Starting phenix.real_space_refine on Tue Feb 13 16:59:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l47_0831/02_2024/6l47_0831_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l47_0831/02_2024/6l47_0831.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l47_0831/02_2024/6l47_0831_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l47_0831/02_2024/6l47_0831_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l47_0831/02_2024/6l47_0831_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l47_0831/02_2024/6l47_0831.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l47_0831/02_2024/6l47_0831.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l47_0831/02_2024/6l47_0831_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l47_0831/02_2024/6l47_0831_updated.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.015 sd= 0.713 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 38 5.16 5 C 4796 2.51 5 N 1066 2.21 5 O 1100 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 7000 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3444 Classifications: {'peptide': 416} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 19, 'TRANS': 396} Chain breaks: 2 Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 67 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 5, 'PHE:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 59 Chain: "B" Number of atoms: 3444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3444 Classifications: {'peptide': 416} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 19, 'TRANS': 396} Chain breaks: 2 Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 67 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 5, 'PHE:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 59 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'CLR': 1, 'E5L': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'CLR': 1, 'E5L': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.25, per 1000 atoms: 0.61 Number of scatterers: 7000 At special positions: 0 Unit cell: (141.075, 86.735, 76.285, 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 38 16.00 O 1100 8.00 N 1066 7.00 C 4796 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 365 " - pdb=" SG CYS A 516 " distance=2.06 Simple disulfide: pdb=" SG CYS A 528 " - pdb=" SG CYS A 548 " distance=2.03 Simple disulfide: pdb=" SG CYS B 365 " - pdb=" SG CYS B 516 " distance=2.06 Simple disulfide: pdb=" SG CYS B 528 " - pdb=" SG CYS B 548 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 2.92 Conformation dependent library (CDL) restraints added in 1.2 seconds 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1604 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 28 helices and 0 sheets defined 71.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.23 Creating SS restraints... Processing helix chain 'A' and resid 128 through 134 removed outlier: 4.219A pdb=" N GLU A 134 " --> pdb=" O ASP A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 164 Processing helix chain 'A' and resid 173 through 177 Processing helix chain 'A' and resid 181 through 212 Proline residue: A 199 - end of helix Processing helix chain 'A' and resid 217 through 246 removed outlier: 3.870A pdb=" N GLY A 238 " --> pdb=" O VAL A 234 " (cutoff:3.500A) Proline residue: A 239 - end of helix removed outlier: 3.637A pdb=" N VAL A 243 " --> pdb=" O PRO A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 284 removed outlier: 3.676A pdb=" N PHE A 254 " --> pdb=" O PRO A 250 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE A 255 " --> pdb=" O ALA A 251 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ILE A 256 " --> pdb=" O SER A 252 " (cutoff:3.500A) Proline residue: A 276 - end of helix Processing helix chain 'A' and resid 294 through 302 removed outlier: 3.934A pdb=" N PHE A 302 " --> pdb=" O LEU A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 345 removed outlier: 3.658A pdb=" N PHE A 335 " --> pdb=" O PHE A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 394 removed outlier: 4.306A pdb=" N ILE A 370 " --> pdb=" O VAL A 366 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N LEU A 371 " --> pdb=" O PHE A 367 " (cutoff:3.500A) Proline residue: A 372 - end of helix Processing helix chain 'A' and resid 413 through 418 Processing helix chain 'A' and resid 422 through 438 Processing helix chain 'A' and resid 446 through 466 removed outlier: 4.393A pdb=" N MET A 449 " --> pdb=" O SER A 446 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ALA A 451 " --> pdb=" O ALA A 448 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N PHE A 453 " --> pdb=" O LEU A 450 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N VAL A 466 " --> pdb=" O ALA A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 486 Processing helix chain 'A' and resid 498 through 527 Processing helix chain 'B' and resid 128 through 134 removed outlier: 4.219A pdb=" N GLU B 134 " --> pdb=" O ASP B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 164 Processing helix chain 'B' and resid 173 through 177 Processing helix chain 'B' and resid 181 through 212 Proline residue: B 199 - end of helix Processing helix chain 'B' and resid 217 through 246 removed outlier: 3.870A pdb=" N GLY B 238 " --> pdb=" O VAL B 234 " (cutoff:3.500A) Proline residue: B 239 - end of helix removed outlier: 3.636A pdb=" N VAL B 243 " --> pdb=" O PRO B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 284 removed outlier: 3.675A pdb=" N PHE B 254 " --> pdb=" O PRO B 250 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE B 255 " --> pdb=" O ALA B 251 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ILE B 256 " --> pdb=" O