Starting phenix.real_space_refine on Wed Sep 17 11:59:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rs7_54212/09_2025/9rs7_54212.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rs7_54212/09_2025/9rs7_54212.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/9rs7_54212/09_2025/9rs7_54212.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rs7_54212/09_2025/9rs7_54212.map" model { file = "/net/cci-nas-00/data/ceres_data/9rs7_54212/09_2025/9rs7_54212.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rs7_54212/09_2025/9rs7_54212.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 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 27 5.16 5 C 5274 2.51 5 N 1437 2.21 5 O 1512 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8250 Number of models: 1 Model: "" Number of chains: 3 Chain: "C" Number of atoms: 1283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1283 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 4, 'TRANS': 157} Chain breaks: 2 Chain: "A" Number of atoms: 3410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3410 Classifications: {'peptide': 437} Link IDs: {'PTRANS': 22, 'TRANS': 414} Chain breaks: 2 Chain: "B" Number of atoms: 3557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3557 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 25, 'TRANS': 427} Chain breaks: 9 Time building chain proxies: 2.22, per 1000 atoms: 0.27 Number of scatterers: 8250 At special positions: 0 Unit cell: (68.68, 108.12, 123.76, 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 27 16.00 O 1512 8.00 N 1437 7.00 C 5274 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.70 Conformation dependent library (CDL) restraints added in 437.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1942 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 7 sheets defined 43.2% alpha, 18.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'C' and resid 67 through 72 removed outlier: 4.192A pdb=" N SER C 72 " --> pdb=" O GLU C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 78 removed outlier: 3.910A pdb=" N PHE C 77 " --> pdb=" O LEU C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 98 removed outlier: 4.291A pdb=" N PHE C 96 " --> pdb=" O ASN C 92 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASP C 97 " --> pdb=" O ALA C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 110 Processing helix chain 'C' and resid 137 through 149 removed outlier: 3.784A pdb=" N PHE C 144 " --> pdb=" O ARG C 140 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N CYS C 145 " --> pdb=" O ALA C 141 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS C 148 " --> pdb=" O PHE C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 167 Processing helix chain 'C' and resid 168 through 177 removed outlier: 4.010A pdb=" N MET C 177 " --> pdb=" O ARG C 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 221 Processing helix chain 'A' and resid 241 through 262 removed outlier: 5.126A pdb=" N SER A 247 " --> pdb=" O SER A 243 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N THR A 248 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 314 Processing helix chain 'A' and resid 315 through 325 Processing helix chain 'A' and resid 337 through 352 removed outlier: 4.184A pdb=" N LEU A 341 " --> pdb=" O GLY A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 359 Processing helix chain 'A' and resid 367 through 381 Processing helix chain 'A' and resid 409 through 421 Processing helix chain 'A' and resid 439 through 444 removed outlier: 3.501A pdb=" N ASN A 444 " --> pdb=" O PRO A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 498 No H-bonds generated for 'chain 'A' and resid 496 through 498' Processing helix chain 'A' and resid 499 through 517 Processing helix chain 'A' and resid 518 through 529 Processing helix chain 'A' and resid 533 through 538 Processing helix chain 'A' and resid 560 through 564 removed outlier: 3.923A pdb=" N SER A 563 " --> pdb=" O SER A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 593 Processing helix chain 'A' and resid 634 through 653 removed outlier: 4.243A pdb=" N GLY A 638 " --> pdb=" O VAL A 634 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARG A 641 " --> pdb=" O ALA A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 658 Processing helix chain 'B' and resid 33 through 37 removed outlier: 3.513A pdb=" N GLN B 37 " --> pdb=" O THR B 33 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 33 through 37' Processing helix chain 'B' and resid 44 through 54 removed outlier: 4.526A pdb=" N GLN B 49 " --> pdb=" O SER B 45 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ALA B 50 " --> pdb=" O THR B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 120 removed outlier: 4.141A pdb=" N SER B 117 " --> pdb=" O GLU B 113 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N PHE B 118 " --> pdb=" O PHE B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 211 Processing helix chain 'B' and resid 214 through 242 removed outlier: 7.741A pdb=" N ARG B 224 " --> pdb=" O ALA B 220 " (cutoff:3.500A) removed outlier: 9.122A pdb=" N ALA B 225 " --> pdb=" O SER B 221 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLN B 226 " --> pdb=" O