain R residue 1044 ASP Chi-restraints excluded: chain R residue 1076 GLN Chi-restraints excluded: chain R residue 445 TYR Chi-restraints excluded: chain R residue 477 LEU Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 123 VAL Chi-restraints excluded: chain H residue 219 THR Chi-restraints excluded: chain K residue 83 MET Chi-restraints excluded: chain K residue 98 ILE Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain L residue 165 VAL Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain L residue 198 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 11 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 83 optimal weight: 0.5980 chunk 1 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 85 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 443 GLN H 169 ASN ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 162 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.146571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.124690 restraints weight = 12304.655| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 2.73 r_work: 0.3470 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7753 Z= 0.171 Angle : 0.645 9.516 10556 Z= 0.324 Chirality : 0.043 0.166 1197 Planarity : 0.005 0.088 1325 Dihedral : 4.609 21.509 1065 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 3.96 % Allowed : 18.81 % Favored : 77.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.20 (0.28), residues: 972 helix: 0.74 (0.30), residues: 324 sheet: 0.40 (0.32), residues: 267 loop : -1.25 (0.35), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 27 TYR 0.027 0.002 TYR R 428 PHE 0.035 0.002 PHE R 224 TRP 0.009 0.001 TRP H 50 HIS 0.005 0.001 HIS L 191 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 7744) covalent geometry : angle 0.64521 (10538) SS BOND : bond 0.00273 ( 9) SS BOND : angle 0.67274 ( 18) hydrogen bonds : bond 0.03530 ( 365) hydrogen bonds : angle 4.43806 ( 1056) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 191 time to evaluate : 0.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 174 ASP cc_start: 0.7397 (t0) cc_final: 0.7133 (t0) REVERT: R 246 MET cc_start: 0.7839 (OUTLIER) cc_final: 0.7539 (ttt) REVERT: R 265 ASN cc_start: 0.7948 (m110) cc_final: 0.7691 (m110) REVERT: R 291 MET cc_start: 0.7499 (mmm) cc_final: 0.7091 (mmm) REVERT: R 325 GLU cc_start: 0.7251 (mm-30) cc_final: 0.6878 (tm-30) REVERT: R 1003 ARG cc_start: 0.7744 (OUTLIER) cc_final: 0.7532 (ptm160) REVERT: R 1009 GLU cc_start: 0.7753 (tp30) cc_final: 0.7545 (tp30) REVERT: R 1033 ASP cc_start: 0.8035 (t0) cc_final: 0.7682 (t0) REVERT: R 1076 GLN cc_start: 0.8194 (OUTLIER) cc_final: 0.7787 (mp10) REVERT: R 1097 GLU cc_start: 0.8099 (pp20) cc_final: 0.7499 (pp20) REVERT: R 1111 LEU cc_start: 0.8177 (OUTLIER) cc_final: 0.7769 (mm) REVERT: R 482 MET cc_start: 0.6464 (mmt) cc_final: 0.6123 (mmt) REVERT: H 21 LEU cc_start: 0.8186 (OUTLIER) cc_final: 0.7902 (tt) REVERT: H 86 MET cc_start: 0.7522 (mtm) cc_final: 0.6835 (mtm) REVERT: H 124 THR cc_start: 0.7862 (p) cc_final: 0.7404 (t) REVERT: H 185 GLN cc_start: 0.8070 (mm-40) cc_final: 0.7858 (mm-40) REVERT: K 34 MET cc_start: 0.7729 (mtt) cc_final: 0.7327 (mtt) REVERT: L 5 MET cc_start: 0.8210 (mmm) cc_final: 0.7736 (mmt) REVERT: L 109 LYS cc_start: 0.8947 (ttmm) cc_final: 0.8713 (ttmt) REVERT: L 149 GLN cc_start: 0.8029 (mm-40) cc_final: 0.7683 (mt0) REVERT: L 158 SER cc_start: 0.8619 (m) cc_final: 0.8273 (t) REVERT: L 211 PHE cc_start: 0.8624 (p90) cc_final: 0.8283 (p90) outliers start: 32 outliers final: 19 residues processed: 212 average time/residue: 0.0865 time to fit residues: 24.8983 Evaluate side-chains 212 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 188 