Starting phenix.real_space_refine on Wed Mar 12 07:46:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9l1s_62753/03_2025/9l1s_62753.cif Found real_map, /net/cci-nas-00/data/ceres_data/9l1s_62753/03_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_62753/03_2025/9l1s_62753.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9l1s_62753/03_2025/9l1s_62753.map" model { file = "/net/cci-nas-00/data/ceres_data/9l1s_62753/03_2025/9l1s_62753.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9l1s_62753/03_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-5624/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: 4.44, per 1000 atoms: 0.59 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: 1.55 Conformation dependent library (CDL) restraints added in 983.1 milliseconds 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: 0.91 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: 2.10 Time building geometry restraints manager: 1.92 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: 0.530 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: 0.270 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 19.600 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:12.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.900 ------------------------------------------------------------------------------- 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 : 0.876 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: 1.1260 time to fit residues: 154.2018 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 : 0.830 ------------------------------------------------------------------------------- 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 = 9885.912| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 3.02 r_work: 0.3577 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 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 : 0.853 Fit side-chains revert: symmetry clash REVERT: A 554 TYR cc_start: 0.6592 (p90) cc_final: 0.6207 (p90) REVERT: B 147 GLN cc_start: 0.7967 (pm20) cc_final: 0.7711 (pm20) REVERT: C 3 GLN cc_start: 0.7856 (pp30) cc_final: 0.7495 (pp30) REVERT: C 99 TYR cc_start: 0.8327 (p90) cc_final: 0.8116 (p90) REVERT: C 102 TYR cc_start: 0.7774 (m-80) cc_final: 0.7503 (m-80) outliers start: 17 outliers final: 7 residues processed: 108 average time/residue: 1.0652 time to fit residues: 122.7098 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 : 0.734 ------------------------------------------------------------------------------- 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: 0.8980 chunk 68 optimal weight: 5.9990 chunk 52 optimal weight: 0.5980 chunk 0 optimal weight: 7.9990 chunk 20 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 chunk 77 optimal weight: 10.0000 chunk 29 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 164 GLN A 176 ASN A 275 ASN A 512 HIS B 137 ASN ** B 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.165995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.119610 restraints weight = 10031.193| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 2.61 r_work: 0.3620 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3480 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7760 Z= 0.187 Angle : 0.619 9.848 10555 Z= 0.318 Chirality : 0.044 0.160 1174 Planarity : 0.005 0.074 1383 Dihedral : 4.817 24.437 1067 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 2.00 % Allowed : 13.88 % Favored : 84.12 % 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: -1.81 (0.26), residues: 981 helix: -3.92 (0.55), residues: 38 sheet: -0.94 (0.33), residues: 252 loop : -1.18 (0.23), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 452 HIS 0.004 0.001 HIS B 189 PHE 0.014 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 110 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 93 time to evaluate : 0.773 Fit side-chains REVERT: A 275 ASN cc_start: 0.7931 (OUTLIER) cc_final: 0.7713 (t0) REVERT: A 512 HIS cc_start: 0.6349 (OUTLIER) cc_final: 0.6122 (p90) REVERT: B 147 GLN cc_start: 0.8116 (pm20) cc_final: 0.7910 (pm20) REVERT: B 189 HIS cc_start: 0.7238 (m90) cc_final: 0.6964 (m-70) REVERT: B 199 GLN cc_start: 0.8817 (tt0) cc_final: 0.8515 (tm130) REVERT: C 3 GLN cc_start: 0.7840 (pp30) cc_final: 0.7406 (pp30) REVERT: C 85 GLU cc_start: 0.7881 (tp30) cc_final: 0.7668 (tp30) REVERT: C 102 TYR cc_start: 0.7854 (m-80) cc_final: 0.7615 (m-80) REVERT: C 195 ILE cc_start: 0.7057 (OUTLIER) cc_final: 0.6718 (mm) outliers start: 17 outliers final: 6 residues processed: 104 average time/residue: 0.9714 time to fit residues: 108.4339 Evaluate side-chains 93 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 84 