Starting phenix.real_space_refine on Thu Jul 18 23:21:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tth_41608/07_2024/8tth_41608.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tth_41608/07_2024/8tth_41608.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tth_41608/07_2024/8tth_41608.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tth_41608/07_2024/8tth_41608.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tth_41608/07_2024/8tth_41608.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tth_41608/07_2024/8tth_41608.cif" } resolution = 3.54 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= 0.002 sd= 0.060 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 26 5.16 5 C 3031 2.51 5 N 729 2.21 5 O 834 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 63": "OD1" <-> "OD2" Residue "A PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 222": "OE1" <-> "OE2" Residue "A PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 323": "OE1" <-> "OE2" Residue "A PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 41": "OD1" <-> "OD2" Residue "D TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 106": "OD1" <-> "OD2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 4620 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2842 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 14, 'TRANS': 355} Chain breaks: 1 Chain: "C" Number of atoms: 991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 991 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 124} Chain: "D" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 787 Classifications: {'peptide': 105} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 99} Time building chain proxies: 3.23, per 1000 atoms: 0.70 Number of scatterers: 4620 At special positions: 0 Unit cell: (60.225, 72.6, 106.425, 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 26 16.00 O 834 8.00 N 729 7.00 C 3031 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS C 48 " - pdb=" SG CYS C 122 " distance=2.03 Simple disulfide: pdb=" SG CYS D 47 " - pdb=" SG CYS D 112 " 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: 1.83 Conformation dependent library (CDL) restraints added in 850.4 milliseconds 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1092 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 6 sheets defined 58.7% alpha, 17.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 2 through 33 removed outlier: 3.715A pdb=" N PHE A 6 " --> pdb=" O ASN A 2 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE A 12 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ILE A 15 " --> pdb=" O ASN A 11 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N VAL A 22 " --> pdb=" O GLY A 18 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N ILE A 23 " --> pdb=" O ILE A 19 " (cutoff:3.500A) Proline residue: A 24 - end of helix Proline residue: A 27 - end of helix removed outlier: 3.917A pdb=" N LEU A 33 " --> pdb=" O TYR A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 66 removed outlier: 3.666A pdb=" N LEU A 40 " --> pdb=" O THR A 36 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N VAL A 44 " --> pdb=" O LEU A 40 " (cutoff:3.500A) Proline residue: A 56 - end of helix Processing helix chain 'A' and resid 66 through 86 removed outlier: 3.837A pdb=" N ALA A 86 " --> pdb=" O GLU A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 120 Proline residue: A 110 - end of helix Processing helix chain 'A' and resid 125 through 150 Proline residue: A 144 - end of helix removed outlier: 3.931A pdb=" N MET A 150 " --> pdb=" O ILE A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 177 removed outlier: 3.543A pdb=" N VAL A 175 " --> pdb=" O ILE A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 233 removed outlier: 4.009A pdb=" N SER A 226 " --> pdb=" O GLU A 222 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU A 227 " --> pdb=" O THR A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 266 removed outlier: 4.022A pdb=" N ILE A 240 " --> pdb=" O SER A 236 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ASP A 260 " --> pdb=" O ILE A 256 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N LYS A 261 " --> pdb=" O TYR A 257 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N TYR A 265 " --> pdb=" O LYS A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 289 removed outlier: 3.996A pdb=" N LEU A 276 " --> pdb=" O ILE A 272 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE A 288 " --> pdb=" O ILE A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 322 removed outlier: 3.639A pdb=" N ILE A 304 " --> pdb=" O PHE A 300 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLY A 305 " --> pdb=" O VAL A 