GLN B 222 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N THR B 241 " --> pdb=" O HIS B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 256 removed outlier: 4.008A pdb=" N PHE B 255 " --> pdb=" O ALA B 251 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLY B 256 " --> pdb=" O CYS B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 290 Processing helix chain 'B' and resid 337 through 354 Processing helix chain 'B' and resid 453 through 455 No H-bonds generated for 'chain 'B' and resid 453 through 455' Processing helix chain 'B' and resid 456 through 467 removed outlier: 3.706A pdb=" N GLU B 462 " --> pdb=" O PRO B 458 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER B 463 " --> pdb=" O THR B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 480 Processing helix chain 'B' and resid 548 through 566 Processing sheet with id=AA1, first strand: chain 'C' and resid 43 through 51 removed outlier: 3.804A pdb=" N GLY C 15 " --> pdb=" O THR C 64 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N CYS C 83 " --> pdb=" O LYS C 10 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL C 87 " --> pdb=" O LEU C 14 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N CYS C 84 " --> pdb=" O VAL C 121 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N LEU C 123 " --> pdb=" O CYS C 84 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N LEU C 86 " --> pdb=" O LEU C 123 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N ILE C 125 " --> pdb=" O LEU C 86 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N PHE C 88 " --> pdb=" O ILE C 125 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 234 through 237 removed outlier: 6.606A pdb=" N SER A 229 " --> pdb=" O PRO A 234 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU A 284 " --> pdb=" O LYS A 281 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE A 278 " --> pdb=" O LEU A 267 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N LEU A 267 " --> pdb=" O ILE A 278 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR B 126 " --> pdb=" O THR A 270 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ALA B 132 " --> pdb=" O THR B 129 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N TRP B 143 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N TRP B 144 " --> pdb=" O ILE B 22 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ILE B 22 " --> pdb=" O TRP B 144 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LEU B 146 " --> pdb=" O LEU B 20 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N LEU B 20 " --> pdb=" O LEU B 146 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N SER B 148 " --> pdb=" O GLY B 18 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 361 through 362 removed outlier: 5.942A pdb=" N LEU A 361 " --> pdb=" O TRP A 556 " (cutoff:3.500A) removed outlier: 8.413A pdb=" N MET A 558 " --> pdb=" O LEU A 361 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN A 555 " --> pdb=" O SER A 550 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL A 601 " --> pdb=" O LYS B 589 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLU B 585 " --> pdb=" O THR A 605 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N TRP B 594 " --> pdb=" O THR B 590 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 396 through 401 removed outlier: 6.423A pdb=" N LEU A 391 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N VAL A 400 " --> pdb=" O GLY A 389 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N GLY A 389 " --> pdb=" O VAL A 400 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 152 through 154 Processing sheet with id=AA6, first strand: chain 'B' and resid 258 through 259 removed outlier: 5.944A pdb=" N ILE B 258 " --> pdb=" O LEU B 514 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N SER B 516 " --> pdb=" O ILE B 258 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 327 through 330 removed outlier: 6.746A pdb=" N VAL B 298 " --> pdb=" O VAL B 329 " (cutoff:3.500A) 427 hydrogen bonds defined for protein. 1230 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.43 Time building geometry restraints manager: 0.94 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: 2696 1.34 - 1.46: 1917 1.46 - 1.58: 3768 1.58 - 1.70: 0 1.70 - 1.82: 42 Bond restraints: 8423 Sorted by residual: bond pdb=" N HIS B 427 " pdb=" CA HIS B 427 " ideal model delta sigma weight residual 1.455 1.487 -0.032 1.38e-02 5.25e+03 5.40e+00 bond pdb=" N ASP B 426 " pdb=" CA ASP B 426 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.60e+00 bond pdb=" CG HIS B 427 " pdb=" CD2 HIS B 427 " ideal model delta sigma weight residual 1.354 1.338 0.016 1.10e-02 8.26e+03 2.22e+00 bond pdb=" CG1 ILE B 562 " pdb=" CD1 ILE B 562 " ideal model delta sigma weight residual 1.513 1.462 0.051 3.90e-02 6.57e+02 1.69e+00 bond pdb=" CB GLU B 462 " pdb=" CG GLU B 462 " ideal model delta sigma weight residual 1.520 1.555 -0.035 3.00e-02 1.11e+03 1.35e+00 ... (remaining 8418 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 11188 1.85 - 3.70: 179 3.70 - 5.55: 40 5.55 - 7.40: 3 7.40 - 9.26: 3 Bond angle restraints: 11413 Sorted by residual: angle pdb=" N VAL A 398 " pdb=" CA VAL A 398 " pdb=" C VAL A 398 " ideal model