time to evaluate : 0.819 ------------------------------------------------------------------------------- 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 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 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: 0.6980 chunk 60 optimal weight: 3.9990 chunk 90 optimal weight: 20.0000 chunk 91 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 chunk 92 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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** B 137 ASN ** B 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.161708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.118005 restraints weight = 10040.577| |-----------------------------------------------------------------------------| r_work (start): 0.3725 rms_B_bonded: 2.71 r_work: 0.3567 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3427 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7760 Z= 0.292 Angle : 0.684 8.028 10555 Z= 0.351 Chirality : 0.046 0.166 1174 Planarity : 0.005 0.062 1383 Dihedral : 5.108 24.539 1067 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.46 % Favored : 91.54 % Rotamer: Outliers : 2.24 % Allowed : 16.00 % Favored : 81.76 % 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: -1.78 (0.26), residues: 981 helix: -3.75 (0.61), residues: 38 sheet: -0.78 (0.33), residues: 252 loop : -1.23 (0.23), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 169 HIS 0.014 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 *********************** 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: 19 poor density : 85 time to evaluate : 0.782 Fit side-chains REVERT: A 509 LEU cc_start: 0.4696 (OUTLIER) cc_final: 0.4190 (pp) REVERT: A 554 TYR cc_start: 0.6072 (p90) cc_final: 0.5779 (p90) REVERT: B 147 GLN cc_start: 0.8102 (pm20) cc_final: 0.7741 (pm20) REVERT: B 199 GLN cc_start: 0.8872 (tt0) cc_final: 0.8456 (tm-30) REVERT: C 3 GLN cc_start: 0.8019 (pp30) cc_final: 0.7560 (pp30) REVERT: C 34 MET cc_start: 0.7464 (OUTLIER) cc_final: 0.7243 (mmm) REVERT: C 85 GLU cc_start: 0.7943 (tp30) cc_final: 0.7727 (tp30) REVERT: C 102 TYR cc_start: 0.7977 (m-80) cc_final: 0.7708 (m-80) REVERT: C 195 ILE cc_start: 0.7043 (OUTLIER) cc_final: 0.6697 (mm) outliers start: 19 outliers final: 12 residues processed: 97 average time/residue: 0.9842 time to fit residues: 102.6390 Evaluate side-chains 94 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 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 146 THR 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 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 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: 0.0570 chunk 89 optimal weight: 30.0000 chunk 80 optimal weight: 0.9990 chunk 9 optimal weight: 6.9990 chunk 35 optimal weight: 9.9990 chunk 41 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 chunk 82 optimal weight: 0.9980 chunk 33 optimal weight: 8.9990 chunk 94 optimal weight: 10.0000 overall best weight: 0.7900 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.165347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.123924 restraints weight = 10012.533| |-----------------------------------------------------------------------------| r_work (start): 0.3793 rms_B_bonded: 2.92 r_work: 0.3594 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3451 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.2696 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 : 0.622 8.467 10555 Z= 0.318 Chirality : 0.044 0.153 1174 Planarity : 0.005 0.055 1383 Dihedral : 4.785 24.578 1067 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 2.82 % Allowed : 17.29 % Favored : 79.88 % 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: -1.61 (0.26), residues: 981 helix: -3.54 (0.61), residues: 38 sheet: -0.61 (0.33), residues: 247 loop : -1.14 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 169 HIS 0.004 0.001 HIS B 189 PHE 0.017 0.001 PHE A 73 TYR 0.009 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 109 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 85 time to evaluate : 0.868 Fit side-chains revert: symmetry clash REVERT: A 509 LEU cc_start: 0.4581 (OUTLIER) cc_final: 0.3894 (pp) REVERT: B 199 GLN cc_start: 0.8887 (tt0) cc_final: 0.8422 (tm-30) REVERT: C 3 GLN cc_start: 0.7926 (pp30) cc_final: 0.7391 (pp30) REVERT: C 85 GLU cc_start: 0.7977 (tp30) cc_final: 0.7647 (tp30) REVERT: C 102 TYR cc_start: 0.7944 (m-80) cc_final: 0.7697 (m-80) REVERT: C 195 ILE cc_start: 0.6980 (OUTLIER) cc_final: 0.6673 (mm) outliers start: 24 outliers final: 13 residues processed: 103 average time/residue: 1.0120 time to fit residues: 111.9835 Evaluate side-chains 91 