Starting phenix.real_space_refine on Fri Dec 27 23:10:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xan_38202/12_2024/8xan_38202.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xan_38202/12_2024/8xan_38202.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xan_38202/12_2024/8xan_38202.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xan_38202/12_2024/8xan_38202.map" model { file = "/net/cci-nas-00/data/ceres_data/8xan_38202/12_2024/8xan_38202.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xan_38202/12_2024/8xan_38202.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.007 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 30 5.16 5 C 4383 2.51 5 N 1164 2.21 5 O 1386 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 54 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 6963 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 2321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2321 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 14, 'TRANS': 291} Chain: "A" Number of atoms: 2321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2321 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 14, 'TRANS': 291} Chain: "C" Number of atoms: 2321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2321 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 14, 'TRANS': 291} Time building chain proxies: 4.73, per 1000 atoms: 0.68 Number of scatterers: 6963 At special positions: 0 Unit cell: (105.6, 108.24, 63.36, 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 30 16.00 O 1386 8.00 N 1164 7.00 C 4383 6.00 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: 1.76 Conformation dependent library (CDL) restraints added in 1.2 seconds 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1668 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 6 sheets defined 6.8% alpha, 24.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'B' and resid 77 through 86 Processing helix chain 'B' and resid 113 through 117 Processing helix chain 'A' and resid 77 through 86 Processing helix chain 'A' and resid 113 through 117 Processing helix chain 'A' and resid 234 through 239 removed outlier: 4.399A pdb=" N LYS A 238 " --> pdb=" O THR A 234 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N PHE A 239 " --> pdb=" O LEU A 235 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 234 through 239' Processing helix chain 'A' and resid 293 through 297 removed outlier: 3.571A pdb=" N ILE A 296 " --> pdb=" O ASP A 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 86 Processing helix chain 'C' and resid 113 through 117 Processing helix chain 'C' and resid 234 through 239 removed outlier: 4.416A pdb=" N LYS C 238 " --> pdb=" O THR C 234 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N PHE C 239 " --> pdb=" O LEU C 235 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 234 through 239' Processing sheet with id=AA1, first strand: chain 'B' and resid 7 through 13 removed outlier: 5.671A pdb=" N LEU B 13 " --> pdb=" O ALA B 25 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ALA B 25 " --> pdb=" O LEU B 13 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 25 through 28 current: chain 'B' and resid 57 through 71 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 57 through 71 current: chain 'B' and resid 119 through 135 removed outlier: 6.531A pdb=" N GLY B 145 " --> pdb=" O ASN B 128 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N MET B 130 " --> pdb=" O THR B 143 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N THR B 143 " --> pdb=" O MET B 130 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N LEU B 132 " --> pdb=" O MET B 141 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N MET B 141 " --> pdb=" O LEU B 132 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ILE B 134 " --> pdb=" O ILE B 139 " (cutoff:3.500A) removed outlier: 8.624A pdb=" N ILE B 139 " --> pdb=" O ILE B 134 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 138 through 148 current: chain 'B' and resid 221 through 229 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 221 through 229 current: chain 'B' and resid 259 through 269 Processing sheet with id=AA2, first strand: chain 'B' and resid 202 through 204 removed outlier: 4.120A pdb=" N LYS B 214 " --> pdb=" O ARG B 204 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 8 through 13 removed outlier: 5.638A pdb=" N LEU A 13 " --> pdb=" O ALA A 25 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ALA A 25 " --> pdb=" O LEU A 13 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 25 through 28 current: chain 'A' and resid 57 through 71 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 57 through 71 current: chain 'A' and resid 119 through 135 removed outlier: 6.477A pdb=" N GLY A 145 " --> pdb=" O ASN A 128 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N MET A 130 " --> pdb=" O THR A 143 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N THR A 143 " --> pdb=" O MET A 130 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N LEU A 132 " --> pdb=" O MET A 141 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N MET A 141 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ILE A 134 " --> pdb=" O ILE A 139 " (cutoff:3.500A) removed outlier: 8.635A pdb=" N ILE A 139 " --> pdb=" O ILE A 134 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 138 through 148 current: chain 'A' and resid 221 through 229 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 221 through 229 current: chain 'A' and resid 262 through 269 Processing sheet with id=AA4, first strand: chain 'A' and resid 202 through 204 removed outlier: 3.972A pdb=" N LYS A 214 " --> pdb=" O ARG A 204 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 8 through 13 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 27 through 28 current: chain 'C' and resid 57 through 71 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 57 through 71 current: chain 'C' and resid 119 through 135 removed outlier: 6.342A pdb=" N GLY C 145 " --> pdb=" O ASN C 128 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N MET C 130 " --> pdb=" O THR C 143 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N THR C 143 " --> pdb=" O MET C 130 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N LEU C 132 " --> pdb=" O MET C 141 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N MET C 141 " --> pdb=" O LEU C 132 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ILE C 134 " --> pdb=" O ILE C 139 " (cutoff:3.500A) removed outlier: 8.487A pdb=" N ILE C 139 " --> pdb=" O ILE C 134 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 138 through 148 current: chain 'C' and resid 221 through 229 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 221 through 229 current: chain 'C' and resid 260 through 269 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 260 through 269 current: chain 'C' and resid 283 through 290 Processing sheet with id=AA6, first strand: chain 'C' and resid 202 through 204 removed outlier: 4.119A pdb=" N LYS C 214 " --> pdb=" O ARG C 204 " (cutoff:3.500A) 53 hydrogen bonds defined for protein. 126 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: 1.52 Time building geometry restraints manager: 2.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1644 1.33 - 1.45: 1367 1.45 - 1.57: 4021 1.57 - 1.69: 3 1.69 - 1.81: 54 Bond restraints: 7089 Sorted by residual: bond pdb=" N GLY C 87 " pdb=" CA GLY C 87 " ideal model delta sigma weight residual 1.442 1.476 -0.034 7.70e-03 1.69e+04 1.95e+01 bond pdb=" N GLY A 97 " pdb=" CA GLY A 97 " ideal model delta sigma weight residual 1.445 1.477 -0.032 8.30e-03 1.45e+04 1.48e+01 bond pdb=" N GLY B 87 " pdb=" CA GLY B 87 " ideal model delta sigma weight residual 1.445 1.476 -0.032 9.20e-03 1.18e+04 1.18e+01 bond pdb=" N ILE A 57 " pdb=" CA ILE A 57 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.11e-02 8.12e+03 1.17e+01 bond pdb=" N ILE A 146 " pdb=" CA ILE A 146 " ideal model delta sigma weight residual 1.456 1.495 -0.039 1.15e-02 7.56e+03 1.16e+01 ... (remaining 7084 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.08: 6587 1.08 - 2.16: 2127 2.16 - 3.25: 772 3.25 - 4.33: 125 4.33 - 5.41: 13 Bond angle restraints: 9624 Sorted by residual: angle pdb=" CA GLY C 56 " pdb=" C GLY C 56 " pdb=" O GLY C 56 " ideal model delta sigma weight residual 122.22 118.13 4.09 6.50e-01 2.37e+00 3.95e+01 angle pdb=" CA GLY A 56 " pdb=" C GLY A 56 " pdb=" O GLY A 56 " ideal model delta sigma weight residual 122.13 118.14 3.99 8.90e-01 1.26e+00 2.01e+01 angle pdb=" N ILE B 296 " pdb=" CA ILE B 296 " pdb=" C ILE B 296 " ideal model delta sigma weight residual 112.83 108.45 4.38 9.90e-01 1.02e+00 1.95e+01 angle pdb=" CA GLY B 87 " pdb=" C GLY B 87 " pdb=" O GLY B 87 " ideal model delta sigma weight residual 122.33 117.90 4.43 1.11e+00 8.12e-01 1.59e+01 angle pdb=" N ASP B 51 " pdb=" CA ASP B 51 " pdb=" C ASP B 51 " ideal model delta sigma weight residual 113.20 108.45 4.75 1.21e+00 