delta sigma weight residual 111.62 109.33 2.29 7.90e-01 1.60e+00 8.38e+00 angle pdb=" CA ASP B 426 " pdb=" CB ASP B 426 " pdb=" CG ASP B 426 " ideal model delta sigma weight residual 112.60 115.38 -2.78 1.00e+00 1.00e+00 7.74e+00 angle pdb=" CA LEU C 8 " pdb=" CB LEU C 8 " pdb=" CG LEU C 8 " ideal model delta sigma weight residual 116.30 125.56 -9.26 3.50e+00 8.16e-02 6.99e+00 angle pdb=" C ASP C 114 " pdb=" CA ASP C 114 " pdb=" CB ASP C 114 " ideal model delta sigma weight residual 111.14 115.20 -4.06 1.56e+00 4.11e-01 6.78e+00 angle pdb=" CB MET C 25 " pdb=" CG MET C 25 " pdb=" SD MET C 25 " ideal model delta sigma weight residual 112.70 120.51 -7.81 3.00e+00 1.11e-01 6.77e+00 ... (remaining 11408 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.43: 4398 17.43 - 34.86: 479 34.86 - 52.29: 113 52.29 - 69.72: 22 69.72 - 87.15: 10 Dihedral angle restraints: 5022 sinusoidal: 2013 harmonic: 3009 Sorted by residual: dihedral pdb=" CA TRP B 547 " pdb=" C TRP B 547 " pdb=" N THR B 548 " pdb=" CA THR B 548 " ideal model delta harmonic sigma weight residual 180.00 161.19 18.81 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" CA VAL B 437 " pdb=" C VAL B 437 " pdb=" N SER B 438 " pdb=" CA SER B 438 " ideal model delta harmonic sigma weight residual 180.00 162.87 17.13 0 5.00e+00 4.00e-02 1.17e+01 dihedral pdb=" CA PRO A 210 " pdb=" C PRO A 210 " pdb=" N ASP A 211 " pdb=" CA ASP A 211 " ideal model delta harmonic sigma weight residual -180.00 -162.97 -17.03 0 5.00e+00 4.00e-02 1.16e+01 ... (remaining 5019 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 969 0.042 - 0.083: 224 0.083 - 0.125: 90 0.125 - 0.167: 13 0.167 - 0.208: 2 Chirality restraints: 1298 Sorted by residual: chirality pdb=" CB ILE C 13 " pdb=" CA ILE C 13 " pdb=" CG1 ILE C 13 " pdb=" CG2 ILE C 13 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA THR B 451 " pdb=" N THR B 451 " pdb=" C THR B 451 " pdb=" CB THR B 451 " both_signs ideal model delta sigma weight residual False 2.53 2.35 0.18 2.00e-01 2.50e+01 7.78e-01 chirality pdb=" CA VAL C 29 " pdb=" N VAL C 29 " pdb=" C VAL C 29 " pdb=" CB VAL C 29 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.67e-01 ... (remaining 1295 not shown) Planarity restraints: 1448 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 598 " 0.008 2.00e-02 2.50e+03 1.00e-02 2.51e+00 pdb=" CG TRP B 598 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 TRP B 598 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP B 598 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 598 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 598 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 598 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 598 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 598 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B 598 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 565 " -0.026 5.00e-02 4.00e+02 3.90e-02 2.44e+00 pdb=" N PRO A 566 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 566 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 566 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 233 " -0.023 5.00e-02 4.00e+02 3.43e-02 1.88e+00 pdb=" N PRO A 234 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 234 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 234 " -0.019 5.00e-02 4.00e+02 ... (remaining 1445 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 340 2.72 - 3.26: 8615 3.26 - 3.81: 14124 3.81 - 4.35: 17242 4.35 - 4.90: 29582 Nonbonded interactions: 69903 Sorted by model distance: nonbonded pdb=" OE1 GLU A 432 " pdb=" OH TYR A 451 " model vdw 2.173 3.040 nonbonded pdb=" OG1 THR A 315 " pdb=" O ASN A 444 " model vdw 2.192 3.040 nonbonded pdb=" NZ LYS C 38 " pdb=" OD1 ASP C 63 " model vdw 2.195 3.120 nonbonded pdb=" N GLN C 27 " pdb=" OE1 GLN C 27 " model vdw 2.218 3.120 nonbonded pdb=" OG1 THR B 152 " pdb=" O SER B 186 " model vdw 2.223 3.040 ... (remaining 69898 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: 6.380 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 9.740 Find NCS groups from input model: 0.060 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:6.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 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 0.051 8423 Z= 0.139 Angle : 0.593 9.256 11413 Z= 0.305 Chirality : 0.043 0.208 1298 Planarity : 0.004 0.039 1448 Dihedral : 15.613 87.152 3080 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 0.67 % Allowed : 16.57 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.29 (0.27), residues: 1020 helix: 1.58 (0.26), residues: 413 sheet: -0.89 (0.36), residues: 218 loop : -0.57 (0.32), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 113 TYR 0.017 0.001 TYR B 401 PHE 0.012 0.001 PHE C 106 TRP 0.026 0.001 TRP B 598 HIS 0.003 0.001 HIS A 589 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 8423) covalent geometry : angle 0.59316 (11413) hydrogen bonds : bond 0.13000 ( 427) hydrogen bonds : angle 6.59342 ( 1230) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 105 time to evaluate : 0.344 Fit side-chains revert: symmetry clash REVERT: C 71 GLN cc_start: 0.8283 (tm-30) cc_final: 0.8046 (tm-30) REVERT: A 246 ASN cc_start: 0.7757 (t0) cc_final: 0.7080 (p0) REVERT: A 321 ASN cc_start: 0.8544 (t0) cc_final: 0.8296 (t0) outliers start: 6 outliers final: 1 residues processed: 109 average time/residue: 0.5016 time to fit residues: 58.9907 Evaluate side-chains 99 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 98 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.5980 chunk 100 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 91 ASN ** C 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 325 HIS A 504 GLN A 598 HIS B 247 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.095532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.077843 restraints weight = 18671.025| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 3.48 r_work: 0.3088 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.0887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8423 Z= 0.171 Angle : 0.588 8.487 11413 Z= 0.297 Chirality : 0.043 0.172 1298 Planarity : 0.004 0.038 1448 Dihedral : 4.176 25.293 1140 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 3.92 % Allowed : 16.57 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.38 (0.27), residues: 1020 helix: 1.79 (0.26), residues: 414 sheet: -0.98 (0.35), residues: 228 loop : -0.59 (0.33), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 238 TYR 0.015 0.001 TYR B 443 PHE 0.011 0.001 PHE A 276 TRP 0.014 0.001 TRP B 595 HIS 0.003 0.001 HIS B 211 Details of bonding type rmsd covalent geometry : bond 0.00388 ( 8423) covalent geometry : angle 0.58789 (11413) hydrogen bonds : bond 0.04278 ( 427) hydrogen bonds : angle 5.55350 ( 1230) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 106 time to evaluate : 0.458 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 6 LYS cc_start: 0.7788 (tppt) cc_final: 0.7575 (mmmm) REVERT: C 71 GLN cc_start: 0.8433 (tm-30) cc_final: 0.8173 (tm-30) REVERT: A 246 ASN cc_start: 0.8300 (t0) cc_final: 0.7139 (p0) REVERT: A 506 MET cc_start: 0.8891 (OUTLIER) cc_final: 0.8063 (tpp) REVERT: B 130 GLU cc_start: 0.8793 (OUTLIER) cc_final: 0.8335 (tm-30) outliers start: 35 outliers final: 16 residues processed: 127 average time/residue: 0.4740 time to fit residues: 65.1037 Evaluate side-chains 110 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 92 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 13 ILE Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 142 GLN Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 258 PHE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 419 MET Chi-restraints excluded: chain A residue 506 MET Chi-restraints excluded: chain A residue 536 SER Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 446 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 27 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 6 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 chunk 95 optimal weight: 1.9990 chunk 84 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 52 optimal weight: 0.5980 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 91 ASN ** C 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 325 HIS A 598 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.095315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.077653 restraints weight = 18648.762| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 3.46 r_work: 0.3089 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.1157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8423 Z= 0.162 Angle : 0.584 8.402 11413 Z= 0.293 Chirality : 0.043 0.171 1298 Planarity : 0.004 0.045 1448 Dihedral : 4.181 22.177 1140 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 4.14 % Allowed : 17.47 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.38 (0.27), residues: 1020 helix: 1.78 (0.26), residues: 418 sheet: -0.95 (0.35), residues: 225 loop : -0.62 (0.33), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 263 TYR 0.013 0.001 TYR B 443 PHE 0.012 0.001 PHE A 276 TRP 0.015 0.001 TRP B 595 HIS 0.002 0.001 HIS B 556 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 8423) covalent geometry : angle 0.58431 (11413) hydrogen bonds : bond 0.03747 ( 427) hydrogen bonds : angle 5.26436 ( 1230) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 100 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 71 GLN cc_start: 0.8505 (tm-30) cc_final: 0.8258 (tm-30) REVERT: C 77 PHE cc_start: 0.7632 (OUTLIER) cc_final: 0.6916 (m-10) REVERT: C 92 ASN cc_start: 0.8342 (t0) cc_final: 0.8129 (t0) REVERT: A 246 ASN cc_start: 0.8379 (t0) cc_final: 0.7196 (p0) REVERT: A 506 MET cc_start: 0.8945 (OUTLIER) cc_final: 0.8217 (tpp) REVERT: A 516 SER cc_start: 0.9345 (m) cc_final: 0.9072 (p) REVERT: A 582 MET cc_start: 0.9204 (tpp) cc_final: 0.8874 (mmm) REVERT: A 595 ARG cc_start: 0.8173 (OUTLIER) cc_final: 0.7793 (mmm160) REVERT: B 130 GLU cc_start: 0.8835 (OUTLIER) cc_final: 0.8347 (tm-30) REVERT: B 373 LEU cc_start: 0.9203 (OUTLIER) cc_final: 0.8870 (tt) outliers start: 37 outliers final: 15 residues processed: 124 average time/residue: 0.4837 time to fit residues: 64.8985 Evaluate side-chains 110 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 90 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 13 ILE Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 77 