Starting phenix.real_space_refine on Mon Sep 30 03:58:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jm9_36410/09_2024/8jm9_36410_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jm9_36410/09_2024/8jm9_36410.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jm9_36410/09_2024/8jm9_36410.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jm9_36410/09_2024/8jm9_36410.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jm9_36410/09_2024/8jm9_36410_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jm9_36410/09_2024/8jm9_36410_neut.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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: 5 Type Number sf(0) Gaussians S 72 5.16 5 C 7824 2.51 5 N 2056 2.21 5 O 2096 1.98 5 H 12472 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 24520 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 6130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 6130 Classifications: {'peptide': 381} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 374} Chain breaks: 1 Restraints were copied for chains: C, B, D Time building chain proxies: 15.05, per 1000 atoms: 0.61 Number of scatterers: 24520 At special positions: 0 Unit cell: (110.67, 110.67, 104.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 72 16.00 O 2096 8.00 N 2056 7.00 C 7824 6.00 H 12472 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.44 Conformation dependent library (CDL) restraints added in 1.9 seconds 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2904 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 8 sheets defined 85.0% alpha, 2.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.83 Creating SS restraints... Processing helix chain 'A' and resid 7 through 17 removed outlier: 3.503A pdb=" N PHE A 11 " --> pdb=" O SER A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 65 Processing helix chain 'A' and resid 73 through 100 Processing helix chain 'A' and resid 101 through 119 Processing helix chain 'A' and resid 120 through 123 Processing helix chain 'A' and resid 124 through 161 Processing helix chain 'A' and resid 168 through 174 removed outlier: 3.765A pdb=" N VAL A 172 " --> pdb=" O THR A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 215 Processing helix chain 'A' and resid 263 through 321 removed outlier: 6.206A pdb=" N ILE A 294 " --> pdb=" O ASN A 290 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N ALA A 295 " --> pdb=" O SER A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 369 Proline residue: A 347 - end of helix removed outlier: 3.753A pdb=" N THR A 358 " --> pdb=" O GLU A 354 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N ILE A 359 " --> pdb=" O SER A 355 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N GLN A 360 " --> pdb=" O ARG A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 387 removed outlier: 4.012A pdb=" N VAL A 387 " --> pdb=" O GLN A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 425 removed outlier: 3.553A pdb=" N THR A 406 " --> pdb=" O ARG A 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 17 removed outlier: 3.503A pdb=" N PHE B 11 " --> pdb=" O SER B 7 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 65 Processing helix chain 'B' and resid 73 through 100 Processing helix chain 'B' and resid 101 through 119 Processing helix chain 'B' and resid 120 through 123 Processing helix chain 'B' and resid 124 through 161 Processing helix chain 'B' and resid 168 through 174 removed outlier: 3.765A pdb=" N VAL B 172 " --> pdb=" O THR B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 215 Processing helix chain 'B' and resid 263 through 321 removed outlier: 6.206A pdb=" N ILE B 294 " --> pdb=" O ASN B 290 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N ALA B 295 " --> pdb=" O SER B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 369 Proline residue: B 347 - end of helix removed outlier: 3.753A pdb=" N THR B 358 " --> pdb=" O GLU B 354 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N ILE B 359 " --> pdb=" O SER B 355 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N GLN B 360 " --> pdb=" O ARG B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 387 removed outlier: 4.012A pdb=" N VAL B 387 " --> pdb=" O GLN B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 425 removed outlier: 3.553A pdb=" N THR B 406 " --> pdb=" O ARG B 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 17 removed outlier: 3.503A pdb=" N PHE C 11 " --> pdb=" O SER C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 65 Processing helix chain 'C' and resid 73 through 100 Processing helix chain 'C' and resid 101 through 119 Processing helix chain 'C' and resid 120 through 123 Processing helix chain 'C' and resid 124 through 161 Processing helix chain 'C' and resid 168 through 174 removed outlier: 3.765A pdb=" N VAL C 172 " --> pdb=" O THR C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 215 Processing helix chain 'C' and resid 263 through 321 removed outlier: 6.206A pdb=" N ILE C 294 " --> pdb=" O ASN C 290 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N ALA C 295 " --> pdb=" O SER C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 369 Proline residue: C 347 - end of helix removed outlier: 3.753A pdb=" N THR C 358 " --> pdb=" O GLU C 354 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N ILE C 359 " --> pdb=" O SER C 355 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N GLN C 360 " --> pdb=" O ARG C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 371 through 387 removed outlier: 4.012A pdb=" N VAL C 387 " --> pdb=" O GLN C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 425 removed outlier: 3.553A pdb=" N THR C 406 " --> pdb=" O ARG C 402 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 17 removed outlier: 3.503A pdb=" N PHE D 11 " --> pdb=" O SER D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 65 Processing helix chain 'D' and resid 73 through 100 Processing helix chain 'D' and resid 101 through 119 Processing helix chain 'D' and resid 120 through 123 Processing helix chain 'D' and resid 124 through 161 Processing helix chain 'D' and resid 168 through 174 removed outlier: 3.765A pdb=" N VAL D 172 " --> pdb=" O THR D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 215 Processing helix chain 'D' and resid 263 through 321 removed outlier: 6.206A pdb=" N ILE D 294 " --> pdb=" O