Starting phenix.real_space_refine on Tue Jan 14 22:39:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9l1s_62753/01_2025/9l1s_62753.cif Found real_map, /net/cci-nas-00/data/ceres_data/9l1s_62753/01_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_62753/01_2025/9l1s_62753.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9l1s_62753/01_2025/9l1s_62753.map" model { file = "/net/cci-nas-00/data/ceres_data/9l1s_62753/01_2025/9l1s_62753.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9l1s_62753/01_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-5571/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: 4.73, 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: 1.66 Conformation dependent library (CDL) restraints added in 1.2 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: 0.97 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: 2.24 Time building geometry restraints manager: 1.98 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: 0.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 20.090 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.040 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:12.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.820 ------------------------------------------------------------------------------- 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 7760 Z= 0.165 Angle : 0.656 8.356 10555 Z= 0.369 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 *********************** 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 : 0.904 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: 1.2137 time to fit residues: 166.0500 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 : 0.880 ------------------------------------------------------------------------------- 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 7760 Z= 0.246 Angle : 0.678 8.742 10555 Z= 0.349 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 *********************** 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 : 0.874 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: 1.1570 time to fit residues: 132.9621 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 : 0.797 ------------------------------------------------------------------------------- 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: 0.9980 chunk 0 optimal weight: 7.9990 chunk 20 optimal weight: 4.9990 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: 1.2184 ------------------------------------------------------------------------------- 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 137 ASN ** B 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.164697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.118690 restraints weight = 10054.606| |-----------------------------------------------------------------------------| r_work (start): 0.3728 rms_B_bonded: 2.52 r_work: 0.3602 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3462 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7760 Z= 0.216 Angle : 0.636 10.033 10555 Z= 0.328 Chirality : 0.045 0.162 1174 Planarity : 0.005 0.074 1383 Dihedral : 4.944 25.017 1067 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 2.35 % Allowed : 13.76 % Favored : 83.88 % 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: -1.84 (0.26), residues: 981 helix: -3.91 (0.56), residues: 38 sheet: -0.94 (0.33), residues: 252 loop : -1.21 (0.23), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 452 HIS 0.004 0.001 HIS B 189 PHE 0.015 0.001 PHE A 73 TYR 0.012 0.001 TYR C 90 ARG 0.009 0.000 ARG B 18 *********************** 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: 20 poor density : 92 time to evaluate : 0.806 Fit side-chains REVERT: A 275 ASN cc_start: 0.7893 (OUTLIER) cc_final: 0.7665 (t0) REVERT: A 512 HIS cc_start: 0.6429 (OUTLIER) cc_final: 0.6213 (p90) REVERT: B 189 HIS cc_start: 0.7290 (m90) cc_final: 0.7010 (m-70) REVERT: B 199 GLN cc_start: 0.8801 (tt0) cc_final: 0.8505 (tm-30) REVERT: C 3 GLN cc_start: 0.7919 (pp30) cc_final: 0.7493 (pp30) REVERT: C 62 ARG cc_start: 0.8145 (ttp-110) cc_final: 0.7742 (ttp-110) REVERT: C 102 TYR cc_start: 