301 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N PHE A 306 " --> pdb=" O VAL A 302 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ARG A 310 " --> pdb=" O PHE A 306 " (cutoff:3.500A) Proline residue: A 311 - end of helix Processing helix chain 'A' and resid 324 through 354 Proline residue: A 344 - end of helix Processing helix chain 'A' and resid 356 through 382 Processing helix chain 'C' and resid 54 through 56 No H-bonds generated for 'chain 'C' and resid 54 through 56' Processing helix chain 'C' and resid 88 through 91 Processing helix chain 'C' and resid 113 through 117 Processing helix chain 'D' and resid 103 through 107 Processing sheet with id=AA1, first strand: chain 'C' and resid 29 through 33 Processing sheet with id=AA2, first strand: chain 'C' and resid 36 through 37 removed outlier: 8.450A pdb=" N ASP C 144 " --> pdb=" O SER C 126 " (cutoff:3.500A) removed outlier: 9.164A pdb=" N SER C 126 " --> pdb=" O ASP C 144 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N TRP C 146 " --> pdb=" O ARG C 124 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N ARG C 124 " --> pdb=" O TRP C 146 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N GLN C 148 " --> pdb=" O CYS C 122 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N CYS C 122 " --> pdb=" O GLN C 148 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N ARG C 64 " --> pdb=" O TRP C 73 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N TRP C 73 " --> pdb=" O ARG C 64 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 130 through 132 Processing sheet with id=AA4, first strand: chain 'D' and resid 28 through 31 Processing sheet with id=AA5, first strand: chain 'D' and resid 34 through 36 removed outlier: 3.663A pdb=" N LEU D 35 " --> pdb=" O LYS D 127 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N TRP D 59 " --> pdb=" O LEU D 71 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 34 through 36 removed outlier: 3.663A pdb=" N LEU D 35 " --> pdb=" O LYS D 127 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN D 114 " --> pdb=" O THR D 121 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR D 121 " --> pdb=" O GLN D 114 " (cutoff:3.500A) 323 hydrogen bonds defined for protein. 915 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: 1.28 Time building geometry restraints manager: 2.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1398 1.34 - 1.46: 1212 1.46 - 1.58: 2078 1.58 - 1.70: 0 1.70 - 1.81: 47 Bond restraints: 4735 Sorted by residual: bond pdb=" CA MET A 150 " pdb=" CB MET A 150 " ideal model delta sigma weight residual 1.528 1.545 -0.017 1.35e-02 5.49e+03 1.60e+00 bond pdb=" C GLN D 103 " pdb=" O GLN D 103 " ideal model delta sigma weight residual 1.236 1.246 -0.010 8.90e-03 1.26e+04 1.22e+00 bond pdb=" CA PHE C 134 " pdb=" CB PHE C 134 " ideal model delta sigma weight residual 1.535 1.548 -0.013 1.37e-02 5.33e+03 8.91e-01 bond pdb=" C LEU D 102 " pdb=" N GLN D 103 " ideal model delta sigma weight residual 1.326 1.335 -0.009 1.12e-02 7.97e+03 7.17e-01 bond pdb=" CB ASN C 110 " pdb=" CG ASN C 110 " ideal model delta sigma weight residual 1.516 1.537 -0.021 2.50e-02 1.60e+03 6.96e-01 ... (remaining 4730 not shown) Histogram of bond angle deviations from ideal: 100.11 - 106.91: 127 106.91 - 113.71: 2569 113.71 - 120.52: 1908 120.52 - 127.32: 1773 127.32 - 134.13: 45 Bond angle restraints: 6422 Sorted by residual: angle pdb=" N VAL D 53 " pdb=" CA VAL D 53 " pdb=" C VAL D 53 " ideal model delta sigma weight residual 113.53 108.33 5.20 9.80e-01 1.04e+00 2.82e+01 angle pdb=" C TYR C 133 " pdb=" N PHE C 134 " pdb=" CA PHE C 134 " ideal model delta sigma weight residual 125.02 130.27 -5.25 1.76e+00 3.23e-01 8.89e+00 angle pdb=" CA LEU A 42 " pdb=" CB LEU A 42 " pdb=" CG LEU A 42 " ideal model delta sigma weight residual 116.30 125.98 -9.68 3.50e+00 8.16e-02 7.64e+00 angle pdb=" CB MET A 150 " pdb=" CG MET A 150 " pdb=" SD MET A 150 " ideal model delta sigma weight residual 112.70 120.88 -8.18 3.00e+00 1.11e-01 7.43e+00 angle pdb=" N LEU D 35 " pdb=" CA LEU D 35 " pdb=" C LEU D 35 " ideal model delta sigma weight residual 107.23 111.65 -4.42 1.67e+00 3.59e-01 7.00e+00 ... (remaining 6417 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.62: 2339 17.62 - 35.23: 314 35.23 - 52.84: 67 52.84 - 70.46: 19 70.46 - 88.07: 1 Dihedral angle restraints: 2740 sinusoidal: 1021 harmonic: 1719 Sorted by residual: dihedral pdb=" CB CYS D 47 " pdb=" SG CYS D 47 " pdb=" SG CYS D 112 " pdb=" CB CYS D 112 " ideal model delta sinusoidal sigma weight residual -86.00 -32.52 -53.48 1 1.00e+01 1.00e-02 3.89e+01 dihedral pdb=" CA TRP C 131 " pdb=" C TRP C 131 " pdb=" N TYR C 132 " pdb=" CA TYR C 132 " ideal