6.83e-01 1.54e+01 ... (remaining 9619 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.96: 3725 14.96 - 29.92: 372 29.92 - 44.88: 94 44.88 - 59.84: 32 59.84 - 74.80: 25 Dihedral angle restraints: 4248 sinusoidal: 1641 harmonic: 2607 Sorted by residual: dihedral pdb=" CD ARG A 219 " pdb=" NE ARG A 219 " pdb=" CZ ARG A 219 " pdb=" NH1 ARG A 219 " ideal model delta sinusoidal sigma weight residual 0.00 35.11 -35.11 1 1.00e+01 1.00e-02 1.75e+01 dihedral pdb=" CD ARG A 49 " pdb=" NE ARG A 49 " pdb=" CZ ARG A 49 " pdb=" NH1 ARG A 49 " ideal model delta sinusoidal sigma weight residual 0.00 29.73 -29.73 1 1.00e+01 1.00e-02 1.26e+01 dihedral pdb=" CD ARG C 101 " pdb=" NE ARG C 101 " pdb=" CZ ARG C 101 " pdb=" NH1 ARG C 101 " ideal model delta sinusoidal sigma weight residual 0.00 27.23 -27.23 1 1.00e+01 1.00e-02 1.06e+01 ... (remaining 4245 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 524 0.044 - 0.088: 252 0.088 - 0.132: 224 0.132 - 0.176: 95 0.176 - 0.219: 39 Chirality restraints: 1134 Sorted by residual: chirality pdb=" CA ILE B 29 " pdb=" N ILE B 29 " pdb=" C ILE B 29 " pdb=" CB ILE B 29 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA ILE A 29 " pdb=" N ILE A 29 " pdb=" C ILE A 29 " pdb=" CB ILE A 29 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA ILE A 267 " pdb=" N ILE A 267 " pdb=" C ILE A 267 " pdb=" CB ILE A 267 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.08e+00 ... (remaining 1131 not shown) Planarity restraints: 1245 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 219 " -0.635 9.50e-02 1.11e+02 2.85e-01 4.94e+01 pdb=" NE ARG A 219 " 0.036 2.00e-02 2.50e+03 pdb=" CZ ARG A 219 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG A 219 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 219 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 49 " -0.526 9.50e-02 1.11e+02 2.36e-01 3.41e+01 pdb=" NE ARG A 49 " 0.033 2.00e-02 2.50e+03 pdb=" CZ ARG A 49 " 0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG A 49 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A 49 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 101 " -0.483 9.50e-02 1.11e+02 2.16e-01 2.87e+01 pdb=" NE ARG C 101 " 0.030 2.00e-02 2.50e+03 pdb=" CZ ARG C 101 " 0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG C 101 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG C 101 " -0.015 2.00e-02 2.50e+03 ... (remaining 1242 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 1896 2.82 - 3.34: 6313 3.34 - 3.86: 12208 3.86 - 4.38: 14060 4.38 - 4.90: 23246 Nonbonded interactions: 57723 Sorted by model distance: nonbonded pdb=" OD1 ASP C 78 " pdb=" OH TYR C 260 " model vdw 2.299 3.040 nonbonded pdb=" N LEU C 43 " pdb=" O ARG C 58 " model vdw 2.402 3.120 nonbonded pdb=" N LEU B 43 " pdb=" O ARG B 58 " model vdw 2.403 3.120 nonbonded pdb=" N LEU A 43 " pdb=" O ARG A 58 " model vdw 2.403 3.120 nonbonded pdb=" OE2 GLU B 14 " pdb=" OG SER B 104 " model vdw 2.419 3.040 ... (remaining 57718 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.430 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: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 19.730 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 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 : 0.011 0.083 7089 Z= 0.718 Angle : 1.186 5.409 9624 Z= 0.899 Chirality : 0.082 0.219 1134 Planarity : 0.021 0.285 1245 Dihedral : 14.665 74.798 2580 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 1.56 % Allowed : 11.72 % Favored : 86.72 % 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: -2.22 (0.25), residues: 912 helix: -2.00 (0.70), residues: 48 sheet: -0.79 (0.26), residues: 372 loop : -1.99 (0.25), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 89 HIS 0.005 0.001 HIS C 7 PHE 0.015 0.001 PHE A 109 TYR 0.008 0.001 TYR C 17 ARG 0.005 0.001 ARG A 101 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 167 time to evaluate : 0.819 Fit side-chains revert: symmetry clash REVERT: B 171 GLU cc_start: 0.5991 (tt0) cc_final: 0.5508 (pt0) REVERT: B 176 PHE cc_start: 0.4933 (m-10) cc_final: 0.4214 (m-10) REVERT: A 53 ASN cc_start: 0.6745 (m-40) cc_final: 0.6492 (m-40) REVERT: A 285 SER cc_start: 0.8697 (t) cc_final: 0.8342 (p) REVERT: C 46 GLU cc_start: 0.8133 (tp30) cc_final: 0.6975 (pp20) REVERT: C 63 GLN cc_start: 0.6534 (pt0) cc_final: 0.6278 (tt0) REVERT: C 186 ASP cc_start: 0.6297 (t0) cc_final: 0.6090 (t0) REVERT: C 293 ASP cc_start: 0.8234 (t70) cc_final: 0.7994 (t0) outliers start: 12 outliers final: 4 residues processed: 172 average time/residue: 0.1963 time to fit residues: 44.4000 Evaluate side-chains 115 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 111 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 187 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 75 optimal weight: 10.0000 chunk 68 optimal weight: 9.9990 chunk 37 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 46 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 27 optimal weight: 9.9990 chunk 42 optimal weight: 0.7980 chunk 52 optimal weight: 6.9990 chunk 81 optimal weight: 2.