Starting phenix.real_space_refine on Sun May 11 05:08:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9l1s_62753/05_2025/9l1s_62753.cif Found real_map, /net/cci-nas-00/data/ceres_data/9l1s_62753/05_2025/9l1s_62753.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9l1s_62753/05_2025/9l1s_62753.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9l1s_62753/05_2025/9l1s_62753.map" model { file = "/net/cci-nas-00/data/ceres_data/9l1s_62753/05_2025/9l1s_62753.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9l1s_62753/05_2025/9l1s_62753.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 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 60 5.16 5 C 4742 2.51 5 N 1319 2.21 5 O 1463 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 7584 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 553, 4266 Classifications: {'peptide': 553} Link IDs: {'PTRANS': 33, 'TRANS': 519} Chain breaks: 1 Chain: "B" Number of atoms: 1657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1657 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 202} Chain: "C" Number of atoms: 1661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1661 Classifications: {'peptide': 222} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 208} Time building chain proxies: 4.71, per 1000 atoms: 0.62 Number of scatterers: 7584 At special positions: 0 Unit cell: (89.232, 113.568, 140.946, 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 60 16.00 O 1463 8.00 N 1319 7.00 C 4742 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 26 " - pdb=" SG CYS A 53 " distance=2.03 Simple disulfide: pdb=" SG CYS A 162 " - pdb=" SG CYS A 192 " distance=2.03 Simple disulfide: pdb=" SG CYS A 195 " - pdb=" SG CYS A 204 " distance=2.03 Simple disulfide: pdb=" SG CYS A 199 " - pdb=" SG CYS A 212 " distance=2.03 Simple disulfide: pdb=" SG CYS A 220 " - pdb=" SG CYS A 227 " distance=2.03 Simple disulfide: pdb=" SG CYS A 224 " - pdb=" SG CYS A 235 " distance=2.03 Simple disulfide: pdb=" SG CYS A 236 " - pdb=" SG CYS A 244 " distance=2.03 Simple disulfide: pdb=" SG CYS A 240 " - pdb=" SG CYS A 252 " distance=2.03 Simple disulfide: pdb=" SG CYS A 255 " - pdb=" SG CYS A 264 " distance=2.03 Simple disulfide: pdb=" SG CYS A 268 " - pdb=" SG CYS A 295 " distance=2.03 Simple disulfide: pdb=" SG CYS A 299 " - pdb=" SG CYS A 311 " distance=2.03 Simple disulfide: pdb=" SG CYS A 315 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 342 " - pdb=" SG CYS A 367 " distance=2.03 Simple disulfide: pdb=" SG CYS A 475 " - pdb=" SG CYS A 504 " distance=2.03 Simple disulfide: pdb=" SG CYS A 511 " - pdb=" SG CYS A 520 " distance=2.03 Simple disulfide: pdb=" SG CYS A 515 " - pdb=" SG CYS A 528 " distance=2.03 Simple disulfide: pdb=" SG CYS A 544 " - pdb=" SG CYS A 560 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.04 Simple disulfide: pdb=" SG CYS B 134 " - pdb=" SG CYS B 194 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS C 140 " - pdb=" SG CYS C 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: 1.82 Conformation dependent library (CDL) restraints added in 1.1 seconds 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1820 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 22 sheets defined 7.0% alpha, 19.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'A' and resid 42 through 48 removed outlier: 3.649A pdb=" N HIS A 48 " --> pdb=" O ASP A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 75 removed outlier: 3.608A pdb=" N GLN A 75 " --> pdb=" O SER A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 111 removed outlier: 3.688A pdb=" N ASP A 110 " --> pdb=" O LEU A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 173 removed outlier: 4.263A pdb=" N ILE A 172 " --> pdb=" O LEU A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 212 removed outlier: 4.231A pdb=" N CYS A 212 " --> pdb=" O SER A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 235 Processing helix chain 'A' and resid 395 through 401 removed outlier: 3.781A pdb=" N GLN A 398 " --> pdb=" O GLU A 395 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL A 399 " --> pdb=" O GLN A 396 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE A 400 " --> pdb=" O LEU A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 439 Processing helix chain 'A' and resid 500 through 506 Processing helix chain 'A' and resid 515 through 519 removed outlier: 3.788A pdb=" N GLY A 518 " --> pdb=" O CYS A 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 187 Processing helix chain 'C' and resid 28 through 32 removed outlier: 3.654A pdb=" N TYR C 32 " --> pdb=" O PHE C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 158 No H-bonds generated for 'chain 'C' and resid 156 through 158' Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 26 removed outlier: 3.575A pdb=" N CYS A 26 " --> pdb=" O VAL A 55 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 60 through 65 removed outlier: 3.552A pdb=" N TYR A 64 " --> pdb=" O ALA A 87 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ASN A 89 " --> pdb=" O TYR A 64 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU A 183 " --> pdb=" O VAL A 153 