model delta harmonic sigma weight residual 180.00 152.91 27.09 0 5.00e+00 4.00e-02 2.94e+01 dihedral pdb=" CA MET A 150 " pdb=" C MET A 150 " pdb=" N ALA A 151 " pdb=" CA ALA A 151 " ideal model delta harmonic sigma weight residual 180.00 159.20 20.80 0 5.00e+00 4.00e-02 1.73e+01 ... (remaining 2737 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 520 0.040 - 0.079: 156 0.079 - 0.119: 49 0.119 - 0.158: 6 0.158 - 0.198: 3 Chirality restraints: 734 Sorted by residual: chirality pdb=" CG LEU A 49 " pdb=" CB LEU A 49 " pdb=" CD1 LEU A 49 " pdb=" CD2 LEU A 49 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 9.80e-01 chirality pdb=" CA PHE C 134 " pdb=" N PHE C 134 " pdb=" C PHE C 134 " pdb=" CB PHE C 134 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.42e-01 chirality pdb=" CB VAL C 90 " pdb=" CA VAL C 90 " pdb=" CG1 VAL C 90 " pdb=" CG2 VAL C 90 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.47e-01 ... (remaining 731 not shown) Planarity restraints: 792 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN D 103 " 0.026 5.00e-02 4.00e+02 4.02e-02 2.58e+00 pdb=" N PRO D 104 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO D 104 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO D 104 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 236 " -0.025 5.00e-02 4.00e+02 3.77e-02 2.27e+00 pdb=" N PRO A 237 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 237 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 237 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET A 157 " 0.022 5.00e-02 4.00e+02 3.37e-02 1.81e+00 pdb=" N PRO A 158 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 158 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 158 " 0.019 5.00e-02 4.00e+02 ... (remaining 789 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 179 2.72 - 3.26: 4770 3.26 - 3.81: 7840 3.81 - 4.35: 8833 4.35 - 4.90: 15676 Nonbonded interactions: 37298 Sorted by model distance: nonbonded pdb=" OE1 GLN D 30 " pdb=" OG1 THR D 126 " model vdw 2.174 2.440 nonbonded pdb=" OH TYR D 60 " pdb=" OE1 GLN D 113 " model vdw 2.216 2.440 nonbonded pdb=" OH TYR A 278 " pdb=" O VAL A 301 " model vdw 2.230 2.440 nonbonded pdb=" OH TYR A 29 " pdb=" O HIS A 155 " model vdw 2.296 2.440 nonbonded pdb=" O PHE C 55 " pdb=" OG SER C 79 " model vdw 2.311 2.440 ... (remaining 37293 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 0.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 17.230 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 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 0.024 4735 Z= 0.171 Angle : 0.687 9.675 6422 Z= 0.369 Chirality : 0.043 0.198 734 Planarity : 0.004 0.040 792 Dihedral : 16.672 88.074 1642 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.20 % Allowed : 31.00 % Favored : 68.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.88 (0.36), residues: 595 helix: 1.66 (0.30), residues: 323 sheet: 0.34 (0.51), residues: 109 loop : -1.40 (0.51), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 293 HIS 0.003 0.001 HIS A 155 PHE 0.018 0.002 PHE C 134 TYR 0.012 0.001 TYR D 73 ARG 0.002 0.000 ARG D 42 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 130 time to evaluate : 0.499 Fit side-chains revert: symmetry clash REVERT: C 61 HIS cc_start: 0.8230 (m170) cc_final: 0.7925 (m170) outliers start: 1 outliers final: 0 residues processed: 131 average time/residue: 0.1368 time to fit residues: 23.6604 Evaluate side-chains 125 residues out of total 500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 49 optimal weight: 7.9990 chunk 44 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 15 optimal weight: 0.0770 chunk 30 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 46 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 overall best weight: 0.9742 ------------------------------------------------------------------------------- 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: 0.7454 moved from start: 0.1105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4735 Z= 0.223 Angle : 0.618 6.991 6422 Z= 0.320 Chirality : 0.044 0.215 734 Planarity : 0.005 0.046 792 Dihedral : 5.133 64.450 643 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 5.00 % Allowed : 27.40 % Favored : 67.