0.7907 (m-80) cc_final: 0.7662 (m-80) REVERT: C 195 ILE cc_start: 0.6971 (OUTLIER) cc_final: 0.6602 (mm) outliers start: 20 outliers final: 9 residues processed: 106 average time/residue: 0.9967 time to fit residues: 113.5417 Evaluate side-chains 93 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 81 time to evaluate : 0.803 ------------------------------------------------------------------------------- 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 512 HIS Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 180 THR 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: 2.9990 chunk 87 optimal weight: 8.9990 chunk 10 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 chunk 90 optimal weight: 9.9990 chunk 91 optimal weight: 5.9990 chunk 66 optimal weight: 0.6980 chunk 92 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 86 optimal weight: 0.9990 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 75 GLN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 106 GLN B 38 GLN B 137 ASN ** B 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.160638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.114314 restraints weight = 10072.415| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 2.50 r_work: 0.3540 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3401 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.2794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 7760 Z= 0.338 Angle : 0.711 8.333 10555 Z= 0.365 Chirality : 0.047 0.172 1174 Planarity : 0.005 0.063 1383 Dihedral : 5.297 25.647 1067 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.77 % Favored : 91.23 % Rotamer: Outliers : 2.71 % Allowed : 16.00 % Favored : 81.29 % 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: -3.77 (0.62), residues: 38 sheet: -0.87 (0.33), residues: 262 loop : -1.22 (0.23), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 205 HIS 0.018 0.002 HIS A 512 PHE 0.017 0.002 PHE A 73 TYR 0.019 0.002 TYR B 94 ARG 0.009 0.001 ARG B 18 *********************** 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 107 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 84 time to evaluate : 0.786 Fit side-chains REVERT: A 282 MET cc_start: 0.7475 (mmm) cc_final: 0.7176 (mmm) REVERT: A 554 TYR cc_start: 0.6125 (p90) cc_final: 0.5778 (p90) REVERT: B 147 GLN cc_start: 0.8072 (pm20) cc_final: 0.7812 (pm20) REVERT: B 199 GLN cc_start: 0.8866 (tt0) cc_final: 0.8457 (tm-30) REVERT: C 3 GLN cc_start: 0.8033 (pp30) cc_final: 0.7659 (pp30) REVERT: C 85 GLU cc_start: 0.7899 (tp30) cc_final: 0.7681 (tp30) REVERT: C 102 TYR cc_start: 0.8001 (m-80) cc_final: 0.7716 (m-80) outliers start: 23 outliers final: 13 residues processed: 99 average time/residue: 1.1102 time to fit residues: 117.4106 Evaluate side-chains 90 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 0.801 ------------------------------------------------------------------------------- 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 541 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 44 optimal weight: 2.9990 chunk 89 optimal weight: 20.0000 chunk 80 optimal weight: 0.4980 chunk 9 optimal weight: 0.9980 chunk 35 optimal weight: 8.9990 chunk 41 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 chunk 82 optimal weight: 0.3980 chunk 33 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 GLN B 27 GLN 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 = 0.4274 r_free = 0.4274 target = 0.164703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.118647 restraints weight = 10017.821| |-----------------------------------------------------------------------------| r_work (start): 0.3728 rms_B_bonded: 2.57 r_work: 0.3598 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3458 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7760 Z= 0.180 Angle : 0.627 8.166 10555 Z= 0.319 Chirality : 0.044 0.153 1174 Planarity : 0.005 0.055 1383 Dihedral : 4.857 24.916 1067 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 2.71 % Allowed : 17.65 % Favored : 79.65 % 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: -1.64 (0.26), residues: 981 helix: -3.50 (0.61), residues: 