PHE Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain A residue 258 PHE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 506 MET Chi-restraints excluded: chain A residue 536 SER Chi-restraints excluded: chain A residue 595 ARG Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 446 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 76 optimal weight: 0.8980 chunk 6 optimal weight: 0.0470 chunk 98 optimal weight: 0.3980 chunk 4 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 30 optimal weight: 0.0670 chunk 15 optimal weight: 0.9980 chunk 1 optimal weight: 7.9990 chunk 60 optimal weight: 2.9990 chunk 63 optimal weight: 10.0000 overall best weight: 0.4616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 91 ASN ** C 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 325 HIS A 598 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.096350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.078624 restraints weight = 18941.270| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 3.50 r_work: 0.3110 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8423 Z= 0.127 Angle : 0.571 8.267 11413 Z= 0.286 Chirality : 0.042 0.175 1298 Planarity : 0.004 0.070 1448 Dihedral : 4.098 25.073 1138 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.36 % Allowed : 19.15 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.43 (0.27), residues: 1020 helix: 1.84 (0.26), residues: 416 sheet: -0.88 (0.35), residues: 223 loop : -0.65 (0.33), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 651 TYR 0.013 0.001 TYR B 443 PHE 0.011 0.001 PHE A 276 TRP 0.017 0.001 TRP B 598 HIS 0.003 0.001 HIS A 589 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 8423) covalent geometry : angle 0.57085 (11413) hydrogen bonds : bond 0.03519 ( 427) hydrogen bonds : angle 5.06972 ( 1230) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 111 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 71 GLN cc_start: 0.8486 (tm-30) cc_final: 0.8200 (tm-30) REVERT: C 77 PHE cc_start: 0.7459 (OUTLIER) cc_final: 0.6738 (m-10) REVERT: C 92 ASN cc_start: 0.8279 (t0) cc_final: 0.8078 (t0) REVERT: A 246 ASN cc_start: 0.8293 (t0) cc_final: 0.7025 (p0) REVERT: A 444 ASN cc_start: 0.8889 (p0) cc_final: 0.8404 (t160) REVERT: A 506 MET cc_start: 0.8959 (OUTLIER) cc_final: 0.8261 (tpp) REVERT: A 516 SER cc_start: 0.9387 (m) cc_final: 0.9124 (p) REVERT: A 540 LYS cc_start: 0.9031 (mmmt) cc_final: 0.8702 (tptp) REVERT: A 595 ARG cc_start: 0.8172 (tpm170) cc_final: 0.7928 (mmm160) REVERT: B 130 GLU cc_start: 0.8839 (tm-30) cc_final: 0.8239 (tm-30) REVERT: B 373 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8816 (tt) outliers start: 30 outliers final: 15 residues processed: 131 average time/residue: 0.4307 time to fit residues: 61.3161 Evaluate side-chains 116 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 98 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 13 ILE Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 77 PHE Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 142 GLN Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 258 PHE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 506 MET Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 446 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 30 optimal weight: 0.9990 chunk 101 optimal weight: 0.1980 chunk 46 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 50 optimal weight: 5.9990 chunk 90 optimal weight: 0.0980 chunk 62 optimal weight: 3.9990 chunk 87 optimal weight: 0.1980 chunk 27 optimal weight: 0.5980 chunk 86 optimal weight: 0.6980 overall best weight: 0.3580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 91 ASN ** C 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 325 HIS A 598 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.097405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.079707 restraints weight = 18719.463| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 3.53 r_work: 0.3123 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8423 Z= 0.121 Angle : 0.574 8.280 11413 Z= 0.287 Chirality : 0.042 0.158 1298 Planarity : 0.004 0.066 1448 Dihedral : 4.003 19.887 1138 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.81 % Allowed : 18.92 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.44 (0.27), residues: 1020 helix: 1.85 (0.26), residues: 422 sheet: -0.78 (0.35), residues: 217 loop : -0.77 (0.32), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 651 TYR 0.024 0.001 TYR B 401 PHE 0.010 0.001 PHE A 276 TRP 0.021 0.001 TRP B 598 HIS 0.003 0.000 HIS A 589 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 8423) covalent geometry : angle 0.57449 (11413) hydrogen bonds : bond 0.03383 ( 427) hydrogen bonds : angle 4.99936 ( 1230) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 110 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 58 THR cc_start: 0.7405 (OUTLIER) cc_final: 0.7018 (p) REVERT: C 63 ASP cc_start: 0.6966 (t0) cc_final: 0.6743 (t0) REVERT: C 71 GLN cc_start: 0.8520 (tm-30) cc_final: 0.8227 (tm-30) REVERT: C 77 PHE cc_start: 0.7399 (OUTLIER) cc_final: 0.6653 (m-80) REVERT: A 246 ASN cc_start: 0.8343 (t0) cc_final: 0.7053 (p0) REVERT: A 432 GLU cc_start: 0.8644 (mm-30) cc_final: 