ASN D 290 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N ALA D 295 " --> pdb=" O SER D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 369 Proline residue: D 347 - end of helix removed outlier: 3.753A pdb=" N THR D 358 " --> pdb=" O GLU D 354 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N ILE D 359 " --> pdb=" O SER D 355 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N GLN D 360 " --> pdb=" O ARG D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 371 through 387 removed outlier: 4.012A pdb=" N VAL D 387 " --> pdb=" O GLN D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 425 removed outlier: 3.553A pdb=" N THR D 406 " --> pdb=" O ARG D 402 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 22 through 26 Processing sheet with id=AA2, first strand: chain 'A' and resid 392 through 393 removed outlier: 4.578A pdb=" N PHE A 392 " --> pdb=" O VAL A 400 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 22 through 26 Processing sheet with id=AA4, first strand: chain 'B' and resid 392 through 393 removed outlier: 4.578A pdb=" N PHE B 392 " --> pdb=" O VAL B 400 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 22 through 26 Processing sheet with id=AA6, first strand: chain 'C' and resid 392 through 393 removed outlier: 4.578A pdb=" N PHE C 392 " --> pdb=" O VAL C 400 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 22 through 26 Processing sheet with id=AA8, first strand: chain 'D' and resid 392 through 393 removed outlier: 4.578A pdb=" N PHE D 392 " --> pdb=" O VAL D 400 " (cutoff:3.500A) 1080 hydrogen bonds defined for protein. 3228 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: 9.14 Time building geometry restraints manager: 7.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 12440 1.03 - 1.22: 32 1.22 - 1.42: 5112 1.42 - 1.61: 7056 1.61 - 1.81: 112 Bond restraints: 24752 Sorted by residual: bond pdb=" CB LYS C 379 " pdb=" CG LYS C 379 " ideal model delta sigma weight residual 1.520 1.546 -0.026 3.00e-02 1.11e+03 7.51e-01 bond pdb=" CB LYS D 379 " pdb=" CG LYS D 379 " ideal model delta sigma weight residual 1.520 1.546 -0.026 3.00e-02 1.11e+03 7.51e-01 bond pdb=" CB LYS B 379 " pdb=" CG LYS B 379 " ideal model delta sigma weight residual 1.520 1.546 -0.026 3.00e-02 1.11e+03 7.51e-01 bond pdb=" CB LYS A 379 " pdb=" CG LYS A 379 " ideal model delta sigma weight residual 1.520 1.546 -0.026 3.00e-02 1.11e+03 7.51e-01 bond pdb=" C LYS B 357 " pdb=" O LYS B 357 " ideal model delta sigma weight residual 1.236 1.246 -0.010 1.31e-02 5.83e+03 6.00e-01 ... (remaining 24747 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.04: 41844 1.04 - 2.08: 2708 2.08 - 3.12: 116 3.12 - 4.16: 40 4.16 - 5.21: 12 Bond angle restraints: 44720 Sorted by residual: angle pdb=" N VAL D 69 " pdb=" CA VAL D 69 " pdb=" C VAL D 69 " ideal model delta sigma weight residual 111.81 109.28 2.53 8.60e-01 1.35e+00 8.67e+00 angle pdb=" N VAL B 69 " pdb=" CA VAL B 69 " pdb=" C VAL B 69 " ideal model delta sigma weight residual 111.81 109.28 2.53 8.60e-01 1.35e+00 8.67e+00 angle pdb=" N VAL A 69 " pdb=" CA VAL A 69 " pdb=" C VAL A 69 " ideal model delta sigma weight residual 111.81 109.28 2.53 8.60e-01 1.35e+00 8.67e+00 angle pdb=" N VAL C 69 " pdb=" CA VAL C 69 " pdb=" C VAL C 69 " ideal model delta sigma weight residual 111.81 109.28 2.53 8.60e-01 1.35e+00 8.67e+00 angle pdb=" CA LYS A 379 " pdb=" CB LYS A 379 " pdb=" CG LYS A 379 " ideal model delta sigma weight residual 114.10 118.99 -4.89 2.00e+00 2.50e-01 5.97e+00 ... (remaining 44715 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.72: 9532 11.72 - 23.45: 1192 23.45 - 35.17: 400 35.17 - 46.89: 220 46.89 - 58.62: 164 Dihedral angle restraints: 11508 sinusoidal: 6176 harmonic: 5332 Sorted by residual: dihedral pdb=" N GLN C 5 " pdb=" CA GLN C 5 " pdb=" CB GLN C 5 " pdb=" CG GLN C 5 " ideal model delta sinusoidal sigma weight residual -60.00 -116.83 56.83 3 1.50e+01 4.44e-03 9.42e+00 dihedral pdb=" N GLN B 5 " pdb=" CA GLN B 5 " pdb=" CB GLN B 5 " pdb=" CG GLN B 5 " ideal model delta sinusoidal sigma weight residual -60.00 -116.83 56.83 3 1.50e+01 4.44e-03 9.42e+00 dihedral pdb=" N GLN D 5 " pdb=" CA GLN D 5 " pdb=" CB GLN D 5 " pdb=" CG GLN D 5 " ideal model delta sinusoidal sigma weight residual -60.00 -116.83 56.83 3 1.50e+01 4.44e-03 9.42e+00 ... (remaining 11505 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1516 0.036 - 0.071: 384 0.071 - 0.107: 80 0.107 - 0.142: 12 0.142 - 0.178: 4 Chirality restraints: 1996 Sorted by residual: chirality pdb=" CB THR B 46 " pdb=" CA THR B 46 " pdb=" OG1 THR B 46 " pdb=" CG2 THR B 46 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 7.88e-01 chirality pdb=" CB THR C 46 " pdb=" CA THR C 46 " pdb=" OG1 THR C 46 " pdb=" CG2 THR C 46 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 7.88e-01 chirality pdb=" CB THR A 46 " pdb=" CA THR A 46 " pdb=" OG1 THR A 46 " pdb=" CG2 THR A 46 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 7.88e-01 ... (remaining 1993 not shown) Planarity restraints: 3532 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP C 83 " 0.005 2.00e-02 2.50e+03 1.01e-02 1.02e+00 pdb=" CG ASP C 83 " -0.017 2.00e-02 2.50e+03 pdb=" OD1 ASP C 83 " 0.006 2.00e-02 2.50e+03 pdb=" OD2 ASP C 83 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP D 83 " 0.005 2.00e-02 2.50e+03 1.01e-02 1.02e+00 pdb=" CG ASP D 83 " -0.017 2.00e-02 2.50e+03 pdb=" OD1 ASP D 83 " 0.006 2.00e-02 2.50e+03 pdb=" OD2 ASP D 83 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP B 83 " -0.005 2.00e-02 2.50e+03 1.01e-02 1.02e+00 pdb=" CG ASP B 83 " 0.017 2.00e-02 2.50e+03 pdb=" OD1 ASP B 83 " -0.006 2.00e-02 2.50e+03 pdb=" OD2 ASP B 83 " -0.006 2.00e-02 2.50e+03 ... (remaining 3529 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.18: 1060 2.18 - 2.78: 49068 2.78 - 3.39: 73844 3.39 - 3.99: 91204 3.99 - 4.60: 146036 Nonbonded interactions: 361212 Sorted by model distance: nonbonded pdb=" OD1 ASN C 207 " pdb=" HG1 THR C 358 " model vdw 1.569 2.450 nonbonded pdb=" OD1 ASN D 207 " pdb=" HG1 THR D 358 " model vdw 1.569 2.450 nonbonded pdb=" OD1 ASN A 207 " pdb=" HG1 THR A 358 " model vdw 1.569 2.450 nonbonded pdb=" OD1 ASN B 207 " pdb=" HG1 THR B 358 " model vdw 1.569 2.450 nonbonded pdb=" OE2 GLU C 346 " pdb=" HE ARG C 402 " model vdw 1.622 2.450 ... (remaining 361207 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.220 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: 0.410 Extract box with map and model: 0.950 Check model and map are aligned: 0.180 Set scattering table: 0.240 Process input model: 54.740 Find NCS groups from input model: 0.700 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: 0.010 Load rotamer database and sin/cos tables:11.