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 53 ASN B 63 GLN B 179 HIS C 110 ASN C 273 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.3676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7089 Z= 0.297 Angle : 0.654 9.288 9624 Z= 0.344 Chirality : 0.048 0.146 1134 Planarity : 0.005 0.050 1245 Dihedral : 4.904 52.784 989 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.56 % Allowed : 14.45 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.26), residues: 912 helix: 0.11 (1.07), residues: 30 sheet: -0.70 (0.25), residues: 399 loop : -1.49 (0.25), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 89 HIS 0.006 0.002 HIS A 7 PHE 0.024 0.002 PHE B 230 TYR 0.014 0.002 TYR B 260 ARG 0.006 0.001 ARG B 6 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 94 time to evaluate : 0.874 Fit side-chains revert: symmetry clash REVERT: B 3 ASP cc_start: 0.8096 (m-30) cc_final: 0.7890 (m-30) REVERT: B 55 MET cc_start: 0.7213 (tpp) cc_final: 0.6914 (tpp) REVERT: B 75 GLU cc_start: 0.6700 (tp30) cc_final: 0.6426 (tp30) REVERT: B 134 ILE cc_start: 0.8662 (mt) cc_final: 0.8261 (tt) REVERT: B 258 ASN cc_start: 0.7935 (OUTLIER) cc_final: 0.7652 (p0) REVERT: A 297 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.8017 (mm) REVERT: C 186 ASP cc_start: 0.6500 (t0) cc_final: 0.6253 (t0) outliers start: 12 outliers final: 4 residues processed: 105 average time/residue: 0.1724 time to fit residues: 25.1551 Evaluate side-chains 72 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 66 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 151 GLN Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 258 ASN Chi-restraints excluded: chain A residue 150 ASN Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain C residue 36 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 45 optimal weight: 1.9990 chunk 25 optimal weight: 10.0000 chunk 68 optimal weight: 9.9990 chunk 55 optimal weight: 8.9990 chunk 22 optimal weight: 7.9990 chunk 81 optimal weight: 10.0000 chunk 88 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 27 optimal weight: 10.0000 chunk 65 optimal weight: 8.9990 chunk 80 optimal weight: 3.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 53 ASN B 63 GLN A 96 ASN A 215 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.4788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 7089 Z= 0.357 Angle : 0.634 8.255 9624 Z= 0.332 Chirality : 0.047 0.142 1134 Planarity : 0.005 0.045 1245 Dihedral : 5.132 55.209 983 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 3.52 % Allowed : 14.71 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.25), residues: 912 helix: 0.29 (1.06), residues: 30 sheet: -0.73 (0.27), residues: 342 loop : -1.54 (0.23), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 89 HIS 0.007 0.002 HIS C 7 PHE 0.024 0.002 PHE A 176 TYR 0.012 0.002 TYR C 229 ARG 0.004 0.001 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 68 time to evaluate : 0.891 Fit side-chains REVERT: B 134 ILE cc_start: 0.8602 (mt) cc_final: 0.8213 (tt) REVERT: B 173 MET cc_start: 0.8048 (mmt) cc_final: 0.7828 (mmt) REVERT: A 297 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.8044 (mm) REVERT: C 52 ARG cc_start: 0.8382 (OUTLIER) cc_final: 0.8112 (ptt90) REVERT: C 186 ASP cc_start: 0.6793 (t0) cc_final: 0.6578 (t0) REVERT: C 285 SER cc_start: 0.8710 (t) cc_final: 0.8433 (p) outliers start: 27 outliers final: 15 residues processed: 90 average time/residue: 0.1825 time to fit residues: 23.1137 Evaluate side-chains 77 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 60 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 150 ASN Chi-restraints excluded: chain B residue 151 GLN Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 150 ASN Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 150 ASN Chi-restraints excluded: chain C residue 258 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 