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.13 (0.37), residues: 595 helix: 1.78 (0.30), residues: 325 sheet: 0.40 (0.51), residues: 110 loop : -1.12 (0.52), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 136 HIS 0.002 0.001 HIS A 155 PHE 0.022 0.002 PHE C 134 TYR 0.016 0.002 TYR C 133 ARG 0.002 0.000 ARG A 324 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 134 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 LYS cc_start: 0.7712 (OUTLIER) cc_final: 0.7499 (pttm) REVERT: A 315 ASN cc_start: 0.7417 (m110) cc_final: 0.7208 (m-40) outliers start: 25 outliers final: 15 residues processed: 149 average time/residue: 0.1285 time to fit residues: 25.3357 Evaluate side-chains 144 residues out of total 500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 128 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 317 PHE Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 135 TYR Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 112 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 29 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 18 optimal weight: 0.0070 chunk 43 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 overall best weight: 0.7000 ------------------------------------------------------------------------------- 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: 0.7441 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4735 Z= 0.186 Angle : 0.579 8.304 6422 Z= 0.301 Chirality : 0.043 0.217 734 Planarity : 0.004 0.046 792 Dihedral : 5.036 61.412 643 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 5.40 % Allowed : 28.20 % Favored : 66.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.21 (0.37), residues: 595 helix: 1.74 (0.30), residues: 328 sheet: 0.58 (0.51), residues: 110 loop : -1.02 (0.53), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 293 HIS 0.002 0.001 HIS A 155 PHE 0.020 0.002 PHE C 134 TYR 0.012 0.001 TYR C 133 ARG 0.002 0.000 ARG A 324 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 135 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 109 MET cc_start: 0.7388 (OUTLIER) cc_final: 0.6526 (mmt) REVERT: D 73 TYR cc_start: 0.7781 (p90) cc_final: 0.7385 (p90) outliers start: 27 outliers final: 19 residues processed: 151 average time/residue: 0.1307 time to fit residues: 26.1185 Evaluate side-chains 150 residues out of total 500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 130 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 317 PHE Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 109 MET Chi-restraints excluded: chain C residue 135 TYR Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 76 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 27 optimal weight: 6.9990 chunk 5 optimal weight: 4.9990 chunk 25 optimal weight: 0.6980 chunk 36 optimal weight: 0.7980 chunk 53 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 51 optimal weight: 4.9990 chunk 15 optimal weight: 0.7980 chunk 47 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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: 0.7468 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4735 Z= 0.203 Angle : 0.592 7.406 6422 Z= 0.306 Chirality : 0.043 0.217 734 Planarity : 0.004 0.047 792 Dihedral : 5.036 61.152 643 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 6.40 % Allowed : 27.60 % Favored : 66.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.13 (0.36), residues: 595 helix: 1.72 (0.30), residues: 328 sheet: 0.53 (0.50), residues: 110 loop : -1.13 (0.52), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 62 HIS 0.003 0.001 HIS A 155 PHE 0.019 0.002 PHE C 134 TYR 0.014 0.002 TYR C 133 ARG 0.001 0.000 ARG A 324 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 136 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 94 PHE cc_start: 0.7699 (m-10) cc_final: 0.7061 (m-10) REVERT: C 109 MET cc_start: 0.7433 (OUTLIER) cc_final: 0.6615 (mmt) REVERT: D 73 TYR cc_start: 0.7824 (p90) cc_final: 0.7462 (p90) outliers start: 32 outliers final: 22 residues processed: 155 average time/residue: 0.1282 time to fit residues: 26.3688 Evaluate side-chains 156 residues out of total 500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 133 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 317 PHE Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain C residue 27 GLU Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 109 MET Chi-restraints excluded: chain C residue 125 MET Chi-restraints excluded: chain C residue 133 TYR Chi-restraints excluded: chain C residue 135 TYR Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 71 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 0 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 23 optimal weight: 0.7980 chunk 48 optimal weight: 0.5980 chunk 39 optimal weight: 0.8980 chunk 29 optimal weight: 0.5980 chunk 51 optimal weight: 6.9990 chunk 14 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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: 0.7461 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4735 Z= 0.188 Angle : 0.585 7.607 6422 Z= 0.302 Chirality : 0.043 0.217 734 Planarity : 0.004 0.046 792 Dihedral : 5.010 60.639 643 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 7.00 % Allowed : 28.00 % Favored : 65.