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 258 through 260 removed outlier: 3.521A pdb=" N PHE A 258 " --> pdb=" O GLU A 265 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 272 through 274 Processing sheet with id=AA5, first strand: chain 'A' and resid 289 through 291 Processing sheet with id=AA6, first strand: chain 'A' and resid 304 through 305 Processing sheet with id=AA7, first strand: chain 'A' and resid 319 through 323 Processing sheet with id=AA8, first strand: chain 'A' and resid 342 through 343 removed outlier: 6.517A pdb=" N CYS A 342 " --> pdb=" O PHE A 371 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 374 through 376 removed outlier: 7.451A pdb=" N LEU A 467 " --> pdb=" O SER A 442 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N THR A 444 " --> pdb=" O LEU A 467 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N HIS A 469 " --> pdb=" O THR A 444 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N GLN A 446 " --> pdb=" O HIS A 469 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ALA A 466 " --> pdb=" O LEU A 494 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 405 through 406 Processing sheet with id=AB2, first strand: chain 'A' and resid 539 through 541 removed outlier: 3.578A pdb=" N GLU A 539 " --> pdb=" O ARG A 536 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE A 534 " --> pdb=" O VAL A 541 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N LEU A 535 " --> pdb=" O CYS A 560 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 552 through 553 Processing sheet with id=AB4, first strand: chain 'B' and resid 5 through 7 removed outlier: 3.634A pdb=" N THR B 74 " --> pdb=" O SER B 63 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 10 through 13 Processing sheet with id=AB6, first strand: chain 'B' and resid 53 through 54 removed outlier: 5.828A pdb=" N LEU B 46 " --> pdb=" O GLN B 37 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N GLN B 37 " --> pdb=" O LEU B 46 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE B 48 " --> pdb=" O TRP B 35 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 129 through 133 Processing sheet with id=AB8, first strand: chain 'B' and resid 145 through 150 removed outlier: 3.511A pdb=" N LYS B 145 " --> pdb=" O THR B 197 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N CYS B 194 " --> pdb=" O LYS B 207 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LYS B 207 " --> pdb=" O CYS B 194 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 5 through 7 Processing sheet with id=AC1, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.043A pdb=" N GLY C 10 " --> pdb=" O THR C 110 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR C 107 " --> pdb=" O TYR C 90 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N MET C 34 " --> pdb=" O ASP C 50 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N ASP C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 122 through 124 removed outlier: 3.691A pdb=" N GLY C 139 " --> pdb=" O LEU C 124 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER C 180 " --> pdb=" O CYS C 140 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 151 through 154 removed outlier: 4.379A pdb=" N TYR C 194 " --> pdb=" O VAL C 211 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LYS C 209 " --> pdb=" O CYS C 196 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 169 through 170 140 hydrogen bonds defined for protein. 333 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: 2.09 Time building geometry restraints manager: 2.15 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: 2518 1.34 - 1.46: 1691 1.46 - 1.58: 3483 1.58 - 1.70: 0 1.70 - 1.82: 68 Bond restraints: 7760 Sorted by residual: bond pdb=" N LEU A 509 " pdb=" CA LEU A 509 " ideal model delta sigma weight residual 1.462 1.489 -0.027 1.46e-02 4.69e+03 3.42e+00 bond pdb=" C ARG A 34 " pdb=" N LEU A 35 " ideal model delta sigma weight residual 1.330 1.352 -0.022 1.47e-02 4.63e+03 2.20e+00 bond pdb=" N ASN C 155 " pdb=" CA ASN C 155 " ideal model delta sigma weight residual 1.457 1.473 -0.016 1.29e-02 6.01e+03 1.51e+00 bond pdb=" C LEU A 509 " pdb=" O LEU A 509 " ideal model delta sigma weight residual 1.232 1.246 -0.014 1.20e-02 6.94e+03 1.38e+00 bond pdb=" CA CYS A 511 " pdb=" C CYS A 511 " ideal model delta sigma weight residual 1.532 1.521 0.011 9.60e-03 1.09e+04 1.33e+00 ... (remaining 7755 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.67: 10237 1.67 - 3.34: 273 3.34 - 5.01: 35 5.01 - 6.69: 4 6.69 - 8.36: 6 Bond angle restraints: 10555 Sorted by residual: angle pdb=" N VAL A 219 " pdb=" CA VAL A 219 " pdb=" C VAL A 219 " ideal model delta sigma weight residual 113.20 108.50 4.70 9.60e-01 1.09e+00 2.39e+01 angle pdb=" C SER A 451 " pdb=" N TRP A 452 " pdb=" CA TRP A 452 " ideal model delta sigma weight residual 121.90 116.10 5.80 1.26e+00 6.30e-01 2.12e+01 angle pdb=" C ARG A 34 " pdb=" N LEU A 35 " pdb=" CA LEU A 35 " ideal model delta sigma weight residual 120.68 127.43 -6.75 1.52e+00 4.33e-01 1.97e+01 angle pdb=" C ASN A 275 " pdb=" N THR A 276 " pdb=" CA THR A 276 " ideal model delta sigma weight residual 121.54 128.25 -6.71 1.91e+00 