61 optimal weight: 6.9990 chunk 42 optimal weight: 7.9990 chunk 9 optimal weight: 10.0000 chunk 39 optimal weight: 3.9990 chunk 54 optimal weight: 7.9990 chunk 82 optimal weight: 5.9990 chunk 86 optimal weight: 9.9990 chunk 77 optimal weight: 10.0000 chunk 23 optimal weight: 10.0000 chunk 72 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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: 0.8117 moved from start: 0.5177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 7089 Z= 0.334 Angle : 0.598 8.466 9624 Z= 0.312 Chirality : 0.047 0.138 1134 Planarity : 0.005 0.034 1245 Dihedral : 5.148 50.510 983 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.99 % Allowed : 16.93 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.25), residues: 912 helix: 0.29 (1.04), residues: 30 sheet: -0.83 (0.26), residues: 351 loop : -1.59 (0.23), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 89 HIS 0.005 0.001 HIS B 179 PHE 0.018 0.002 PHE B 176 TYR 0.022 0.002 TYR C 17 ARG 0.006 0.001 ARG A 52 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 68 time to evaluate : 0.761 Fit side-chains REVERT: B 75 GLU cc_start: 0.7884 (tp30) cc_final: 0.7582 (tp30) REVERT: B 134 ILE cc_start: 0.8606 (mt) cc_final: 0.8238 (tt) REVERT: B 173 MET cc_start: 0.8071 (mmt) cc_final: 0.7768 (mmt) REVERT: A 51 ASP cc_start: 0.8061 (t0) cc_final: 0.7667 (t0) REVERT: A 75 GLU cc_start: 0.7914 (tp30) cc_final: 0.7675 (tp30) REVERT: A 114 SER cc_start: 0.8627 (p) cc_final: 0.8349 (t) REVERT: A 297 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.7886 (mm) REVERT: C 17 TYR cc_start: 0.8652 (t80) cc_final: 0.8416 (t80) REVERT: C 285 SER cc_start: 0.8839 (t) cc_final: 0.8551 (p) outliers start: 23 outliers final: 15 residues processed: 88 average time/residue: 0.1488 time to fit residues: 19.0615 Evaluate side-chains 77 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 61 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 150 ASN Chi-restraints excluded: chain B residue 151 GLN Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 150 ASN Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 258 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 1 optimal weight: 5.9990 chunk 64 optimal weight: 10.0000 chunk 35 optimal weight: 8.9990 chunk 74 optimal weight: 9.9990 chunk 60 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 44 optimal weight: 8.9990 chunk 78 optimal weight: 6.9990 chunk 21 optimal weight: 8.9990 chunk 29 optimal weight: 1.9990 chunk 17 optimal weight: 9.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- 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: 0.8169 moved from start: 0.5634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.033 7089 Z= 0.467 Angle : 0.688 7.609 9624 Z= 0.360 Chirality : 0.049 0.159 1134 Planarity : 0.006 0.050 1245 Dihedral : 5.741 44.806 983 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 4.30 % Allowed : 16.93 % Favored : 78.78 % 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: -2.15 (0.24), residues: 912 helix: -0.12 (1.02), residues: 30 sheet: -1.09 (0.26), residues: 351 loop : -1.76 (0.22), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 89 HIS 0.008 0.002 HIS A 7 PHE 0.024 0.002 PHE B 176 TYR 0.019 0.002 TYR B 229 ARG 0.006 0.001 ARG A 52 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 70 time to evaluate : 0.884 Fit side-chains REVERT: B 75 GLU cc_start: 0.8031 (tp30) cc_final: 0.7772 (tp30) REVERT: B 134 ILE cc_start: 0.8681 (mt) cc_final: 0.8337 (tt) REVERT: B 157 THR cc_start: 0.8365 (m) cc_final: 0.8101 (p) REVERT: A 114 SER cc_start: 0.8617 (p) cc_final: 0.8375 (t) REVERT: A 215 GLN cc_start: 0.8292 (OUTLIER) cc_final: 0.6920 (mm110) REVERT: C 17 TYR cc_start: 0.8656 (t80) cc_final: 0.8434 (t80) REVERT: C 30 ARG cc_start: 0.8511 (OUTLIER) cc_final: 0.8191 (mtp180) REVERT: C 52 ARG cc_start: 0.8525 (OUTLIER) cc_final: 0.8107 (ptm-80) REVERT: C 157 THR cc_start: 0.8397 (m) cc_final: 0.7988 (p) REVERT: C 187 ILE cc_start: 0.7141 (mm) cc_final: 0.6916 (mm) REVERT: C 285 SER cc_start: 0.8885 (t) cc_final: 0.8651 (p) outliers start: 33 outliers final: 26 residues processed: 101 average time/residue: 0.1461 time to fit residues: 21.2274 Evaluate side-chains 95 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 66 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 150 ASN Chi-restraints excluded: chain B residue 151 GLN Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 126 GLU Chi-restraints excluded: chain A residue 150 ASN Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 215 GLN Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain C residue 30 ARG Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 150 ASN Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 258 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 51 optimal weight: 2.9990 chunk 21 optimal weight: 7.9990 chunk 87 optimal weight: 6.9990 chunk 72 optimal weight: 2.9990 chunk 40 optimal weight: 8.9990 chunk 7 optimal weight: 8.9990 chunk 28 optimal weight: 0.6980 chunk 45 optimal weight: 9.9990 chunk 83 optimal weight: 0.3980 chunk 9 optimal weight: 9.9990 chunk 49 optimal weight: 7.