Starting phenix.real_space_refine on Thu Feb 13 04:32:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7r8d_24316/02_2025/7r8d_24316.cif Found real_map, /net/cci-nas-00/data/ceres_data/7r8d_24316/02_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7r8d_24316/02_2025/7r8d_24316.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7r8d_24316/02_2025/7r8d_24316.map" model { file = "/net/cci-nas-00/data/ceres_data/7r8d_24316/02_2025/7r8d_24316.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7r8d_24316/02_2025/7r8d_24316.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 5.48, per 1000 atoms: 0.63 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: 2.41 Conformation dependent library (CDL) restraints added in 996.6 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: 1.00 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: 2.66 Time building geometry restraints manager: 2.76 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: 0.04 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: 0.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 23.310 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.480 ------------------------------------------------------------------------------- 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 8962 Z= 0.139 Angle : 0.655 7.436 12162 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (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 TRP 0.001 0.000 TRP B 480 HIS 0.001 0.000 HIS B 618 PHE 0.006 0.001 PHE A 570 TYR 0.005 0.001 TYR A 510 ARG 0.001 0.000 ARG B 150 *********************** 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 : 0.906 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: 0.2160 time to fit residues: 59.9065 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 : 0.868 ------------------------------------------------------------------------------- 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 91 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 43 optimal weight: 0.1980 chunk 84 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 63 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 overall best weight: 2.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN A 337 ASN A 392 GLN A 620 GLN B 336 GLN B 337 ASN ** B 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 620 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.115236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.089990 restraints weight = 10255.372| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 1.91 r_work: 0.2775 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2631 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.042 8962 Z= 0.442 Angle : 0.684 6.621 12162 Z= 0.334 Chirality : 0.046 0.156 1420 Planarity : 0.004 0.048 1474 Dihedral : 7.423 59.269 1728 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 5.90 % Allowed : 12.12 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.26), residues: 1078 helix: 0.76 (0.21), residues: 650 sheet: -0.57 (0.52), residues: 78 loop : -2.35 (0.32), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 511 HIS 0.005 0.001 HIS B 183 PHE 0.019 0.002 PHE B 570 TYR 0.014 0.002 TYR B 602 ARG 0.005 0.001 ARG B 156 *********************** 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 180 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 125 time to evaluate : 1.066 Fit side-chains REVERT: A 166 ASP cc_start: 0.7522 (m-30) cc_final: 0.7095 (m-30) REVERT: A 198 LYS cc_start: 0.8189 (tttp) cc_final: 0.7673 (ttpt) REVERT: A 285 ASP cc_start: 0.8657 (m-30) cc_final: 0.8450 (m-30) REVERT: A 591 ARG cc_start: 0.8131 (OUTLIER) cc_final: 0.7562 (ttt-90) REVERT: A 618 HIS cc_start: 0.8013 (t70) cc_final: 0.7786 (t-170) REVERT: A 659 ARG cc_start: 0.7451 (ttt-90) cc_final: 0.6945 (ttm170) REVERT: B 166 ASP cc_start: 0.7499 (m-30) cc_final: 0.7055 (m-30) REVERT: B 198 LYS cc_start: 0.8211 (tttp) cc_final: 0.7723 (ttpt) REVERT: B 584 MET cc_start: 0.8188 (mtt) cc_final: 0.7911 (mtt) REVERT: B 591 ARG cc_start: 0.8135 (OUTLIER) cc_final: 0.7561 (ttt-90) REVERT: B 618 HIS cc_start: 0.8061 (t70) cc_final: 0.7806 (t-170) REVERT: B 659 ARG cc_start: 0.7466 (ttt-90) cc_final: 0.6966 (ttm170) outliers start: 55 outliers final: 38 residues processed: 161 average time/residue: 0.2004 time to fit residues: 45.8904 Evaluate side-chains 157 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 117 time to evaluate : 1.045 ------------------------------------------------------------------------------- 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 202 THR 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 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 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 202 THR 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 405 MET 