2.74e-01 1.24e+01 angle pdb=" N GLY C 97 " pdb=" CA GLY C 97 " pdb=" C GLY C 97 " ideal model delta sigma weight residual 112.34 105.53 6.81 2.04e+00 2.40e-01 1.11e+01 ... (remaining 10550 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 4291 17.96 - 35.92: 312 35.92 - 53.88: 57 53.88 - 71.84: 22 71.84 - 89.80: 15 Dihedral angle restraints: 4697 sinusoidal: 1854 harmonic: 2843 Sorted by residual: dihedral pdb=" CA MET A 347 " pdb=" C MET A 347 " pdb=" N GLU A 348 " pdb=" CA GLU A 348 " ideal model delta harmonic sigma weight residual -180.00 -154.63 -25.37 0 5.00e+00 4.00e-02 2.57e+01 dihedral pdb=" CA PRO C 98 " pdb=" C PRO C 98 " pdb=" N SER C 99 " pdb=" CA SER C 99 " ideal model delta harmonic sigma weight residual 180.00 157.27 22.73 0 5.00e+00 4.00e-02 2.07e+01 dihedral pdb=" CB CYS B 23 " pdb=" SG CYS B 23 " pdb=" SG CYS B 88 " pdb=" CB CYS B 88 " ideal model delta sinusoidal sigma weight residual 93.00 55.34 37.66 1 1.00e+01 1.00e-02 2.00e+01 ... (remaining 4694 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 838 0.043 - 0.086: 260 0.086 - 0.129: 70 0.129 - 0.172: 5 0.172 - 0.216: 1 Chirality restraints: 1174 Sorted by residual: chirality pdb=" CA LEU A 509 " pdb=" N LEU A 509 " pdb=" C LEU A 509 " pdb=" CB LEU A 509 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CA VAL A 314 " pdb=" N VAL A 314 " pdb=" C VAL A 314 " pdb=" CB VAL A 314 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.59e-01 chirality pdb=" CG LEU A 535 " pdb=" CB LEU A 535 " pdb=" CD1 LEU A 535 " pdb=" CD2 LEU A 535 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.82e-01 ... (remaining 1171 not shown) Planarity restraints: 1383 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN B 79 " 0.088 5.00e-02 4.00e+02 1.34e-01 2.87e+01 pdb=" N PRO B 80 " -0.232 5.00e-02 4.00e+02 pdb=" CA PRO B 80 " 0.073 5.00e-02 4.00e+02 pdb=" CD PRO B 80 " 0.071 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 118 " 0.068 5.00e-02 4.00e+02 1.02e-01 1.67e+01 pdb=" N PRO B 119 " -0.176 5.00e-02 4.00e+02 pdb=" CA PRO B 119 " 0.054 5.00e-02 4.00e+02 pdb=" CD PRO B 119 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 246 " -0.031 5.00e-02 4.00e+02 4.65e-02 3.46e+00 pdb=" N PRO A 247 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 247 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 247 " -0.026 5.00e-02 4.00e+02 ... (remaining 1380 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 39 2.54 - 3.13: 5514 3.13 - 3.72: 11225 3.72 - 4.31: 16019 4.31 - 4.90: 26919 Nonbonded interactions: 59716 Sorted by model distance: nonbonded pdb=" O CYS A 504 " pdb=" CD1 LEU A 509 " model vdw 1.945 3.460 nonbonded pdb=" OH TYR A 301 " pdb=" OE2 GLU A 460 " model vdw 2.191 3.040 nonbonded pdb=" OG1 THR A 290 " pdb=" O GLY A 309 " model vdw 2.226 3.040 nonbonded pdb=" O PRO A 420 " pdb=" N SER A 451 " model vdw 2.272 3.120 nonbonded pdb=" OE2 GLU A 321 " pdb=" NE2 GLN A 329 " model vdw 2.280 3.120 ... (remaining 59711 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: 0.400 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: 0.020 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 20.010 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 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:10.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 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 0.054 7781 Z= 0.132 Angle : 0.657 8.356 10597 Z= 0.370 Chirality : 0.044 0.216 1174 Planarity : 0.006 0.134 1383 Dihedral : 14.050 89.804 2814 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 0.24 % Allowed : 0.35 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.26), residues: 981 helix: -3.77 (0.60), residues: 38 sheet: -1.37 (0.33), residues: 253 loop : -1.33 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 169 HIS 0.007 0.001 HIS B 189 PHE 0.013 0.001 PHE B 118 TYR 0.012 0.001 TYR A 64 ARG 0.007 0.000 ARG A 143 Details of bonding type rmsd hydrogen bonds : bond 0.28712 ( 140) hydrogen bonds : angle 10.99563 ( 333) SS BOND : bond 0.00190 ( 21) SS BOND : angle 0.97131 ( 42) covalent geometry : bond 0.00254 ( 7760) covalent geometry : angle 0.65554 (10555) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 128 time to evaluate : 0.857 Fit side-chains REVERT: A 554 TYR cc_start: 0.6348 (p90) cc_final: 0.6044 (p90) REVERT: B 137 ASN cc_start: 0.7723 (t0) cc_final: 0.7369 (t160) outliers start: 2 outliers final: 2 residues processed: 129 average time/residue: 1.1106 time to fit residues: 151.9266 Evaluate side-chains 80 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 78 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 488 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 5.9990 chunk 74 optimal weight: 30.0000 chunk 41 optimal weight: 0.0030 chunk 25 optimal weight: 2.9990 chunk 50 optimal weight: 9.9990 chunk 39 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 29 optimal weight: 0.5980 chunk 46 optimal weight: 2.9990 chunk 57 optimal weight: 0.5980 chunk 88 optimal weight: 6.9990 overall best weight: 1.