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 76 time to evaluate : 0.786 ------------------------------------------------------------------------------- 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 171 ASP 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 180 THR Chi-restraints excluded: chain C residue 138 LEU 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: 4.9990 chunk 63 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 chunk 4 optimal weight: 0.7980 chunk 76 optimal weight: 5.9990 chunk 68 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 93 optimal weight: 0.7980 chunk 53 optimal weight: 0.4980 chunk 36 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 overall best weight: 2.2184 ------------------------------------------------------------------------------- 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 38 GLN B 137 ASN C 39 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.160161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.113268 restraints weight = 10126.770| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 2.60 r_work: 0.3523 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3385 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.3116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 7760 Z= 0.324 Angle : 0.710 8.570 10555 Z= 0.362 Chirality : 0.047 0.154 1174 Planarity : 0.005 0.052 1383 Dihedral : 5.234 24.789 1067 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.26 % Favored : 91.74 % Rotamer: Outliers : 3.53 % Allowed : 17.41 % Favored : 79.06 % 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: -1.65 (0.26), residues: 981 helix: -3.27 (0.68), residues: 38 sheet: -0.83 (0.32), residues: 267 loop : -1.09 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 169 HIS 0.005 0.001 HIS B 189 PHE 0.019 0.002 PHE A 73 TYR 0.019 0.002 TYR B 94 ARG 0.010 0.001 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 115 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 85 time to evaluate : 0.869 Fit side-chains revert: symmetry clash REVERT: A 509 LEU cc_start: 0.5043 (OUTLIER) cc_final: 0.4461 (pp) REVERT: A 533 GLN cc_start: 0.8938 (mp10) cc_final: 0.8061 (mp10) REVERT: B 145 LYS cc_start: 0.8850 (OUTLIER) cc_final: 0.8519 (ptmm) REVERT: B 199 GLN cc_start: 0.8890 (tt0) cc_final: 0.8434 (tm-30) REVERT: C 3 GLN cc_start: 0.8096 (pp30) cc_final: 0.7773 (pp30) REVERT: C 34 MET cc_start: 0.7585 (OUTLIER) cc_final: 0.7343 (mmm) REVERT: C 85 GLU cc_start: 0.8054 (tp30) cc_final: 0.7836 (tp30) REVERT: C 102 TYR cc_start: 0.8031 (m-80) cc_final: 0.7771 (m-80) outliers start: 30 outliers final: 12 residues processed: 104 average time/residue: 0.9260 time to fit residues: 103.9010 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 : 0.841 ------------------------------------------------------------------------------- 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 97 optimal weight: 20.0000 chunk 56 optimal weight: 9.9990 chunk 52 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 69 optimal weight: 5.9990 chunk 17 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 137 ASN ** B 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.160560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.113781 restraints weight = 10074.070| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 2.62 r_work: 0.3536 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3397 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.3200 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= 0.289 Angle : 0.687 8.836 10555 Z= 0.351 Chirality : 0.046 0.145 1174 Planarity : 0.005 0.052 1383 Dihedral : 5.176 26.907 1067 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 2.94 % Allowed : 19.29 % 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: -1.61 (0.26), residues: 981 helix: -2.99 (0.74), residues: 38 sheet: -0.67 (0.33), residues: 254 loop : -1.15 (0.23), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 205 HIS 0.004 0.001 HIS A 48 PHE 0.021 0.002 PHE A 73 TYR 0.014 0.002 TYR B 94 ARG 0.012 0.001 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 105 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 80 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 509 LEU cc_start: 0.4939 (OUTLIER) cc_final: 0.4354 (pp) REVERT: B 19 VAL cc_start: 0.7487 (OUTLIER) cc_final: 0.7248 (p) REVERT: B 145 LYS cc_start: 0.8874 (OUTLIER) cc_final: 0.8513 (ptmm) REVERT: B 199 GLN cc_start: 0.8854 (tt0) cc_final: 0.8311 (tm130) REVERT: C 34 MET cc_start: 0.7503 (OUTLIER) cc_final: 0.7258 (mmm) REVERT: C 102 TYR cc_start: 0.8056 (m-80) cc_final: 0.7792 (m-80) REVERT: C 144 ASP cc_start: 0.7703 (m-30) cc_final: 0.7322 (t0) outliers start: 25 outliers final: 12 residues processed: 97 average time/residue: 0.9909 time to fit residues: 103.5100 Evaluate side-chains 95 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 79 time to evaluate : 0.899 ------------------------------------------------------------------------------- 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 94 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 48 optimal weight: 5.9990 chunk 32 optimal weight: 0.9980 chunk 29 optimal weight: 6.9990 chunk 66 optimal weight: 9.9990 chunk 52 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 2 optimal weight: 4.