38 sheet: -0.73 (0.33), residues: 252 loop : -1.12 (0.23), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 169 HIS 0.004 0.001 HIS B 189 PHE 0.016 0.001 PHE A 73 TYR 0.011 0.001 TYR C 90 ARG 0.009 0.000 ARG B 18 *********************** 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 106 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 83 time to evaluate : 0.790 Fit side-chains revert: symmetry clash REVERT: A 282 MET cc_start: 0.7332 (mmm) cc_final: 0.6989 (mmm) REVERT: A 509 LEU cc_start: 0.4540 (OUTLIER) cc_final: 0.3806 (pp) REVERT: B 147 GLN cc_start: 0.7888 (pm20) cc_final: 0.7666 (pm20) REVERT: B 199 GLN cc_start: 0.8878 (tt0) cc_final: 0.8432 (tm130) REVERT: C 3 GLN cc_start: 0.7969 (pp30) cc_final: 0.7448 (pp30) REVERT: C 85 GLU cc_start: 0.7986 (tp30) cc_final: 0.7722 (tp30) REVERT: C 102 TYR cc_start: 0.7934 (m-80) cc_final: 0.7659 (m-80) REVERT: C 195 ILE cc_start: 0.6992 (OUTLIER) cc_final: 0.6662 (mm) outliers start: 23 outliers final: 10 residues processed: 102 average time/residue: 0.9832 time to fit residues: 108.1535 Evaluate side-chains 88 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 0.854 ------------------------------------------------------------------------------- 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 156 SER 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 0.0170 chunk 63 optimal weight: 5.9990 chunk 55 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 chunk 68 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 93 optimal weight: 4.9990 chunk 53 optimal weight: 6.9990 chunk 36 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 overall best weight: 1.6026 ------------------------------------------------------------------------------- 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 137 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.161689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.115325 restraints weight = 10084.489| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 2.50 r_work: 0.3555 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3418 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7760 Z= 0.256 Angle : 0.665 8.441 10555 Z= 0.338 Chirality : 0.045 0.164 1174 Planarity : 0.005 0.051 1383 Dihedral : 5.016 24.014 1067 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.95 % Favored : 92.05 % Rotamer: Outliers : 3.41 % Allowed : 18.12 % Favored : 78.47 % 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: -1.66 (0.26), residues: 981 helix: -3.12 (0.71), residues: 38 sheet: -0.87 (0.32), residues: 262 loop : -1.10 (0.24), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 169 HIS 0.004 0.001 HIS B 189 PHE 0.018 0.002 PHE A 73 TYR 0.014 0.001 TYR B 94 ARG 0.010 0.000 ARG B 18 *********************** 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 114 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 85 time to evaluate : 0.787 Fit side-chains revert: symmetry clash REVERT: A 94 VAL cc_start: 0.7519 (t) cc_final: 0.7257 (p) REVERT: A 509 LEU cc_start: 0.4643 (OUTLIER) cc_final: 0.3959 (pp) REVERT: A 533 GLN cc_start: 0.8968 (mp10) cc_final: 0.8082 (mp10) REVERT: B 147 GLN cc_start: 0.7937 (pm20) cc_final: 0.7706 (pm20) REVERT: B 199 GLN cc_start: 0.8878 (tt0) cc_final: 0.8409 (tm130) REVERT: C 3 GLN cc_start: 0.8045 (pp30) cc_final: 0.7621 (pp30) REVERT: C 34 MET cc_start: 0.7523 (OUTLIER) cc_final: 0.7252 (mmm) REVERT: C 85 GLU cc_start: 0.7976 (tp30) cc_final: 0.7646 (tp30) REVERT: C 102 TYR cc_start: 0.7989 (m-80) cc_final: 0.7716 (m-80) REVERT: C 117 LYS cc_start: 0.8736 (mtpm) cc_final: 0.7589 (mtpp) REVERT: C 144 ASP cc_start: 0.7685 (OUTLIER) cc_final: 0.7319 (t0) outliers start: 29 outliers final: 14 residues processed: 102 average time/residue: 0.9767 time to fit residues: 107.3965 Evaluate side-chains 100 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 83 time to evaluate : 0.818 ------------------------------------------------------------------------------- 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 509 LEU Chi-restraints excluded: chain A residue 541 VAL 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 