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 GLN A 239 GLN A 473 HIS B 199 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.164567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.122483 restraints weight = 9885.875| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 3.02 r_work: 0.3576 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7781 Z= 0.156 Angle : 0.686 8.742 10597 Z= 0.353 Chirality : 0.046 0.240 1174 Planarity : 0.006 0.095 1383 Dihedral : 5.029 24.291 1071 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.24 % Favored : 92.66 % Rotamer: Outliers : 2.00 % Allowed : 11.06 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.26), residues: 981 helix: -3.78 (0.60), residues: 38 sheet: -1.18 (0.32), residues: 265 loop : -1.20 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 205 HIS 0.011 0.001 HIS A 512 PHE 0.021 0.002 PHE A 534 TYR 0.013 0.001 TYR B 94 ARG 0.006 0.001 ARG B 108 Details of bonding type rmsd hydrogen bonds : bond 0.03764 ( 140) hydrogen bonds : angle 7.18447 ( 333) SS BOND : bond 0.00563 ( 21) SS BOND : angle 1.86605 ( 42) covalent geometry : bond 0.00375 ( 7760) covalent geometry : angle 0.67761 (10555) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 95 time to evaluate : 0.857 Fit side-chains revert: symmetry clash REVERT: A 554 TYR cc_start: 0.6589 (p90) cc_final: 0.6200 (p90) REVERT: B 147 GLN cc_start: 0.7967 (pm20) cc_final: 0.7711 (pm20) REVERT: C 3 GLN cc_start: 0.7859 (pp30) cc_final: 0.7496 (pp30) REVERT: C 99 TYR cc_start: 0.8325 (p90) cc_final: 0.8114 (p90) REVERT: C 102 TYR cc_start: 0.7776 (m-80) cc_final: 0.7506 (m-80) outliers start: 17 outliers final: 7 residues processed: 108 average time/residue: 1.0680 time to fit residues: 123.2683 Evaluate side-chains 94 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 87 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 151 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 27 optimal weight: 0.9990 chunk 68 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 20 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 25 optimal weight: 0.3980 chunk 1 optimal weight: 4.9990 chunk 77 optimal weight: 9.9990 chunk 29 optimal weight: 0.6980 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 GLN A 176 ASN A 275 ASN A 512 HIS B 38 GLN B 137 ASN ** B 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.161982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.119836 restraints weight = 10083.888| |-----------------------------------------------------------------------------| r_work (start): 0.3739 rms_B_bonded: 2.82 r_work: 0.3546 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3404 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7781 Z= 0.176 Angle : 0.680 10.478 10597 Z= 0.351 Chirality : 0.046 0.170 1174 Planarity : 0.005 0.075 1383 Dihedral : 5.192 26.138 1067 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % Rotamer: Outliers : 2.59 % Allowed : 13.88 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.26), residues: 981 helix: -3.93 (0.56), residues: 38 sheet: -1.03 (0.32), residues: 260 loop : -1.25 (0.23), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 205 HIS 0.004 0.001 HIS A 512 PHE 0.016 0.002 PHE A 73 TYR 0.016 0.002 TYR B 94 ARG 0.008 0.001 ARG B 18 Details of bonding type rmsd hydrogen bonds : bond 0.03561 ( 140) hydrogen bonds : angle 6.70817 ( 333) SS BOND : bond 0.00435 ( 21) SS BOND : angle 1.41333 ( 42) covalent geometry : bond 0.00428 ( 7760) covalent geometry : angle 0.67575 (10555) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 90 time to evaluate : 0.813 Fit side-chains REVERT: A 275 ASN cc_start: 0.7796 (OUTLIER) cc_final: 0.7551 (t0) REVERT: A 509 LEU cc_start: 0.4681 (OUTLIER) cc_final: 0.4321 (pp) REVERT: A 512 HIS cc_start: 0.6475 (OUTLIER) cc_final: 0.6263 (p-80) REVERT: B 147 GLN cc_start: 0.8097 (pm20) cc_final: 0.7674 (pm20) REVERT: B 189 HIS cc_start: 0.7323 (m90) cc_final: 0.7025 (m-70) REVERT: B 199 GLN cc_start: 0.8845 (tt0) cc_final: 0.8531 (tm-30) REVERT: C 3 GLN cc_start: 0.7991 (pp30) cc_final: 0.7661 (pp30) REVERT: C 85 GLU cc_start: 0.7944 (tp30) cc_final: 0.7738 (tp30) REVERT: C 102 TYR cc_start: 0.7978 (m-80) cc_final: 0.7721 (m-80) REVERT: C 195 ILE cc_start: 0.7021 (OUTLIER) cc_final: 0.6670 (mm) outliers start: 22 outliers final: 11 residues processed: 105 average time/residue: 0.9444 time to fit residues: 106.6731 Evaluate side-chains 97 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 82 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 275 ASN Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 512 HIS Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 144 ASP Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 195 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 81 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 10 optimal weight: 0.4980 chunk 60 optimal weight: 3.9990 chunk 90 optimal weight: 10.0000 chunk 91 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 92 optimal weight: 6.9990 chunk 2 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN A 512 HIS B 137 ASN B 160 GLN C 76 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.163736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.117922 restraints weight = 