Starting phenix.real_space_refine on Mon Nov 17 21:28:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7r8d_24316/11_2025/7r8d_24316.cif Found real_map, /net/cci-nas-00/data/ceres_data/7r8d_24316/11_2025/7r8d_24316.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7r8d_24316/11_2025/7r8d_24316.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7r8d_24316/11_2025/7r8d_24316.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7r8d_24316/11_2025/7r8d_24316.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7r8d_24316/11_2025/7r8d_24316.map" } resolution = 3.2 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 ------------------------------------------------------------------------------- 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= 0.005 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 68 5.16 5 C 5756 2.51 5 N 1414 2.21 5 O 1524 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 74 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8762 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 545, 4269 Classifications: {'peptide': 545} Link IDs: {'PTRANS': 18, 'TRANS': 526} Chain breaks: 2 Chain: "B" Number of atoms: 4269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 545, 4269 Classifications: {'peptide': 545} Link IDs: {'PTRANS': 18, 'TRANS': 526} Chain breaks: 2 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 112 Unusual residues: {'CLR': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 112 Unusual residues: {'CLR': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 2.06, per 1000 atoms: 0.24 Number of scatterers: 8762 At special positions: 0 Unit cell: (102.459, 72.471, 120.785, 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 68 16.00 O 1524 8.00 N 1414 7.00 C 5756 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 611 " - pdb=" SG CYS A 617 " distance=2.03 Simple disulfide: pdb=" SG CYS B 611 " - pdb=" SG CYS B 617 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.76 Conformation dependent library (CDL) restraints added in 314.8 milliseconds 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2016 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 4 sheets defined 60.9% alpha, 7.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 123 through 131 Processing helix chain 'A' and resid 154 through 157 Processing helix chain 'A' and resid 173 through 186 Processing helix chain 'A' and resid 189 through 204 Processing helix chain 'A' and resid 213 through 217 Processing helix chain 'A' and resid 218 through 231 Processing helix chain 'A' and resid 248 through 265 Processing helix chain 'A' and resid 277 through 282 Processing helix chain 'A' and resid 303 through 310 removed outlier: 3.639A pdb=" N TYR A 307 " --> pdb=" O ASN A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 330 Processing helix chain 'A' and resid 336 through 346 Processing helix chain 'A' and resid 388 through 405 removed outlier: 3.512A pdb=" N GLN A 392 " --> pdb=" O SER A 388 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N CYS A 394 " --> pdb=" O LEU A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 429 Processing helix chain 'A' and resid 438 through 478 Proline residue: A 460 - end of helix Proline residue: A 466 - end of helix removed outlier: 3.764A pdb=" N ASN A 478 " --> pdb=" O ARG A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 510 removed outlier: 3.907A pdb=" N TYR A 486 " --> pdb=" O SER A 482 " (cutoff:3.500A) Proline residue: A 496 - end of helix Proline residue: A 502 - end of helix removed outlier: 4.006A pdb=" N ILE A 508 " --> pdb=" O ALA A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 546 Processing helix chain 'A' and resid 549 through 567 removed outlier: 3.582A pdb=" N ALA A 553 " --> pdb=" O SER A 549 " (cutoff:3.500A) Proline residue: A 558 - end of helix Proline residue: A 563 - end of helix removed outlier: 3.655A pdb=" N LEU A 566 " --> pdb=" O ILE A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 587 removed outlier: 4.241A pdb=" N TRP A 583 " --> pdb=" O THR A 579 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N MET A 584 " --> pdb=" O TYR A 580 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N SER A 585 " --> pdb=" O LEU A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 602 Processing helix chain 'A' and resid 623 through 629 Processing helix chain 'A' and resid 635 through 666 removed outlier: 3.731A pdb=" N ASP A 639 " --> pdb=" O LYS A 635 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 131 Processing helix chain 'B' and resid 154 through 157 Processing helix chain 'B' and resid 173 through 186 Processing helix chain 'B' and resid 189 through 204 Processing helix chain 'B' and resid 213 through 217 Processing helix chain 'B' and resid 218 through 231 Processing helix chain 'B' and resid 248 through 265 Processing helix chain 'B' and resid 277 through 282 Processing helix chain 'B' and resid 303 through 310 removed outlier: 3.639A pdb=" N TYR B 307 " --> pdb=" O ASN B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 330 Processing helix chain 'B' and resid 336 through 346 Processing helix chain 'B' and resid 388 through 405 removed outlier: 3.512A pdb=" N GLN B 392 " --> pdb=" O SER B 388 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N CYS B 394 " --> pdb=" O LEU B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 429 Processing helix chain 'B' and resid 438 through 478 Proline residue: B 460 - end of helix Proline residue: B 466 - end of helix removed outlier: 3.764A pdb=" N ASN B 478 " --> pdb=" O ARG B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 510 removed outlier: 3.907A pdb=" N TYR B 486 " --> pdb=" O SER B 482 " (cutoff:3.500A) Proline