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 636 LEU 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 97 optimal weight: 0.9980 chunk 70 optimal weight: 0.3980 chunk 12 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 86 optimal weight: 0.8980 chunk 61 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 87 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 ASN B 337 ASN ** B 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.119664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.094706 restraints weight = 10205.709| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 1.88 r_work: 0.3044 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8962 Z= 0.178 Angle : 0.529 5.743 12162 Z= 0.261 Chirality : 0.039 0.141 1420 Planarity : 0.004 0.045 1474 Dihedral : 6.970 58.857 1724 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 4.18 % Allowed : 14.48 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.27), residues: 1078 helix: 1.33 (0.22), residues: 644 sheet: -0.31 (0.53), residues: 78 loop : -2.09 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 583 HIS 0.002 0.000 HIS B 171 PHE 0.012 0.001 PHE B 570 TYR 0.007 0.001 TYR A 602 ARG 0.002 0.000 ARG A 156 *********************** 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 162 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 123 time to evaluate : 0.745 Fit side-chains revert: symmetry clash REVERT: A 166 ASP cc_start: 0.7503 (m-30) cc_final: 0.7093 (m-30) REVERT: A 198 LYS cc_start: 0.8335 (tttp) cc_final: 0.7822 (ttpt) REVERT: A 285 ASP cc_start: 0.8659 (m-30) cc_final: 0.8413 (m-30) REVERT: A 568 SER cc_start: 0.8779 (t) cc_final: 0.8536 (t) REVERT: A 591 ARG cc_start: 0.8122 (OUTLIER) cc_final: 0.7618 (tmt-80) REVERT: A 659 ARG cc_start: 0.7557 (ttt-90) cc_final: 0.7100 (ttm170) REVERT: B 166 ASP cc_start: 0.7493 (m-30) cc_final: 0.7082 (m-30) REVERT: B 198 LYS cc_start: 0.8313 (tttp) cc_final: 0.7836 (ttpt) REVERT: B 568 SER cc_start: 0.8774 (t) cc_final: 0.8549 (t) REVERT: B 584 MET cc_start: 0.8225 (mtt) cc_final: 0.7961 (mtt) REVERT: B 591 ARG cc_start: 0.8120 (OUTLIER) cc_final: 0.7637 (tmt-80) REVERT: B 659 ARG cc_start: 0.7547 (ttt-90) cc_final: 0.7069 (ttm170) outliers start: 39 outliers final: 28 residues processed: 151 average time/residue: 0.1908 time to fit residues: 40.7487 Evaluate side-chains 150 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 120 time to evaluate : 1.131 ------------------------------------------------------------------------------- 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 469 MET Chi-restraints excluded: chain A residue 509 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 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 469 MET Chi-restraints excluded: chain B residue 509 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 46 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 chunk 96 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 chunk 24 optimal weight: 0.4980 chunk 54 optimal weight: 6.9990 chunk 94 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3287 r_free = 0.3287 target = 0.120047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.095016 restraints weight = 10135.227| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 1.88 r_work: 0.2850 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2707 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8962 Z= 0.175 Angle : 0.518 5.824 12162 Z= 0.255 Chirality : 0.039 0.138 1420 Planarity : 0.003 0.045 1474 Dihedral : 6.472 57.802 1718 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 4.72 % Allowed : 15.45 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.27), residues: 1078 helix: 1.53 (0.22), residues: 648 sheet: -0.09 (0.55), residues: 78 loop : -1.94 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 583 HIS 0.002 0.001 HIS B 171 PHE 0.012 0.001 PHE A 570 TYR 0.008 0.001 TYR A 602 ARG 0.002 0.000 ARG A 156 *********************** 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 170 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 126 time to evaluate : 0.931 Fit side-chains REVERT: A 166 ASP cc_start: 0.7356 (m-30) cc_final: 0.6947 (m-30) REVERT: A 198 LYS cc_start: 0.8119 (tttp) cc_final: 0.7597 (ttpt) REVERT: A 285 ASP cc_start: 0.8594 (m-30) cc_final: 0.8293 (m-30) REVERT: A 568 SER cc_start: 0.8891 (t) cc_final: 0.8658 (t) REVERT: A 591 ARG cc_start: 0.7925 (OUTLIER) cc_final: 0.7521 (tmt-80) REVERT: A 659 ARG cc_start: 0.7275 (ttt-90) cc_final: 0.6801 (ttm170) REVERT: B 166 ASP cc_start: 0.7348 (m-30) cc_final: 0.6929 (m-30) REVERT: B 198 LYS cc_start: 0.8080 (tttp) cc_final: 0.7581 (ttpt) REVERT: B 568 SER cc_start: 0.8876 (t) cc_final: 0.8655 (t) REVERT: B 584 MET cc_start: 0.7985 (mtt) cc_final: 0.7687 (mtt) REVERT: B 591 ARG cc_start: 0.7925 (OUTLIER) cc_final: 