SER B 252 " (cutoff:3.500A) Proline residue: B 276 - end of helix Processing helix chain 'B' and resid 294 through 302 removed outlier: 3.934A pdb=" N PHE B 302 " --> pdb=" O LEU B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 345 removed outlier: 3.658A pdb=" N PHE B 335 " --> pdb=" O PHE B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 394 removed outlier: 4.306A pdb=" N ILE B 370 " --> pdb=" O VAL B 366 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N LEU B 371 " --> pdb=" O PHE B 367 " (cutoff:3.500A) Proline residue: B 372 - end of helix Processing helix chain 'B' and resid 413 through 418 Processing helix chain 'B' and resid 422 through 438 Processing helix chain 'B' and resid 446 through 466 removed outlier: 4.393A pdb=" N MET B 449 " --> pdb=" O SER B 446 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ALA B 451 " --> pdb=" O ALA B 448 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N PHE B 453 " --> pdb=" O LEU B 450 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N VAL B 466 " --> pdb=" O ALA B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 486 Processing helix chain 'B' and resid 498 through 527 430 hydrogen bonds defined for protein. 1206 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: 1.90 Time building geometry restraints manager: 3.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1940 1.34 - 1.46: 2208 1.46 - 1.58: 3064 1.58 - 1.70: 0 1.70 - 1.82: 60 Bond restraints: 7272 Sorted by residual: bond pdb=" N E5L B1001 " pdb=" C3 E5L B1001 " ideal model delta sigma weight residual 1.454 1.335 0.119 2.00e-02 2.50e+03 3.52e+01 bond pdb=" N E5L A1001 " pdb=" C3 E5L A1001 " ideal model delta sigma weight residual 1.454 1.335 0.119 2.00e-02 2.50e+03 3.52e+01 bond pdb=" N E5L A1001 " pdb=" C E5L A1001 " ideal model delta sigma weight residual 1.454 1.353 0.101 2.00e-02 2.50e+03 2.56e+01 bond pdb=" N E5L B1001 " pdb=" C E5L B1001 " ideal model delta sigma weight residual 1.454 1.353 0.101 2.00e-02 2.50e+03 2.56e+01 bond pdb=" C E5L B1001 " pdb=" C1 E5L B1001 " ideal model delta sigma weight residual 1.386 1.485 -0.099 2.00e-02 2.50e+03 2.45e+01 ... (remaining 7267 not shown) Histogram of bond angle deviations from ideal: 100.43 - 107.15: 247 107.15 - 113.88: 3904 113.88 - 120.60: 3225 120.60 - 127.32: 2450 127.32 - 134.04: 108 Bond angle restraints: 9934 Sorted by residual: angle pdb=" O E5L B1001 " pdb=" C1 E5L B1001 " pdb=" C6 E5L B1001 " ideal model delta sigma weight residual 103.61 120.64 -17.03 3.00e+00 1.11e-01 3.22e+01 angle pdb=" O E5L A1001 " pdb=" C1 E5L A1001 " pdb=" C6 E5L A1001 " ideal model delta sigma weight residual 103.61 120.63 -17.02 3.00e+00 1.11e-01 3.22e+01 angle pdb=" C E5L A1001 " pdb=" C1 E5L A1001 " pdb=" O E5L A1001 " ideal model delta sigma weight residual 136.26 120.75 15.51 3.00e+00 1.11e-01 2.67e+01 angle pdb=" C E5L B1001 " pdb=" C1 E5L B1001 " pdb=" O E5L B1001 " ideal model delta sigma weight residual 136.26 120.78 15.48 3.00e+00 1.11e-01 2.66e+01 angle pdb=" C HIS A 386 " pdb=" N CYS A 387 " pdb=" CA CYS A 387 " ideal model delta sigma weight residual 120.68 115.11 5.57 1.70e+00 3.46e-01 1.07e+01 ... (remaining 9929 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.28: 3970 26.28 - 52.55: 156 52.55 - 78.83: 12 78.83 - 105.10: 0 105.10 - 131.37: 8 Dihedral angle restraints: 4146 sinusoidal: 1660 harmonic: 2486 Sorted by residual: dihedral pdb=" CA ARG A 309 " pdb=" C ARG A 309 " pdb=" N ASP A 310 " pdb=" CA ASP A 310 " ideal model delta harmonic sigma weight residual 180.00 -158.38 -21.62 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CA ARG B 309 " pdb=" C ARG B 309 " pdb=" N ASP B 310 " pdb=" CA ASP B 310 " ideal model delta harmonic sigma weight residual -180.00 -158.40 -21.60 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" C16 E5L A1001 " pdb=" C17 E5L A1001 " pdb=" C18 E5L A1001 " pdb=" C19 E5L A1001 " ideal model delta sinusoidal sigma weight residual 182.95 51.58 131.37 1 3.00e+01 1.11e-03 1.77e+01 ... (remaining 4143 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 890 0.057 - 0.115: 164 0.115 - 0.172: 12 0.172 - 0.230: 2 0.230 - 0.287: 2 Chirality restraints: 1070 Sorted by residual: chirality pdb=" C17 CLR A1002 " pdb=" C13 CLR A1002 " pdb=" C16 CLR A1002 " pdb=" C20 CLR A1002 " both_signs ideal model delta sigma weight residual False 2.55 2.27 0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" C17 CLR B1002 " pdb=" C13 CLR B1002 " pdb=" C16 CLR B1002 " pdb=" C20 CLR B1002 " both_signs ideal model delta sigma weight residual False 2.55 2.27 0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" C20 CLR A1002 " pdb=" C17 CLR A1002 " pdb=" C21 CLR A1002 " pdb=" C22 CLR A1002 " both_signs ideal model delta sigma weight residual False 2.59 2.81 -0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 1067 not shown) Planarity restraints: 1180 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" N E5L A1001 " 0.201 2.00e-02 2.50e+03 1.26e-01 2.00e+02 pdb=" C E5L A1001 " -0.158 2.00e-02 2.50e+03 pdb=" C3 E5L A1001 " 0.045 2.00e-02 2.50e+03 pdb=" C4 E5L A1001 " -0.110 2.00e-02 2.50e+03 pdb=" O3 E5L A1001 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" N E5L B1001 " -0.201 2.00e-02 2.50e+03 1.26e-01 2.00e+02 pdb=" C E5L B1001 " 0.157 2.00e-02 2.50e+03 pdb=" C3 E5L B1001 " -0.046 2.00e-02 2.50e+03 pdb=" C4 E5L B1001 " 0.110 2.00e-02 2.50e+03 pdb=" O3 E5L B1001 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 385 " -0.013 2.00e-02 2.50e+03 2.58e-02 6.67e+00 pdb=" C LEU B 385 " 0.045 2.00e-02 2.50e+03 pdb=" O LEU B 385 " -0.017 2.00e-02 2.50e+03 pdb=" N HIS B 386 " -0.015 2.00e-02 2.50e+03 ... (remaining 1177 