residue: B 496 - end of helix Proline residue: B 502 - end of helix removed outlier: 4.006A pdb=" N ILE B 508 " --> pdb=" O ALA B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 546 Processing helix chain 'B' and resid 549 through 567 removed outlier: 3.582A pdb=" N ALA B 553 " --> pdb=" O SER B 549 " (cutoff:3.500A) Proline residue: B 558 - end of helix Proline residue: B 563 - end of helix removed outlier: 3.655A pdb=" N LEU B 566 " --> pdb=" O ILE B 562 " (cutoff:3.500A) Processing helix chain 'B' and resid 578 through 587 removed outlier: 4.242A pdb=" N TRP B 583 " --> pdb=" O THR B 579 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N MET B 584 " --> pdb=" O TYR B 580 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N SER B 585 " --> pdb=" O LEU B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 602 Processing helix chain 'B' and resid 623 through 629 Processing helix chain 'B' and resid 635 through 666 removed outlier: 3.731A pdb=" N ASP B 639 " --> pdb=" O LYS B 635 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 101 through 108 removed outlier: 6.996A pdb=" N LYS A 102 " --> pdb=" O SER A 83 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N SER A 83 " --> pdb=" O LYS A 102 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N ILE A 104 " --> pdb=" O ASP A 81 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ARG A 80 " --> pdb=" O ALA A 142 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA A 142 " --> pdb=" O ARG A 80 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 159 through 162 removed outlier: 6.566A pdb=" N CYS A 160 " --> pdb=" O PHE A 239 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N ASP A 241 " --> pdb=" O CYS A 160 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N ILE A 162 " --> pdb=" O ASP A 241 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N TYR A 297 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N SER A 291 " --> pdb=" O CYS A 295 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N CYS A 295 " --> pdb=" O SER A 291 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 101 through 108 removed outlier: 6.996A pdb=" N LYS B 102 " --> pdb=" O SER B 83 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N SER B 83 " --> pdb=" O LYS B 102 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N ILE B 104 " --> pdb=" O ASP B 81 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ARG B 80 " --> pdb=" O ALA B 142 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA B 142 " --> pdb=" O ARG B 80 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 159 through 162 removed outlier: 6.567A pdb=" N CYS B 160 " --> pdb=" O PHE B 239 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N ASP B 241 " --> pdb=" O CYS B 160 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N ILE B 162 " --> pdb=" O ASP B 241 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N TYR B 297 " --> pdb=" O VAL B 289 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N SER B 291 " --> pdb=" O CYS B 295 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N CYS B 295 " --> pdb=" O SER B 291 " (cutoff:3.500A) 486 hydrogen bonds defined for protein. 1422 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: 1.45 Time building geometry restraints manager: 1.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2700 1.34 - 1.46: 1937 1.46 - 1.58: 4215 1.58 - 1.69: 0 1.69 - 1.81: 110 Bond restraints: 8962 Sorted by residual: bond pdb=" C ILE A 562 " pdb=" N PRO A 563 " ideal model delta sigma weight residual 1.337 1.357 -0.020 9.80e-03 1.04e+04 4.13e+00 bond pdb=" C ILE B 562 " pdb=" N PRO B 563 " ideal model delta sigma weight residual 1.337 1.356 -0.019 9.80e-03 1.04e+04 3.84e+00 bond pdb=" C3 CLR A 801 " pdb=" O1 CLR A 801 " ideal model delta sigma weight residual 1.413 1.392 0.021 2.00e-02 2.50e+03 1.14e+00 bond pdb=" C3 CLR B 703 " pdb=" O1 CLR B 703 " ideal model delta sigma weight residual 1.413 1.392 0.021 2.00e-02 2.50e+03 1.13e+00 bond pdb=" C3 CLR B 701 " pdb=" O1 CLR B 701 " ideal model delta sigma weight residual 1.413 1.392 0.021 2.00e-02 2.50e+03 1.12e+00 ... (remaining 8957 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.49: 11737 1.49 - 2.97: 323 2.97 - 4.46: 53 4.46 - 5.95: 33 5.95 - 7.44: 16 Bond angle restraints: 12162 Sorted by residual: angle pdb=" C GLN B 620 " pdb=" N LYS B 621 " pdb=" CA LYS B 621 " ideal model delta sigma weight residual 121.54 127.56 -6.02 1.91e+00 2.74e-01 9.93e+00 angle pdb=" C GLN A 620 " pdb=" N LYS A 621 " pdb=" CA LYS A 621 " ideal model delta sigma weight residual 121.54 127.54 -6.00 1.91e+00 2.74e-01 9.86e+00 angle pdb=" N GLY A 299 " pdb=" CA GLY A 299 " pdb=" C GLY A 299 " ideal model delta sigma weight residual 110.38 114.70 -4.32 1.42e+00 4.96e-01 9.27e+00 angle pdb=" N GLY B 299 " pdb=" CA GLY B 299 " pdb=" C GLY B 299 " ideal model delta sigma weight residual 110.38 114.69 -4.31 1.42e+00 4.96e-01 9.21e+00 angle pdb=" C13 CLR B 701 " pdb=" C17 CLR B 701 " pdb=" C20 CLR B 701 " ideal model delta sigma weight residual 119.60 112.16 7.44 3.00e+00 1.11e-01 6.14e+00 ... (remaining 12157 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.52: 5116 17.52 - 35.04: 452 35.04 - 52.56: 116 52.56 - 70.07: 14 70.07 - 87.59: 12 Dihedral angle restraints: 5710 sinusoidal: 2564 harmonic: 3146 Sorted by residual: dihedral pdb=" CB GLU B 628 " pdb=" CG GLU B 628 " pdb=" CD GLU B 628 " pdb=" OE1 GLU B 628 " ideal model delta sinusoidal sigma weight residual 0.00 87.59 -87.59 1 3.00e+01 1.11e-03 1.02e+01 dihedral pdb=" CB GLU A 628 " pdb=" CG GLU A 628 " pdb=" CD GLU A 628 " pdb=" OE1 GLU A 628 " ideal model delta sinusoidal sigma weight residual 0.00 87.55 -87.55 1 3.00e+01 1.11e-03 1.02e+01 dihedral