34 MET 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 97 optimal weight: 6.9990 chunk 56 optimal weight: 9.9990 chunk 52 optimal weight: 6.9990 chunk 83 optimal weight: 0.8980 chunk 68 optimal weight: 5.9990 chunk 41 optimal weight: 0.0970 chunk 45 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 32 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- 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 176 ASN B 137 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.161476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.119510 restraints weight = 10041.983| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 2.91 r_work: 0.3545 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3401 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.3161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7760 Z= 0.253 Angle : 0.659 8.565 10555 Z= 0.335 Chirality : 0.045 0.208 1174 Planarity : 0.005 0.050 1383 Dihedral : 5.043 25.200 1067 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 3.18 % Allowed : 18.82 % Favored : 78.00 % 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: -1.59 (0.26), residues: 981 helix: -2.97 (0.73), residues: 38 sheet: -0.56 (0.34), residues: 239 loop : -1.17 (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 A 48 PHE 0.019 0.002 PHE A 73 TYR 0.014 0.001 TYR B 94 ARG 0.012 0.000 ARG B 18 *********************** 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 107 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 80 time to evaluate : 0.818 Fit side-chains REVERT: A 351 ARG cc_start: 0.8205 (OUTLIER) cc_final: 0.7468 (mtt-85) REVERT: B 19 VAL cc_start: 0.7385 (OUTLIER) cc_final: 0.7124 (p) REVERT: B 147 GLN cc_start: 0.7883 (pm20) cc_final: 0.7672 (pm20) REVERT: B 189 HIS cc_start: 0.7247 (m90) cc_final: 0.6784 (m-70) REVERT: B 199 GLN cc_start: 0.8879 (tt0) cc_final: 0.8316 (tm130) REVERT: C 85 GLU cc_start: 0.8038 (tp30) cc_final: 0.7731 (tp30) REVERT: C 102 TYR cc_start: 0.7971 (m-80) cc_final: 0.7709 (m-80) REVERT: C 117 LYS cc_start: 0.8775 (mtpm) cc_final: 0.7708 (mtpp) REVERT: C 144 ASP cc_start: 0.7687 (OUTLIER) cc_final: 0.7269 (t0) outliers start: 27 outliers final: 13 residues processed: 99 average time/residue: 1.0885 time to fit residues: 115.7665 Evaluate side-chains 94 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 78 time to evaluate : 0.809 ------------------------------------------------------------------------------- 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 B residue 19 VAL 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: 0.9990 chunk 30 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 48 optimal weight: 4.9990 chunk 32 optimal weight: 0.6980 chunk 29 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 52 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 81 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 491 GLN B 137 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.164352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.123637 restraints weight = 10176.533| |-----------------------------------------------------------------------------| r_work (start): 0.3790 rms_B_bonded: 2.98 r_work: 0.3599 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3460 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7760 Z= 0.185 Angle : 0.637 10.359 10555 Z= 0.319 Chirality : 0.044 0.165 1174 Planarity : 0.005 0.052 1383 Dihedral : 4.767 23.074 1067 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 2.24 % Allowed : 20.12 % Favored : 77.65 % 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: -1.46 (0.27), residues: 981 helix: -2.67 (0.80), residues: 38 sheet: -0.50 (0.34), residues: 239 loop : -1.08 (0.23), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 169 HIS 0.003 0.001 HIS B 189 PHE 0.019 0.001 PHE A 73 TYR 0.011 0.001 TYR A 554 ARG 0.012 0.000 ARG B 18 *********************** 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: 19 poor density : 86 time to evaluate : 0.788 Fit side-chains revert: symmetry clash REVERT: A 94 VAL cc_start: 0.7476 (t) cc_final: 0.7203 (p) REVERT: A 351 ARG cc_start: 