10017.692| |-----------------------------------------------------------------------------| r_work (start): 0.3716 rms_B_bonded: 2.51 r_work: 0.3590 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3451 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7781 Z= 0.130 Angle : 0.639 8.130 10597 Z= 0.328 Chirality : 0.045 0.160 1174 Planarity : 0.005 0.063 1383 Dihedral : 4.976 24.784 1067 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 2.12 % Allowed : 16.00 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.26), residues: 981 helix: -3.64 (0.63), residues: 38 sheet: -0.81 (0.33), residues: 252 loop : -1.20 (0.23), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 169 HIS 0.011 0.001 HIS A 512 PHE 0.016 0.001 PHE A 73 TYR 0.011 0.001 TYR C 90 ARG 0.009 0.000 ARG B 18 Details of bonding type rmsd hydrogen bonds : bond 0.02956 ( 140) hydrogen bonds : angle 6.29640 ( 333) SS BOND : bond 0.00276 ( 21) SS BOND : angle 1.29590 ( 42) covalent geometry : bond 0.00314 ( 7760) covalent geometry : angle 0.63489 (10555) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 86 time to evaluate : 0.864 Fit side-chains REVERT: A 509 LEU cc_start: 0.4757 (OUTLIER) cc_final: 0.4109 (pp) REVERT: A 554 TYR cc_start: 0.6203 (p90) cc_final: 0.5779 (p90) REVERT: B 145 LYS cc_start: 0.8586 (OUTLIER) cc_final: 0.8334 (ptmm) REVERT: B 199 GLN cc_start: 0.8879 (tt0) cc_final: 0.8454 (tm-30) REVERT: C 3 GLN cc_start: 0.7970 (pp30) cc_final: 0.7583 (pp30) REVERT: C 85 GLU cc_start: 0.7891 (tp30) cc_final: 0.7574 (tp30) REVERT: C 102 TYR cc_start: 0.7950 (m-80) cc_final: 0.7677 (m-80) REVERT: C 195 ILE cc_start: 0.7020 (OUTLIER) cc_final: 0.6684 (mm) outliers start: 18 outliers final: 10 residues processed: 98 average time/residue: 1.0659 time to fit residues: 111.5947 Evaluate side-chains 91 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 78 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 MET Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 145 LYS Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 195 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 44 optimal weight: 3.9990 chunk 89 optimal weight: 30.0000 chunk 80 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 67 optimal weight: 7.9990 chunk 82 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 94 optimal weight: 9.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 106 GLN A 512 HIS B 27 GLN B 137 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.159722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.113391 restraints weight = 10086.786| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 2.51 r_work: 0.3528 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3390 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 7781 Z= 0.212 Angle : 0.711 9.183 10597 Z= 0.364 Chirality : 0.047 0.152 1174 Planarity : 0.005 0.055 1383 Dihedral : 5.336 26.308 1067 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % Rotamer: Outliers : 4.12 % Allowed : 16.35 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.26), residues: 981 helix: -3.80 (0.58), residues: 44 sheet: -0.87 (0.32), residues: 267 loop : -1.19 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 169 HIS 0.005 0.001 HIS B 189 PHE 0.018 0.002 PHE A 73 TYR 0.019 0.002 TYR B 94 ARG 0.008 0.001 ARG B 18 Details of bonding type rmsd hydrogen bonds : bond 0.03332 ( 140) hydrogen bonds : angle 6.54727 ( 333) SS BOND : bond 0.00446 ( 21) SS BOND : angle 1.30922 ( 42) covalent geometry : bond 0.00515 ( 7760) covalent geometry : angle 0.70763 (10555) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 85 time to evaluate : 0.900 Fit side-chains revert: symmetry clash REVERT: A 209 SER cc_start: 0.8538 (p) cc_final: 0.8229 (t) REVERT: A 282 MET cc_start: 0.7473 (mmm) cc_final: 0.7194 (mmm) REVERT: A 509 LEU cc_start: 0.5033 (OUTLIER) cc_final: 0.4430 (pp) REVERT: B 145 LYS cc_start: 0.8864 (OUTLIER) cc_final: 0.8510 (ptmm) REVERT: B 199 GLN cc_start: 0.8871 (tt0) cc_final: 0.8439 (tm130) REVERT: C 85 GLU cc_start: 0.8015 (tp30) cc_final: 0.7765 (tp30) REVERT: C 102 TYR cc_start: 0.8021 (m-80) cc_final: 0.7760 (m-80) outliers start: 35 outliers final: 15 residues processed: 110 average time/residue: 0.9514 time to fit residues: 112.3330 Evaluate side-chains 94 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 77 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain B residue 145 LYS Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 144 ASP Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 195 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 7.9990 chunk 63 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 76 optimal weight: 4.9990 chunk 68 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 93 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 36 optimal weight: 0.0570 chunk 21 optimal weight: 0.9980 overall best weight: 0.8900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 137 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.163849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.122231 restraints weight = 10062.033| |-----------------------------------------------------------------------------| r_work (start): 0.3771 rms_B_bonded: 2.87 r_work: 0.3582 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3442 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.3019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7781 Z= 0.122 Angle : 0.641 9.008 10597 Z= 0.327 Chirality : 0.044 0.141 1174 Planarity : 0.005 0.053 1383 Dihedral : 4.923 24.897 1067 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 2.12 % Allowed : 19.29 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.26), residues: 981 helix: -3.07 (0.70), residues: 38 sheet: -0.71 (0.33), residues: 252 loop : -1.12 (0.23), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 452 HIS 0.004 0.001 HIS B 189 PHE 0.025 0.002 PHE A 534 TYR 0.010 0.001 TYR C 90 ARG 0.010 0.000 ARG B 18 Details of bonding type rmsd hydrogen bonds : bond 0.02704 ( 140) hydrogen bonds : angle 5.93893 ( 333) SS BOND : bond 0.00264 ( 21) SS BOND : angle 0.98110 ( 42) covalent geometry : bond 0.00298 ( 7760) covalent geometry : angle 0.63884 (10555) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 86 time to evaluate : 0.968 Fit side-chains revert: symmetry clash REVERT: A 533 GLN cc_start: 0.9003 (mp10) cc_final: 0.8142 (mp10) REVERT: B 145 LYS cc_start: 0.8844 (OUTLIER) cc_final: 0.8466 (ptmm) REVERT: B 199 GLN cc_start: 0.8890 (tt0) cc_final: 0.8351 (tm130) REVERT: C 3 GLN cc_start: 0.7989 (pp30) cc_final: 0.7531 (pp30) REVERT: C 85 GLU cc_start: 0.8003 (tp30) cc_final: 0.7801 (tp30) REVERT: C 102 TYR cc_start: 0.7945 (m-80) cc_final: 0.7694 (m-80) REVERT: C 195 ILE cc_start: 0.6970 (OUTLIER) cc_final: 0.6576 (mm) outliers start: 18 outliers final: 11 residues processed: 97 average time/residue: 0.9665 time to fit residues: 100.8102 Evaluate side-chains 95 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 MET Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain B residue 145 LYS Chi-restraints excluded: chain B residue 167 ASP Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 195 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 97 optimal weight: 20.0000 chunk 56 optimal weight: 4.9990 chunk 52 optimal weight: 10.0000 chunk 83 optimal weight: 0.9990 chunk 68 optimal weight: 7.9990 chunk 41 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 69 optimal weight: 0.0370 chunk 17 optimal weight: 5.9990 chunk 32 optimal weight: 8.9990 chunk 10 optimal weight: 0.6980 overall best weight: 1.9464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN A 176 ASN B 137 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.160823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.114192 restraints weight = 10119.037| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 2.60 r_work: 0.3539 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3401 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.3231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 7781 Z= 0.184 Angle : 0.691 8.987 10597 Z= 0.350 Chirality : 0.046 0.170 1174 Planarity : 0.005 0.052 1383 Dihedral : 5.118 25.005 1067 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 3.65 % Allowed : 18.59 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.26), residues: 981 helix: -3.31 (0.67), residues: 44 sheet: -0.72 (0.34), residues: 249 loop : -1.16 (0.23), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 169 HIS 0.004 0.001 HIS A 48 PHE 0.022 0.002 PHE A 534 TYR 0.020 0.002 TYR B 140 ARG 0.011 0.001 ARG B 18 Details of bonding type rmsd hydrogen bonds : bond 0.03000 ( 140) hydrogen bonds : angle 6.09696 ( 333) SS BOND : bond 0.00304 ( 21) SS BOND : angle 1.19033 ( 42) covalent geometry : bond 0.00451 ( 7760) covalent geometry : angle 0.68833 (10555) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 87 time to evaluate : 0.824 Fit side-chains REVERT: A 282 MET cc_start: 0.7494 (mmm) cc_final: 0.7227 (mmm) REVERT: A 351 ARG cc_start: 0.8262 (OUTLIER) cc_final: 0.7490 (mtt-85) REVERT: A 509 LEU cc_start: 0.4857 (OUTLIER) cc_final: 0.4229 (pp) REVERT: B 18 ARG cc_start: 0.8437 (ptm160) cc_final: 0.8096 (ptm-80) REVERT: B 19 VAL cc_start: 0.7512 (OUTLIER) cc_final: 0.7281 (p) REVERT: B 145 LYS cc_start: 0.8843 (OUTLIER) cc_final: 0.8495 (ptmm) REVERT: B 189 HIS cc_start: 0.7266 (m90) cc_final: 0.6809 (m-70) REVERT: B 199 GLN cc_start: 0.8842 (tt0) cc_final: 0.8304 (tm130) REVERT: C 102 TYR cc_start: 0.8057 (m-80) cc_final: 0.7771 (m-80) REVERT: C 144 ASP cc_start: 0.7638 (OUTLIER) cc_final: 0.7325 (t0) outliers start: 31 outliers final: 15 residues processed: 108 average time/residue: 1.0052 time to fit residues: 116.0638 Evaluate side-chains 99 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 79 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 MET Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 351 ARG Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 145 LYS Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 144 ASP Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 195 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 94 optimal weight: 7.9990 chunk 30 optimal weight: 0.0970 chunk 20 optimal weight: 0.7980 chunk 48 optimal weight: 3.9990 chunk 32 optimal weight: 0.2980 chunk 29 optimal weight: 6.9990 