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN B 137 ASN ** B 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.163262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.117462 restraints weight = 10188.610| |-----------------------------------------------------------------------------| r_work (start): 0.3717 rms_B_bonded: 2.53 r_work: 0.3588 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3448 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.3212 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= 0.207 Angle : 0.661 9.821 10555 Z= 0.334 Chirality : 0.044 0.139 1174 Planarity : 0.005 0.050 1383 Dihedral : 4.908 24.299 1067 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 2.47 % Allowed : 20.12 % 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: -1.48 (0.27), residues: 981 helix: -2.68 (0.81), residues: 38 sheet: -0.48 (0.35), residues: 239 loop : -1.11 (0.23), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 169 HIS 0.003 0.001 HIS B 189 PHE 0.019 0.001 PHE A 73 TYR 0.010 0.001 TYR B 94 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: 21 poor density : 84 time to evaluate : 0.888 Fit side-chains revert: symmetry clash REVERT: A 533 GLN cc_start: 0.8952 (mp10) cc_final: 0.8117 (mp10) REVERT: B 137 ASN cc_start: 0.8322 (t0) cc_final: 0.8004 (t160) REVERT: B 145 LYS cc_start: 0.8831 (OUTLIER) cc_final: 0.8456 (ptmm) REVERT: B 189 HIS cc_start: 0.7237 (m90) cc_final: 0.6900 (m90) REVERT: B 199 GLN cc_start: 0.8885 (tt0) cc_final: 0.8320 (tm130) REVERT: C 34 MET cc_start: 0.7329 (OUTLIER) cc_final: 0.7100 (mmm) REVERT: C 102 TYR cc_start: 0.7921 (m-80) cc_final: 0.7676 (m-80) REVERT: C 144 ASP cc_start: 0.7696 (m-30) cc_final: 0.7281 (t0) REVERT: C 195 ILE cc_start: 0.6965 (OUTLIER) cc_final: 0.6593 (mm) outliers start: 21 outliers final: 12 residues processed: 96 average time/residue: 1.0268 time to fit residues: 105.7219 Evaluate side-chains 93 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 78 time to evaluate : 0.849 ------------------------------------------------------------------------------- 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 92 optimal weight: 10.0000 chunk 13 optimal weight: 2.9990 chunk 30 optimal weight: 0.2980 chunk 80 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 24 optimal weight: 0.3980 chunk 44 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 9 optimal weight: 6.9990 chunk 69 optimal weight: 0.8980 chunk 95 optimal weight: 0.3980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 ASN ** B 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.164622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.118680 restraints weight = 10205.493| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 2.59 r_work: 0.3602 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3461 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.3234 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= 0.189 Angle : 0.656 9.885 10555 Z= 0.329 Chirality : 0.044 0.140 1174 Planarity : 0.005 0.051 1383 Dihedral : 4.785 24.145 1067 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 2.59 % Allowed : 19.88 % Favored : 77.53 % 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: -1.40 (0.27), residues: 981 helix: -2.62 (0.81), residues: 38 sheet: -0.44 (0.35), residues: 239 loop : -1.05 (0.24), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 169 HIS 0.003 0.001 HIS A 48 PHE 0.019 0.001 PHE A 73 TYR 0.019 0.001 TYR B 140 ARG 0.013 0.001 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 : 0.675 Fit side-chains revert: symmetry clash REVERT: A 94 VAL cc_start: 0.7449 (t) cc_final: 0.7188 (p) REVERT: A 351 ARG cc_start: 0.8213 (OUTLIER) cc_final: 0.7429 (mtt-85) REVERT: A 533 GLN cc_start: 0.8915 (mp10) cc_final: 0.8115 (mp10) REVERT: B 19 VAL cc_start: 0.7404 (OUTLIER) cc_final: 0.7185 (p) REVERT: B 145 LYS cc_start: 0.8792 (OUTLIER) cc_final: 0.8379 (ptmm) REVERT: B 189 HIS cc_start: 0.7113 (m90) cc_final: 0.6736 (m90) REVERT: B 199 GLN cc_start: 0.8892 (tt0) cc_final: 0.8322 (tm130) REVERT: C 34 