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 171 ILE Chi-restraints excluded: chain R residue 246 MET Chi-restraints excluded: chain R residue 306 ILE Chi-restraints excluded: chain R residue 309 ILE Chi-restraints excluded: chain R residue 347 LEU Chi-restraints excluded: chain R residue 358 SER Chi-restraints excluded: chain R residue 1003 ARG Chi-restraints excluded: chain R residue 1044 ASP Chi-restraints excluded: chain R residue 1076 GLN Chi-restraints excluded: chain R residue 1111 LEU Chi-restraints excluded: chain R residue 445 TYR Chi-restraints excluded: chain R residue 477 LEU Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 123 VAL Chi-restraints excluded: chain H residue 219 THR Chi-restraints excluded: chain K residue 83 MET Chi-restraints excluded: chain K residue 98 ILE Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain L residue 165 VAL Chi-restraints excluded: chain L residue 198 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 17 optimal weight: 0.4980 chunk 96 optimal weight: 7.9990 chunk 60 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 7 optimal weight: 0.2980 chunk 30 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 48 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 443 GLN ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 162 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.147084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.125270 restraints weight = 12136.334| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 2.72 r_work: 0.3485 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7753 Z= 0.146 Angle : 0.629 8.033 10556 Z= 0.317 Chirality : 0.043 0.155 1197 Planarity : 0.005 0.094 1325 Dihedral : 4.546 21.801 1065 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 3.47 % Allowed : 19.18 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.09 (0.28), residues: 972 helix: 0.80 (0.30), residues: 324 sheet: 0.59 (0.33), residues: 254 loop : -1.20 (0.34), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 27 TYR 0.028 0.002 TYR R 428 PHE 0.039 0.002 PHE R 224 TRP 0.009 0.001 TRP H 50 HIS 0.005 0.001 HIS L 191 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 7744) covalent geometry : angle 0.62862 (10538) SS BOND : bond 0.00267 ( 9) SS BOND : angle 0.62010 ( 18) hydrogen bonds : bond 0.03395 ( 365) hydrogen bonds : angle 4.38950 ( 1056) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 191 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 174 ASP cc_start: 0.7384 (t0) cc_final: 0.7116 (t0) REVERT: R 246 MET cc_start: 0.7822 (OUTLIER) cc_final: 0.7521 (ttt) REVERT: R 265 ASN cc_start: 0.7944 (m110) cc_final: 0.7714 (m110) REVERT: R 291 MET cc_start: 0.7469 (mmm) cc_final: 0.7057 (mmm) REVERT: R 321 SER cc_start: 0.8400 (p) cc_final: 0.8067 (p) REVERT: R 325 GLU cc_start: 0.7255 (mm-30) cc_final: 0.6872 (tm-30) REVERT: R 351 LYS cc_start: 0.8545 (mttm) cc_final: 0.8142 (mtpp) REVERT: R 1003 ARG cc_start: 0.7731 (OUTLIER) cc_final: 0.7527 (ptm160) REVERT: R 1009 GLU cc_start: 0.7732 (tp30) cc_final: 0.7513 (tp30) REVERT: R 1033 ASP cc_start: 0.7990 (t0) cc_final: 0.7643 (t0) REVERT: R 1076 GLN cc_start: 0.8182 (OUTLIER) cc_final: 0.7779 (mp10) REVERT: R 1097 GLU cc_start: 0.8075 (pp20) cc_final: 0.7509 (pp20) REVERT: R 1111 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7745 (mm) REVERT: R 482 MET cc_start: 0.6404 (mmt) cc_final: 0.6099 (mmt) REVERT: H 21 LEU cc_start: 0.8198 (OUTLIER) cc_final: 0.7939 (tt) REVERT: H 86 MET cc_start: 0.7553 (mtm) cc_final: 0.6908 (mtm) REVERT: H 124 THR cc_start: 0.7905 (p) cc_final: 0.7454 (t) REVERT: H 185 GLN cc_start: 0.8020 (mm-40) cc_final: 0.7819 (mm-40) REVERT: K 34 MET cc_start: 0.7691 (mtt) cc_final: 