0.8224 (OUTLIER) cc_final: 0.7440 (mtt-85) REVERT: A 533 GLN cc_start: 0.8941 (mp10) cc_final: 0.8094 (mp10) REVERT: B 137 ASN cc_start: 0.8375 (t0) cc_final: 0.8042 (t160) REVERT: B 199 GLN cc_start: 0.8874 (tt0) cc_final: 0.8303 (tm130) REVERT: C 34 MET cc_start: 0.7245 (OUTLIER) cc_final: 0.6922 (mmm) REVERT: C 85 GLU cc_start: 0.7962 (tp30) cc_final: 0.7720 (tp30) REVERT: C 102 TYR cc_start: 0.7921 (m-80) cc_final: 0.7694 (m-80) REVERT: C 117 LYS cc_start: 0.8798 (mtpm) cc_final: 0.7752 (mtpp) REVERT: C 144 ASP cc_start: 0.7672 (m-30) cc_final: 0.7292 (t0) REVERT: C 195 ILE cc_start: 0.7010 (OUTLIER) cc_final: 0.6688 (mp) outliers start: 19 outliers final: 11 residues processed: 100 average time/residue: 1.0108 time to fit residues: 108.6134 Evaluate side-chains 96 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 0.845 ------------------------------------------------------------------------------- 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 272 VAL Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 351 ARG Chi-restraints excluded: chain B residue 126 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 92 optimal weight: 8.9990 chunk 13 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 24 optimal weight: 0.0470 chunk 44 optimal weight: 5.9990 chunk 26 optimal weight: 0.9990 chunk 9 optimal weight: 6.9990 chunk 69 optimal weight: 0.9980 chunk 95 optimal weight: 0.8980 overall best weight: 0.7680 ------------------------------------------------------------------------------- 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 = 0.4280 r_free = 0.4280 target = 0.164891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.124391 restraints weight = 10249.361| |-----------------------------------------------------------------------------| r_work (start): 0.3801 rms_B_bonded: 2.99 r_work: 0.3612 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3473 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.3230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7760 Z= 0.188 Angle : 0.645 9.878 10555 Z= 0.324 Chirality : 0.044 0.171 1174 Planarity : 0.005 0.051 1383 Dihedral : 4.695 23.182 1067 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 2.59 % Allowed : 20.00 % Favored : 77.41 % 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: -1.42 (0.27), residues: 981 helix: -2.58 (0.81), residues: 38 sheet: -0.50 (0.34), residues: 239 loop : -1.05 (0.23), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 169 HIS 0.003 0.001 HIS A 48 PHE 0.019 0.001 PHE A 73 TYR 0.010 0.001 TYR A 554 ARG 0.012 0.000 ARG B 18 *********************** 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 109 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 87 time to evaluate : 0.858 Fit side-chains revert: symmetry clash REVERT: A 54 GLN cc_start: 0.7437 (OUTLIER) cc_final: 0.7044 (mm-40) REVERT: A 94 VAL cc_start: 0.7598 (t) cc_final: 0.7300 (p) REVERT: A 351 ARG cc_start: 0.8186 (OUTLIER) cc_final: 0.7400 (mtt-85) REVERT: A 509 LEU cc_start: 0.4452 (OUTLIER) cc_final: 0.4081 (pp) REVERT: A 533 GLN cc_start: 0.8975 (mp10) cc_final: 0.8084 (mp10) REVERT: B 19 VAL cc_start: 0.7429 (OUTLIER) cc_final: 0.7181 (m) REVERT: B 137 ASN cc_start: 0.8423 (t0) cc_final: 0.8125 (t0) REVERT: B 181 LEU cc_start: 0.6344 (OUTLIER) cc_final: 0.5990 (pp) REVERT: C 85 GLU cc_start: 0.7937 (tp30) cc_final: 0.7730 (tp30) REVERT: C 102 TYR cc_start: 0.7900 (m-80) cc_final: 0.7682 (m-80) REVERT: C 117 LYS cc_start: 0.8833 (mtpm) cc_final: 0.7826 (mtpp) REVERT: C 144 ASP cc_start: 0.7719 (m-30) cc_final: 0.7340 (t0) REVERT: C 195 ILE cc_start: 0.7083 (OUTLIER) cc_final: 0.6776 (mp) outliers start: 22 outliers final: 13 residues processed: 103 average time/residue: 1.0676 time to fit residues: 117.4865 Evaluate side-chains 100 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 81 time to evaluate : 0.859 ------------------------------------------------------------------------------- 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 54 GLN 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 19 VAL Chi-restraints excluded: chain B residue 126 