chunk 66 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 chunk 28 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 137 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.164232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.118770 restraints weight = 10179.984| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 2.53 r_work: 0.3606 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3468 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.3193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7781 Z= 0.119 Angle : 0.656 9.482 10597 Z= 0.331 Chirality : 0.044 0.163 1174 Planarity : 0.005 0.052 1383 Dihedral : 4.835 24.573 1067 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 2.47 % Allowed : 20.71 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.27), residues: 981 helix: -2.67 (0.80), residues: 38 sheet: -0.49 (0.35), residues: 239 loop : -1.07 (0.23), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 169 HIS 0.003 0.001 HIS B 189 PHE 0.020 0.001 PHE A 534 TYR 0.012 0.001 TYR A 554 ARG 0.010 0.000 ARG B 18 Details of bonding type rmsd hydrogen bonds : bond 0.02588 ( 140) hydrogen bonds : angle 5.69221 ( 333) SS BOND : bond 0.00234 ( 21) SS BOND : angle 0.91913 ( 42) covalent geometry : bond 0.00287 ( 7760) covalent geometry : angle 0.65495 (10555) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 84 time to evaluate : 0.832 Fit side-chains revert: symmetry clash REVERT: A 94 VAL cc_start: 0.7526 (t) cc_final: 0.7250 (p) REVERT: A 351 ARG cc_start: 0.8211 (OUTLIER) cc_final: 0.7417 (mtt-85) REVERT: A 533 GLN cc_start: 0.8957 (mp10) cc_final: 0.8099 (mp10) REVERT: B 18 ARG cc_start: 0.8425 (ptm160) cc_final: 0.8053 (ptm-80) REVERT: B 19 VAL cc_start: 0.7445 (OUTLIER) cc_final: 0.7220 (p) REVERT: B 106 ILE cc_start: 0.7446 (pp) cc_final: 0.7197 (pp) REVERT: B 137 ASN cc_start: 0.8315 (t0) cc_final: 0.7991 (t160) REVERT: B 145 LYS cc_start: 0.8816 (OUTLIER) cc_final: 0.8478 (ptmm) REVERT: B 189 HIS cc_start: 0.7243 (m90) cc_final: 0.6924 (m90) REVERT: B 199 GLN cc_start: 0.8869 (tt0) cc_final: 0.8321 (tm130) REVERT: C 102 TYR cc_start: 0.7941 (m-80) cc_final: 0.7658 (m-80) REVERT: C 144 ASP cc_start: 0.7625 (m-30) cc_final: 0.7302 (t0) REVERT: C 195 ILE cc_start: 0.6996 (OUTLIER) cc_final: 0.6585 (mm) outliers start: 21 outliers final: 11 residues processed: 100 average time/residue: 0.9939 time to fit residues: 106.6302 Evaluate side-chains 95 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 MET Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 351 ARG Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 145 LYS Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 195 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 92 optimal weight: 8.9990 chunk 13 optimal weight: 0.8980 chunk 30 optimal weight: 4.9990 chunk 80 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 26 optimal weight: 0.0370 chunk 9 optimal weight: 6.9990 chunk 69 optimal weight: 1.9990 chunk 95 optimal weight: 0.0870 overall best weight: 0.8038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.164667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.118649 restraints weight = 10239.635| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 2.63 r_work: 0.3603 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3463 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.3237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7781 Z= 0.119 Angle : 0.651 9.925 10597 Z= 0.328 Chirality : 0.044 0.161 1174 Planarity : 0.005 0.051 1383 Dihedral : 4.758 23.004 1067 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 2.24 % Allowed : 20.94 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.27), residues: 981 helix: -2.63 (0.80), residues: 38 sheet: -0.43 (0.35), residues: 241 loop : -1.05 (0.24), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 169 HIS 0.003 0.001 HIS A 48 PHE 0.020 0.001 PHE A 73 TYR 0.011 0.001 TYR A 554 ARG 0.009 0.000 ARG A 143 Details of bonding type rmsd hydrogen bonds : bond 0.02575 ( 140) hydrogen bonds : angle 5.61808 ( 333) SS BOND : bond 0.00221 ( 21) SS BOND : angle 0.91386 ( 42) covalent geometry : bond 0.00289 ( 7760) covalent geometry : angle 0.65024 (10555) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 84 time to evaluate : 0.792 Fit side-chains revert: symmetry clash REVERT: A 94 VAL cc_start: 0.7475 (t) cc_final: 0.7212 (p) REVERT: A 351 ARG cc_start: 0.8190 (OUTLIER) cc_final: 0.7396 (mtt-85) REVERT: A 533 GLN cc_start: 0.8936 (mp10) cc_final: 0.8130 (mp10) REVERT: B 18 ARG cc_start: 0.8416 (ptm160) cc_final: 0.8010 (ptm-80) REVERT: B 19 VAL cc_start: 0.7416 (OUTLIER) cc_final: 0.7162 (m) REVERT: B 137 ASN cc_start: 0.8390 (t0) cc_final: 0.8158 (t0) REVERT: B 145 LYS cc_start: 0.8767 (OUTLIER) cc_final: 0.8358 (ptmm) REVERT: B 199 GLN cc_start: 0.8906 (tt0) cc_final: 0.8323 (tm130) REVERT: C 85 GLU cc_start: 0.8488 (mp0) cc_final: 0.8086 (tp30) REVERT: C 102 TYR cc_start: 0.7904 (m-80) cc_final: 0.7564 (m-80) REVERT: C 144 ASP cc_start: 0.7716 (m-30) cc_final: 0.7344 (t0) REVERT: C 195 ILE cc_start: 0.7058 (OUTLIER) cc_final: 0.6680 (mm) outliers start: 19 outliers final: 12 residues