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 179 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.5623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 7089 Z= 0.215 Angle : 0.543 8.517 9624 Z= 0.280 Chirality : 0.045 0.154 1134 Planarity : 0.004 0.029 1245 Dihedral : 5.050 48.093 983 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.99 % Allowed : 19.53 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.26), residues: 912 helix: 0.44 (1.07), residues: 30 sheet: -0.68 (0.25), residues: 405 loop : -1.60 (0.24), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 89 HIS 0.006 0.001 HIS B 179 PHE 0.011 0.001 PHE B 176 TYR 0.013 0.001 TYR C 17 ARG 0.004 0.000 ARG A 52 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 71 time to evaluate : 0.843 Fit side-chains REVERT: B 75 GLU cc_start: 0.7845 (tp30) cc_final: 0.7634 (tp30) REVERT: B 134 ILE cc_start: 0.8644 (mt) cc_final: 0.8242 (tt) REVERT: B 157 THR cc_start: 0.8322 (m) cc_final: 0.8064 (p) REVERT: B 268 LYS cc_start: 0.8796 (ptpt) cc_final: 0.8328 (mtpt) REVERT: A 51 ASP cc_start: 0.8103 (t0) cc_final: 0.7656 (t70) REVERT: C 52 ARG cc_start: 0.8471 (OUTLIER) cc_final: 0.8127 (ptm-80) REVERT: C 157 THR cc_start: 0.8308 (m) cc_final: 0.7942 (p) REVERT: C 187 ILE cc_start: 0.7121 (mm) cc_final: 0.6847 (mm) REVERT: C 285 SER cc_start: 0.8736 (t) cc_final: 0.8491 (p) outliers start: 23 outliers final: 18 residues processed: 93 average time/residue: 0.1550 time to fit residues: 21.0752 Evaluate side-chains 83 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 64 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 126 GLU Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 150 ASN Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 150 ASN Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 252 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 63 optimal weight: 6.9990 chunk 49 optimal weight: 6.9990 chunk 73 optimal weight: 8.9990 chunk 48 optimal weight: 3.9990 chunk 86 optimal weight: 10.0000 chunk 54 optimal weight: 10.0000 chunk 52 optimal weight: 6.9990 chunk 40 optimal weight: 10.0000 chunk 53 optimal weight: 4.9990 chunk 34 optimal weight: 8.9990 chunk 51 optimal weight: 0.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.5829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 7089 Z= 0.348 Angle : 0.605 7.632 9624 Z= 0.315 Chirality : 0.046 0.162 1134 Planarity : 0.005 0.034 1245 Dihedral : 5.332 56.133 983 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 4.04 % Allowed : 17.58 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.26), residues: 912 helix: 0.32 (1.07), residues: 30 sheet: -0.70 (0.25), residues: 405 loop : -1.68 (0.25), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 89 HIS 0.008 0.001 HIS B 179 PHE 0.019 0.002 PHE B 176 TYR 0.012 0.002 TYR B 229 ARG 0.005 0.000 ARG A 52 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 63 time to evaluate : 1.018 Fit side-chains REVERT: B 75 GLU cc_start: 0.7896 (tp30) cc_final: 0.7652 (tp30) REVERT: B 134 ILE cc_start: 0.8655 (mt) cc_final: 0.8306 (tt) REVERT: B 157 THR cc_start: 0.8288 (m) cc_final: 0.8082 (p) REVERT: B 268 LYS cc_start: 0.8815 (ptpt) cc_final: 0.8528 (mtpt) REVERT: A 114 SER cc_start: 0.8605 (p) cc_final: 0.8353 (t) REVERT: A 126 GLU cc_start: 0.8862 (OUTLIER) cc_final: 0.8553 (mt-10) REVERT: C 30 ARG cc_start: 0.8556 (OUTLIER) cc_final: 0.8279 (mtp180) REVERT: C 52 ARG cc_start: 0.8433 (OUTLIER) cc_final: 0.7947 (ptm-80) REVERT: C 157 THR cc_start: 0.8256 (m) cc_final: 0.7889 (p) REVERT: C 187 ILE cc_start: 0.7045 (mm) cc_final: 0.6776 (mm) REVERT: C 194 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7551 (tp30) REVERT: C 285 SER cc_start: 0.8766 (t) cc_final: 0.8513 (p) outliers start: 31 outliers final: 24 residues processed: 91 average time/residue: 