0.8309 (mm-30) REVERT: A 444 ASN cc_start: 0.8841 (p0) cc_final: 0.8513 (t160) REVERT: A 506 MET cc_start: 0.8986 (OUTLIER) cc_final: 0.8254 (tpp) REVERT: A 516 SER cc_start: 0.9389 (m) cc_final: 0.9128 (p) REVERT: A 540 LYS cc_start: 0.9005 (mmmt) cc_final: 0.8702 (tptp) REVERT: B 130 GLU cc_start: 0.8854 (tm-30) cc_final: 0.8359 (tm-30) REVERT: B 150 ASP cc_start: 0.8269 (m-30) cc_final: 0.7118 (p0) REVERT: B 373 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8753 (tt) outliers start: 34 outliers final: 16 residues processed: 131 average time/residue: 0.4165 time to fit residues: 59.4608 Evaluate side-chains 110 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 90 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 13 ILE Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 77 PHE Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 142 GLN Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 258 PHE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 419 MET Chi-restraints excluded: chain A residue 506 MET Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 547 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 81 optimal weight: 2.9990 chunk 87 optimal weight: 0.0010 chunk 32 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 41 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 89 optimal weight: 0.6980 overall best weight: 1.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 91 ASN ** C 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 325 HIS A 598 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.092899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.075270 restraints weight = 18826.276| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 3.39 r_work: 0.3043 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 8423 Z= 0.253 Angle : 0.647 8.513 11413 Z= 0.326 Chirality : 0.044 0.175 1298 Planarity : 0.004 0.063 1448 Dihedral : 4.198 20.450 1138 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.70 % Allowed : 21.05 % Favored : 75.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.37 (0.28), residues: 1020 helix: 1.77 (0.26), residues: 422 sheet: -0.94 (0.35), residues: 225 loop : -0.67 (0.33), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 404 TYR 0.020 0.002 TYR B 401 PHE 0.014 0.002 PHE C 88 TRP 0.019 0.002 TRP B 598 HIS 0.003 0.001 HIS B 211 Details of bonding type rmsd covalent geometry : bond 0.00586 ( 8423) covalent geometry : angle 0.64715 (11413) hydrogen bonds : bond 0.03770 ( 427) hydrogen bonds : angle 5.20854 ( 1230) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 88 time to evaluate : 0.316 Fit side-chains revert: symmetry clash REVERT: C 56 GLN cc_start: 0.8403 (pp30) cc_final: 0.7750 (pp30) REVERT: C 59 MET cc_start: 0.8017 (OUTLIER) cc_final: 0.7739 (mtt) REVERT: C 71 GLN cc_start: 0.8603 (tm-30) cc_final: 0.8360 (tm-30) REVERT: A 506 MET cc_start: 0.9023 (OUTLIER) cc_final: 0.8342 (tpp) REVERT: A 516 SER cc_start: 0.9414 (m) cc_final: 0.9154 (p) REVERT: B 130 GLU cc_start: 0.8893 (OUTLIER) cc_final: 0.8334 (tm-30) REVERT: B 373 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8710 (tt) REVERT: B 594 TRP cc_start: 0.5981 (t-100) cc_final: 0.5777 (t-100) outliers start: 33 outliers final: 19 residues processed: 110 average time/residue: 0.4400 time to fit residues: 52.5252 Evaluate side-chains 115 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 92 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 13 ILE Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 59 MET Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 142 GLN Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 258 PHE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 506 MET Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 628 CYS Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 547 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 26 optimal weight: 0.6980 chunk 94 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 72 optimal weight: 0.7980 chunk 82 optimal weight: 0.0050 chunk 70 optimal weight: 0.9990 chunk 95 optimal weight: 0.6980 chunk 96 optimal weight: 4.9990 chunk 14 optimal weight: 0.7980 chunk 77 optimal weight: 0.3980 chunk 11 optimal weight: 0.9980 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 91 ASN ** C 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 325 HIS A 598 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.095410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.077665 restraints weight = 18807.664| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 3.50 r_work: 0.3112 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8423 Z= 0.139 Angle : 0.608 9.380 11413 Z= 0.303 Chirality : 0.043 0.212 1298 Planarity : 0.004 0.061 1448 Dihedral : 4.125 19.608 1138 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.47 % Allowed : 21.72 % Favored : 74.