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6697 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12280 Z= 0.193 Angle : 0.466 5.206 16656 Z= 0.263 Chirality : 0.034 0.178 1996 Planarity : 0.002 0.017 2040 Dihedral : 15.463 58.615 4376 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 0.61 % Allowed : 19.76 % Favored : 79.64 % 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: 3.59 (0.21), residues: 1508 helix: 2.97 (0.14), residues: 1256 sheet: 0.61 (0.68), residues: 48 loop : -1.37 (0.44), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 38 HIS 0.001 0.000 HIS B 306 PHE 0.013 0.001 PHE C 125 TYR 0.008 0.001 TYR D 56 ARG 0.003 0.000 ARG D 129 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 188 time to evaluate : 2.005 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: symmetry clash REVERT: A 57 ARG cc_start: 0.6196 (tpt170) cc_final: 0.5099 (tpp-160) REVERT: A 78 VAL cc_start: 0.7240 (t) cc_final: 0.6845 (p) REVERT: A 328 TRP cc_start: 0.5594 (m100) cc_final: 0.5281 (m-90) REVERT: A 399 ARG cc_start: 0.7231 (mtm-85) cc_final: 0.6965 (ttp80) REVERT: A 403 THR cc_start: 0.7874 (m) cc_final: 0.7644 (p) REVERT: B 57 ARG cc_start: 0.6197 (tpt170) cc_final: 0.5100 (tpp-160) REVERT: B 78 VAL cc_start: 0.7241 (t) cc_final: 0.6846 (p) REVERT: B 328 TRP cc_start: 0.5592 (m100) cc_final: 0.5280 (m-90) REVERT: B 399 ARG cc_start: 0.7231 (mtm-85) cc_final: 0.6964 (ttp80) REVERT: B 403 THR cc_start: 0.7873 (m) cc_final: 0.7642 (p) REVERT: C 57 ARG cc_start: 0.6196 (tpt170) cc_final: 0.5098 (tpp-160) REVERT: C 78 VAL cc_start: 0.7240 (t) cc_final: 0.6846 (p) REVERT: C 328 TRP cc_start: 0.5593 (m100) cc_final: 0.5280 (m-90) REVERT: C 399 ARG cc_start: 0.7230 (mtm-85) cc_final: 0.6964 (ttp80) REVERT: C 403 THR cc_start: 0.7874 (m) cc_final: 0.7643 (p) REVERT: D 57 ARG cc_start: 0.6197 (tpt170) cc_final: 0.5098 (tpp-160) REVERT: D 78 VAL cc_start: 0.7240 (t) cc_final: 0.6846 (p) REVERT: D 328 TRP cc_start: 0.5592 (m100) cc_final: 0.5280 (m-90) REVERT: D 399 ARG cc_start: 0.7229 (mtm-85) cc_final: 0.6963 (ttp80) REVERT: D 403 THR cc_start: 0.7875 (m) cc_final: 0.7645 (p) outliers start: 8 outliers final: 8 residues processed: 196 average time/residue: 2.6911 time to fit residues: 573.0860 Evaluate side-chains 180 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 172 time to evaluate : 1.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain D residue 279 GLU Chi-restraints excluded: chain D residue 345 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 1.9990 chunk 115 optimal weight: 0.3980 chunk 63 optimal weight: 2.9990 chunk 39 optimal weight: 0.3980 chunk 77 optimal weight: 0.2980 chunk 61 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 72 optimal weight: 3.9990 chunk 88 optimal weight: 7.9990 chunk 138 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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: 0.6689 moved from start: 0.0735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 12280 Z= 0.159 Angle : 0.438 4.726 16656 Z= 0.242 Chirality : 0.033 0.128 1996 Planarity : 0.002 0.020 2040 Dihedral : 4.381 50.685 1676 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.91 % Allowed : 17.33 % Favored : 81.76 % 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: 3.69 (0.21), residues: 1508 helix: 3.04 (0.14), residues: 1260 sheet: 0.46 (0.71), residues: 48 loop : -1.38 (0.44), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 38 HIS 0.002 0.001 HIS A 306 PHE 0.009 0.001 PHE A 125 TYR 0.007 0.001 TYR A 175 ARG 0.002 0.000 ARG C 129 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 192 time to evaluate : 2.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ARG cc_start: 0.6179 (tpt170) cc_final: 0.5087 (tpp-160) REVERT: A 67 ILE cc_start: 0.7608 (OUTLIER) cc_final: 0.7274 (tt) REVERT: A 78 VAL cc_start: 0.7236 (t) cc_final: 0.6826 (p) REVERT: A 110 ASP cc_start: 0.6863 (t0) cc_final: 0.6504 (m-30) REVERT: A 120 ASN cc_start: 0.7021 (p0) cc_final: 0.6122 (t160) REVERT: A 159 GLN cc_start: 0.5911 (OUTLIER) cc_final: 0.5510 (mt0) REVERT: A 328 TRP cc_start: 0.5583 (m100) cc_final: 0.5368 (m-90) REVERT: A 346 GLU cc_start: 0.7659 (mm-30) cc_final: 0.7407 (mm-30) REVERT: A 399 ARG cc_start: 0.7254 (mtm-85) cc_final: 0.6593 (mtt90) REVERT: A 403 THR cc_start: 0.7962 (m) cc_final: 0.7676 (p) REVERT: B 57 ARG cc_start: 0.6179 (tpt170) cc_final: 0.5087 (tpp-160) REVERT: B 67 ILE cc_start: 0.7607 (OUTLIER) cc_final: 0.7273 (tt) REVERT: B 78 VAL cc_start: 0.7236 (t) cc_final: 0.6826 (p) REVERT: B 110 ASP cc_start: 0.6865 (t0) cc_final: 0.6504 (m-30) REVERT: B 120 ASN cc_start: 0.7020 (p0) cc_final: 0.6119 (t160) REVERT: B 159 GLN cc_start: 0.5910 (OUTLIER) cc_final: 0.5510 (mt0) REVERT: B 328 TRP cc_start: 0.5581 (m100) cc_final: 0.5368 (m-90) REVERT: B 346 GLU cc_start: 0.7659 (mm-30) cc_final: 0.7407 (mm-30) REVERT: B 399 ARG cc_start: 0.7253 (mtm-85) cc_final: 0.6593 (mtt90) REVERT: B 403 THR cc_start: 0.7963 (m) cc_final: 0.7676 (p) REVERT: C 57 ARG cc_start: 0.6180 (tpt170) cc_final: 0.5087 (tpp-160) REVERT: C 67 ILE cc_start: 0.7606 (OUTLIER) cc_final: 0.7273 (tt) REVERT: C 78 VAL cc_start: 0.7237 (t) cc_final: 0.6827 (p) REVERT: C 110 ASP cc_start: 0.6864 (t0) cc_final: 0.6505 (m-30) REVERT: C 120 ASN cc_start: 0.7021 (p0) cc_final: 0.6119 (t160) REVERT: C 159 GLN cc_start: 0.5911 (OUTLIER) cc_final: 0.5510 (mt0) REVERT: C 328 TRP cc_start: 0.5581 (m100) cc_final: 0.5368 (m-90) REVERT: C 346 GLU cc_start: 0.7659 (mm-30) cc_final: 0.7407 (mm-30) REVERT: C 399 ARG cc_start: 0.7253 (mtm-85) cc_final: 0.6592 (mtt90) REVERT: C 403 THR cc_start: 0.7964 (m) cc_final: 0.7678 (p) REVERT: D 57 ARG cc_start: 0.6180 (tpt170) cc_final: 0.5087 (tpp-160) REVERT: D 67 ILE cc_start: 0.7606 (OUTLIER) cc_final: 0.7273 (tt) REVERT: D 78 VAL cc_start: 0.7236 (t) cc_final: 0.6826 (p) REVERT: D 110 ASP cc_start: 0.6862 (t0) cc_final: 0.6504 (m-30) REVERT: D 120 ASN cc_start: 0.7023 (p0) cc_final: 0.6123 (t160) REVERT: D 159 GLN cc_start: 0.5911 (OUTLIER) cc_final: 0.5510 (mt0) REVERT: D 328 TRP cc_start: 0.5582 (m100) cc_final: 0.5367 (m-90) REVERT: D 346 GLU cc_start: 0.7658 (mm-30) cc_final: 0.7406 (mm-30) REVERT: D 399 ARG cc_start: 0.7252 (mtm-85) cc_final: 0.6591 (mtt90) REVERT: D 403 THR cc_start: 0.7964 (m) cc_final: 0.7679 (p) outliers start: 12 outliers final: 0 residues processed: 204 average time/residue: 2.5744 time to fit residues: 573.4652 Evaluate side-chains 192 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 184 time to evaluate : 2.