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.19 (0.37), residues: 595 helix: 1.72 (0.30), residues: 328 sheet: 0.51 (0.50), residues: 110 loop : -0.97 (0.54), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 293 HIS 0.003 0.001 HIS A 155 PHE 0.018 0.002 PHE C 134 TYR 0.013 0.001 TYR C 133 ARG 0.001 0.000 ARG A 380 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 136 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 174 ILE cc_start: 0.7216 (OUTLIER) cc_final: 0.6757 (mm) REVERT: A 323 GLU cc_start: 0.7704 (pm20) cc_final: 0.6923 (tt0) REVERT: A 378 GLN cc_start: 0.6516 (tt0) cc_final: 0.6154 (mt0) REVERT: C 94 PHE cc_start: 0.7707 (m-10) cc_final: 0.7076 (m-10) REVERT: C 106 TYR cc_start: 0.7140 (m-80) cc_final: 0.6289 (m-80) REVERT: C 109 MET cc_start: 0.7502 (OUTLIER) cc_final: 0.6545 (mmt) REVERT: D 73 TYR cc_start: 0.7839 (p90) cc_final: 0.7425 (p90) outliers start: 35 outliers final: 26 residues processed: 157 average time/residue: 0.1177 time to fit residues: 24.9407 Evaluate side-chains 163 residues out of total 500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 135 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 317 PHE Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain C residue 27 GLU Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 109 MET Chi-restraints excluded: chain C residue 125 MET Chi-restraints excluded: chain C residue 133 TYR Chi-restraints excluded: chain C residue 135 TYR Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 76 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 14 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 29 optimal weight: 0.6980 chunk 55 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 41 optimal weight: 0.0670 overall best weight: 0.9122 ------------------------------------------------------------------------------- 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: 0.7488 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4735 Z= 0.219 Angle : 0.626 10.265 6422 Z= 0.318 Chirality : 0.044 0.217 734 Planarity : 0.004 0.048 792 Dihedral : 5.074 60.376 643 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 7.80 % Allowed : 28.40 % Favored : 63.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.08 (0.36), residues: 595 helix: 1.68 (0.30), residues: 327 sheet: 0.45 (0.50), residues: 110 loop : -1.09 (0.53), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 293 HIS 0.003 0.001 HIS A 155 PHE 0.021 0.002 PHE A 161 TYR 0.015 0.001 TYR C 133 ARG 0.001 0.000 ARG A 324 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 134 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 378 GLN cc_start: 0.6559 (tt0) cc_final: 0.6179 (mt0) REVERT: C 94 PHE cc_start: 0.7798 (m-10) cc_final: 0.7213 (m-10) REVERT: C 106 TYR cc_start: 0.7131 (m-80) cc_final: 0.6285 (m-80) REVERT: C 109 MET cc_start: 0.7526 (OUTLIER) cc_final: 0.6529 (mmt) REVERT: D 73 TYR cc_start: 0.7900 (p90) cc_final: 0.7490 (p90) outliers start: 39 outliers final: 32 residues processed: 157 average time/residue: 0.1216 time to fit residues: 25.6886 Evaluate side-chains 163 residues out of total 500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 130 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 315 ASN Chi-restraints excluded: chain A residue 317 PHE Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain C residue 27 GLU Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 109 MET Chi-restraints excluded: chain C residue 125 MET Chi-restraints excluded: chain C residue 133 TYR Chi-restraints excluded: chain C residue 135 TYR Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 76 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 32 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 chunk 34 optimal weight: 4.9990 chunk 26 optimal weight: 0.7980 chunk 22 optimal weight: 0.2980 chunk 33 optimal weight: 0.8980 chunk 17 optimal weight: 0.0170 chunk 11 optimal weight: 3.9990 overall best weight: 0.5218 ------------------------------------------------------------------------------- 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: 0.7444 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4735 Z= 0.178 Angle : 0.617 8.431 6422 Z= 0.311 Chirality : 0.044 0.216 734 Planarity : 0.004 0.050 792 Dihedral : 5.037 60.581 643 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 7.20 % Allowed : 29.40 % Favored : 63.