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (0.27), residues: 1020 helix: 1.70 (0.26), residues: 426 sheet: -0.83 (0.35), residues: 222 loop : -0.75 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 263 TYR 0.020 0.001 TYR B 401 PHE 0.017 0.001 PHE C 88 TRP 0.027 0.001 TRP B 598 HIS 0.003 0.001 HIS A 589 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 8423) covalent geometry : angle 0.60808 (11413) hydrogen bonds : bond 0.03505 ( 427) hydrogen bonds : angle 5.07339 ( 1230) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 101 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 56 GLN cc_start: 0.8411 (pp30) cc_final: 0.7655 (pp30) REVERT: C 71 GLN cc_start: 0.8562 (tm-30) cc_final: 0.8342 (tm-30) REVERT: A 213 GLU cc_start: 0.8732 (pm20) cc_final: 0.8517 (pm20) REVERT: A 432 GLU cc_start: 0.8617 (mm-30) cc_final: 0.8329 (mm-30) REVERT: A 506 MET cc_start: 0.9040 (OUTLIER) cc_final: 0.8325 (tpp) REVERT: A 516 SER cc_start: 0.9426 (m) cc_final: 0.9168 (p) REVERT: A 540 LYS cc_start: 0.9006 (mmmt) cc_final: 0.8689 (tptp) REVERT: B 130 GLU cc_start: 0.8869 (tm-30) cc_final: 0.8369 (tm-30) outliers start: 31 outliers final: 18 residues processed: 123 average time/residue: 0.4503 time to fit residues: 60.1879 Evaluate side-chains 112 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 93 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 13 ILE Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 142 GLN Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 258 PHE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 506 MET Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 434 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 94 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 20 optimal weight: 0.3980 chunk 89 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 96 optimal weight: 0.9990 chunk 98 optimal weight: 0.0970 chunk 93 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 325 HIS A 598 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.094454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.076755 restraints weight = 18752.984| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 3.49 r_work: 0.3072 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 8423 Z= 0.181 Angle : 0.644 11.470 11413 Z= 0.319 Chirality : 0.043 0.198 1298 Planarity : 0.004 0.060 1448 Dihedral : 4.133 21.188 1138 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 2.58 % Allowed : 23.29 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.37 (0.28), residues: 1020 helix: 1.68 (0.26), residues: 424 sheet: -0.85 (0.35), residues: 223 loop : -0.64 (0.34), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 263 TYR 0.020 0.001 TYR B 401 PHE 0.016 0.002 PHE C 88 TRP 0.029 0.002 TRP B 598 HIS 0.002 0.001 HIS B 556 Details of bonding type rmsd covalent geometry : bond 0.00424 ( 8423) covalent geometry : angle 0.64445 (11413) hydrogen bonds : bond 0.03537 ( 427) hydrogen bonds : angle 5.09507 ( 1230) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 94 time to evaluate : 0.340 Fit side-chains revert: symmetry clash REVERT: A 246 ASN cc_start: 0.8484 (t0) cc_final: 0.7283 (p0) REVERT: A 432 GLU cc_start: 0.8613 (mm-30) cc_final: 0.8350 (mm-30) REVERT: A 506 MET cc_start: 0.9042 (OUTLIER) cc_final: 0.8375 (tpp) REVERT: A 516 SER cc_start: 0.9429 (m) cc_final: 0.9174 (p) REVERT: A 582 MET cc_start: 0.9190 (tpp) cc_final: 0.8881 (mmm) REVERT: B 130 GLU cc_start: 0.8871 (tm-30) cc_final: 0.8364 (tm-30) REVERT: B 150 ASP cc_start: 0.8295 (m-30) cc_final: 0.7110 (p0) outliers start: 23 outliers final: 18 residues processed: 111 average time/residue: 0.4409 time to fit residues: 53.2692 Evaluate side-chains 107 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 88 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 13 ILE Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 142 GLN Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 258 PHE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 506 MET Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 446 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 43 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 82 optimal weight: 0.8980 chunk 70 optimal weight: 0.2980 chunk 37 optimal weight: 0.4980 chunk 51 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 325 HIS A 598 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.095771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.077975 restraints weight = 18741.411| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 3.49 r_work: 0.3091 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 8423 Z= 0.155 Angle : 0.658 11.744 11413 Z= 0.328 Chirality : 0.043 0.208 1298 Planarity : 0.004 0.056 1448 Dihedral : 4.170 23.167 1138 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.46 % Allowed : 23.74 % Favored : 73.