0.7287 (mtt) REVERT: L 5 MET cc_start: 0.8195 (mmm) cc_final: 0.7723 (mmm) REVERT: L 109 LYS cc_start: 0.8939 (ttmm) cc_final: 0.8699 (ttmt) REVERT: L 147 LYS cc_start: 0.8374 (pttp) cc_final: 0.8082 (pttp) REVERT: L 149 GLN cc_start: 0.7996 (mm-40) cc_final: 0.7685 (mt0) REVERT: L 158 SER cc_start: 0.8606 (m) cc_final: 0.8249 (t) REVERT: L 211 PHE cc_start: 0.8603 (p90) cc_final: 0.8279 (p90) outliers start: 28 outliers final: 19 residues processed: 208 average time/residue: 0.0952 time to fit residues: 26.7774 Evaluate side-chains 214 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 190 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 171 ILE Chi-restraints excluded: chain R residue 193 TYR Chi-restraints excluded: chain R residue 246 MET Chi-restraints excluded: chain R residue 306 ILE Chi-restraints excluded: chain R residue 347 LEU Chi-restraints excluded: chain R residue 358 SER Chi-restraints excluded: chain R residue 1003 ARG Chi-restraints excluded: chain R residue 1044 ASP Chi-restraints excluded: chain R residue 1076 GLN Chi-restraints excluded: chain R residue 1111 LEU Chi-restraints excluded: chain R residue 445 TYR Chi-restraints excluded: chain R residue 477 LEU Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 123 VAL Chi-restraints excluded: chain H residue 219 THR Chi-restraints excluded: chain K residue 83 MET Chi-restraints excluded: chain K residue 98 ILE Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain L residue 165 VAL Chi-restraints excluded: chain L residue 198 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 53 optimal weight: 2.9990 chunk 14 optimal weight: 0.5980 chunk 66 optimal weight: 5.9990 chunk 6 optimal weight: 0.5980 chunk 62 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 78 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 443 GLN H 169 ASN ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 162 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.145516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.123488 restraints weight = 12151.029| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 2.73 r_work: 0.3453 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 7753 Z= 0.197 Angle : 0.664 8.202 10556 Z= 0.335 Chirality : 0.044 0.152 1197 Planarity : 0.005 0.099 1325 Dihedral : 4.702 21.310 1065 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 3.22 % Allowed : 20.54 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.16 (0.28), residues: 972 helix: 0.75 (0.29), residues: 320 sheet: 0.55 (0.33), residues: 255 loop : -1.24 (0.33), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 27 TYR 0.029 0.002 TYR R 428 PHE 0.050 0.002 PHE R 224 TRP 0.011 0.002 TRP H 50 HIS 0.005 0.001 HIS L 191 Details of bonding type rmsd covalent geometry : bond 0.00452 ( 7744) covalent geometry : angle 0.66433 (10538) SS BOND : bond 0.00284 ( 9) SS BOND : angle 0.74151 ( 18) hydrogen bonds : bond 0.03688 ( 365) hydrogen bonds : angle 4.49099 ( 1056) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 196 time to evaluate : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 174 ASP cc_start: 0.7455 (t0) cc_final: 0.7179 (t0) REVERT: R 246 MET cc_start: 0.7867 (OUTLIER) cc_final: 0.7546 (ttt) REVERT: R 265 ASN cc_start: 0.7894 (m110) cc_final: 0.7627 (m110) REVERT: R 291 MET cc_start: 0.7522 (mmm) cc_final: 0.7080 (mmm) REVERT: R 292 ILE cc_start: 0.8183 (tt) cc_final: 0.7837 (pt) REVERT: R 321 SER cc_start: 0.8373 (p) cc_final: 0.8042 (p) REVERT: R 325 GLU cc_start: 0.7331 (mm-30) cc_final: 0.6919 (tm-30) REVERT: R 351 LYS cc_start: 0.8606 (mttm) cc_final: 0.8209 (mtpp) REVERT: R 1003 ARG cc_start: 0.7755 (OUTLIER) cc_final: 0.7537 (ptt90) REVERT: R 1009 GLU