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 159 GLN Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 159 GLN Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 159 GLN Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 159 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 76 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 chunk 114 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 138 optimal weight: 2.9990 chunk 149 optimal weight: 0.4980 chunk 123 optimal weight: 2.9990 chunk 137 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 110 optimal weight: 4.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- 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: 0.6724 moved from start: 0.0987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 12280 Z= 0.307 Angle : 0.482 4.899 16656 Z= 0.268 Chirality : 0.035 0.136 1996 Planarity : 0.003 0.023 2040 Dihedral : 3.368 11.590 1660 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.22 % Allowed : 15.20 % Favored : 83.59 % 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 (0.21), residues: 1508 helix: 2.66 (0.13), residues: 1256 sheet: 0.20 (0.68), residues: 48 loop : -1.72 (0.43), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 154 HIS 0.003 0.001 HIS A 278 PHE 0.024 0.002 PHE A 422 TYR 0.011 0.001 TYR A 56 ARG 0.004 0.000 ARG B 111 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 184 time to evaluate : 1.866 Fit side-chains REVERT: A 57 ARG cc_start: 0.6254 (tpt170) cc_final: 0.5122 (tpp-160) REVERT: A 78 VAL cc_start: 0.7175 (t) cc_final: 0.6800 (p) REVERT: A 110 ASP cc_start: 0.7021 (OUTLIER) cc_final: 0.6562 (m-30) REVERT: A 120 ASN cc_start: 0.6943 (p0) cc_final: 0.6004 (t0) REVERT: A 276 ASP cc_start: 0.7281 (t0) cc_final: 0.6881 (m-30) REVERT: A 328 TRP cc_start: 0.5642 (m100) cc_final: 0.5430 (m-90) REVERT: A 346 GLU cc_start: 0.7820 (mm-30) cc_final: 0.7529 (mm-30) REVERT: A 399 ARG cc_start: 0.7491 (mtm-85) cc_final: 0.6823 (mtt90) REVERT: B 57 ARG cc_start: 0.6254 (tpt170) cc_final: 0.5123 (tpp-160) REVERT: B 78 VAL cc_start: 0.7177 (t) cc_final: 0.6802 (p) REVERT: B 110 ASP cc_start: 0.7021 (OUTLIER) cc_final: 0.6560 (m-30) REVERT: B 120 ASN cc_start: 0.6942 (p0) cc_final: 0.6001 (t0) REVERT: B 276 ASP cc_start: 0.7281 (t0) cc_final: 0.6882 (m-30) REVERT: B 328 TRP cc_start: 0.5640 (m100) cc_final: 0.5430 (m-90) REVERT: B 346 GLU cc_start: 0.7822 (mm-30) cc_final: 0.7531 (mm-30) REVERT: B 399 ARG cc_start: 0.7491 (mtm-85) cc_final: 0.6823 (mtt90) REVERT: C 57 ARG cc_start: 0.6254 (tpt170) cc_final: 0.5123 (tpp-160) REVERT: C 78 VAL cc_start: 0.7177 (t) cc_final: 0.6803 (p) REVERT: C 110 ASP cc_start: 0.7021 (OUTLIER) cc_final: 0.6560 (m-30) REVERT: C 120 ASN cc_start: 0.6942 (p0) cc_final: 0.6001 (t0) REVERT: C 276 ASP cc_start: 0.7283 (t0) cc_final: 0.6883 (m-30) REVERT: C 328 TRP cc_start: 0.5641 (m100) cc_final: 0.5432 (m-90) REVERT: C 346 GLU cc_start: 0.7821 (mm-30) cc_final: 0.7579 (mm-30) REVERT: C 399 ARG cc_start: 0.7492 (mtm-85) cc_final: 0.6822 (mtt90) REVERT: D 57 ARG cc_start: 0.6255 (tpt170) cc_final: 0.5123 (tpp-160) REVERT: D 78 VAL cc_start: 0.7175 (t) cc_final: 0.6801 (p) REVERT: D 110 ASP cc_start: 0.7022 (OUTLIER) cc_final: 0.6562 (m-30) REVERT: D 120 ASN cc_start: 0.6943 (p0) cc_final: 0.6003 (t0) REVERT: D 276 ASP cc_start: 0.7283 (t0) cc_final: 0.6883 (m-30) REVERT: D 328 TRP cc_start: 0.5642 (m100) cc_final: 0.5431 (m-90) REVERT: D 346 GLU cc_start: 0.7819 (mm-30) cc_final: 0.7529 (mm-30) REVERT: D 399 ARG cc_start: 0.7491 (mtm-85) cc_final: 0.6821 (mtt90) outliers start: 16 outliers final: 0 residues processed: 188 average time/residue: 2.9284 time to fit residues: 595.4606 Evaluate side-chains 184 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 180 time to evaluate : 1.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain D residue 110 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 136 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 chunk 71 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 92 optimal weight: 20.0000 chunk 138 optimal weight: 2.9990 chunk 146 optimal weight: 7.9990 chunk 72 optimal weight: 3.9990 chunk 131 optimal weight: 0.9980 chunk 39 optimal weight: 0.1980 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN B 117 ASN C 117 ASN D 117 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6714 moved from start: 0.1081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12280 Z= 0.237 Angle : 0.461 5.142 16656 Z= 0.254 Chirality : 0.034 0.131 1996 Planarity : 0.004 0.052 2040 Dihedral : 3.377 11.751 1660 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.22 % Allowed : 14.82 % Favored : 83.97 % 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: 3.12 (0.21), residues: 1508 helix: 2.64 (0.13), residues: 1260 sheet: 0.27 (0.71), residues: 48 loop : -1.53 (0.43), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 154 HIS 0.002 0.001 HIS B 278 PHE 0.023 0.002 PHE C 422 TYR 0.008 0.001 TYR C 56 ARG 0.006 0.000 ARG D 129 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 192 time to evaluate : 2.046 Fit side-chains REVERT: A 57 ARG cc_start: 0.6283 (tpt170) cc_final: 0.5083 (tpp-160) REVERT: A 78 VAL cc_start: 0.7168 (t) cc_final: 0.6791 (p) REVERT: A 110 ASP cc_start: 0.6929 (OUTLIER) cc_final: 0.6538 (m-30) REVERT: A 120 ASN cc_start: 0.6934 (p0) cc_final: 0.5981 (t0) REVERT: A 276 ASP cc_start: 0.7261 (t0) cc_final: 0.6887 (m-30) REVERT: A 328 TRP cc_start: 0.5602 (m100) cc_final: 0.5382 (m-90) REVERT: A 346 GLU cc_start: 0.7852 (mm-30) cc_final: 0.7592 (mm-30) REVERT: A 399 ARG cc_start: 0.7493 (mtm-85) cc_final: 0.6827 (mtt90) REVERT: B 57 ARG cc_start: 0.6283 (tpt170) cc_final: 0.5085 (tpp-160) REVERT: B 78 VAL cc_start: 0.7168 (t) cc_final: 0.6791 (p) REVERT: B 110 ASP cc_start: 0.6930 (OUTLIER) cc_final: 0.6538 (m-30) REVERT: B 120 ASN cc_start: 