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.22 (0.37), residues: 595 helix: 1.73 (0.30), residues: 327 sheet: 0.54 (0.50), residues: 110 loop : -0.89 (0.54), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 293 HIS 0.003 0.001 HIS A 155 PHE 0.016 0.001 PHE C 134 TYR 0.017 0.001 TYR A 292 ARG 0.001 0.000 ARG A 324 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 132 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 323 GLU cc_start: 0.7375 (pm20) cc_final: 0.6725 (tt0) REVERT: A 378 GLN cc_start: 0.6500 (tt0) cc_final: 0.6116 (mt0) REVERT: C 94 PHE cc_start: 0.7735 (m-10) cc_final: 0.7183 (m-10) REVERT: C 106 TYR cc_start: 0.7026 (m-80) cc_final: 0.6236 (m-80) REVERT: C 109 MET cc_start: 0.7534 (OUTLIER) cc_final: 0.6549 (mmt) REVERT: D 73 TYR cc_start: 0.7891 (p90) cc_final: 0.7441 (p90) outliers start: 36 outliers final: 27 residues processed: 157 average time/residue: 0.1239 time to fit residues: 26.2035 Evaluate side-chains 158 residues out of total 500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 130 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 317 PHE Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain C residue 27 GLU Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 109 MET Chi-restraints excluded: chain C residue 125 MET Chi-restraints excluded: chain C residue 133 TYR Chi-restraints excluded: chain C residue 135 TYR Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 128 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 11 optimal weight: 5.9990 chunk 36 optimal weight: 0.8980 chunk 38 optimal weight: 8.9990 chunk 28 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 51 optimal weight: 7.9990 chunk 54 optimal weight: 0.0980 chunk 49 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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: 0.7471 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4735 Z= 0.203 Angle : 0.622 8.402 6422 Z= 0.315 Chirality : 0.044 0.216 734 Planarity : 0.004 0.046 792 Dihedral : 5.054 60.750 643 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 8.00 % Allowed : 28.60 % Favored : 63.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.36), residues: 595 helix: 1.70 (0.30), residues: 326 sheet: 0.43 (0.49), residues: 110 loop : -1.01 (0.53), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 293 HIS 0.003 0.001 HIS A 155 PHE 0.023 0.002 PHE A 161 TYR 0.023 0.001 TYR A 292 ARG 0.001 0.000 ARG A 380 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 135 time to evaluate : 0.504 Fit side-chains revert: symmetry clash REVERT: A 323 GLU cc_start: 0.7374 (pm20) cc_final: 0.6691 (tt0) REVERT: A 378 GLN cc_start: 0.6526 (tt0) cc_final: 0.6150 (mt0) REVERT: C 94 PHE cc_start: 0.7765 (m-10) cc_final: 0.7223 (m-10) REVERT: C 106 TYR cc_start: 0.7025 (m-80) cc_final: 0.6275 (m-80) REVERT: C 109 MET cc_start: 0.7578 (OUTLIER) cc_final: 0.6565 (mmt) REVERT: D 73 TYR cc_start: 0.7940 (p90) cc_final: 0.7475 (p90) outliers start: 40 outliers final: 31 residues processed: 160 average time/residue: 0.1230 time to fit residues: 26.4141 Evaluate side-chains 162 residues out of total 500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 130 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 TYR Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain C residue 27 GLU Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 109 MET Chi-restraints excluded: chain C residue 125 MET Chi-restraints excluded: chain C residue 133 TYR Chi-restraints excluded: chain C residue 135 TYR Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 128 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 23 optimal weight: 0.5980 chunk 41 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 50 optimal weight: 0.0470 chunk 52 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 56 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 38 optimal weight: 7.9990 chunk 58 optimal weight: 2.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- 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: 0.7452 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4735 Z= 0.191 Angle : 0.633 9.308 6422 Z= 0.321 Chirality : 0.044 0.216 734 Planarity : 0.004 0.047 792 Dihedral : 5.089 60.320 643 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 7.20 % Allowed : 30.20 % Favored : 62.