pdb=" N LEU B 636 " pdb=" CA LEU B 636 " pdb=" CB LEU B 636 " pdb=" CG LEU B 636 " ideal model delta sinusoidal sigma weight residual -180.00 -120.23 -59.77 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 5707 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 1300 0.072 - 0.144: 94 0.144 - 0.215: 3 0.215 - 0.287: 15 0.287 - 0.359: 8 Chirality restraints: 1420 Sorted by residual: chirality pdb=" C14 CLR A 804 " pdb=" C13 CLR A 804 " pdb=" C15 CLR A 804 " pdb=" C8 CLR A 804 " both_signs ideal model delta sigma weight residual False -2.32 -2.68 0.36 2.00e-01 2.50e+01 3.22e+00 chirality pdb=" C14 CLR B 701 " pdb=" C13 CLR B 701 " pdb=" C15 CLR B 701 " pdb=" C8 CLR B 701 " both_signs ideal model delta sigma weight residual False -2.32 -2.68 0.36 2.00e-01 2.50e+01 3.22e+00 chirality pdb=" C14 CLR B 702 " pdb=" C13 CLR B 702 " pdb=" C15 CLR B 702 " pdb=" C8 CLR B 702 " both_signs ideal model delta sigma weight residual False -2.32 -2.67 0.35 2.00e-01 2.50e+01 3.12e+00 ... (remaining 1417 not shown) Planarity restraints: 1474 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 465 " -0.025 5.00e-02 4.00e+02 3.70e-02 2.19e+00 pdb=" N PRO A 466 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO A 466 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 466 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 465 " 0.025 5.00e-02 4.00e+02 3.70e-02 2.19e+00 pdb=" N PRO B 466 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO B 466 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 466 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR B 416 " 0.005 2.00e-02 2.50e+03 1.01e-02 1.03e+00 pdb=" C THR B 416 " -0.018 2.00e-02 2.50e+03 pdb=" O THR B 416 " 0.007 2.00e-02 2.50e+03 pdb=" N SER B 417 " 0.006 2.00e-02 2.50e+03 ... (remaining 1471 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 688 2.74 - 3.28: 8712 3.28 - 3.82: 14454 3.82 - 4.36: 16851 4.36 - 4.90: 30052 Nonbonded interactions: 70757 Sorted by model distance: nonbonded pdb=" O ILE A 404 " pdb=" OG1 THR A 411 " model vdw 2.202 3.040 nonbonded pdb=" O ILE B 404 " pdb=" OG1 THR B 411 " model vdw 2.202 3.040 nonbonded pdb=" OE1 GLN B 164 " pdb=" OE1 GLN B 242 " model vdw 2.223 3.040 nonbonded pdb=" OE1 GLN A 164 " pdb=" OE1 GLN A 242 " model vdw 2.225 3.040 nonbonded pdb=" O SER A 386 " pdb=" OG SER A 386 " model vdw 2.243 3.040 ... (remaining 70752 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.510 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: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.270 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 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 : 0.002 0.021 8964 Z= 0.129 Angle : 0.655 7.436 12166 Z= 0.339 Chirality : 0.052 0.359 1420 Planarity : 0.003 0.037 1474 Dihedral : 14.260 87.593 3688 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 1.93 % Allowed : 11.16 % Favored : 86.91 % 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 are not related in a simple way. whole: -1.18 (0.24), residues: 1078 helix: 0.39 (0.20), residues: 620 sheet: -0.65 (0.53), residues: 78 loop : -2.83 (0.28), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 150 TYR 0.005 0.001 TYR A 510 PHE 0.006 0.001 PHE A 570 TRP 0.001 0.000 TRP B 480 HIS 0.001 0.000 HIS B 618 Details of bonding type rmsd covalent geometry : bond 0.00220 ( 8962) covalent geometry : angle 0.65492 (12162) SS BOND : bond 0.00057 ( 2) SS BOND : angle 0.84988 ( 4) hydrogen bonds : bond 0.10340 ( 486) hydrogen bonds : angle 4.75071 ( 1422) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 194 time to evaluate : 0.400 Fit side-chains REVERT: A 166 ASP cc_start: 0.7231 (m-30) cc_final: 0.6919 (m-30) REVERT: A 198 LYS cc_start: 0.8073 (tttp) cc_final: 0.7721 (ttpt) REVERT: A 618 HIS cc_start: 0.7980 (t70) cc_final: 0.7528 (t-170) REVERT: A 659 ARG cc_start: 0.7024 (ttt-90) cc_final: 0.6703 (ttm170) REVERT: B 166 ASP cc_start: 0.7197 (m-30) cc_final: 0.6914 (m-30) REVERT: B 198 LYS cc_start: 0.8046 (tttp) cc_final: 0.7744 (ttpt) REVERT: B 618 HIS cc_start: 0.7984 (t70) cc_final: 0.7497 (t-170) REVERT: B 659 ARG cc_start: 0.7027 (ttt-90) cc_final: 0.6700 (ttm170) outliers start: 18 outliers final: 14 residues processed: 204 average time/residue: 0.0932 time to fit residues: 26.1831 Evaluate side-chains 158 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 144 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 445 PHE Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 445 PHE Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain B residue 636 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 0.4980 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 chunk 106 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN A 392 GLN A 620 GLN B 336 GLN ** B 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 620 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.119539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.093798 restraints weight = 10234.624| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 2.00 r_work: 0.2826 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2680 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8964 Z= 0.173 Angle : 0.599 5.684 12166 Z= 0.293 Chirality : 0.042 0.147 1420 Planarity : 0.004 0.045 1474 Dihedral : 7.273 59.658 1728 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 4.94 % Allowed : 13.09 % Favored : 81.97 % 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 are not related in a simple way. whole: -0.20 (0.26), residues: 1078 helix: 1.07 (0.21), residues: 644 sheet: -0.54 (0.51), residues: 78 loop : -2.33 (0.31), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 156 TYR 0.012 0.001 TYR B 602 PHE 0.017 0.002 PHE A 