MET cc_start: 0.7338 (OUTLIER) cc_final: 0.7107 (mmm) REVERT: C 85 GLU cc_start: 0.8478 (mp0) cc_final: 0.8101 (tp30) REVERT: C 102 TYR cc_start: 0.7932 (m-80) cc_final: 0.7701 (m-80) REVERT: C 144 ASP cc_start: 0.7650 (m-30) cc_final: 0.7243 (t0) REVERT: C 195 ILE cc_start: 0.6955 (OUTLIER) cc_final: 0.6593 (mm) outliers start: 22 outliers final: 11 residues processed: 103 average time/residue: 0.9660 time to fit residues: 106.7041 Evaluate side-chains 100 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 84 time to evaluate : 0.783 ------------------------------------------------------------------------------- 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: 0.5980 chunk 90 optimal weight: 8.9990 chunk 70 optimal weight: 10.0000 chunk 83 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 59 optimal weight: 0.6980 chunk 39 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 137 ASN ** B 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.163909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.117307 restraints weight = 10149.011| |-----------------------------------------------------------------------------| r_work (start): 0.3717 rms_B_bonded: 2.62 r_work: 0.3590 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3450 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.3359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7760 Z= 0.212 Angle : 0.674 10.326 10555 Z= 0.337 Chirality : 0.045 0.174 1174 Planarity : 0.005 0.057 1383 Dihedral : 4.827 23.186 1067 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 2.12 % Allowed : 20.94 % Favored : 76.94 % 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: -1.39 (0.27), residues: 981 helix: -2.58 (0.81), residues: 38 sheet: -0.42 (0.34), residues: 241 loop : -1.05 (0.24), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 169 HIS 0.003 0.001 HIS A 48 PHE 0.021 0.001 PHE A 73 TYR 0.011 0.001 TYR B 94 ARG 0.013 0.001 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 102 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 84 time to evaluate : 0.991 Fit side-chains revert: symmetry clash REVERT: A 94 VAL cc_start: 0.7483 (t) cc_final: 0.7239 (p) REVERT: A 351 ARG cc_start: 0.8222 (OUTLIER) cc_final: 0.7443 (mtt-85) REVERT: A 533 GLN cc_start: 0.8921 (mp10) cc_final: 0.8118 (mp10) REVERT: B 19 VAL cc_start: 0.7361 (OUTLIER) cc_final: 0.7140 (p) REVERT: B 106 ILE cc_start: 0.7402 (pp) cc_final: 0.6934 (mp) REVERT: B 118 PHE cc_start: 0.7786 (m-80) cc_final: 0.7394 (m-80) REVERT: B 137 ASN cc_start: 0.8446 (t0) cc_final: 0.8131 (t160) REVERT: B 145 LYS cc_start: 0.8691 (OUTLIER) cc_final: 0.8328 (ptmm) REVERT: C 34 MET cc_start: 0.7400 (OUTLIER) cc_final: 0.7163 (mmm) REVERT: C 85 GLU cc_start: 0.8440 (mp0) cc_final: 0.7992 (tp30) REVERT: C 102 TYR cc_start: 0.7915 (m-80) cc_final: 0.7684 (m-80) REVERT: C 144 ASP cc_start: 0.7664 (m-30) cc_final: 0.7279 (t0) REVERT: C 195 ILE cc_start: 0.7012 (OUTLIER) cc_final: 0.6661 (mm) outliers start: 18 outliers final: 12 residues processed: 96 average time/residue: 1.0158 time to fit residues: 104.7646 Evaluate side-chains 99 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 82 time to evaluate : 0.840 ------------------------------------------------------------------------------- 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 124 LEU 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: 0.8980 chunk 52 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 83 optimal weight: 0.0470 chunk 88 optimal weight: 7.9990 chunk 69 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 74 optimal weight: 9.9990 overall best weight: 0.7480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.165787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.124503 restraints weight = 10096.308| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 3.00 r_work: 0.3617 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3476 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.3396 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= 0.186 Angle : 0.670 10.452 10555 Z= 0.334 Chirality : 0.044 0.155 1174 Planarity : 0.005 0.056 1383 Dihedral : 4.707 23.226 1067 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % 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: -1.33 (0.27), residues: 981 helix: -2.55 (0.81), residues: 38 sheet: -0.36 (0.35), residues: 241 loop : -1.02 (0.24), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 169 HIS 0.003 0.001 HIS A 48 PHE 0.019 0.001 PHE A 73 TYR 0.009 0.001 TYR C 90 ARG 0.013 0.001 ARG B 18 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7425.74 seconds wall clock time: 126 minutes 46.61 seconds (7606.61 seconds total)