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 1886 2.79 - 3.32: 6908 3.32 - 3.85: 11908 3.85 - 4.37: 12872 4.37 - 4.90: 21617 Nonbonded interactions: 55191 Sorted by model distance: nonbonded pdb=" OE1 GLU B 284 " pdb=" OG SER B 286 " model vdw 2.266 2.440 nonbonded pdb=" OE1 GLU A 284 " pdb=" OG SER A 286 " model vdw 2.266 2.440 nonbonded pdb=" O THR B 419 " pdb=" OG1 THR B 419 " model vdw 2.279 2.440 nonbonded pdb=" O THR A 419 " pdb=" OG1 THR A 419 " model vdw 2.279 2.440 nonbonded pdb=" O PRO A 216 " pdb=" N SER A 220 " model vdw 2.295 2.520 ... (remaining 55186 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.360 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: 2.130 Check model and map are aligned: 0.110 Set scattering table: 0.060 Process input model: 23.100 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.030 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 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 : 0.005 0.119 7272 Z= 0.297 Angle : 0.819 17.025 9934 Z= 0.400 Chirality : 0.045 0.287 1070 Planarity : 0.008 0.126 1180 Dihedral : 14.765 131.375 2530 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.73 % Favored : 89.27 % Rotamer: Outliers : 3.34 % Allowed : 10.58 % Favored : 86.07 % 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: -3.09 (0.26), residues: 820 helix: -1.17 (0.19), residues: 586 sheet: None (None), residues: 0 loop : -4.15 (0.37), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 407 HIS 0.004 0.001 HIS A 425 PHE 0.020 0.002 PHE B 230 TYR 0.016 0.002 TYR A 308 ARG 0.003 0.000 ARG B 418 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 235 time to evaluate : 0.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 266 LYS cc_start: 0.8063 (ptpt) cc_final: 0.7802 (ptpp) REVERT: A 273 GLU cc_start: 0.8523 (tm-30) cc_final: 0.8152 (tm-30) REVERT: A 339 TYR cc_start: 0.8712 (m-80) cc_final: 0.8279 (m-80) REVERT: A 342 GLU cc_start: 0.7980 (tm-30) cc_final: 0.7277 (tm-30) REVERT: A 371 LEU cc_start: 0.8659 (tm) cc_final: 0.7921 (mm) REVERT: A 422 VAL cc_start: 0.9067 (OUTLIER) cc_final: 0.8447 (p) REVERT: A 426 ASP cc_start: 0.8349 (m-30) cc_final: 0.8024 (m-30) REVERT: B 223 HIS cc_start: 0.8844 (m90) cc_final: 0.8626 (m170) REVERT: B 273 GLU cc_start: 0.8580 (tm-30) cc_final: 0.8215 (tm-30) REVERT: B 339 TYR cc_start: 0.8716 (m-80) cc_final: 0.8278 (m-80) REVERT: B 342 GLU cc_start: 0.7947 (tm-30) cc_final: 0.7267 (tm-30) REVERT: B 371 LEU cc_start: 0.8656 (tm) cc_final: 0.7906 (mm) REVERT: B 422 VAL cc_start: 0.9037 (OUTLIER) cc_final: 0.8440 (p) REVERT: B 426 ASP cc_start: 0.8359 (m-30) cc_final: 0.8051 (m-30) outliers start: 24 outliers final: 10 residues processed: 251 average time/residue: 0.1981 time to fit residues: 64.2848 Evaluate side-chains 178 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 166 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 414 SER Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 548 CYS Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 414 SER Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 548 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 69 optimal weight: 5.9990 chunk 62 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 41 optimal weight: 10.0000 chunk 33 optimal weight: 0.0970 chunk 64 optimal weight: 0.9990 chunk 24 optimal weight: 9.9990 chunk 39 optimal weight: 2.9990 chunk 47 optimal weight: 9.9990 chunk 74 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 460 HIS B 460 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7272 Z= 0.188 Angle : 0.688 8.130 9934 Z= 0.349 Chirality : 0.041 0.158 1070 Planarity : 0.006 0.051 1180 Dihedral : 10.757 80.553 1090 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.90 % Favored : 91.10 % Rotamer: Outliers : 6.27 % Allowed : 16.99 % Favored : 76.74 % 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: -1.61 (0.30), residues: 820 helix: -0.15 (0.21), residues: 588 sheet: None (None), residues: 0 loop : -3.38 (0.43), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 438 HIS 0.003 0.001 HIS A 143 PHE 0.027 0.002 PHE B 270 TYR 0.028 0.002 TYR A 308 ARG 0.007 0.001 ARG B 272 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 179 time to evaluate : 0.834 Fit side-chains REVERT: A 146 ILE cc_start: 0.8886 (pt) cc_final: 0.8516 (mt) REVERT: A 180 LYS cc_start: 0.7983 (mttt) cc_final: 0.7726 (mtmm) REVERT: A 260 GLN cc_start: 0.9148 (pt0) cc_final: 0.8716 (tt0) REVERT: A 262 ARG cc_start: 0.7811 (ttp80) cc_final: 0.6542 (ttm170) REVERT: A 327 PHE cc_start: 0.8945 (OUTLIER) cc_final: 0.8501 (m-80) REVERT: A 342 GLU cc_start: 0.7989 (tm-30) cc_final: 0.7427 (tm-30) REVERT: A 396 LEU cc_start: 0.9443 (tp) cc_final: 0.9239 (tp) REVERT: A 422 VAL cc_start: 0.9082 (OUTLIER) cc_final: 0.8513 (p) REVERT: A 426 ASP cc_start: 0.8402 (m-30) cc_final: 0.8090 (m-30) REVERT: A 471 PHE cc_start: 0.6762 (p90) cc_final: 0.6369 (m-80) REVERT: B 146 ILE cc_start: 0.8846 (pt) cc_final: 0.8486 (mt) REVERT: B 180 LYS cc_start: 0.7971 (mttt) cc_final: 0.7721 (mtmm) REVERT: B 201 PHE cc_start: 0.8619 (t80) cc_final: 0.8391 (t80) REVERT: B 223 HIS cc_start: 0.8862 (m90) cc_final: 0.8605 (m170) REVERT: B 260 GLN cc_start: 0.9122 (pt0) cc_final: 0.8653 (tt0) REVERT: B 327 PHE cc_start: 0.8935 (OUTLIER) cc_final: 0.8458 (m-80) REVERT: B 342 GLU cc_start: 0.7985 (tm-30) cc_final: 0.7441 (tm-30) REVERT: B 396 LEU cc_start: 0.9435 (tp) cc_final: 0.9210 (tp) REVERT: B 405 LYS cc_start: 0.7871 (OUTLIER) cc_final: 0.7588 (mmtp) REVERT: B 422 VAL cc_start: 0.9037 (OUTLIER) cc_final: 0.8477 (p) REVERT: B 426 ASP cc_start: 0.8367 (m-30) cc_final: 0.8052 (m-30) REVERT: B 471 PHE cc_start: 0.6808 (p90) cc_final: 0.6396 (m-80) outliers start: 45 outliers final: 25 residues processed: 204 average time/residue: 0.1758 time to fit residues: 48.1469 Evaluate side-chains 178 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 148 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 311 SER Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 526 GLN Chi-restraints excluded: chain A residue 548 CYS Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 311 SER Chi-restraints excluded: chain B residue 327 PHE Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 405 LYS Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 526 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 41 optimal weight: 10.0000 chunk 23 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 50 optimal weight: 30.0000 chunk 20 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 73 optimal weight: 9.9990 chunk 25 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7272 Z= 0.209 Angle : 0.647 7.176 9934 Z= 0.333 Chirality : 0.041 0.163 1070 Planarity : 0.005 0.045 1180 Dihedral : 9.056 73.741 1087 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.39 % Favored : 90.61 % Rotamer: Outliers : 5.15 % Allowed : 20.75 % Favored : 74.09 % 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: -1.10 (0.30), residues: 820 helix: 0.29 (0.21), residues: 590 sheet: None (None), residues: 0 loop : -3.43 (0.44), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 438 HIS 0.005 0.001 HIS B 425 PHE 0.032 0.002 PHE B 270 TYR 0.028 0.002 TYR A 308 ARG 0.006 0.001 ARG A 262 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 158 time to evaluate : 0.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8911 (tt) REVERT: A 327 PHE cc_start: 0.8895 (OUTLIER) cc_final: 0.8430 (m-80) REVERT: A 342 GLU cc_start: 0.8096 (tm-30) cc_final: 0.7483 (tm-30) REVERT: A 422 VAL cc_start: 0.9168 (OUTLIER) cc_final: 0.8515 (p) REVERT: A 426 ASP cc_start: 0.8377 (m-30) cc_final: 0.8090 (m-30) REVERT: B 132 LEU cc_start: 0.9174 (OUTLIER) cc_final: 0.8920 (tt) REVERT: B 160 ASP cc_start: 0.8192 (t0) cc_final: 0.7990 (t0) REVERT: B 223 HIS cc_start: 0.8854 (m90) cc_final: 0.8597 (m170) REVERT: B 273 GLU cc_start: 0.8490 (tm-30) cc_final: 0.8094 (tm-30) REVERT: B 327 PHE cc_start: 0.8876 (OUTLIER) cc_final: 0.8411 (m-80) REVERT: B 342 GLU cc_start: 0.8092 (tm-30) cc_final: 0.7481 (tm-30) REVERT: B 422 VAL cc_start: 0.9160 (OUTLIER) cc_final: 0.8510 (p) REVERT: B 426 ASP cc_start: 0.8359 (m-30) cc_final: 0.8092 (m-30) outliers start: 37 outliers final: 25 residues processed: 184 average time/residue: 0.1717 time to fit residues: 42.9522 Evaluate side-chains 181 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 150 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 131 GLU Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 311 SER Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 526 GLN Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 131 GLU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 311 SER Chi-restraints excluded: chain B residue 327 PHE Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 526 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 73 optimal weight: 8.9990 chunk 56 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 35 optimal weight: 0.4980 chunk 50 optimal weight: 10.0000 chunk 74 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 70 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 329 GLN B 329 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.3344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7272 Z= 0.183 Angle : 0.649 9.946 9934 Z= 0.327 Chirality : 0.040 0.162 1070 Planarity : 0.006 0.057 1180 Dihedral : 8.444 72.135 1086 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.88 % Favored : 90.12 % Rotamer: Outliers : 5.99 % Allowed : 21.45 % Favored : 72.56 % 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: -0.77 (0.31), residues: 820 helix: 0.59 (0.21), residues: 592 sheet: None (None), residues: 0 loop : -3.55 (0.44), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 438 HIS 0.003 0.001 HIS B 425 PHE 0.029 0.002 PHE B 270 TYR 0.027 0.002 TYR A 308 ARG 0.004 0.000 ARG B 418 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 167 time to evaluate : 0.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8881 (tt) REVERT: A 201 PHE cc_start: 0.8698 (t80) cc_final: 0.8370 (t80) REVERT: A 266 LYS cc_start: 0.8226 (ptpt) cc_final: 0.7944 (mtmt) REVERT: A 279 LEU cc_start: 0.9502 (OUTLIER) cc_final: 0.9158 (tt) REVERT: A 327 PHE cc_start: 0.8852 (OUTLIER) cc_final: 0.8363 (m-80) REVERT: A 342 GLU cc_start: 0.8170 (tm-30) cc_final: 0.7573 (tm-30) REVERT: A 402 MET cc_start: 0.8491 (ppp) cc_final: 0.7922 (ppp) REVERT: A 422 VAL cc_start: 0.9167 (OUTLIER) cc_final: 0.8568 (p) REVERT: A 426 ASP cc_start: 0.8347 (m-30) cc_final: 0.8014 (m-30) REVERT: B 132 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8886 (tt) REVERT: B 273 GLU cc_start: 0.8529 (tm-30) cc_final: 0.7910 (tm-30) REVERT: B 327 PHE cc_start: 0.8824 (OUTLIER) cc_final: 0.8370 (m-80) REVERT: B 342 GLU cc_start: 0.8166 (tm-30) cc_final: 0.7571 (tm-30) REVERT: B 422 VAL cc_start: 0.9200 (OUTLIER) cc_final: 0.8756 (p) REVERT: B 426 ASP cc_start: 0.8329 (m-30) cc_final: 0.8058 (m-30) outliers start: 43 outliers final: 28 residues processed: 197 average time/residue: 0.1604 time to fit residues: 43.0609 Evaluate side-chains 186 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 151 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 230 PHE Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 260 GLN Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 311 