570 TRP 0.004 0.001 TRP A 511 HIS 0.003 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00416 ( 8962) covalent geometry : angle 0.59879 (12162) SS BOND : bond 0.00011 ( 2) SS BOND : angle 0.06628 ( 4) hydrogen bonds : bond 0.03753 ( 486) hydrogen bonds : angle 3.99971 ( 1422) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 130 time to evaluate : 0.315 Fit side-chains revert: symmetry clash REVERT: A 166 ASP cc_start: 0.7449 (m-30) cc_final: 0.7067 (m-30) REVERT: A 198 LYS cc_start: 0.8199 (tttp) cc_final: 0.7676 (ttpt) REVERT: A 285 ASP cc_start: 0.8591 (m-30) cc_final: 0.8370 (m-30) REVERT: A 568 SER cc_start: 0.8869 (t) cc_final: 0.8622 (t) REVERT: A 584 MET cc_start: 0.8086 (mtt) cc_final: 0.7830 (mtt) REVERT: A 591 ARG cc_start: 0.8013 (OUTLIER) cc_final: 0.7511 (ttt-90) REVERT: A 659 ARG cc_start: 0.7373 (ttt-90) cc_final: 0.6872 (ttm170) REVERT: B 166 ASP cc_start: 0.7441 (m-30) cc_final: 0.6995 (m-30) REVERT: B 198 LYS cc_start: 0.8187 (tttp) cc_final: 0.7722 (ttpt) REVERT: B 568 SER cc_start: 0.8911 (t) cc_final: 0.8675 (t) REVERT: B 584 MET cc_start: 0.8065 (mtt) cc_final: 0.7834 (mtt) REVERT: B 591 ARG cc_start: 0.8011 (OUTLIER) cc_final: 0.7529 (ttt-90) REVERT: B 618 HIS cc_start: 0.8051 (t70) cc_final: 0.7754 (t-170) REVERT: B 659 ARG cc_start: 0.7432 (ttt-90) cc_final: 0.6908 (ttm170) outliers start: 46 outliers final: 32 residues processed: 163 average time/residue: 0.0920 time to fit residues: 20.8401 Evaluate side-chains 159 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 125 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 591 ARG Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 632 GLU Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 665 GLU Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 405 MET Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain B residue 591 ARG Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain B residue 632 GLU Chi-restraints excluded: chain B residue 665 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 45 optimal weight: 0.8980 chunk 25 optimal weight: 8.9990 chunk 91 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 92 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 ASN ** B 392 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 = 0.3285 r_free = 0.3285 target = 0.119749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.094125 restraints weight = 10129.751| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 1.98 r_work: 0.2918 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8964 Z= 0.137 Angle : 0.538 5.925 12166 Z= 0.263 Chirality : 0.040 0.140 1420 Planarity : 0.003 0.044 1474 Dihedral : 6.788 58.798 1720 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 4.51 % Allowed : 14.06 % Favored : 81.44 % 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 are not related in a simple way. whole: 0.26 (0.27), residues: 1078 helix: 1.37 (0.22), residues: 646 sheet: -0.25 (0.53), residues: 78 loop : -2.05 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 651 TYR 0.009 0.001 TYR B 592 PHE 0.012 0.001 PHE A 570 TRP 0.004 0.001 TRP A 583 HIS 0.002 0.001 HIS A 183 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 8962) covalent geometry : angle 0.53762 (12162) SS BOND : bond 0.00022 ( 2) SS BOND : angle 0.37136 ( 4) hydrogen bonds : bond 0.03431 ( 486) hydrogen bonds : angle 3.89063 ( 1422) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 131 time to evaluate : 0.332 Fit side-chains REVERT: A 166 ASP cc_start: 0.7441 (m-30) cc_final: 0.7029 (m-30) REVERT: A 198 LYS cc_start: 0.8280 (tttp) cc_final: 0.7756 (ttpt) REVERT: A 285 ASP cc_start: 0.8643 (m-30) cc_final: 0.8396 (m-30) REVERT: A 568 SER cc_start: 0.8797 (t) cc_final: 0.8581 (t) REVERT: A 591 ARG cc_start: 0.8087 (OUTLIER) cc_final: 0.7623 (tmt-80) REVERT: A 659 ARG cc_start: 0.7458 (ttt-90) cc_final: 0.6990 (ttm170) REVERT: B 166 ASP cc_start: 0.7435 (m-30) cc_final: 0.7008 (m-30) REVERT: B 198 LYS cc_start: 0.8270 (tttp) cc_final: 0.7793 (ttpt) REVERT: B 568 SER cc_start: 0.8799 (t) cc_final: 0.8588 (t) REVERT: B 584 MET cc_start: 0.8172 (mtt) cc_final: 0.7881 (mtt) REVERT: B 591 ARG cc_start: 0.8071 (OUTLIER) cc_final: 0.7628 (tmt-80) REVERT: B 618 HIS cc_start: 0.8107 (t70) cc_final: 0.7777 (t-170) REVERT: B 659 ARG cc_start: 0.7459 (ttt-90) cc_final: 0.6973 (ttm170) outliers start: 42 outliers final: 32 residues processed: 157 average time/residue: 0.0814 time to fit residues: 18.4184 Evaluate side-chains 158 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 124 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 389 CYS Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 591 ARG Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 632 GLU Chi-restraints excluded: chain A residue 665 GLU Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain B residue 591 ARG Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain B residue 632 GLU Chi-restraints excluded: chain B residue 665 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 27 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 102 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 95 optimal weight: 0.8980 chunk 31 optimal weight: 0.4980 chunk 32 optimal weight: 0.6980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 392 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 = 0.3271 r_free = 0.3271 target = 0.118750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.093891 restraints weight = 10297.941| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 1.85 r_work: 0.2832 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2691 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8964 Z= 0.141 Angle : 0.539 5.888 12166 Z= 0.264 Chirality : 0.040 0.138 1420 Planarity : 0.004 0.046 1474 Dihedral : 6.535 58.084 1718 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 5.26 % Allowed : 13.73 % Favored : 81.01 % 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 are not related in a simple way. whole: 0.42 (0.27), residues: 1078 helix: 1.39 (0.21), residues: 658 sheet: -0.08 (0.54), residues: 78 loop : -1.88 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 339 TYR 0.009 0.001 TYR B 592 PHE 0.013 0.001 PHE B 570 TRP 0.005 0.001 TRP A 583 HIS 0.002 0.001 HIS A 618 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 8962) covalent geometry : angle 0.53909 (12162) SS BOND : bond 0.00015 ( 2) SS BOND : angle 0.17877 ( 4) hydrogen bonds : bond 0.03398 ( 486) hydrogen bonds : angle 3.82185 ( 1422) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 130 time to evaluate : 0.305 Fit side-chains revert: symmetry clash REVERT: A 166 ASP cc_start: 0.7365 (m-30) cc_final: 0.6957 (m-30) REVERT: A 198 LYS cc_start: 0.8136 (tttp) cc_final: 0.7608 (ttpt) REVERT: A 285 ASP cc_start: 0.8600 (m-30) cc_final: 0.8311 (m-30) REVERT: A 568 SER cc_start: 0.8944 (t) cc_final: 0.8730 (t) REVERT: A 591 ARG cc_start: 0.7964 (OUTLIER) cc_final: 0.7562 (tmt-80) REVERT: A 659 ARG cc_start: 0.7294 (ttt-90) cc_final: 0.6805 (ttm170) REVERT: B 166 ASP cc_start: 0.7371 (m-30) cc_final: 0.6948 (m-30) REVERT: B 198 LYS cc_start: 0.8072 (tttp) cc_final: 0.7575 (ttpt) REVERT: B 568 SER cc_start: 0.8942 (t) cc_final: 0.8734 (t) REVERT: B 591 ARG cc_start: 0.7968 (OUTLIER) cc_final: 0.7556 (tmt-80) REVERT: B 618 HIS cc_start: 0.8109 (t70) cc_final: 0.7826 (t-170) REVERT: B 659 ARG cc_start: 0.7278 (ttt-90) cc_final: 0.6771 (ttm170) outliers start: 49 outliers final: 38 residues processed: 165 average time/residue: 0.0745 time to fit residues: 17.9498 Evaluate side-chains 162 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 122 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 389 CYS Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 591 ARG Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 632 GLU Chi-restraints excluded: chain A residue 665 GLU Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 389 CYS Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain B residue 591 ARG Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain B residue 632 GLU Chi-restraints excluded: chain B residue 665 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 65 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 80 optimal weight: 0.0030 chunk 10 optimal weight: 4.9990 chunk 90 optimal weight: 0.8980 chunk 7 optimal weight: 0.0770 chunk 4 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 overall best weight: 0.9952 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 392 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 = 0.3278 r_free = 0.3278 target = 0.119325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.093679 restraints weight = 10185.701| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 1.98 r_work: 0.2827 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2683 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8964 Z= 0.127 Angle : 0.525 6.265 12166 Z= 0.257 Chirality : 0.039 0.138 1420 Planarity : 0.003 0.044 1474 Dihedral : 6.458 59.895 1718 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 5.69 % Allowed : 14.70 % Favored : 79.61 % 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 are not related in a simple way. whole: 0.60 (0.27), residues: 1078 helix: 1.53 (0.21), residues: 654 sheet: 0.04 (0.55), residues: 78 loop : -1.77 (0.35), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 651 TYR 0.008 0.001 TYR A 592 PHE 0.012 0.001 PHE B 570 TRP 0.004 0.001 TRP A 583 HIS 0.002 0.001 HIS B 171 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 8962) covalent geometry : angle 0.52543 (12162) SS BOND : bond 0.00032 ( 2) SS BOND : angle 0.11191 ( 4) hydrogen bonds : bond 0.03283 ( 486) hydrogen bonds : angle 3.76689 ( 1422) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 124 time to evaluate : 0.325 Fit side-chains revert: symmetry clash REVERT: A 166 ASP cc_start: 0.7407 (m-30) cc_final: 0.6972 (m-30) REVERT: A 198 LYS cc_start: 0.8217 (tttp) cc_final: 0.7691 (ttpt) REVERT: A 285 ASP cc_start: 0.8652 (m-30) cc_final: 0.8377 (m-30) REVERT: A 591 ARG cc_start: 0.8029 (OUTLIER) cc_final: 0.7643 (tmt-80) REVERT: A 659 ARG cc_start: 0.7409 (ttt-90) cc_final: 0.6933 (ttm170) REVERT: B 82 LEU cc_start: 0.7955 (OUTLIER) cc_final: 0.7697 (tt) REVERT: B 166 ASP cc_start: 0.7383 (m-30) cc_final: 0.6931 (m-30) REVERT: B 198 LYS cc_start: 0.8170 (tttp) cc_final: 0.7680 (ttpt) REVERT: B 584 MET cc_start: 0.8089 (mtt) cc_final: 0.7771 (mtt) REVERT: B 591 ARG cc_start: 0.8013 (OUTLIER) cc_final: 0.7630 (tmt-80) REVERT: B 618 HIS cc_start: 0.8175 (t70) cc_final: 0.7927 (t-170) REVERT: B 659 ARG cc_start: 0.7417 (ttt-90) cc_final: 0.6926 (ttm170) outliers start: 53 outliers final: 38 residues processed: 161 average time/residue: 0.0816 time to fit residues: 18.9772 Evaluate side-chains 160 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 119 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 389 CYS Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 591 ARG Chi-restraints excluded: chain A residue 632 GLU Chi-restraints excluded: chain A residue 665 GLU Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain B residue 591 ARG Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 632 GLU Chi-restraints excluded: chain B residue 665 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 13 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 76 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 60 