cc_start: 0.7764 (tp30) cc_final: 0.7528 (tp30) REVERT: R 1033 ASP cc_start: 0.8068 (t0) cc_final: 0.7738 (t0) REVERT: R 1076 GLN cc_start: 0.8248 (OUTLIER) cc_final: 0.7814 (mp10) REVERT: R 1097 GLU cc_start: 0.8135 (pp20) cc_final: 0.7548 (pp20) REVERT: R 1111 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.7830 (mm) REVERT: R 482 MET cc_start: 0.6456 (mmt) cc_final: 0.6056 (mmt) REVERT: H 21 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7878 (tt) REVERT: H 86 MET cc_start: 0.7565 (mtm) cc_final: 0.6871 (mtm) REVERT: H 124 THR cc_start: 0.7914 (p) cc_final: 0.7456 (t) REVERT: K 34 MET cc_start: 0.7740 (mtt) cc_final: 0.7318 (mtt) REVERT: L 5 MET cc_start: 0.8237 (mmm) cc_final: 0.7739 (mmt) REVERT: L 109 LYS cc_start: 0.8946 (ttmm) cc_final: 0.8706 (ttmt) REVERT: L 147 LYS cc_start: 0.8396 (pttp) cc_final: 0.8074 (pttp) REVERT: L 149 GLN cc_start: 0.8017 (mm-40) cc_final: 0.7636 (mt0) REVERT: L 158 SER cc_start: 0.8664 (m) cc_final: 0.8315 (t) REVERT: L 211 PHE cc_start: 0.8646 (p90) cc_final: 0.8326 (p90) outliers start: 26 outliers final: 20 residues processed: 212 average time/residue: 0.0933 time to fit residues: 26.7978 Evaluate side-chains 220 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 195 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 171 ILE Chi-restraints excluded: chain R residue 246 MET Chi-restraints excluded: chain R residue 306 ILE Chi-restraints excluded: chain R residue 309 ILE Chi-restraints excluded: chain R residue 347 LEU Chi-restraints excluded: chain R residue 358 SER Chi-restraints excluded: chain R residue 387 VAL Chi-restraints excluded: chain R residue 1003 ARG Chi-restraints excluded: chain R residue 1044 ASP Chi-restraints excluded: chain R residue 1076 GLN Chi-restraints excluded: chain R residue 1111 LEU Chi-restraints excluded: chain R residue 445 TYR Chi-restraints excluded: chain R residue 477 LEU Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 123 VAL Chi-restraints excluded: chain H residue 219 THR Chi-restraints excluded: chain K residue 83 MET Chi-restraints excluded: chain K residue 98 ILE Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain L residue 165 VAL Chi-restraints excluded: chain L residue 198 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 25 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 38 optimal weight: 6.9990 chunk 94 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 443 GLN ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 162 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.144968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.122917 restraints weight = 12190.096| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 2.70 r_work: 0.3446 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 7753 Z= 0.222 Angle : 0.684 8.610 10556 Z= 0.345 Chirality : 0.045 0.155 1197 Planarity : 0.005 0.099 1325 Dihedral : 4.822 21.958 1065 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 3.22 % Allowed : 21.04 % Favored : 75.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.20 (0.28), residues: 972 helix: 0.69 (0.29), residues: 321 sheet: 0.38 (0.32), residues: 269 loop : -1.18 (0.34), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 27 TYR 0.031 0.002 TYR R 428 PHE 0.053 0.002 PHE R 224 TRP 0.013 0.002 TRP H 50 HIS 0.007 0.001 HIS L 191 Details of bonding type rmsd covalent geometry : bond 0.00504 ( 7744) covalent geometry : angle 0.68383 (10538) SS BOND : bond 0.00283 ( 9) SS BOND : angle 0.78795 ( 18) hydrogen bonds : bond 0.03822 ( 365) hydrogen bonds : angle 4.58173 ( 1056) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1768.78 seconds wall clock time: 31 minutes 12.59 seconds (1872.59 seconds total)