SER Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 230 PHE Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 260 GLN Chi-restraints excluded: chain B residue 311 SER Chi-restraints excluded: chain B residue 327 PHE Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 514 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 66 optimal weight: 0.9980 chunk 44 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 67 optimal weight: 0.7980 chunk 54 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 40 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 20 optimal weight: 10.0000 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 ASN ** B 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 390 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.3594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7272 Z= 0.247 Angle : 0.663 7.398 9934 Z= 0.342 Chirality : 0.042 0.170 1070 Planarity : 0.005 0.044 1180 Dihedral : 8.423 75.369 1086 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 15.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.71 % Favored : 88.29 % Rotamer: Outliers : 6.82 % Allowed : 20.61 % Favored : 72.56 % 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: -0.53 (0.31), residues: 820 helix: 0.86 (0.22), residues: 582 sheet: None (None), residues: 0 loop : -3.53 (0.41), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 438 HIS 0.006 0.001 HIS A 425 PHE 0.028 0.002 PHE B 270 TYR 0.021 0.002 TYR B 308 ARG 0.004 0.001 ARG A 262 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 154 time to evaluate : 0.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8941 (tt) REVERT: A 160 ASP cc_start: 0.8306 (t0) cc_final: 0.8060 (t0) REVERT: A 265 MET cc_start: 0.8548 (ttm) cc_final: 0.8029 (ttm) REVERT: A 266 LYS cc_start: 0.8425 (ptpt) cc_final: 0.8179 (mtmt) REVERT: A 279 LEU cc_start: 0.9478 (OUTLIER) cc_final: 0.9183 (tt) REVERT: A 327 PHE cc_start: 0.9002 (OUTLIER) cc_final: 0.8562 (m-80) REVERT: A 342 GLU cc_start: 0.8151 (tm-30) cc_final: 0.7528 (tm-30) REVERT: A 402 MET cc_start: 0.8653 (ppp) cc_final: 0.8059 (ppp) REVERT: A 418 ARG cc_start: 0.8409 (ttm-80) cc_final: 0.7883 (mtm-85) REVERT: A 422 VAL cc_start: 0.9269 (OUTLIER) cc_final: 0.8723 (p) REVERT: A 426 ASP cc_start: 0.8292 (m-30) cc_final: 0.8071 (m-30) REVERT: B 132 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8943 (tt) REVERT: B 160 ASP cc_start: 0.8307 (t0) cc_final: 0.8059 (t0) REVERT: B 265 MET cc_start: 0.8671 (ttm) cc_final: 0.8136 (ttm) REVERT: B 327 PHE cc_start: 0.8972 (OUTLIER) cc_final: 0.8557 (m-80) REVERT: B 342 GLU cc_start: 0.8138 (tm-30) cc_final: 0.7507 (tm-30) REVERT: B 418 ARG cc_start: 0.8398 (ttm-80) cc_final: 0.8160 (ttm-80) REVERT: B 422 VAL cc_start: 0.9292 (OUTLIER) cc_final: 0.8818 (p) REVERT: B 426 ASP cc_start: 0.8288 (m-30) cc_final: 0.8078 (m-30) outliers start: 49 outliers final: 30 residues processed: 187 average time/residue: 0.1664 time to fit residues: 42.4204 Evaluate side-chains 187 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 150 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 230 PHE Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 260 GLN Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 311 SER Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 526 GLN Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 230 PHE Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 260 GLN Chi-restraints excluded: chain B residue 311 SER Chi-restraints excluded: chain B residue 327 PHE Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 526 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 26 optimal weight: 0.7980 chunk 71 optimal weight: 6.9990 chunk 15 optimal weight: 8.9990 chunk 46 optimal weight: 8.9990 chunk 19 optimal weight: 0.2980 chunk 79 optimal weight: 0.7980 chunk 65 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 6 optimal weight: 6.9990 chunk 41 optimal weight: 10.0000 chunk 76 optimal weight: 6.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 ASN A 390 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.3840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7272 Z= 0.183 Angle : 0.672 11.141 9934 Z= 0.333 Chirality : 0.042 0.271 1070 Planarity : 0.005 0.042 1180 Dihedral : 8.084 67.702 1082 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.12 % Favored : 89.88 % Rotamer: Outliers : 5.15 % Allowed : 23.12 % Favored : 71.73 % 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: -0.62 (0.31), residues: 820 helix: 0.70 (0.21), residues: 592 sheet: None (None), residues: 0 loop : -3.46 (0.43), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 438 HIS 0.005 0.001 HIS A 425 PHE 0.030 0.001 PHE B 270 TYR 0.025 0.002 TYR B 336 ARG 0.002 0.000 ARG A 262 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 168 time to evaluate : 0.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8888 (tt) REVERT: A 160 ASP cc_start: 0.8257 (t0) cc_final: 0.8008 (t0) REVERT: A 265 MET cc_start: 0.8476 (ttm) cc_final: 0.8041 (ttm) REVERT: A 273 GLU cc_start: 0.8472 (tm-30) cc_final: 0.8264 (tm-30) REVERT: A 279 LEU cc_start: 0.9477 (OUTLIER) cc_final: 0.9185 (tt) REVERT: A 308 TYR cc_start: 0.7941 (t80) cc_final: 0.7729 (t80) REVERT: A 327 PHE cc_start: 0.8878 (OUTLIER) cc_final: 0.8396 (m-80) REVERT: A 342 GLU cc_start: 0.8132 (tm-30) cc_final: 0.7511 (tm-30) REVERT: A 371 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.7618 (mm) REVERT: A 402 MET cc_start: 0.8615 (ppp) cc_final: 0.8015 (ppp) REVERT: A 418 ARG cc_start: 0.8420 (ttm-80) cc_final: 0.7848 (mtm-85) REVERT: A 422 VAL cc_start: 0.9157 (OUTLIER) cc_final: 0.8263 (p) REVERT: A 426 ASP cc_start: 0.8322 (m-30) cc_final: 