0.6921 (p0) cc_final: 0.5976 (t0) REVERT: B 276 ASP cc_start: 0.7262 (t0) cc_final: 0.6889 (m-30) REVERT: B 328 TRP cc_start: 0.5602 (m100) cc_final: 0.5381 (m-90) REVERT: B 346 GLU cc_start: 0.7853 (mm-30) cc_final: 0.7593 (mm-30) REVERT: B 399 ARG cc_start: 0.7493 (mtm-85) cc_final: 0.6827 (mtt90) REVERT: C 57 ARG cc_start: 0.6285 (tpt170) cc_final: 0.5085 (tpp-160) REVERT: C 78 VAL cc_start: 0.7171 (t) cc_final: 0.6795 (p) REVERT: C 110 ASP cc_start: 0.6932 (OUTLIER) cc_final: 0.6540 (m-30) REVERT: C 120 ASN cc_start: 0.6921 (p0) cc_final: 0.5982 (t0) REVERT: C 276 ASP cc_start: 0.7263 (t0) cc_final: 0.6889 (m-30) REVERT: C 328 TRP cc_start: 0.5602 (m100) cc_final: 0.5382 (m-90) REVERT: C 346 GLU cc_start: 0.7852 (mm-30) cc_final: 0.7591 (mm-30) REVERT: C 399 ARG cc_start: 0.7493 (mtm-85) cc_final: 0.6826 (mtt90) REVERT: D 57 ARG cc_start: 0.6284 (tpt170) cc_final: 0.5083 (tpp-160) REVERT: D 78 VAL cc_start: 0.7168 (t) cc_final: 0.6792 (p) REVERT: D 110 ASP cc_start: 0.6930 (OUTLIER) cc_final: 0.6540 (m-30) REVERT: D 120 ASN cc_start: 0.6923 (p0) cc_final: 0.5984 (t0) REVERT: D 276 ASP cc_start: 0.7263 (t0) cc_final: 0.6890 (m-30) REVERT: D 328 TRP cc_start: 0.5604 (m100) cc_final: 0.5382 (m-90) REVERT: D 346 GLU cc_start: 0.7851 (mm-30) cc_final: 0.7592 (mm-30) REVERT: D 399 ARG cc_start: 0.7493 (mtm-85) cc_final: 0.6826 (mtt90) outliers start: 16 outliers final: 8 residues processed: 200 average time/residue: 2.6003 time to fit residues: 568.9097 Evaluate side-chains 198 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 186 time to evaluate : 1.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 110 ASP Chi-restraints excluded: chain D residue 345 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 122 optimal weight: 0.7980 chunk 83 optimal weight: 5.9990 chunk 2 optimal weight: 4.9990 chunk 109 optimal weight: 6.9990 chunk 60 optimal weight: 4.9990 chunk 125 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 131 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN B 117 ASN C 117 ASN D 117 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6717 moved from start: 0.1196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12280 Z= 0.255 Angle : 0.461 4.464 16656 Z= 0.256 Chirality : 0.034 0.131 1996 Planarity : 0.004 0.047 2040 Dihedral : 3.422 11.328 1660 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.22 % Allowed : 15.05 % Favored : 83.74 % 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: 3.05 (0.21), residues: 1508 helix: 2.60 (0.13), residues: 1260 sheet: 0.24 (0.72), residues: 48 loop : -1.55 (0.43), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 154 HIS 0.002 0.001 HIS A 278 PHE 0.031 0.002 PHE B 422 TYR 0.009 0.001 TYR A 56 ARG 0.008 0.000 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 198 time to evaluate : 1.902 Fit side-chains REVERT: A 57 ARG cc_start: 0.6285 (tpt170) cc_final: 0.5065 (tpp-160) REVERT: A 78 VAL cc_start: 0.7113 (t) cc_final: 0.6738 (p) REVERT: A 120 ASN cc_start: 0.6933 (p0) cc_final: 0.5946 (t0) REVERT: A 276 ASP cc_start: 0.7247 (t0) cc_final: 0.6924 (m-30) REVERT: A 328 TRP cc_start: 0.5562 (m100) cc_final: 0.5272 (m-90) REVERT: A 346 GLU cc_start: 0.7893 (mm-30) cc_final: 0.7669 (mm-30) REVERT: A 399 ARG cc_start: 0.7496 (mtm-85) cc_final: 0.6802 (mtt90) REVERT: B 57 ARG cc_start: 0.6285 (tpt170) cc_final: 0.5065 (tpp-160) REVERT: B 78 VAL cc_start: 0.7115 (t) cc_final: 0.6740 (p) REVERT: B 120 ASN cc_start: 0.6931 (p0) cc_final: 0.5945 (t0) REVERT: B 276 ASP cc_start: 0.7249 (t0) cc_final: 0.6924 (m-30) REVERT: B 328 TRP cc_start: 0.5562 (m100) cc_final: 0.5273 (m-90) REVERT: B 346 GLU cc_start: 0.7893 (mm-30) cc_final: 0.7669 (mm-30) REVERT: B 399 ARG cc_start: 0.7496 (mtm-85) cc_final: 0.6803 (mtt90) REVERT: C 57 ARG cc_start: 0.6287 (tpt170) cc_final: 0.5066 (tpp-160) REVERT: C 78 VAL cc_start: 0.7117 (t) cc_final: 0.6741 (p) REVERT: C 120 ASN cc_start: 0.6930 (p0) cc_final: 0.5944 (t0) REVERT: C 276 ASP cc_start: 0.7249 (t0) cc_final: 0.6925 (m-30) REVERT: C 328 TRP cc_start: 0.5563 (m100) cc_final: 0.5275 (m-90) REVERT: C 346 GLU cc_start: 0.7893 (mm-30) cc_final: 0.7669 (mm-30) REVERT: C 399 ARG cc_start: 0.7496 (mtm-85) cc_final: 0.6803 (mtt90) REVERT: D 57 ARG cc_start: 0.6285 (tpt170) cc_final: 0.5064 (tpp-160) REVERT: D 78 VAL cc_start: 0.7115 (t) cc_final: 0.6739 (p) REVERT: D 110 ASP cc_start: 0.6942 (OUTLIER) cc_final: 0.6533 (m-30) REVERT: D 120 ASN cc_start: 0.6933 (p0) cc_final: 0.5947 (t0) REVERT: D 276 ASP cc_start: 0.7249 (t0) cc_final: 0.6925 (m-30) REVERT: D 328 TRP cc_start: 0.5563 (m100) cc_final: 0.5273 (m-90) REVERT: D 346 GLU cc_start: 0.7892 (mm-30) cc_final: 0.7668 (mm-30) REVERT: D 399 ARG cc_start: 0.7495 (mtm-85) cc_final: 0.6801 (mtt90) outliers start: 16 outliers final: 11 residues processed: 206 average time/residue: 2.7126 time to fit residues: 607.9680 Evaluate side-chains 198 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 186 time to evaluate : 1.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 110 ASP Chi-restraints excluded: chain D residue 345 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 49 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 147 optimal weight: 6.9990 chunk 122 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 chunk 12 optimal weight: 7.9990 chunk 48 optimal weight: 0.9980 chunk 77 optimal weight: 0.2980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN B 117 ASN C 117 ASN D 117 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6704 moved from start: 0.1193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12280 Z= 0.188 Angle : 0.444 5.756 16656 Z= 0.244 Chirality : 0.033 0.128 1996 Planarity : 0.003 0.053 2040 Dihedral : 3.337 10.825 1660 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.91 % Allowed : 15.81 % Favored : 83.28 % 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: 3.33 (0.21), residues: 1508 helix: 2.79 (0.14), residues: 1260 sheet: 0.25 (0.72), residues: 48 loop : -1.43 (0.44), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 154 HIS 0.001 0.001 HIS A 278 PHE 0.031 0.002 PHE C 422 TYR 0.007 0.001 TYR A 56 ARG 0.009 0.000 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 180 time to evaluate : 2.094 Fit side-chains REVERT: A 57 ARG cc_start: 0.6277 (tpt170) cc_final: 0.5053 (tpp-160) REVERT: A 67 ILE cc_start: 0.7715 (OUTLIER) cc_final: 