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 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 = 0.3242 r_free = 0.3242 target = 0.116509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.091297 restraints weight = 10299.056| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 1.92 r_work: 0.2796 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2653 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8964 Z= 0.175 Angle : 0.573 6.666 12166 Z= 0.279 Chirality : 0.041 0.139 1420 Planarity : 0.004 0.045 1474 Dihedral : 6.511 57.076 1718 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 5.90 % Allowed : 15.56 % Favored : 78.54 % 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 are not related in a simple way. whole: 0.47 (0.27), residues: 1078 helix: 1.42 (0.21), residues: 656 sheet: -0.03 (0.53), residues: 78 loop : -1.82 (0.35), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 406 TYR 0.010 0.001 TYR B 592 PHE 0.013 0.001 PHE B 570 TRP 0.004 0.001 TRP B 480 HIS 0.003 0.001 HIS B 171 Details of bonding type rmsd covalent geometry : bond 0.00433 ( 8962) covalent geometry : angle 0.57311 (12162) SS BOND : bond 0.00007 ( 2) SS BOND : angle 0.07793 ( 4) hydrogen bonds : bond 0.03672 ( 486) hydrogen bonds : angle 3.88500 ( 1422) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 124 time to evaluate : 0.280 Fit side-chains REVERT: A 166 ASP cc_start: 0.7437 (m-30) cc_final: 0.6993 (m-30) REVERT: A 198 LYS cc_start: 0.8207 (tttp) cc_final: 0.7690 (ttpt) REVERT: A 285 ASP cc_start: 0.8682 (m-30) cc_final: 0.8429 (m-30) REVERT: A 591 ARG cc_start: 0.8150 (OUTLIER) cc_final: 0.7713 (ttt-90) REVERT: A 659 ARG cc_start: 0.7484 (ttt-90) cc_final: 0.6996 (ttm170) REVERT: B 166 ASP cc_start: 0.7435 (m-30) cc_final: 0.6977 (m-30) REVERT: B 198 LYS cc_start: 0.8243 (tttp) cc_final: 0.7727 (ttpt) REVERT: B 591 ARG cc_start: 0.8143 (OUTLIER) cc_final: 0.7697 (ttt-90) REVERT: B 659 ARG cc_start: 0.7484 (ttt-90) cc_final: 0.6979 (ttm170) outliers start: 55 outliers final: 39 residues processed: 162 average time/residue: 0.0863 time to fit residues: 20.1649 Evaluate side-chains 161 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 120 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 389 CYS Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 568 SER Chi-restraints excluded: chain A residue 591 ARG Chi-restraints excluded: chain A residue 665 GLU Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 389 CYS Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 508 ILE Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain B residue 568 SER Chi-restraints excluded: chain B residue 591 ARG Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 665 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 11 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 102 optimal weight: 0.0050 chunk 10 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 1 optimal weight: 0.6980 chunk 98 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 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 = 0.3286 r_free = 0.3286 target = 0.120047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.094952 restraints weight = 10204.147| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 1.88 r_work: 0.2848 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2706 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8964 Z= 0.104 Angle : 0.517 7.363 12166 Z= 0.252 Chirality : 0.038 0.138 1420 Planarity : 0.003 0.044 1474 Dihedral : 6.283 56.620 1718 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 4.72 % Allowed : 16.63 % Favored : 78.65 % 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 are not related in a simple way. whole: 0.84 (0.27), residues: 1078 helix: 1.72 (0.22), residues: 654 sheet: 0.15 (0.54), residues: 78 loop : -1.67 (0.35), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 651 TYR 0.006 0.001 TYR B 602 PHE 0.010 0.001 PHE B 570 TRP 0.004 0.001 TRP A 583 HIS 0.010 0.001 HIS B 618 Details of bonding type rmsd covalent geometry : bond 0.00234 ( 8962) covalent geometry : angle 0.51680 (12162) SS BOND : bond 0.00049 ( 2) SS BOND : angle 0.09846 ( 4) hydrogen bonds : bond 0.03136 ( 486) hydrogen bonds : angle 3.67227 ( 1422) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 128 time to evaluate : 0.334 Fit side-chains REVERT: A 166 ASP cc_start: 0.7294 (m-30) cc_final: 0.6853 (m-30) REVERT: A 198 LYS cc_start: 0.8065 (tttp) cc_final: 0.7538 (ttpt) REVERT: A 285 ASP cc_start: 0.8627 (m-30) cc_final: 0.8356 (m-30) REVERT: A 591 ARG cc_start: 0.7975 (OUTLIER) cc_final: 0.7687 (tmt-80) REVERT: A 659 ARG cc_start: 0.7288 (ttt-90) cc_final: 0.6803 (ttm170) REVERT: B 166 ASP cc_start: 0.7278 (m-30) cc_final: 0.6826 (m-30) REVERT: B 198 LYS cc_start: 0.8082 (tttp) cc_final: 0.7567 (ttpt) REVERT: B 584 MET cc_start: 0.7920 (mtt) cc_final: 0.7594 (mtt) REVERT: B 591 ARG cc_start: 0.7983 (OUTLIER) cc_final: 0.7656 (tmt-80) REVERT: B 628 GLU cc_start: 0.8039 (tp30) cc_final: 0.7680 (tp30) REVERT: B 659 ARG cc_start: 0.7275 (ttt-90) cc_final: 0.6784 (ttm170) outliers start: 44 outliers final: 29 residues processed: 157 average time/residue: 0.0832 time to fit residues: 18.9175 Evaluate side-chains 155 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 124 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 389 CYS Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 591 ARG Chi-restraints excluded: chain A residue 665 GLU Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 389 CYS Chi-restraints excluded: chain B residue 405 MET Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 591 ARG Chi-restraints excluded: chain B residue 665 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 46 