LYS Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 181 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 25 optimal weight: 0.7980 chunk 90 optimal weight: 20.0000 chunk 70 optimal weight: 0.2980 chunk 83 optimal weight: 0.0370 chunk 3 optimal weight: 0.5980 chunk 18 optimal weight: 6.9990 chunk 46 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 95 optimal weight: 8.9990 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.167349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.121937 restraints weight = 10196.919| |-----------------------------------------------------------------------------| r_work (start): 0.3771 rms_B_bonded: 2.61 r_work: 0.3643 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3502 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.3304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7760 Z= 0.174 Angle : 0.654 10.343 10555 Z= 0.323 Chirality : 0.044 0.157 1174 Planarity : 0.005 0.057 1383 Dihedral : 4.532 23.216 1067 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 7.71 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: -1.31 (0.27), residues: 981 helix: -2.49 (0.82), residues: 38 sheet: -0.33 (0.34), residues: 241 loop : -1.01 (0.24), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 169 HIS 0.004 0.000 HIS B 189 PHE 0.018 0.001 PHE A 73 TYR 0.014 0.001 TYR B 140 ARG 0.013 0.000 ARG B 18 ********************** 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 106 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 87 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 GLN cc_start: 0.7332 (OUTLIER) cc_final: 0.6916 (mm-40) REVERT: A 94 VAL cc_start: 0.7290 (t) cc_final: 0.7054 (p) REVERT: A 351 ARG cc_start: 0.8127 (OUTLIER) cc_final: 0.7302 (mtt-85) REVERT: A 533 GLN cc_start: 0.8946 (mp10) cc_final: 0.8088 (mp10) REVERT: B 19 VAL cc_start: 0.7384 (OUTLIER) cc_final: 0.7141 (m) REVERT: B 118 PHE cc_start: 0.7708 (m-80) cc_final: 0.7403 (m-80) REVERT: B 137 ASN cc_start: 0.8519 (t0) cc_final: 0.8249 (t0) REVERT: C 85 GLU cc_start: 0.7937 (tp30) cc_final: 0.7722 (tp30) REVERT: C 102 TYR cc_start: 0.7835 (m-80) cc_final: 0.7518 (m-80) REVERT: C 117 LYS cc_start: 0.8840 (mtpm) cc_final: 0.7857 (mtpp) REVERT: C 144 ASP cc_start: 0.7709 (m-30) cc_final: 0.7323 (t0) REVERT: C 195 ILE cc_start: 0.7123 (OUTLIER) cc_final: 0.6806 (mm) outliers start: 19 outliers final: 10 residues processed: 101 average time/residue: 1.0390 time to fit residues: 112.1048 Evaluate side-chains 96 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 0.945 ------------------------------------------------------------------------------- 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 54 GLN Chi-restraints excluded: chain A residue 55 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 63 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 chunk 88 optimal weight: 9.9990 chunk 69 optimal weight: 6.9990 chunk 46 optimal weight: 4.9990 chunk 74 optimal weight: 10.0000 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 ASN A 97 GLN A 176 ASN A 491 GLN B 137 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.161779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.115630 restraints weight = 10180.383| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 2.52 r_work: 0.3566 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3428 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.3517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 7760 Z= 0.297 Angle : 0.729 10.336 10555 Z= 0.364 Chirality : 0.046 0.202 1174 Planarity : 0.005 0.063 1383 Dihedral : 4.968 24.033 1067 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 2.71 % Allowed : 20.82 % Favored : 76.47 % 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: -2.72 (0.79), residues: 38 sheet: -0.42 (0.34), residues: 246 loop : -1.06 (0.24), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP A 169 HIS 0.003 0.001 HIS B 189 PHE 0.021 0.002 PHE A 73 TYR 0.017 0.002 TYR B 94 ARG 0.014 0.001 ARG B 18 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7271.62 seconds wall clock time: 129 minutes 24.71 seconds (7764.71 seconds total)