0.7336 (tt) REVERT: A 78 VAL cc_start: 0.7105 (t) cc_final: 0.6723 (p) REVERT: A 110 ASP cc_start: 0.6882 (OUTLIER) cc_final: 0.6540 (m-30) REVERT: A 120 ASN cc_start: 0.6865 (p0) cc_final: 0.5926 (t0) REVERT: A 276 ASP cc_start: 0.7242 (t0) cc_final: 0.6895 (m-30) REVERT: A 328 TRP cc_start: 0.5559 (m100) cc_final: 0.4914 (m-10) REVERT: A 346 GLU cc_start: 0.7892 (mm-30) cc_final: 0.7663 (mm-30) REVERT: A 399 ARG cc_start: 0.7514 (mtm-85) cc_final: 0.6815 (mtt90) REVERT: B 57 ARG cc_start: 0.6276 (tpt170) cc_final: 0.5053 (tpp-160) REVERT: B 67 ILE cc_start: 0.7718 (OUTLIER) cc_final: 0.7338 (tt) REVERT: B 78 VAL cc_start: 0.7106 (t) cc_final: 0.6724 (p) REVERT: B 110 ASP cc_start: 0.6884 (OUTLIER) cc_final: 0.6540 (m-30) REVERT: B 120 ASN cc_start: 0.6866 (p0) cc_final: 0.5926 (t0) REVERT: B 276 ASP cc_start: 0.7250 (t0) cc_final: 0.6904 (m-30) REVERT: B 328 TRP cc_start: 0.5560 (m100) cc_final: 0.4915 (m-10) REVERT: B 346 GLU cc_start: 0.7894 (mm-30) cc_final: 0.7664 (mm-30) REVERT: B 399 ARG cc_start: 0.7515 (mtm-85) cc_final: 0.6817 (mtt90) REVERT: C 57 ARG cc_start: 0.6278 (tpt170) cc_final: 0.5053 (tpp-160) REVERT: C 67 ILE cc_start: 0.7718 (OUTLIER) cc_final: 0.7338 (tt) REVERT: C 78 VAL cc_start: 0.7107 (t) cc_final: 0.6726 (p) REVERT: C 110 ASP cc_start: 0.6883 (OUTLIER) cc_final: 0.6540 (m-30) REVERT: C 120 ASN cc_start: 0.6866 (p0) cc_final: 0.5926 (t0) REVERT: C 276 ASP cc_start: 0.7250 (t0) cc_final: 0.6904 (m-30) REVERT: C 328 TRP cc_start: 0.5561 (m100) cc_final: 0.4917 (m-10) REVERT: C 346 GLU cc_start: 0.7892 (mm-30) cc_final: 0.7662 (mm-30) REVERT: C 399 ARG cc_start: 0.7513 (mtm-85) cc_final: 0.6817 (mtt90) REVERT: D 57 ARG cc_start: 0.6276 (tpt170) cc_final: 0.5051 (tpp-160) REVERT: D 67 ILE cc_start: 0.7719 (OUTLIER) cc_final: 0.7337 (tt) REVERT: D 78 VAL cc_start: 0.7105 (t) cc_final: 0.6724 (p) REVERT: D 110 ASP cc_start: 0.6883 (OUTLIER) cc_final: 0.6540 (m-30) REVERT: D 120 ASN cc_start: 0.6866 (p0) cc_final: 0.5928 (t0) REVERT: D 276 ASP cc_start: 0.7244 (t0) cc_final: 0.6896 (m-30) REVERT: D 328 TRP cc_start: 0.5561 (m100) cc_final: 0.4914 (m-10) REVERT: D 346 GLU cc_start: 0.7891 (mm-30) cc_final: 0.7662 (mm-30) REVERT: D 399 ARG cc_start: 0.7511 (mtm-85) cc_final: 0.6814 (mtt90) outliers start: 12 outliers final: 4 residues processed: 184 average time/residue: 2.6995 time to fit residues: 541.2623 Evaluate side-chains 198 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 186 time to evaluate : 2.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 110 ASP Chi-restraints excluded: chain D residue 345 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 141 optimal weight: 7.9990 chunk 16 optimal weight: 7.9990 chunk 83 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 123 optimal weight: 2.9990 chunk 82 optimal weight: 7.9990 chunk 146 optimal weight: 8.9990 chunk 91 optimal weight: 0.7980 chunk 89 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN B 117 ASN C 117 ASN D 117 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6725 moved from start: 0.1334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 12280 Z= 0.312 Angle : 0.482 5.052 16656 Z= 0.267 Chirality : 0.035 0.131 1996 Planarity : 0.004 0.039 2040 Dihedral : 3.489 11.468 1660 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.13 % Allowed : 14.29 % Favored : 83.59 % 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: 2.95 (0.21), residues: 1508 helix: 2.52 (0.13), residues: 1260 sheet: 0.20 (0.70), residues: 48 loop : -1.53 (0.43), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 154 HIS 0.003 0.001 HIS D 286 PHE 0.028 0.002 PHE C 422 TYR 0.009 0.001 TYR B 56 ARG 0.006 0.000 ARG C 129 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 189 time to evaluate : 1.863 Fit side-chains REVERT: A 57 ARG cc_start: 0.6324 (tpt170) cc_final: 0.5083 (tpp-160) REVERT: A 59 LEU cc_start: 0.6433 (OUTLIER) cc_final: 0.6008 (mp) REVERT: A 78 VAL cc_start: 0.7116 (t) cc_final: 0.6743 (p) REVERT: A 110 ASP cc_start: 0.7013 (OUTLIER) cc_final: 0.6578 (m-30) REVERT: A 120 ASN cc_start: 0.6819 (p0) cc_final: 0.5840 (t0) REVERT: A 129 ARG cc_start: 0.6884 (ttm-80) cc_final: 0.6662 (ttm110) REVERT: A 276 ASP cc_start: 0.7252 (t0) cc_final: 0.6928 (m-30) REVERT: A 328 TRP cc_start: 0.5551 (m100) cc_final: 0.4911 (m-10) REVERT: A 346 GLU cc_start: 0.7869 (mm-30) cc_final: 0.7644 (mm-30) REVERT: A 399 ARG cc_start: 0.7518 (mtm-85) cc_final: 0.7271 (mtm110) REVERT: B 57 ARG cc_start: 0.6323 (tpt170) cc_final: 0.5083 (tpp-160) REVERT: B 59 LEU cc_start: 0.6431 (OUTLIER) cc_final: 0.6005 (mp) REVERT: B 78 VAL cc_start: 0.7117 (t) cc_final: 0.6744 (p) REVERT: B 110 ASP cc_start: 0.7014 (OUTLIER) cc_final: 0.6578 (m-30) REVERT: B 120 ASN cc_start: 0.6816 (p0) cc_final: 0.5837 (t0) REVERT: B 129 ARG cc_start: 0.6884 (ttm-80) cc_final: 0.6661 (ttm110) REVERT: B 276 ASP cc_start: 0.7252 (t0) cc_final: 0.6928 (m-30) REVERT: B 328 TRP cc_start: 0.5552 (m100) cc_final: 0.4913 (m-10) REVERT: B 346 GLU cc_start: 0.7871 (mm-30) cc_final: 0.7645 (mm-30) REVERT: B 399 ARG cc_start: 0.7516 (mtm-85) cc_final: 0.7284 (mtm110) REVERT: C 57 ARG cc_start: 0.6325 (tpt170) cc_final: 0.5084 (tpp-160) REVERT: C 59 LEU cc_start: 0.6432 (OUTLIER) cc_final: 0.6007 (mp) REVERT: C 78 VAL cc_start: 0.7120 (t) cc_final: 0.6747 (p) REVERT: C 110 ASP cc_start: 0.7013 (OUTLIER) cc_final: 0.6578 (m-30) REVERT: C 120 ASN cc_start: 0.6816 (p0) cc_final: 0.5837 (t0) REVERT: C 129 ARG cc_start: 0.6880 (ttm-80) cc_final: 0.6661 (ttm110) REVERT: C 276 ASP cc_start: 0.7253 (t0) cc_final: 0.6929 (m-30) REVERT: C 328 TRP cc_start: 0.5552 (m100) cc_final: 0.4913 (m-10) REVERT: C 346 GLU cc_start: 0.7870 (mm-30) cc_final: 0.7644 (mm-30) REVERT: C 399 ARG cc_start: 0.7516 (mtm-85) cc_final: 0.7284 (mtm110) REVERT: D 57 ARG cc_start: 0.6324 (tpt170) cc_final: 0.5082 (tpp-160) REVERT: D 59 LEU cc_start: 0.6429 (OUTLIER) cc_final: 0.6005 (mp) REVERT: D 78 VAL cc_start: 0.7117 (t) cc_final: 0.6744 (p) REVERT: D 110 ASP cc_start: 0.7013 (OUTLIER) cc_final: 0.6579 (m-30) REVERT: D 120 ASN cc_start: 0.6819 (p0) cc_final: 0.5840 (t0) REVERT: D 129 ARG cc_start: 0.6884 (ttm-80) cc_final: 0.6663 (ttm110) REVERT: D 276 ASP cc_start: 0.7252 (t0) cc_final: 0.6929 (m-30) REVERT: D 328 TRP cc_start: 0.5553 (m100) cc_final: 0.4913 (m-10) REVERT: D 346 GLU cc_start: 0.7868 (mm-30) cc_final: 0.7643 (mm-30) REVERT: D 399 ARG cc_start: 0.7517 (mtm-85) cc_final: 0.7271 (mtm110) outliers start: 28 outliers final: 8 residues processed: 201 average time/residue: 2.6092 time to fit residues: 571.7519 Evaluate side-chains 200 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 184 time to evaluate : 2.