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 6 optimal weight: 8.9990 chunk 2 optimal weight: 5.9990 chunk 82 optimal weight: 0.7980 chunk 103 optimal weight: 0.0570 chunk 37 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 88 optimal weight: 0.9990 chunk 60 optimal weight: 8.9990 overall best weight: 1.5704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 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 = 0.3239 r_free = 0.3239 target = 0.116280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.091223 restraints weight = 10309.424| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 1.91 r_work: 0.2793 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2650 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8964 Z= 0.175 Angle : 0.590 7.716 12166 Z= 0.283 Chirality : 0.042 0.138 1420 Planarity : 0.004 0.045 1474 Dihedral : 6.314 53.687 1716 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 4.51 % Allowed : 16.95 % Favored : 78.54 % 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 are not related in a simple way. whole: 0.66 (0.27), residues: 1078 helix: 1.55 (0.21), residues: 652 sheet: 0.09 (0.54), residues: 78 loop : -1.67 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 339 TYR 0.009 0.001 TYR A 592 PHE 0.013 0.001 PHE B 465 TRP 0.004 0.001 TRP B 480 HIS 0.009 0.001 HIS B 618 Details of bonding type rmsd covalent geometry : bond 0.00434 ( 8962) covalent geometry : angle 0.58967 (12162) SS BOND : bond 0.00063 ( 2) SS BOND : angle 0.40581 ( 4) hydrogen bonds : bond 0.03678 ( 486) hydrogen bonds : angle 3.85573 ( 1422) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 126 time to evaluate : 0.338 Fit side-chains REVERT: A 166 ASP cc_start: 0.7412 (m-30) cc_final: 0.6975 (m-30) REVERT: A 198 LYS cc_start: 0.8169 (tttp) cc_final: 0.7658 (ttpt) REVERT: A 285 ASP cc_start: 0.8686 (m-30) cc_final: 0.8406 (m-30) REVERT: A 319 HIS cc_start: 0.8823 (OUTLIER) cc_final: 0.8515 (m-70) REVERT: A 591 ARG cc_start: 0.8117 (OUTLIER) cc_final: 0.7713 (ttt-90) REVERT: A 659 ARG cc_start: 0.7444 (ttt-90) cc_final: 0.6948 (ttm170) REVERT: B 166 ASP cc_start: 0.7403 (m-30) cc_final: 0.6949 (m-30) REVERT: B 198 LYS cc_start: 0.8152 (tttp) cc_final: 0.7641 (ttpt) REVERT: B 319 HIS cc_start: 0.8828 (OUTLIER) cc_final: 0.8514 (m-70) REVERT: B 591 ARG cc_start: 0.8112 (OUTLIER) cc_final: 0.7701 (ttt-90) REVERT: B 628 GLU cc_start: 0.8199 (tp30) cc_final: 0.7749 (tp30) REVERT: B 659 ARG cc_start: 0.7452 (ttt-90) cc_final: 0.6948 (ttm170) outliers start: 42 outliers final: 32 residues processed: 155 average time/residue: 0.0837 time to fit residues: 18.5972 Evaluate side-chains 157 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 121 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 319 HIS Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 389 CYS Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 591 ARG Chi-restraints excluded: chain A residue 665 GLU Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 319 HIS Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 389 CYS Chi-restraints excluded: chain B residue 405 MET Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 591 ARG Chi-restraints excluded: chain B residue 665 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 47 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 13 optimal weight: 0.7980 chunk 26 optimal weight: 7.9990 chunk 80 optimal weight: 8.9990 chunk 95 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 91 optimal weight: 0.4980 chunk 81 optimal weight: 0.6980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 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 = 0.3262 r_free = 0.3262 target = 0.118234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.093507 restraints weight = 10202.253| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 1.84 r_work: 0.2831 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2690 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8964 Z= 0.129 Angle : 0.554 8.156 12166 Z= 0.268 Chirality : 0.040 0.138 1420 Planarity : 0.004 0.044 1474 Dihedral : 6.175 52.978 1716 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 4.29 % Allowed : 17.17 % Favored : 78.54 % 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 are not related in a simple way. whole: 0.83 (0.27), residues: 1078 helix: 1.67 (0.21), residues: 654 sheet: 0.20 (0.55), residues: 78 loop : -1.60 (0.35), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 406 TYR 0.007 0.001 TYR A 429 PHE 0.011 0.001 PHE B 570 TRP 0.004 0.001 TRP A 583 HIS 0.010 0.001 HIS B 618 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 8962) covalent geometry : angle 0.55379 (12162) SS BOND : bond 0.00014 ( 2) SS BOND : angle 0.52556 ( 4) hydrogen bonds : bond 0.03360 ( 486) hydrogen bonds : angle 3.77422 ( 1422) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 124 time to evaluate : 0.314 Fit side-chains REVERT: A 166 ASP cc_start: 0.7315 (m-30) cc_final: 0.6879 (m-30) REVERT: A 198 LYS cc_start: 0.8093 (tttp) cc_final: 0.7581 (ttpt) REVERT: A 285 ASP cc_start: 0.8620 (m-30) cc_final: 0.8331 (m-30) REVERT: A 319 HIS cc_start: 0.8781 (OUTLIER) cc_final: 0.8471 (m-70) REVERT: A 591 ARG cc_start: 0.8038 (OUTLIER) cc_final: 0.7697 (tmt-80) REVERT: A 628 GLU cc_start: 0.8065 (tp30) cc_final: 0.7738 (tp30) REVERT: A 659 ARG cc_start: 0.7318 (ttt-90) cc_final: 0.6826 (ttm170) REVERT: B 166 ASP cc_start: 0.7298 (m-30) cc_final: 0.6852 (m-30) REVERT: B 198 LYS cc_start: 0.8112 (tttp) cc_final: 0.7598 (ttpt) REVERT: B 319 HIS cc_start: 0.8740 (OUTLIER) cc_final: 0.8436 (m-70) REVERT: B 591 ARG cc_start: 0.8043 (OUTLIER) cc_final: 0.7695 (tmt-80) REVERT: B 628 GLU cc_start: 0.8006 (tp30) cc_final: 0.7695 (tp30) REVERT: B 659 ARG cc_start: 0.7308 (ttt-90) cc_final: 0.6817 (ttm170) outliers start: 40 outliers final: 30 residues processed: 154 average time/residue: 0.0778 time to fit residues: 17.1525 Evaluate side-chains 156 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 122 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 319 HIS Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 389 CYS Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 591 ARG Chi-restraints excluded: chain A residue 665 GLU Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 319 HIS Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 389 CYS Chi-restraints excluded: chain B residue 405 MET Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 591 ARG Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 665 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 89 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 6 optimal weight: 6.9990 chunk 18 optimal weight: 0.4980 chunk 58 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 60 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 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 = 0.3264 r_free = 0.3264 target = 0.118419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.092995 restraints weight = 10185.013| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 1.98 r_work: 0.2826 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2681 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8964 Z= 0.130 Angle : 0.552 8.428 12166 Z= 0.268 Chirality : 0.040 0.137 1420 Planarity : 0.003 0.045 1474 Dihedral : 6.143 51.987 1716 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 3.76 % Allowed : 17.60 % Favored : 78.65 % 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 are not related in a simple way. whole: 0.92 (0.27), residues: 1078 helix: 1.75 (0.21), residues: 650 sheet: 0.21 (0.55), residues: 78 loop : -1.53 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 651 TYR 0.007 0.001 TYR B 602 PHE 0.011 0.001 PHE A 570 TRP 0.003 0.001 TRP A 583 HIS 0.009 0.001 HIS B 618 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 8962) covalent geometry : angle 0.55245 (12162) SS BOND : bond 0.00071 ( 2) SS BOND : angle 0.51009 ( 4) hydrogen bonds : bond 0.03343 ( 486) hydrogen bonds : angle 3.74905 ( 1422) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 124 time to evaluate : 0.317 Fit side-chains REVERT: A 166 ASP cc_start: 0.7378 (m-30) cc_final: 0.6930 (m-30) REVERT: A 198 LYS cc_start: 0.8179 (tttp) cc_final: 0.7674 (ttpt) REVERT: A 285 ASP cc_start: 0.8667 (m-30) cc_final: 0.8401 (m-30) REVERT: A 319 HIS cc_start: 0.8848 (OUTLIER) cc_final: 0.8554 (m-70) REVERT: A 591 ARG cc_start: 0.8114 (OUTLIER) cc_final: 0.7796 (tmt-80) REVERT: A 628 GLU cc_start: 0.8134 (tp30) cc_final: 0.7821 (tp30) REVERT: A 659 ARG cc_start: 0.7454 (ttt-90) cc_final: 0.6970 (ttm170) REVERT: B 166 ASP cc_start: 0.7359 (m-30) cc_final: 0.6903 (m-30) REVERT: B 198 LYS cc_start: 0.8205 (tttp) cc_final: 0.7692 (ttpt) REVERT: B 319 HIS cc_start: 0.8807 (OUTLIER) cc_final: 0.8454 (m-70) REVERT: B 591 ARG cc_start: 0.8113 (OUTLIER) cc_final: 0.7794 (tmt-80) REVERT: B 628 GLU cc_start: 0.8080 (tp30) cc_final: 0.7766 (tp30) REVERT: B 659 ARG cc_start: 0.7441 (ttt-90) cc_final: 0.6958 (ttm170) outliers start: 35 outliers final: 30 residues processed: 149 average time/residue: 0.0807 time to fit residues: 17.5195 Evaluate side-chains 155 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 121 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 319 HIS Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 389 CYS Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 591 ARG Chi-restraints excluded: chain A residue 665 GLU Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 319 HIS Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 389 CYS Chi-restraints excluded: chain B residue 405 MET Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 591 ARG Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 665 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 78 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 98 optimal weight: 0.3980 chunk 34 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 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 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 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 = 0.3264 r_free = 0.3264 target = 0.118423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.093010 restraints weight = 10157.228| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 1.97 r_work: 0.2816 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2673 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8964 Z= 0.133 Angle : 0.555 8.446 12166 Z= 0.268 Chirality : 0.040 0.137 1420 Planarity : 0.003 0.044 1474 Dihedral : 6.131 51.028 1716 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 3.86 % Allowed : 17.49 % Favored : 78.65 % 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 are not related in a simple way. whole: 0.96 (0.27), residues: 1078 helix: 1.77 (0.21), residues: 650 sheet: 0.21 (0.55), residues: 78 loop : -1.49 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 339 TYR 0.007 0.001 TYR A 429 PHE 0.011 0.001 PHE A 465 TRP 0.003 0.001 TRP A 583 HIS 0.010 0.001 HIS B 618 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 8962) covalent geometry : angle 0.55528 (12162) SS BOND : bond 0.00038 ( 2) SS BOND : angle 0.53793 ( 4) hydrogen bonds : bond 0.03350 ( 486) hydrogen bonds : angle 3.75328 ( 1422) =============================================================================== Job complete usr+sys time: 2159.38 seconds wall clock time: 37 minutes 43.29 seconds (2263.29 seconds total)