0.8041 (m-30) REVERT: B 132 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8894 (tt) REVERT: B 160 ASP cc_start: 0.8262 (t0) cc_final: 0.8009 (t0) REVERT: B 265 MET cc_start: 0.8550 (ttm) cc_final: 0.7953 (ttm) REVERT: B 279 LEU cc_start: 0.9432 (OUTLIER) cc_final: 0.9215 (tt) REVERT: B 327 PHE cc_start: 0.8842 (OUTLIER) cc_final: 0.8376 (m-80) REVERT: B 342 GLU cc_start: 0.8113 (tm-30) cc_final: 0.7485 (tm-30) REVERT: B 371 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.7623 (mm) REVERT: B 402 MET cc_start: 0.8472 (ppp) cc_final: 0.7974 (ppp) REVERT: B 418 ARG cc_start: 0.8399 (ttm-80) cc_final: 0.7821 (mtm-85) REVERT: B 422 VAL cc_start: 0.9181 (OUTLIER) cc_final: 0.8469 (p) REVERT: B 426 ASP cc_start: 0.8278 (m-30) cc_final: 0.8033 (m-30) outliers start: 37 outliers final: 21 residues processed: 195 average time/residue: 0.1704 time to fit residues: 44.8126 Evaluate side-chains 186 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 155 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 230 PHE Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 260 GLN Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 311 SER Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 230 PHE Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 260 GLN Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 311 SER Chi-restraints excluded: chain B residue 327 PHE Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 422 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 8 optimal weight: 5.9990 chunk 45 optimal weight: 0.0370 chunk 57 optimal weight: 10.0000 chunk 44 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 79 optimal weight: 0.7980 chunk 49 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 36 optimal weight: 9.9990 chunk 31 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 overall best weight: 1.3462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.3964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7272 Z= 0.205 Angle : 0.685 10.271 9934 Z= 0.335 Chirality : 0.041 0.166 1070 Planarity : 0.005 0.042 1180 Dihedral : 8.122 69.515 1082 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.61 % Favored : 89.39 % Rotamer: Outliers : 5.99 % Allowed : 22.70 % Favored : 71.31 % 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: -0.43 (0.31), residues: 820 helix: 0.81 (0.21), residues: 596 sheet: None (None), residues: 0 loop : -3.36 (0.44), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 438 HIS 0.004 0.001 HIS A 425 PHE 0.032 0.001 PHE B 270 TYR 0.023 0.001 TYR A 308 ARG 0.005 0.000 ARG A 262 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 165 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8905 (tt) REVERT: A 160 ASP cc_start: 0.8319 (t0) cc_final: 0.8045 (t0) REVERT: A 265 MET cc_start: 0.8475 (ttm) cc_final: 0.8040 (ttm) REVERT: A 273 GLU cc_start: 0.8437 (tm-30) cc_final: 0.8155 (tm-30) REVERT: A 279 LEU cc_start: 0.9478 (OUTLIER) cc_final: 0.9177 (tt) REVERT: A 308 TYR cc_start: 0.8056 (t80) cc_final: 0.7842 (t80) REVERT: A 327 PHE cc_start: 0.8905 (OUTLIER) cc_final: 0.8478 (m-80) REVERT: A 342 GLU cc_start: 0.8127 (tm-30) cc_final: 0.7521 (tm-30) REVERT: A 371 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.7539 (mm) REVERT: A 402 MET cc_start: 0.8637 (ppp) cc_final: 0.8036 (ppp) REVERT: A 418 ARG cc_start: 0.8381 (ttm-80) cc_final: 0.7806 (mtm-85) REVERT: A 422 VAL cc_start: 0.9195 (OUTLIER) cc_final: 0.8477 (p) REVERT: A 426 ASP cc_start: 0.8288 (m-30) cc_final: 0.8031 (m-30) REVERT: A 484 MET cc_start: 0.6905 (ttt) cc_final: 0.6678 (ttm) REVERT: B 132 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8912 (tt) REVERT: B 160 ASP cc_start: 0.8345 (t0) cc_final: 0.8058 (t0) REVERT: B 180 LYS cc_start: 0.7794 (mttt) cc_final: 0.7488 (mtmm) REVERT: B 253 ARG cc_start: 0.9107 (mtt90) cc_final: 0.8493 (mtt-85) REVERT: B 265 MET cc_start: 0.8482 (ttm) cc_final: 0.7935 (ttm) REVERT: B 327 PHE cc_start: 0.8872 (OUTLIER) cc_final: 0.8447 (m-80) REVERT: B 342 GLU cc_start: 0.8127 (tm-30) cc_final: 0.7518 (tm-30) REVERT: B 371 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.7534 (mm) REVERT: B 402 MET cc_start: 0.8495 (ppp) cc_final: 0.8014 (ppp) REVERT: B 418 ARG cc_start: 0.8395 (ttm-80) cc_final: 0.8144 (ttm-80) REVERT: B 422 VAL cc_start: 0.9219 (OUTLIER) cc_final: 0.8521 (p) REVERT: B 426 ASP cc_start: 0.8273 (m-30) cc_final: 0.8032 (m-30) outliers start: 43 outliers final: 30 residues processed: 196 average time/residue: 0.1651 time to fit residues: 44.7036 Evaluate side-chains 191 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 152 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 230 PHE Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 260 GLN Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 311 SER Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 230 PHE Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 260 GLN Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 311 SER Chi-restraints excluded: chain B residue 327 PHE Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 514 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 23 optimal weight: 0.5980 chunk 15 optimal weight: 3.9990 chunk 50 optimal weight: 0.0170 chunk 53 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 7 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 71 optimal weight: 9.9990 chunk 75 optimal weight: 9.9990 chunk 69 optimal weight: 6.9990 chunk 73 optimal weight: 4.9990 overall best weight: 1.9224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.4106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7272 Z= 0.228 Angle : 0.720 11.217 9934 Z= 0.349 Chirality : 0.042 