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 110 ASP Chi-restraints excluded: chain D residue 345 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 58 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 99 optimal weight: 0.9990 chunk 72 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 115 optimal weight: 0.4980 chunk 133 optimal weight: 2.9990 chunk 140 optimal weight: 3.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN B 117 ASN C 117 ASN D 117 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6719 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12280 Z= 0.261 Angle : 0.467 4.704 16656 Z= 0.258 Chirality : 0.034 0.130 1996 Planarity : 0.003 0.037 2040 Dihedral : 3.483 11.338 1660 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.52 % Allowed : 15.05 % Favored : 83.43 % 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: 3.01 (0.21), residues: 1508 helix: 2.55 (0.13), residues: 1260 sheet: 0.23 (0.72), residues: 48 loop : -1.45 (0.44), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 154 HIS 0.002 0.001 HIS B 278 PHE 0.032 0.002 PHE C 422 TYR 0.007 0.001 TYR D 56 ARG 0.005 0.000 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 184 time to evaluate : 2.017 Fit side-chains REVERT: A 26 ARG cc_start: 0.7007 (ttm170) cc_final: 0.6802 (ttm170) REVERT: A 57 ARG cc_start: 0.6313 (tpt170) cc_final: 0.5051 (tpp-160) REVERT: A 59 LEU cc_start: 0.6422 (OUTLIER) cc_final: 0.5995 (mp) REVERT: A 78 VAL cc_start: 0.7169 (t) cc_final: 0.6795 (p) REVERT: A 110 ASP cc_start: 0.6988 (OUTLIER) cc_final: 0.6588 (m-30) REVERT: A 120 ASN cc_start: 0.6810 (p0) cc_final: 0.5824 (t0) REVERT: A 129 ARG cc_start: 0.6880 (ttm-80) cc_final: 0.6675 (ttm110) REVERT: A 276 ASP cc_start: 0.7248 (t0) cc_final: 0.6935 (m-30) REVERT: A 328 TRP cc_start: 0.5509 (m100) cc_final: 0.4902 (m-10) REVERT: A 399 ARG cc_start: 0.7546 (mtm-85) cc_final: 0.7309 (mtm110) REVERT: B 26 ARG cc_start: 0.7010 (ttm170) cc_final: 0.6805 (ttm170) REVERT: B 57 ARG cc_start: 0.6313 (tpt170) cc_final: 0.5052 (tpp-160) REVERT: B 59 LEU cc_start: 0.6420 (OUTLIER) cc_final: 0.5993 (mp) REVERT: B 78 VAL cc_start: 0.7170 (t) cc_final: 0.6796 (p) REVERT: B 110 ASP cc_start: 0.6989 (OUTLIER) cc_final: 0.6588 (m-30) REVERT: B 120 ASN cc_start: 0.6811 (p0) cc_final: 0.5822 (t0) REVERT: B 276 ASP cc_start: 0.7245 (t0) cc_final: 0.6927 (m-30) REVERT: B 328 TRP cc_start: 0.5511 (m100) cc_final: 0.4903 (m-10) REVERT: B 399 ARG cc_start: 0.7510 (mtm-85) cc_final: 0.7268 (mtm110) REVERT: C 57 ARG cc_start: 0.6314 (tpt170) cc_final: 0.5052 (tpp-160) REVERT: C 59 LEU cc_start: 0.6421 (OUTLIER) cc_final: 0.5994 (mp) REVERT: C 78 VAL cc_start: 0.7170 (t) cc_final: 0.6797 (p) REVERT: C 110 ASP cc_start: 0.6988 (OUTLIER) cc_final: 0.6588 (m-30) REVERT: C 120 ASN cc_start: 0.6812 (p0) cc_final: 0.5824 (t0) REVERT: C 276 ASP cc_start: 0.7253 (t0) cc_final: 0.6914 (m-30) REVERT: C 328 TRP cc_start: 0.5510 (m100) cc_final: 0.4904 (m-10) REVERT: C 399 ARG cc_start: 0.7510 (mtm-85) cc_final: 0.7268 (mtm110) REVERT: D 26 ARG cc_start: 0.7008 (ttm170) cc_final: 0.6802 (ttm170) REVERT: D 57 ARG cc_start: 0.6313 (tpt170) cc_final: 0.5050 (tpp-160) REVERT: D 59 LEU cc_start: 0.6420 (OUTLIER) cc_final: 0.6003 (mp) REVERT: D 78 VAL cc_start: 0.7169 (t) cc_final: 0.6796 (p) REVERT: D 110 ASP cc_start: 0.6990 (OUTLIER) cc_final: 0.6590 (m-30) REVERT: D 120 ASN cc_start: 0.6813 (p0) cc_final: 0.5827 (t0) REVERT: D 276 ASP cc_start: 0.7250 (t0) cc_final: 0.6936 (m-30) REVERT: D 328 TRP cc_start: 0.5511 (m100) cc_final: 0.4903 (m-10) REVERT: D 399 ARG cc_start: 0.7544 (mtm-85) cc_final: 0.7308 (mtm110) outliers start: 20 outliers final: 12 residues processed: 196 average time/residue: 2.6971 time to fit residues: 575.3456 Evaluate side-chains 205 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 185 time to evaluate : 2.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 110 ASP Chi-restraints excluded: chain D residue 345 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 0.6980 chunk 136 optimal weight: 4.9990 chunk 140 optimal weight: 3.9990 chunk 82 optimal weight: 0.8980 chunk 59 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 chunk 123 optimal weight: 3.9990 chunk 129 optimal weight: 4.9990 chunk 89 optimal weight: 4.9990 chunk 144 optimal weight: 0.5980 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN B 117 ASN C 117 ASN D 117 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6709 moved from start: 0.1344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12280 Z= 0.206 Angle : 0.447 4.265 16656 Z= 0.247 Chirality : 0.033 0.130 1996 Planarity : 0.004 0.067 2040 Dihedral : 3.416 10.963 1660 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.82 % Allowed : 14.74 % Favored : 83.43 % 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: 3.24 (0.21), residues: 1508 helix: 2.71 (0.14), residues: 1260 sheet: 0.24 (0.72), residues: 48 loop : -1.32 (0.45), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 154 HIS 0.002 0.001 HIS C 278 PHE 0.040 0.002 PHE A 422 TYR 0.007 0.001 TYR C 56 ARG 0.012 0.000 ARG C 129 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 185 time to evaluate : 4.956 Fit side-chains REVERT: A 57 ARG cc_start: 0.6308 (tpt170) cc_final: 0.5044 (tpp-160) REVERT: A 59 LEU cc_start: 0.6355 (OUTLIER) cc_final: 0.5926 (mp) REVERT: A 67 ILE cc_start: 0.7705 (OUTLIER) cc_final: 0.7337 (tt) REVERT: A 78 VAL cc_start: 0.7086 (t) cc_final: 0.6713 (p) REVERT: A 110 ASP cc_start: 0.6940 (OUTLIER) cc_final: 0.6591 (m-30) REVERT: A 129 ARG cc_start: 0.6869 (ttm-80) cc_final: 0.6662 (ttm110) REVERT: A 276 ASP cc_start: 0.7219 (t0) cc_final: 0.6890 (m-30) REVERT: A 328 TRP cc_start: 0.5507 (m100) cc_final: 0.4909 (m-10) REVERT: A 399 ARG cc_start: 0.7549 (mtm-85) cc_final: 0.7318 (mtm110) REVERT: B 57 ARG cc_start: 0.6309 (tpt170) cc_final: 0.5044 (tpp-160) REVERT: B 59 LEU cc_start: 0.6353 (OUTLIER) cc_final: 0.5925 (mp) REVERT: B 67 ILE cc_start: 0.7705 (OUTLIER) cc_final: 0.7336 (tt) REVERT: B 78 VAL cc_start: 0.7087 (t) cc_final: 0.6714 (p) REVERT: B 