processed: 97 average time/residue: 1.0046 time to fit residues: 104.6281 Evaluate side-chains 98 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 82 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 351 ARG Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 145 LYS Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 167 ASP Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 34 MET Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 195 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 25 optimal weight: 0.9980 chunk 90 optimal weight: 7.9990 chunk 70 optimal weight: 0.7980 chunk 83 optimal weight: 0.8980 chunk 3 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 35 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 95 optimal weight: 6.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 137 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.165311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.123860 restraints weight = 10169.221| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 2.84 r_work: 0.3609 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3470 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.3317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7781 Z= 0.121 Angle : 0.664 10.382 10597 Z= 0.332 Chirality : 0.044 0.158 1174 Planarity : 0.005 0.051 1383 Dihedral : 4.737 23.013 1067 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 2.35 % Allowed : 21.53 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.27), residues: 981 helix: -2.58 (0.80), residues: 38 sheet: -0.45 (0.35), residues: 238 loop : -1.00 (0.24), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 169 HIS 0.003 0.001 HIS B 189 PHE 0.020 0.001 PHE A 73 TYR 0.010 0.001 TYR A 554 ARG 0.009 0.000 ARG A 143 Details of bonding type rmsd hydrogen bonds : bond 0.02601 ( 140) hydrogen bonds : angle 5.61099 ( 333) SS BOND : bond 0.00223 ( 21) SS BOND : angle 0.89314 ( 42) covalent geometry : bond 0.00295 ( 7760) covalent geometry : angle 0.66320 (10555) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 84 time to evaluate : 0.794 Fit side-chains revert: symmetry clash REVERT: A 94 VAL cc_start: 0.7460 (t) cc_final: 0.7205 (p) REVERT: A 351 ARG cc_start: 0.8178 (OUTLIER) cc_final: 0.7387 (mtt-85) REVERT: A 509 LEU cc_start: 0.4654 (OUTLIER) cc_final: 0.4339 (pp) REVERT: A 533 GLN cc_start: 0.8919 (mp10) cc_final: 0.8119 (mp10) REVERT: B 18 ARG cc_start: 0.8403 (ptm160) cc_final: 0.7984 (ptm-80) REVERT: B 19 VAL cc_start: 0.7432 (OUTLIER) cc_final: 0.7189 (m) REVERT: B 145 LYS cc_start: 0.8629 (OUTLIER) cc_final: 0.8289 (ptmm) REVERT: C 85 GLU cc_start: 0.8447 (mp0) cc_final: 0.8005 (tp30) REVERT: C 102 TYR cc_start: 0.7892 (m-80) cc_final: 0.7646 (m-80) REVERT: C 144 ASP cc_start: 0.7694 (m-30) cc_final: 0.7356 (t0) REVERT: C 195 ILE cc_start: 0.7051 (OUTLIER) cc_final: 0.6703 (mm) REVERT: C 206 LYS cc_start: 0.6653 (tptp) cc_final: 0.6423 (tptp) outliers start: 20 outliers final: 13 residues processed: 98 average time/residue: 0.9628 time to fit residues: 101.2518 Evaluate side-chains 99 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 81 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 351 ARG Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 145 LYS Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 167 ASP Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 34 MET Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 195 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 63 optimal weight: 0.9980 chunk 52 optimal weight: 7.9990 chunk 39 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 83 optimal weight: 0.0040 chunk 88 optimal weight: 10.0000 chunk 69 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 74 optimal weight: 20.0000 overall best weight: 1.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.163083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.117313 restraints weight = 10142.932| |-----------------------------------------------------------------------------| r_work (start): 0.3717 rms_B_bonded: 2.52 r_work: 0.3589 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3451 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.3421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7781 Z= 0.153 Angle : 0.701 10.494 10597 Z= 0.349 Chirality : 0.045 0.176 1174 Planarity : 0.005 0.055 1383 Dihedral : 4.900 23.751 1067 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 2.47 % Allowed : 21.41 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.27), residues: 981 helix: -2.62 (0.80), residues: 38 sheet: -0.41 (0.35), residues: 240 loop : -1.07 (0.24), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 169 HIS 0.003 0.001 HIS A 48 PHE 0.022 0.001 PHE A 73 TYR 0.014 0.001 TYR B 94 ARG 0.009 0.001 ARG A 143 Details of bonding type rmsd hydrogen bonds : bond 0.02824 ( 140) hydrogen bonds : angle 5.73974 ( 333) SS BOND : bond 0.00243 ( 21) SS BOND : angle 1.01237 ( 42) covalent geometry : bond 0.00375 ( 7760) covalent geometry : angle 0.69981 (10555) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7344.48 seconds wall clock time: 126 minutes 42.60 seconds (7602.60 seconds total)