0.7507 (tmt-80) REVERT: B 659 ARG cc_start: 0.7281 (ttt-90) cc_final: 0.6784 (ttm170) outliers start: 44 outliers final: 33 residues processed: 155 average time/residue: 0.1850 time to fit residues: 40.9737 Evaluate side-chains 152 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 117 time to evaluate : 0.767 ------------------------------------------------------------------------------- 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 389 CYS Chi-restraints excluded: chain A residue 405 MET Chi-restraints excluded: chain A residue 410 LEU 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 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 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 410 LEU 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 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 81 optimal weight: 4.9990 chunk 15 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 104 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 13 optimal weight: 0.0570 chunk 4 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 overall best weight: 1.3904 ------------------------------------------------------------------------------- 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 = 0.3255 r_free = 0.3255 target = 0.117407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.091682 restraints weight = 10186.337| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 1.99 r_work: 0.2795 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2651 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 8962 Z= 0.250 Angle : 0.562 6.209 12162 Z= 0.275 Chirality : 0.041 0.142 1420 Planarity : 0.004 0.045 1474 Dihedral : 6.520 59.757 1718 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 5.58 % Allowed : 15.56 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.27), residues: 1078 helix: 1.45 (0.21), residues: 648 sheet: 0.03 (0.56), residues: 78 loop : -1.84 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 583 HIS 0.002 0.001 HIS A 171 PHE 0.014 0.001 PHE B 570 TYR 0.010 0.001 TYR A 592 ARG 0.002 0.000 ARG A 156 *********************** 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: 52 poor density : 125 time to evaluate : 0.929 Fit side-chains REVERT: A 166 ASP cc_start: 0.7463 (m-30) cc_final: 0.7032 (m-30) REVERT: A 198 LYS cc_start: 0.8169 (tttp) cc_final: 0.7643 (ttpt) REVERT: A 285 ASP cc_start: 0.8647 (m-30) cc_final: 0.8385 (m-30) REVERT: A 591 ARG cc_start: 0.8054 (OUTLIER) cc_final: 0.7656 (ttt-90) REVERT: A 659 ARG cc_start: 0.7428 (ttt-90) cc_final: 0.6942 (ttm170) REVERT: B 82 LEU cc_start: 0.7946 (OUTLIER) cc_final: 0.7690 (tt) REVERT: B 166 ASP cc_start: 0.7464 (m-30) cc_final: 0.7023 (m-30) REVERT: B 198 LYS cc_start: 0.8196 (tttp) cc_final: 0.7690 (ttpt) REVERT: B 591 ARG cc_start: 0.8048 (OUTLIER) cc_final: 0.7645 (ttt-90) REVERT: B 659 ARG cc_start: 0.7426 (ttt-90) cc_final: 0.6927 (ttm170) outliers start: 52 outliers final: 41 residues processed: 159 average time/residue: 0.1987 time to fit residues: 45.2875 Evaluate side-chains 165 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 121 time to evaluate : 0.912 ------------------------------------------------------------------------------- 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 405 MET Chi-restraints excluded: chain A residue 410 LEU 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 508 ILE 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 591 ARG 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 82 LEU 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 432 ILE Chi-restraints excluded: chain B residue 495 VAL 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 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 101 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 49 optimal weight: 6.9990 chunk 57 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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 = 0.3220 r_free = 0.3220 target = 0.114866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.089346 restraints weight = 10290.364| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 1.98 r_work: 0.2760 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2618 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 8962 Z= 0.337 Angle : 0.610 6.572 12162 Z= 0.298 Chirality : 0.043 0.144 1420 Planarity : 0.004 0.046 1474 Dihedral : 6.590 55.445 1718 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 6.44 % Allowed : 15.45 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.27), residues: 1078 helix: 1.32 (0.21), residues: 650 sheet: -0.06 (0.54), residues: 78 loop : -1.92 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 480 HIS 0.003 0.001 HIS A 171 PHE 0.015 0.002 PHE A 570 TYR 0.011 0.001 TYR A 592 ARG 0.003 0.000 ARG A 156 *********************** 