0.176 1070 Planarity : 0.005 0.042 1180 Dihedral : 8.284 71.415 1082 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.49 % Favored : 89.51 % Rotamer: Outliers : 5.99 % Allowed : 23.54 % Favored : 70.47 % 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 (0.31), residues: 820 helix: 0.82 (0.21), residues: 598 sheet: None (None), residues: 0 loop : -3.54 (0.44), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 438 HIS 0.004 0.001 HIS A 425 PHE 0.031 0.001 PHE B 270 TYR 0.025 0.002 TYR B 322 ARG 0.004 0.000 ARG A 262 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 156 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8925 (tt) REVERT: A 160 ASP cc_start: 0.8362 (t0) cc_final: 0.8067 (t0) REVERT: A 180 LYS cc_start: 0.7815 (mttt) cc_final: 0.7534 (mtmm) REVERT: A 253 ARG cc_start: 0.9079 (mtt90) cc_final: 0.8480 (mtt-85) REVERT: A 265 MET cc_start: 0.8496 (ttm) cc_final: 0.8081 (ttm) REVERT: A 273 GLU cc_start: 0.8415 (tm-30) cc_final: 0.8086 (tm-30) REVERT: A 279 LEU cc_start: 0.9493 (OUTLIER) cc_final: 0.9195 (tt) REVERT: A 308 TYR cc_start: 0.8111 (t80) cc_final: 0.7877 (t80) REVERT: A 327 PHE cc_start: 0.8956 (OUTLIER) cc_final: 0.8500 (m-80) REVERT: A 342 GLU cc_start: 0.8158 (tm-30) cc_final: 0.7519 (tm-30) REVERT: A 371 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.7738 (mm) REVERT: A 402 MET cc_start: 0.8688 (ppp) cc_final: 0.8050 (ppp) REVERT: A 422 VAL cc_start: 0.9212 (OUTLIER) cc_final: 0.8498 (p) REVERT: A 426 ASP cc_start: 0.8284 (m-30) cc_final: 0.8027 (m-30) REVERT: A 472 TYR cc_start: 0.8235 (t80) cc_final: 0.8024 (t80) REVERT: A 484 MET cc_start: 0.6853 (ttt) cc_final: 0.6592 (ttm) REVERT: B 132 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8934 (tt) REVERT: B 164 GLU cc_start: 0.8293 (mm-30) cc_final: 0.8037 (mm-30) REVERT: B 253 ARG cc_start: 0.9055 (mtt90) cc_final: 0.8455 (mtt-85) REVERT: B 265 MET cc_start: 0.8496 (ttm) cc_final: 0.7978 (ttm) REVERT: B 327 PHE cc_start: 0.8924 (OUTLIER) cc_final: 0.8521 (m-80) REVERT: B 342 GLU cc_start: 0.8155 (tm-30) cc_final: 0.7539 (tm-30) REVERT: B 371 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.7742 (mm) REVERT: B 402 MET cc_start: 0.8548 (ppp) cc_final: 0.8067 (ppp) REVERT: B 422 VAL cc_start: 0.9240 (OUTLIER) cc_final: 0.8544 (p) REVERT: B 426 ASP cc_start: 0.8268 (m-30) cc_final: 0.8020 (m-30) REVERT: B 472 TYR cc_start: 0.8239 (t80) cc_final: 0.8016 (t80) outliers start: 43 outliers final: 34 residues processed: 188 average time/residue: 0.1765 time to fit residues: 44.9037 Evaluate side-chains 194 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 151 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 230 PHE Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 260 GLN Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 311 SER Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 230 PHE Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 260 GLN Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 311 SER Chi-restraints excluded: chain B residue 327 PHE Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 514 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 75 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 chunk 32 optimal weight: 0.0030 chunk 57 optimal weight: 7.9990 chunk 22 optimal weight: 7.9990 chunk 66 optimal weight: 0.5980 chunk 69 optimal weight: 0.9990 chunk 73 optimal weight: 9.9990 chunk 48 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 overall best weight: 0.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.4274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7272 Z= 0.186 Angle : 0.684 9.896 9934 Z= 0.332 Chirality : 0.041 0.190 1070 Planarity : 0.005 0.042 1180 Dihedral : 8.076 68.341 1082 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.12 % Favored : 89.88 % Rotamer: Outliers : 5.15 % Allowed : 24.51 % Favored : 70.33 % 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: -0.38 (0.31), residues: 820 helix: 0.88 (0.21), residues: 598 sheet: None (None), residues: 0 loop : -3.52 (0.43), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 438 HIS 0.004 0.001 HIS A 425 PHE 0.030 0.001 PHE B 270 TYR 0.027 0.001 TYR B 322 ARG 0.001 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 171 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 164 GLU cc_start: 0.8258 (mm-30) cc_final: 0.8037 (mm-30) REVERT: A 180 LYS cc_start: 0.7666 (mttt) cc_final: 0.7442 (mtmm) REVERT: A 253 ARG cc_start: 0.9066 (mtt90) cc_final: 0.8538 (mtt-85) REVERT: A 265 MET cc_start: 0.8420 (ttm) cc_final: 0.8014 (ttm) REVERT: A 279 LEU cc_start: 0.9518 (OUTLIER) cc_final: 0.9183 (tt) REVERT: A 327 PHE cc_start: 0.8831 (OUTLIER) cc_final: 0.8400 (m-80) REVERT: A 342 GLU cc_start: 0.8196 (tm-30) cc_final: 0.7534 (tm-30) REVERT: A 371 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.7618 (mm) REVERT: A 402 MET cc_start: 0.8627 (ppp) cc_final: 0.8053 (ppp) REVERT: A 418 ARG cc_start: 0.8348 (ttm-80) cc_final: 0.8131 (ttm-80) REVERT: A 422 VAL cc_start: 0.9191 (OUTLIER) cc_final: 0.8470 (p) REVERT: A 426 ASP cc_start: 0.8224 (m-30) cc_final: 0.7994 (m-30) REVERT: A 462 TYR cc_start: 0.8762 (t80) cc_final: 0.8388 (t80) REVERT: A 484 MET cc_start: 0.6846 (ttt) cc_final: 0.6612 (ttm) REVERT: B 180 LYS cc_start: 0.7705 (mttt) cc_final: 0.7456 (mtmm) REVERT: B 253 ARG cc_start: 0.9040 (mtt90) cc_final: 0.8551 (mtt-85) REVERT: B 259 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.8321 (mp0) REVERT: B 265 MET cc_start: 0.8438 (ttm) cc_final: 0.7834 (ttm) REVERT: B 327 PHE cc_start: 0.8819 (OUTLIER) cc_final: 0.8439 (m-80) REVERT: B 342 GLU cc_start: 0.8194 (tm-30) cc_final: 0.7527 (tm-30) REVERT: B 371 