0.1694 time to fit residues: 22.3936 Evaluate side-chains 91 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 63 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 126 GLU Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 150 ASN Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain C residue 30 ARG Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 150 ASN Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 194 GLU Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 252 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 26 optimal weight: 5.9990 chunk 17 optimal weight: 9.9990 chunk 16 optimal weight: 7.9990 chunk 55 optimal weight: 9.9990 chunk 59 optimal weight: 3.9990 chunk 42 optimal weight: 10.0000 chunk 8 optimal weight: 9.9990 chunk 68 optimal weight: 0.9980 chunk 78 optimal weight: 0.2980 chunk 83 optimal weight: 10.0000 chunk 75 optimal weight: 3.9990 overall best weight: 3.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 179 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.5834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 7089 Z= 0.231 Angle : 0.539 8.281 9624 Z= 0.279 Chirality : 0.045 0.152 1134 Planarity : 0.004 0.031 1245 Dihedral : 4.767 37.380 983 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.26 % Allowed : 19.01 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.26), residues: 912 helix: 0.51 (1.08), residues: 30 sheet: -0.56 (0.26), residues: 405 loop : -1.58 (0.25), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 89 HIS 0.007 0.001 HIS B 179 PHE 0.011 0.001 PHE A 176 TYR 0.019 0.002 TYR C 17 ARG 0.004 0.000 ARG A 52 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 69 time to evaluate : 0.838 Fit side-chains revert: symmetry clash REVERT: B 75 GLU cc_start: 0.7893 (tp30) cc_final: 0.7671 (tp30) REVERT: B 134 ILE cc_start: 0.8605 (mt) cc_final: 0.8250 (tt) REVERT: B 268 LYS cc_start: 0.8799 (ptpt) cc_final: 0.8218 (mtpt) REVERT: A 114 SER cc_start: 0.8555 (p) cc_final: 0.8286 (t) REVERT: A 126 GLU cc_start: 0.8934 (OUTLIER) cc_final: 0.8719 (mt-10) REVERT: C 17 TYR cc_start: 0.8510 (t80) cc_final: 0.7876 (t80) REVERT: C 30 ARG cc_start: 0.8555 (OUTLIER) cc_final: 0.8286 (mtp180) REVERT: C 52 ARG cc_start: 0.8415 (OUTLIER) cc_final: 0.7961 (ptm-80) REVERT: C 157 THR cc_start: 0.8229 (m) cc_final: 0.7887 (p) REVERT: C 187 ILE cc_start: 0.7141 (mm) cc_final: 0.6899 (mm) REVERT: C 285 SER cc_start: 0.8725 (t) cc_final: 0.8469 (p) outliers start: 25 outliers final: 19 residues processed: 92 average time/residue: 0.1614 time to fit residues: 21.4133 Evaluate side-chains 85 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 63 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 126 GLU Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 150 ASN Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain C residue 30 ARG Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 252 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 80 optimal weight: 0.0070 chunk 83 optimal weight: 9.9990 chunk 48 optimal weight: 10.0000 chunk 35 optimal weight: 8.9990 chunk 63 optimal weight: 8.9990 chunk 24 optimal weight: 0.8980 chunk 73 optimal weight: 0.9980 chunk 76 optimal weight: 4.9990 chunk 53 optimal weight: 8.9990 chunk 85 optimal weight: 0.0070 chunk 52 optimal weight: 7.9990 overall best weight: 1.3818 ------------------------------------------------------------------------------- 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: 0.8092 moved from start: 0.5814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7089 Z= 0.135 Angle : 0.493 8.515 9624 Z= 0.253 Chirality : 0.043 0.192 1134 Planarity : 0.004 0.029 1245 Dihedral : 4.083 19.914 983 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.21 % Allowed : 20.18 % Favored : 77.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.27), residues: 912 helix: 0.82 (1.08), residues: 30 sheet: -0.29 (0.27), residues: 399 loop : -1.48 (0.25), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP C 89 HIS 0.007 0.001 HIS B 179 PHE 0.007 0.001 PHE C 74 TYR 0.018 0.001 TYR C 17 ARG 0.004 0.000 ARG A 52 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 59 time to evaluate : 0.832 Fit side-chains revert: symmetry clash REVERT: B 75 GLU cc_start: 0.7928 (tp30) cc_final: 0.7641 (tp30) REVERT: B 134 ILE cc_start: 0.8536 (mt) cc_final: 0.8112 (tt) REVERT: B 268 LYS cc_start: 0.8785 (ptpt) cc_final: 0.8264 (mtpt) REVERT: A 46 GLU cc_start: 0.5208 (pp20) cc_final: 0.4228 (mm-30) REVERT: C 17 TYR cc_start: 0.8427 (t80) cc_final: 0.7872 (t80) REVERT: C 52 ARG cc_start: 0.8400 (OUTLIER) cc_final: 0.8003 (ptm-80) REVERT: C 157 THR cc_start: 0.8157 (m) cc_final: 0.7821 (p) REVERT: C 187 ILE cc_start: 0.7146 (mm) cc_final: 0.6917 (mm) outliers start: 17 outliers final: 13 residues processed: 75 average time/residue: 0.1549 time to fit residues: 17.0293 Evaluate side-chains 71 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 57 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 126 GLU Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 252 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 40 optimal weight: 1.9990 chunk 59 optimal weight: 6.9990 chunk 89 optimal weight: 3.9990 chunk 82 optimal weight: 9.9990 chunk 71 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 55 optimal weight: 9.9990 chunk 43 optimal weight: 7.9990 chunk 56 optimal weight: 4.9990 chunk 76 optimal weight: 10.0000 chunk 21 optimal weight: 10.0000 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 63 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.5860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7089 Z= 0.203 Angle : 0.521 8.213 9624 Z= 0.270 Chirality : 0.044 0.179 1134 Planarity : 0.004 0.031 1245 Dihedral : 4.191 13.987 981 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.47 % Allowed : 19.79 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.27), residues: 912 helix: 0.71 (1.08), residues: 30 sheet: -0.29 (0.27), residues: 405 loop : -1.45 (0.25), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP C 89 HIS 0.009 0.001 HIS B 179 PHE 0.010 0.001 PHE B 176 TYR 0.019 0.001 TYR C 17 ARG 0.003 0.000 ARG A 52 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 64 time to evaluate : 0.882 Fit side-chains revert: symmetry clash REVERT: B 75 GLU cc_start: 0.7914 (tp30) cc_final: 0.7593 (tp30) REVERT: B 134 ILE cc_start: 0.8569 (mt) cc_final: 0.8156 (tt) REVERT: B 268 LYS cc_start: 0.8784 (ptpt) cc_final: 0.8189 (mtpt) REVERT: A 46 GLU cc_start: 0.5438 (pp20) cc_final: 0.4403 (mm-30) REVERT: A 51 ASP cc_start: 0.8030 (t0) cc_final: 0.7573 (t70) REVERT: A 114 SER cc_start: 0.8553 (p) cc_final: 0.8292 (t) REVERT: A 273 GLN cc_start: 0.8102 (tt0) cc_final: 0.7703 (tt0) REVERT: A 275 ASP cc_start: 0.7937 (m-30) cc_final: 0.7568 (m-30) REVERT: C 17 TYR cc_start: 0.8520 (t80) cc_final: 0.8013 (t80) REVERT: C 52 ARG cc_start: 0.8484 (OUTLIER) cc_final: 0.8274 (ptm-80) REVERT: C 157 THR cc_start: 0.8182 (m) cc_final: 0.7863 (p) REVERT: C 187 ILE cc_start: 0.7050 (mm) cc_final: 0.6838 (mm) REVERT: C 194 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.7476 (tp30) outliers start: 19 outliers final: 15 residues processed: 82 average time/residue: 0.1500 time to fit residues: 17.9386 Evaluate side-chains 78 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 61 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 126 GLU Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 194 GLU Chi-restraints excluded: chain C residue 252 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 65 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 19 optimal weight: 8.9990 chunk 71 optimal weight: 9.9990 chunk 29 optimal weight: 4.9990 chunk 73 optimal weight: 6.9990 chunk 9 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 51 optimal weight: 10.0000 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 179 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.103447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.093815 restraints weight = 12603.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.096128 restraints weight = 7092.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.097656 restraints weight = 4630.005| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.5940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 7089 Z= 0.237 Angle : 0.553 9.379 9624 Z= 0.283 Chirality : 0.044 0.175 1134 Planarity : 0.004 0.032 1245 Dihedral : 4.407 14.405 981 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.73 % Allowed : 19.53 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.27), residues: 912 helix: 0.62 (1.08), residues: 30 sheet: -0.30 (0.27), residues: 405 loop : -1.49 (0.25), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 89 HIS 0.009 0.001 HIS B 179 PHE 0.015 0.001 PHE B 176 TYR 0.018 0.001 TYR C 17 ARG 0.004 0.000 ARG A 52 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1452.12 seconds wall clock time: 27 minutes 34.51 seconds (1654.51 seconds total)