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.17 (0.36), residues: 595 helix: 1.68 (0.30), residues: 327 sheet: 0.49 (0.49), residues: 110 loop : -0.87 (0.54), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 293 HIS 0.003 0.001 HIS A 155 PHE 0.016 0.001 PHE C 134 TYR 0.025 0.002 TYR A 292 ARG 0.001 0.000 ARG A 380 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 131 time to evaluate : 0.515 Fit side-chains revert: symmetry clash REVERT: C 94 PHE cc_start: 0.7759 (m-10) cc_final: 0.7225 (m-10) REVERT: C 106 TYR cc_start: 0.7014 (m-80) cc_final: 0.6273 (m-80) REVERT: C 109 MET cc_start: 0.7516 (OUTLIER) cc_final: 0.6475 (mmt) REVERT: D 73 TYR cc_start: 0.7917 (p90) cc_final: 0.7459 (p90) outliers start: 36 outliers final: 31 residues processed: 154 average time/residue: 0.1277 time to fit residues: 26.2918 Evaluate side-chains 161 residues out of total 500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 129 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 TYR Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 317 PHE Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain C residue 27 GLU Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 109 MET Chi-restraints excluded: chain C residue 125 MET Chi-restraints excluded: chain C residue 133 TYR Chi-restraints excluded: chain C residue 135 TYR Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 76 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 54 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 49 optimal weight: 3.9990 chunk 14 optimal weight: 0.0970 chunk 43 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 13 optimal weight: 0.6980 overall best weight: 0.6378 ------------------------------------------------------------------------------- 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: 0.7450 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4735 Z= 0.193 Angle : 0.637 9.618 6422 Z= 0.323 Chirality : 0.044 0.216 734 Planarity : 0.005 0.049 792 Dihedral : 5.090 61.062 643 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 6.80 % Allowed : 30.80 % Favored : 62.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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 (0.36), residues: 595 helix: 1.66 (0.30), residues: 328 sheet: 0.49 (0.49), residues: 110 loop : -1.05 (0.54), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 293 HIS 0.004 0.001 HIS A 155 PHE 0.016 0.002 PHE C 134 TYR 0.023 0.002 TYR A 292 ARG 0.001 0.000 ARG A 380 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 130 time to evaluate : 0.471 Fit side-chains revert: symmetry clash REVERT: A 68 LYS cc_start: 0.7644 (pttm) cc_final: 0.7318 (pttt) REVERT: A 323 GLU cc_start: 0.7318 (pm20) cc_final: 0.6658 (tt0) REVERT: C 94 PHE cc_start: 0.7769 (m-10) cc_final: 0.7233 (m-10) REVERT: C 106 TYR cc_start: 0.6926 (m-80) cc_final: 0.6241 (m-80) REVERT: C 109 MET cc_start: 0.7426 (OUTLIER) cc_final: 0.6365 (mmt) REVERT: D 73 TYR cc_start: 0.7961 (p90) cc_final: 0.7436 (p90) outliers start: 34 outliers final: 28 residues processed: 151 average time/residue: 0.1212 time to fit residues: 24.5432 Evaluate side-chains 157 residues out of total 500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 128 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 TYR Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 317 PHE Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain C residue 27 GLU Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 109 MET Chi-restraints excluded: chain C residue 125 MET Chi-restraints excluded: chain C residue 133 TYR Chi-restraints excluded: chain C residue 135 TYR Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 128 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 46 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 48 optimal weight: 0.2980 chunk 5 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 53 optimal weight: 0.0770 chunk 31 optimal weight: 0.7980 chunk 40 optimal weight: 0.5980 overall best weight: 0.5138 ------------------------------------------------------------------------------- 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 = 0.4090 r_free = 0.4090 target = 0.185439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.158537 restraints weight = 6290.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.163552 restraints weight = 3490.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.166961 restraints weight = 2367.693| |-----------------------------------------------------------------------------| r_work (final): 0.3892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4735 Z= 0.179 Angle : 0.631 9.733 6422 Z= 0.317 Chirality : 0.044 0.216 734 Planarity : 0.004 0.044 792 Dihedral : 5.015 60.828 643 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 7.40 % Allowed : 30.40 % Favored : 62.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.24 (0.36), residues: 595 helix: 1.71 (0.30), residues: 328 sheet: 0.59 (0.49), residues: 110 loop : -0.85 (0.54), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 293 HIS 0.004 0.001 HIS A 155 PHE 0.016 0.001 PHE C 134 TYR 0.027 0.001 TYR A 292 ARG 0.001 0.000 ARG A 380 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1315.28 seconds wall clock time: 24 minutes 9.50 seconds (1449.50 seconds total)