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (0.28), residues: 1020 helix: 1.72 (0.26), residues: 422 sheet: -0.82 (0.35), residues: 222 loop : -0.74 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 263 TYR 0.032 0.001 TYR B 401 PHE 0.016 0.001 PHE C 88 TRP 0.034 0.002 TRP B 598 HIS 0.002 0.001 HIS A 589 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 8423) covalent geometry : angle 0.65807 (11413) hydrogen bonds : bond 0.03518 ( 427) hydrogen bonds : angle 5.09453 ( 1230) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 95 time to evaluate : 0.298 Fit side-chains revert: symmetry clash REVERT: C 49 GLU cc_start: 0.8523 (mp0) cc_final: 0.8092 (mp0) REVERT: C 109 GLN cc_start: 0.8052 (mm-40) cc_final: 0.7678 (tm-30) REVERT: A 246 ASN cc_start: 0.8473 (t0) cc_final: 0.7278 (p0) REVERT: A 432 GLU cc_start: 0.8601 (mm-30) cc_final: 0.8331 (mm-30) REVERT: A 444 ASN cc_start: 0.8944 (p0) cc_final: 0.8424 (t0) REVERT: A 506 MET cc_start: 0.9059 (OUTLIER) cc_final: 0.8383 (tpp) REVERT: A 516 SER cc_start: 0.9428 (m) cc_final: 0.9175 (p) REVERT: A 582 MET cc_start: 0.9189 (tpp) cc_final: 0.8867 (mmm) REVERT: B 130 GLU cc_start: 0.8864 (tm-30) cc_final: 0.8334 (tm-30) REVERT: B 150 ASP cc_start: 0.8303 (m-30) cc_final: 0.7114 (p0) outliers start: 22 outliers final: 17 residues processed: 111 average time/residue: 0.4684 time to fit residues: 56.3502 Evaluate side-chains 107 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 89 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 13 ILE Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 142 GLN Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 258 PHE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 506 MET Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 446 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 101 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 83 optimal weight: 4.9990 chunk 59 optimal weight: 0.0970 chunk 63 optimal weight: 5.9990 chunk 86 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 1 optimal weight: 8.9990 chunk 53 optimal weight: 0.8980 chunk 13 optimal weight: 9.9990 chunk 99 optimal weight: 0.6980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 325 HIS A 598 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.095969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.078178 restraints weight = 18659.532| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 3.50 r_work: 0.3094 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 8423 Z= 0.160 Angle : 0.682 11.864 11413 Z= 0.337 Chirality : 0.043 0.226 1298 Planarity : 0.004 0.049 1448 Dihedral : 4.186 22.955 1138 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.35 % Allowed : 24.30 % Favored : 73.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (0.28), residues: 1020 helix: 1.71 (0.26), residues: 422 sheet: -0.88 (0.35), residues: 229 loop : -0.69 (0.34), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 332 TYR 0.030 0.001 TYR B 401 PHE 0.016 0.001 PHE C 88 TRP 0.041 0.002 TRP B 594 HIS 0.002 0.001 HIS B 556 Details of bonding type rmsd covalent geometry : bond 0.00377 ( 8423) covalent geometry : angle 0.68160 (11413) hydrogen bonds : bond 0.03520 ( 427) hydrogen bonds : angle 5.11322 ( 1230) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 91 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 49 GLU cc_start: 0.8560 (mp0) cc_final: 0.8225 (mp0) REVERT: C 59 MET cc_start: 0.7805 (mtm) cc_final: 0.7478 (mtt) REVERT: A 246 ASN cc_start: 0.8425 (t0) cc_final: 0.7248 (p0) REVERT: A 432 GLU cc_start: 0.8589 (mm-30) cc_final: 0.8321 (mm-30) REVERT: A 444 ASN cc_start: 0.8933 (p0) cc_final: 0.8448 (t160) REVERT: A 506 MET cc_start: 0.9063 (OUTLIER) cc_final: 0.8398 (tpp) REVERT: A 516 SER cc_start: 0.9425 (m) cc_final: 0.9173 (p) REVERT: A 582 MET cc_start: 0.9193 (tpp) cc_final: 0.8886 (mmm) REVERT: B 130 GLU cc_start: 0.8861 (tm-30) cc_final: 0.8329 (tm-30) REVERT: B 150 ASP cc_start: 0.8296 (m-30) cc_final: 0.7119 (p0) outliers start: 21 outliers final: 17 residues processed: 106 average time/residue: 0.4736 time to fit residues: 54.5040 Evaluate side-chains 109 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 91 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 13 ILE Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 142 GLN Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 258 PHE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 506 MET Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 446 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 22 optimal weight: 0.5980 chunk 28 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 63 optimal weight: 5.9990 chunk 18 optimal weight: 0.4980 chunk 43 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 325 HIS A 598 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.095713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.077871 restraints weight = 18726.228| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 3.49 r_work: 0.3086 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 8423 Z= 0.168 Angle : 0.699 12.108 11413 Z= 0.347 Chirality : 0.044 0.244 1298 Planarity : 0.004 0.047 1448 Dihedral : 4.225 21.842 1138 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.35 % Allowed : 24.41 % Favored : 73.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.37 (0.28), residues: 1020 helix: 1.79 (0.26), residues: 416 sheet: -0.88 (0.35), residues: 229 loop : -0.70 (0.33), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 113 TYR 0.030 0.001 TYR B 401 PHE 0.016 0.001 PHE C 88 TRP 0.044 0.002 TRP B 594 HIS 0.003 0.001 HIS A 325 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 8423) covalent geometry : angle 0.69948 (11413) hydrogen bonds : bond 0.03505 ( 427) hydrogen bonds : angle 5.12734 ( 1230) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2607.24 seconds wall clock time: 45 minutes 30.35 seconds (2730.35 seconds total)