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.7614 (mm) REVERT: B 402 MET cc_start: 0.8474 (ppp) cc_final: 0.8013 (ppp) REVERT: B 418 ARG cc_start: 0.8353 (ttm-80) cc_final: 0.8125 (ttm-80) REVERT: B 422 VAL cc_start: 0.9227 (OUTLIER) cc_final: 0.8520 (p) REVERT: B 484 MET cc_start: 0.6902 (ttt) cc_final: 0.6640 (ttm) outliers start: 37 outliers final: 26 residues processed: 194 average time/residue: 0.1834 time to fit residues: 47.6578 Evaluate side-chains 188 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 154 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 230 PHE Chi-restraints excluded: chain A residue 260 GLN Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 311 SER Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 230 PHE Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 260 GLN Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 311 SER Chi-restraints excluded: chain B residue 327 PHE Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 452 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 36 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 6 optimal weight: 6.9990 chunk 50 optimal weight: 20.0000 chunk 39 optimal weight: 3.9990 chunk 51 optimal weight: 9.9990 chunk 69 optimal weight: 9.9990 chunk 19 optimal weight: 7.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 390 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.4332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 7272 Z= 0.292 Angle : 0.745 12.362 9934 Z= 0.371 Chirality : 0.044 0.201 1070 Planarity : 0.005 0.044 1180 Dihedral : 8.418 76.483 1082 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.98 % Favored : 89.02 % Rotamer: Outliers : 5.43 % Allowed : 24.93 % Favored : 69.64 % 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: -0.41 (0.31), residues: 820 helix: 0.85 (0.21), residues: 598 sheet: None (None), residues: 0 loop : -3.48 (0.44), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 438 HIS 0.005 0.001 HIS A 223 PHE 0.032 0.002 PHE B 270 TYR 0.025 0.002 TYR B 322 ARG 0.003 0.001 ARG A 262 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 153 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 ARG cc_start: 0.9089 (mtt90) cc_final: 0.8429 (mtt-85) REVERT: A 265 MET cc_start: 0.8552 (ttm) cc_final: 0.8169 (ttm) REVERT: A 273 GLU cc_start: 0.8645 (tm-30) cc_final: 0.8422 (tm-30) REVERT: A 279 LEU cc_start: 0.9543 (OUTLIER) cc_final: 0.9216 (tt) REVERT: A 327 PHE cc_start: 0.9078 (OUTLIER) cc_final: 0.8641 (m-80) REVERT: A 342 GLU cc_start: 0.8203 (tm-30) cc_final: 0.7583 (tm-30) REVERT: A 402 MET cc_start: 0.8790 (ppp) cc_final: 0.8074 (ppp) REVERT: A 422 VAL cc_start: 0.9244 (OUTLIER) cc_final: 0.8561 (p) REVERT: A 426 ASP cc_start: 0.8214 (m-30) cc_final: 0.7987 (m-30) REVERT: A 484 MET cc_start: 0.6850 (ttt) cc_final: 0.6645 (ttm) REVERT: B 253 ARG cc_start: 0.9074 (mtt90) cc_final: 0.8424 (mtt-85) REVERT: B 259 GLU cc_start: 0.8842 (OUTLIER) cc_final: 0.8456 (mp0) REVERT: B 265 MET cc_start: 0.8580 (ttm) cc_final: 0.8118 (ttm) REVERT: B 327 PHE cc_start: 0.9121 (OUTLIER) cc_final: 0.8708 (m-80) REVERT: B 342 GLU cc_start: 0.8189 (tm-30) cc_final: 0.7573 (tm-30) REVERT: B 371 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.7897 (mm) REVERT: B 402 MET cc_start: 0.8640 (ppp) cc_final: 0.8113 (ppp) REVERT: B 484 MET cc_start: 0.6988 (ttt) cc_final: 0.6744 (ttm) outliers start: 39 outliers final: 28 residues processed: 178 average time/residue: 0.1710 time to fit residues: 41.3113 Evaluate side-chains 179 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 145 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 230 PHE Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 260 GLN Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 311 SER Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 230 PHE Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 260 GLN Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 311 SER Chi-restraints excluded: chain B residue 327 PHE Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 514 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 59 optimal weight: 0.2980 chunk 9 optimal weight: 0.7980 chunk 18 optimal weight: 0.0010 chunk 65 optimal weight: 10.0000 chunk 27 optimal weight: 0.0670 chunk 66 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 3 optimal weight: 4.9990 chunk 47 optimal weight: 0.9980 overall best weight: 0.4324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.119557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.101509 restraints weight = 15662.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.104839 restraints weight = 7339.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.107013 restraints weight = 4472.589| |-----------------------------------------------------------------------------| r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.4516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7272 Z= 0.185 Angle : 0.703 11.238 9934 Z= 0.343 Chirality : 0.043 0.196 1070 Planarity : 0.005 0.043 1180 Dihedral : 8.034 67.458 1081 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.15 % Favored : 90.85 % Rotamer: Outliers : 3.90 % Allowed : 27.16 % Favored : 68.94 % 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: -0.34 (0.31), residues: 820 helix: 0.88 (0.21), residues: 600 sheet: None (None), residues: 0 loop : -3.44 (0.44), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 438 HIS 0.012 0.001 HIS A 223 PHE 0.031 0.001 PHE B 270 TYR 0.032 0.002 TYR A 472 ARG 0.003 0.000 ARG B 139 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1668.17 seconds wall clock time: 30 minutes 53.34 seconds (1853.34 seconds total)