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: 60 poor density : 119 time to evaluate : 1.015 Fit side-chains REVERT: A 166 ASP cc_start: 0.7482 (m-30) cc_final: 0.7042 (m-30) REVERT: A 198 LYS cc_start: 0.8164 (tttp) cc_final: 0.7653 (ttpt) REVERT: A 285 ASP cc_start: 0.8674 (m-30) cc_final: 0.8434 (m-30) REVERT: A 591 ARG cc_start: 0.8182 (OUTLIER) cc_final: 0.7723 (ttt-90) REVERT: A 659 ARG cc_start: 0.7475 (ttt-90) cc_final: 0.7013 (ttm170) REVERT: B 82 LEU cc_start: 0.7943 (OUTLIER) cc_final: 0.7694 (tt) REVERT: B 166 ASP cc_start: 0.7452 (m-30) cc_final: 0.7000 (m-30) REVERT: B 198 LYS cc_start: 0.8159 (tttp) cc_final: 0.7645 (ttpt) REVERT: B 591 ARG cc_start: 0.8170 (OUTLIER) cc_final: 0.7703 (ttt-90) REVERT: B 659 ARG cc_start: 0.7476 (ttt-90) cc_final: 0.7006 (ttm170) outliers start: 60 outliers final: 46 residues processed: 160 average time/residue: 0.1838 time to fit residues: 43.0588 Evaluate side-chains 163 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 114 time to evaluate : 0.964 ------------------------------------------------------------------------------- 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 405 MET Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 469 MET Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 508 ILE 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 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 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 432 ILE Chi-restraints excluded: chain B residue 469 MET 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 632 GLU 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 50 optimal weight: 0.9980 chunk 91 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 96 optimal weight: 0.5980 chunk 36 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3267 r_free = 0.3267 target = 0.118586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.093749 restraints weight = 10183.301| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 1.85 r_work: 0.2833 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2693 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8962 Z= 0.183 Angle : 0.531 7.224 12162 Z= 0.260 Chirality : 0.039 0.139 1420 Planarity : 0.004 0.045 1474 Dihedral : 6.290 54.741 1718 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 4.61 % Allowed : 17.38 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.27), residues: 1078 helix: 1.64 (0.22), residues: 646 sheet: 0.09 (0.54), residues: 78 loop : -1.78 (0.34), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 583 HIS 0.003 0.001 HIS A 171 PHE 0.010 0.001 PHE A 570 TYR 0.007 0.001 TYR B 602 ARG 0.001 0.000 ARG B 651 *********************** 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 167 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 124 time to evaluate : 1.018 Fit side-chains REVERT: A 166 ASP cc_start: 0.7336 (m-30) cc_final: 0.6908 (m-30) REVERT: A 198 LYS cc_start: 0.8077 (tttp) cc_final: 0.7572 (ttpt) REVERT: A 285 ASP cc_start: 0.8630 (m-30) cc_final: 0.8321 (m-30) REVERT: A 591 ARG cc_start: 0.8027 (OUTLIER) cc_final: 0.7686 (tmt-80) REVERT: A 628 GLU cc_start: 0.8006 (tp30) cc_final: 0.7687 (tp30) REVERT: A 659 ARG cc_start: 0.7323 (ttt-90) cc_final: 0.6840 (ttm170) REVERT: B 166 ASP cc_start: 0.7312 (m-30) cc_final: 0.6881 (m-30) REVERT: B 198 LYS cc_start: 0.8116 (tttp) cc_final: 0.7602 (ttpt) REVERT: B 591 ARG cc_start: 0.8037 (OUTLIER) cc_final: 0.7685 (tmt-80) REVERT: B 628 GLU cc_start: 0.8135 (tp30) cc_final: 0.7776 (tp30) REVERT: B 659 ARG cc_start: 0.7303 (ttt-90) cc_final: 0.6823 (ttm170) outliers start: 43 outliers final: 32 residues processed: 152 average time/residue: 0.1953 time to fit residues: 42.6094 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 : 0.959 ------------------------------------------------------------------------------- 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 410 LEU Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 469 MET 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 564 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 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 432 ILE Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 469 MET 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 665 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 81 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 7 optimal weight: 0.0270 chunk 69 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 19 optimal weight: 0.9980 overall best weight: 0.7638 ------------------------------------------------------------------------------- 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 = 0.3279 r_free = 0.3279 target = 0.119578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.094684 restraints weight = 10303.892| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 