110 ASP cc_start: 0.6941 (OUTLIER) cc_final: 0.6592 (m-30) REVERT: B 276 ASP cc_start: 0.7250 (t0) cc_final: 0.6906 (m-30) REVERT: B 328 TRP cc_start: 0.5508 (m100) cc_final: 0.4910 (m-10) REVERT: B 399 ARG cc_start: 0.7539 (mtm-85) cc_final: 0.7305 (mtm110) REVERT: C 57 ARG cc_start: 0.6309 (tpt170) cc_final: 0.5044 (tpp-160) REVERT: C 59 LEU cc_start: 0.6353 (OUTLIER) cc_final: 0.5924 (mp) REVERT: C 67 ILE cc_start: 0.7704 (OUTLIER) cc_final: 0.7337 (tt) REVERT: C 78 VAL cc_start: 0.7089 (t) cc_final: 0.6716 (p) REVERT: C 110 ASP cc_start: 0.6941 (OUTLIER) cc_final: 0.6592 (m-30) REVERT: C 276 ASP cc_start: 0.7251 (t0) cc_final: 0.6907 (m-30) REVERT: C 328 TRP cc_start: 0.5509 (m100) cc_final: 0.4911 (m-10) REVERT: C 399 ARG cc_start: 0.7536 (mtm-85) cc_final: 0.7304 (mtm110) REVERT: D 57 ARG cc_start: 0.6308 (tpt170) cc_final: 0.5041 (tpp-160) REVERT: D 59 LEU cc_start: 0.6359 (OUTLIER) cc_final: 0.5921 (mp) REVERT: D 67 ILE cc_start: 0.7704 (OUTLIER) cc_final: 0.7337 (tt) REVERT: D 78 VAL cc_start: 0.7087 (t) cc_final: 0.6713 (p) REVERT: D 110 ASP cc_start: 0.6941 (OUTLIER) cc_final: 0.6592 (m-30) REVERT: D 276 ASP cc_start: 0.7220 (t0) cc_final: 0.6890 (m-30) REVERT: D 328 TRP cc_start: 0.5510 (m100) cc_final: 0.4910 (m-10) REVERT: D 399 ARG cc_start: 0.7548 (mtm-85) cc_final: 0.7318 (mtm110) outliers start: 24 outliers final: 4 residues processed: 201 average time/residue: 2.7097 time to fit residues: 602.5289 Evaluate side-chains 197 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 181 time to evaluate : 1.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 110 ASP Chi-restraints excluded: chain D residue 345 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 88 optimal weight: 0.7980 chunk 68 optimal weight: 0.7980 chunk 100 optimal weight: 2.9990 chunk 151 optimal weight: 0.9990 chunk 139 optimal weight: 2.9990 chunk 120 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 128 optimal weight: 0.4980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN B 117 ASN C 117 ASN D 117 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6686 moved from start: 0.1358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 12280 Z= 0.151 Angle : 0.438 5.985 16656 Z= 0.239 Chirality : 0.033 0.128 1996 Planarity : 0.003 0.055 2040 Dihedral : 3.242 10.666 1660 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.46 % Allowed : 15.96 % Favored : 83.59 % 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: 3.63 (0.21), residues: 1508 helix: 2.98 (0.14), residues: 1260 sheet: 0.23 (0.74), residues: 48 loop : -1.17 (0.46), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 130 HIS 0.002 0.001 HIS B 306 PHE 0.030 0.001 PHE A 422 TYR 0.006 0.001 TYR A 122 ARG 0.009 0.000 ARG C 129 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 193 time to evaluate : 2.082 Fit side-chains revert: symmetry clash REVERT: A 26 ARG cc_start: 0.7048 (ttm170) cc_final: 0.6830 (ttm170) REVERT: A 57 ARG cc_start: 0.6349 (tpt170) cc_final: 0.5088 (tpp-160) REVERT: A 67 ILE cc_start: 0.7707 (OUTLIER) cc_final: 0.7352 (tt) REVERT: A 78 VAL cc_start: 0.7083 (t) cc_final: 0.6700 (p) REVERT: A 110 ASP cc_start: 0.6809 (OUTLIER) cc_final: 0.6533 (m-30) REVERT: A 276 ASP cc_start: 0.7238 (t0) cc_final: 0.6909 (m-30) REVERT: A 399 ARG cc_start: 0.7388 (mtm-85) cc_final: 0.6714 (mtt90) REVERT: B 26 ARG cc_start: 0.7061 (ttm170) cc_final: 0.6832 (ttm170) REVERT: B 57 ARG cc_start: 0.6349 (tpt170) cc_final: 0.5088 (tpp-160) REVERT: B 67 ILE cc_start: 0.7708 (OUTLIER) cc_final: 0.7353 (tt) REVERT: B 78 VAL cc_start: 0.7085 (t) cc_final: 0.6701 (p) REVERT: B 110 ASP cc_start: 0.6774 (t70) cc_final: 0.6491 (m-30) REVERT: B 276 ASP cc_start: 0.7237 (t0) cc_final: 0.6907 (m-30) REVERT: B 399 ARG cc_start: 0.7388 (mtm-85) cc_final: 0.7154 (mtm110) REVERT: C 57 ARG cc_start: 0.6351 (tpt170) cc_final: 0.5089 (tpp-160) REVERT: C 67 ILE cc_start: 0.7708 (OUTLIER) cc_final: 0.7353 (tt) REVERT: C 78 VAL cc_start: 0.7085 (t) cc_final: 0.6703 (p) REVERT: C 110 ASP cc_start: 0.6774 (OUTLIER) cc_final: 0.6492 (m-30) REVERT: C 159 GLN cc_start: 0.5774 (pt0) cc_final: 0.5514 (mt0) REVERT: C 276 ASP cc_start: 0.7201 (t0) cc_final: 0.6872 (m-30) REVERT: C 399 ARG cc_start: 0.7387 (mtm-85) cc_final: 0.7154 (mtm110) REVERT: D 26 ARG cc_start: 0.7078 (ttm170) cc_final: 0.6852 (ttm170) REVERT: D 57 ARG cc_start: 0.6350 (tpt170) cc_final: 0.5088 (tpp-160) REVERT: D 67 ILE cc_start: 0.7707 (OUTLIER) cc_final: 0.7352 (tt) REVERT: D 78 VAL cc_start: 0.7083 (t) cc_final: 0.6700 (p) REVERT: D 110 ASP cc_start: 0.6812 (t70) cc_final: 0.6535 (m-30) REVERT: D 276 ASP cc_start: 0.7202 (t0) cc_final: 0.6873 (m-30) REVERT: D 399 ARG cc_start: 0.7386 (mtm-85) cc_final: 0.6712 (mtt90) outliers start: 6 outliers final: 0 residues processed: 193 average time/residue: 2.5607 time to fit residues: 541.3306 Evaluate side-chains 195 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 189 time to evaluate : 1.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain D residue 67 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 36 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 120 optimal weight: 7.9990 chunk 50 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 22 optimal weight: 0.9980 chunk 106 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN B 117 ASN C 117 ASN D 117 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.138992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.097565 restraints weight = 37609.851| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 1.93 r_work: 0.2935 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2793 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12280 Z= 0.277 Angle : 0.478 5.718 16656 Z= 0.264 Chirality : 0.035 0.129 1996 Planarity : 0.004 0.057 2040 Dihedral : 3.407 11.223 1660 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.91 % Allowed : 15.20 % Favored : 83.89 % 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: 3.25 (0.21), residues: 1508 helix: 2.71 (0.13), residues: 1260 sheet: 0.18 (0.73), residues: 48 loop : -1.28 (0.45), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 154 HIS 0.003 0.001 HIS C 286 PHE 0.036 0.002 PHE A 422 TYR 0.009 0.001 TYR B 56 ARG 0.008 0.000 ARG B 129 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9443.17 seconds wall clock time: 163 minutes 42.79 seconds (9822.79 seconds total)