1.86 r_work: 0.2846 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2706 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8962 Z= 0.170 Angle : 0.533 7.842 12162 Z= 0.259 Chirality : 0.039 0.139 1420 Planarity : 0.003 0.045 1474 Dihedral : 6.212 53.643 1718 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 4.18 % Allowed : 17.70 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.27), residues: 1078 helix: 1.76 (0.22), residues: 648 sheet: 0.24 (0.55), residues: 78 loop : -1.61 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 583 HIS 0.003 0.001 HIS A 171 PHE 0.010 0.001 PHE A 570 TYR 0.006 0.001 TYR A 602 ARG 0.001 0.000 ARG B 651 *********************** 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 166 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 127 time to evaluate : 0.939 Fit side-chains REVERT: A 166 ASP cc_start: 0.7288 (m-30) cc_final: 0.6857 (m-30) REVERT: A 198 LYS cc_start: 0.8076 (tttp) cc_final: 0.7562 (ttpt) REVERT: A 285 ASP cc_start: 0.8623 (m-30) cc_final: 0.8303 (m-30) REVERT: A 591 ARG cc_start: 0.8000 (OUTLIER) cc_final: 0.7683 (tmt-80) REVERT: A 628 GLU cc_start: 0.7993 (tp30) cc_final: 0.7646 (tp30) REVERT: A 659 ARG cc_start: 0.7324 (ttt-90) cc_final: 0.6846 (ttm170) REVERT: B 166 ASP cc_start: 0.7284 (m-30) cc_final: 0.6850 (m-30) REVERT: B 198 LYS cc_start: 0.8116 (tttp) cc_final: 0.7602 (ttpt) REVERT: B 591 ARG cc_start: 0.8015 (OUTLIER) cc_final: 0.7655 (tmt-80) REVERT: B 628 GLU cc_start: 0.8122 (tp30) cc_final: 0.7756 (tp30) REVERT: B 659 ARG cc_start: 0.7309 (ttt-90) cc_final: 0.6835 (ttm170) outliers start: 39 outliers final: 33 residues processed: 153 average time/residue: 0.2053 time to fit residues: 45.0793 Evaluate side-chains 158 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 123 time to evaluate : 1.110 ------------------------------------------------------------------------------- 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 207 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 389 CYS Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 469 MET 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 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 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 432 ILE Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 469 MET 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 95 optimal weight: 3.9990 chunk 54 optimal weight: 6.9990 chunk 48 optimal weight: 0.0980 chunk 65 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 98 optimal weight: 0.2980 chunk 87 optimal weight: 0.7980 chunk 41 optimal weight: 0.8980 overall best weight: 0.6182 ------------------------------------------------------------------------------- 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 = 0.3297 r_free = 0.3297 target = 0.121013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.095333 restraints weight = 10122.065| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 2.00 r_work: 0.2889 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2745 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8962 Z= 0.149 Angle : 0.518 8.300 12162 Z= 0.252 Chirality : 0.038 0.139 1420 Planarity : 0.003 0.045 1474 Dihedral : 6.034 53.160 1716 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.65 % Allowed : 18.24 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.27), residues: 1078 helix: 1.88 (0.22), residues: 648 sheet: 0.35 (0.55), residues: 78 loop : -1.52 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 583 HIS 0.003 0.000 HIS A 171 PHE 0.009 0.001 PHE A 570 TYR 0.006 0.001 TYR B 429 ARG 0.003 0.000 ARG A 339 *********************** 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 163 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 129 time to evaluate : 0.905 Fit side-chains REVERT: A 166 ASP cc_start: 0.7304 (m-30) cc_final: 0.6854 (m-30) REVERT: A 198 LYS cc_start: 0.8186 (tttp) cc_final: 0.7668 (ttpt) REVERT: A 285 ASP cc_start: 0.8633 (m-30) cc_final: 0.8329 (m-30) REVERT: A 591 ARG cc_start: 0.8056 (OUTLIER) cc_final: 0.7821 (tmt-80) REVERT: A 628 GLU cc_start: 0.7995 (tp30) cc_final: 0.7668 (tp30) REVERT: A 659 ARG cc_start: 0.7444 (ttt-90) cc_final: 0.6952 (ttm170) REVERT: B 166 ASP cc_start: 0.7285 (m-30) cc_final: 0.6840 (m-30) REVERT: B 198 LYS cc_start: 0.8209 (tttp) cc_final: 0.7710 (ttpt) REVERT: B 591 ARG cc_start: 0.8057 (OUTLIER) cc_final: 0.7814 (tmt-80) REVERT: B 628 GLU cc_start: 0.8131 (tp30) cc_final: 0.7771 (tp30) REVERT: B 659 ARG cc_start: 0.7444 (ttt-90) cc_final: 0.6947 (ttm170) outliers start: 34 outliers final: 31 residues processed: 154 average time/residue: 0.1840 time to fit residues: 40.8038 Evaluate side-chains 159 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 126 time to evaluate : 0.977 ------------------------------------------------------------------------------- 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 344 VAL Chi-restraints excluded: chain A residue 389 CYS Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 439 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 597 VAL 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 207 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 432 ILE Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 469 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 94 optimal weight: 3.9990 chunk 6 optimal weight: 6.9990 chunk 13 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 80 optimal weight: 8.9990 chunk 86 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 overall best weight: 1.3986 ------------------------------------------------------------------------------- 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 = 0.3248 r_free = 0.3248 target = 0.117014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.091507 restraints weight = 10296.407| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 1.98 r_work: 0.2793 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2650 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8962 Z= 0.256 Angle : 0.580 8.313 12162 Z= 0.280 Chirality : 0.041 0.138 1420 Planarity : 0.004 0.045 1474 Dihedral : 6.216 50.326 1716 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 4.08 % Allowed : 17.60 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.27), residues: 1078 helix: 1.75 (0.21), residues: 648 sheet: 0.22 (0.54), residues: 78 loop : -1.57 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 480 HIS 0.003 0.001 HIS B 171 PHE 0.013 0.001 PHE A 465 TYR 0.008 0.001 TYR A 429 ARG 0.001 0.000 ARG A 406 ********************** 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 162 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 124 time to evaluate : 0.880 Fit side-chains REVERT: A 166 ASP cc_start: 0.7348 (m-30) cc_final: 0.6904 (m-30) REVERT: A 198 LYS cc_start: 0.8144 (tttp) cc_final: 0.7624 (ttpt) REVERT: A 285 ASP cc_start: 0.8678 (m-30) cc_final: 0.8396 (m-30) REVERT: A 591 ARG cc_start: 0.8093 (OUTLIER) cc_final: 0.7729 (ttt-90) REVERT: A 628 GLU cc_start: 0.8115 (tp30) cc_final: 0.7761 (tp30) REVERT: A 659 ARG cc_start: 0.7443 (ttt-90) cc_final: 0.6953 (ttm170) REVERT: B 166 ASP cc_start: 0.7335 (m-30) cc_final: 0.6896 (m-30) REVERT: B 198 LYS cc_start: 0.8136 (tttp) cc_final: 0.7618 (ttpt) REVERT: B 591 ARG cc_start: 0.8088 (OUTLIER) cc_final: 0.7717 (ttt-90) REVERT: B 628 GLU cc_start: 0.8261 (tp30) cc_final: 0.7799 (tp30) REVERT: B 659 ARG cc_start: 0.7436 (ttt-90) cc_final: 0.6946 (ttm170) outliers start: 38 outliers final: 33 residues processed: 151 average time/residue: 0.1848 time to fit residues: 40.3144 Evaluate side-chains 156 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 121 time to evaluate : 0.987 ------------------------------------------------------------------------------- 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 207 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 389 CYS Chi-restraints excluded: chain A residue 410 LEU 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 597 VAL 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 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 432 ILE Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 469 MET 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 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 58 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 99 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 1 optimal weight: 0.0010 chunk 31 optimal weight: 0.2980 overall best weight: 0.6188 ------------------------------------------------------------------------------- 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 = 0.3296 r_free = 0.3296 target = 0.120944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.095275 restraints weight = 10178.218| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 1.99 r_work: 0.2905 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8962 Z= 0.149 Angle : 0.522 8.608 12162 Z= 0.253 Chirality : 0.038 0.139 1420 Planarity : 0.003 0.045 1474 Dihedral : 6.012 51.377 1716 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 3.43 % Allowed : 18.13 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.27), residues: 1078 helix: 1.91 (0.22), residues: 648 sheet: 0.37 (0.55), residues: 78 loop : -1.48 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 583 HIS 0.003 0.001 HIS A 171 PHE 0.008 0.001 PHE B 465 TYR 0.006 0.001 TYR B 429 ARG 0.001 0.000 ARG B 627 =============================================================================== Job complete usr+sys time: 4105.19 seconds wall clock time: 73 minutes 41.39 seconds (4421.39 seconds total)