Starting phenix.real_space_refine on Sat Dec 28 00:59:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8b9f_15930/12_2024/8b9f_15930.cif Found real_map, /net/cci-nas-00/data/ceres_data/8b9f_15930/12_2024/8b9f_15930.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8b9f_15930/12_2024/8b9f_15930.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8b9f_15930/12_2024/8b9f_15930.map" model { file = "/net/cci-nas-00/data/ceres_data/8b9f_15930/12_2024/8b9f_15930.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8b9f_15930/12_2024/8b9f_15930.cif" } resolution = 3.93 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= 0.070 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1946 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Se 1 7.20 5 S 47 5.16 5 C 3516 2.51 5 N 931 2.21 5 O 1038 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 5533 Number of models: 1 Model: "" Number of chains: 5 Chain: "E" Number of atoms: 1946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 1946 Classifications: {'peptide': 251} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 227} Chain: "B" Number of atoms: 1579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1579 Classifications: {'peptide': 204} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 194} Chain: "C" Number of atoms: 1501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1501 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 10, 'TRANS': 184} Chain: "A" Number of atoms: 486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 486 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 5, 'TRANS': 53} Chain breaks: 1 Chain: "A" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'SPH': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.30, per 1000 atoms: 0.78 Number of scatterers: 5533 At special positions: 0 Unit cell: (74.55, 105, 137.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Se 1 33.99 S 47 16.00 O 1038 8.00 N 931 7.00 C 3516 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS E 36 " - pdb=" SG CYS E 81 " distance=2.03 Simple disulfide: pdb=" SG CYS E 65 " - pdb=" SG CYS E 94 " distance=2.03 Simple disulfide: pdb=" SG CYS E 98 " - pdb=" SG CYS E 145 " distance=2.03 Simple disulfide: pdb=" SG CYS E 129 " - pdb=" SG CYS E 158 " distance=2.04 Simple disulfide: pdb=" SG CYS E 163 " - pdb=" SG CYS E 204 " distance=2.03 Simple disulfide: pdb=" SG CYS E 190 " - pdb=" SG CYS E 220 " distance=2.03 Simple disulfide: pdb=" SG CYS E 225 " - pdb=" SG CYS E 267 " distance=2.02 Simple disulfide: pdb=" SG CYS E 253 " - pdb=" SG CYS E 283 " distance=2.04 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: 1.42 Conformation dependent library (CDL) restraints added in 818.7 milliseconds 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1314 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 16 sheets defined 9.7% alpha, 30.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'E' and resid 112 through 116 Processing helix chain 'B' and resid 83 through 87 Processing helix chain 'B' and resid 89 through 99 Processing helix chain 'B' and resid 142 through 147 Processing helix chain 'B' and resid 178 through 185 removed outlier: 4.161A pdb=" N THR B 183 " --> pdb=" O GLY B 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 48 Processing helix chain 'C' and resid 65 through 69 Processing helix chain 'C' and resid 98 through 105 Processing helix chain 'C' and resid 144 through 150 removed outlier: 3.690A pdb=" N LEU C 150 " --> pdb=" O LYS C 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 108 Processing sheet with id=AA1, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.640A pdb=" N GLN E 86 " --> pdb=" O LEU E 82 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 70 through 71 Processing sheet with id=AA3, first strand: chain 'E' and resid 107 through 109 Processing sheet with id=AA4, first strand: chain 'E' and resid 133 through 135 Processing sheet with id=AA5, first strand: chain 'E' and resid 172 through 175 Processing sheet with id=AA6, first strand: chain 'E' and resid 194 through 197 Processing sheet with id=AA7, first strand: chain 'E' and resid 234 through 236 Processing sheet with id=AA8, first strand: chain 'E' and resid 258 through 260 Processing sheet with id=AA9, first strand: chain 'B' and resid 64 through 65 removed outlier: 4.495A pdb=" N VAL B 239 " --> pdb=" O TRP B 71 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 64 through 65 removed outlier: 4.105A pdb=" N ALA B 250 " --> pdb=" O ARG B 103 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ARG B 103 " --> pdb=" O ALA B 250 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N TYR B 252 " --> pdb=" O LEU B 101 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LEU B 101 " --> pdb=" O TYR B 252 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 153 through 154 removed outlier: 6.758A pdb=" N CYS B 121 " --> pdb=" O PHE B 226 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N SER B 228 " --> pdb=" O GLN B 119 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N GLN B 119 " --> pdb=" O SER B 228 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 51 through 52 Processing sheet with id=AB4, first strand: chain 'C' and resid 51 through 52 Processing sheet with id=AB5, first strand: chain 'C' and resid 83 through 86 removed outlier: 3.907A pdb=" N PHE C 83 " --> pdb=" O CYS C 192 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N LYS C 129 " --> pdb=" O GLN C 195 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N GLY C 197 " --> pdb=" O THR C 127 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N THR C 127 " --> pdb=" O GLY C 197 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 177 through 178 removed outlier: 6.136A pdb=" N TYR C 107 " --> pdb=" O LEU C 225 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N LEU C 225 " --> pdb=" O TYR C 107 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 110 through 112 removed outlier: 6.192A pdb=" N PHE A 110 " --> pdb=" O PRO A 250 " (cutoff:3.500A) 154 hydrogen bonds defined for protein. 369 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: 1.38 Time building geometry restraints manager: 1.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 1815 1.36 - 1.51: 1747 1.51 - 1.66: 2050 1.66 - 1.80: 39 1.80 - 1.95: 27 Bond restraints: 5678 Sorted by residual: bond pdb=" C4 SPH A 300 " pdb=" C5 SPH A 300 " ideal model delta sigma weight residual 1.334 1.463 -0.129 2.00e-02 2.50e+03 4.15e+01 bond pdb=" CA LYS E 161 " pdb=" C LYS E 161 " ideal model delta sigma weight residual 1.523 1.474 0.049 1.28e-02 6.10e+03 1.47e+01 bond pdb=" N ARG E 96 " pdb=" CA ARG E 96 " ideal model delta sigma weight residual 1.454 1.495 -0.041 1.16e-02 7.43e+03 1.24e+01 bond pdb=" N ILE C 70 " pdb=" CA ILE C 70 " ideal model delta sigma weight residual 1.461 1.490 -0.029 9.10e-03 1.21e+04 1.01e+01 bond pdb=" N SER E 162 " pdb=" CA SER E 162 " ideal model delta sigma weight residual 1.454 1.491 -0.037 1.17e-02 7.31e+03 9.77e+00 ... (remaining 5673 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 7539 2.19 - 4.37: 171 4.37 - 6.56: 10 6.56 - 8.74: 4 8.74 - 10.93: 3 Bond angle restraints: 7727 Sorted by residual: angle pdb=" N MET C 65 " pdb=" CA MET C 65 " pdb=" C MET C 65 " ideal model delta sigma weight residual 113.23 104.79 8.44 1.24e+00 6.50e-01 4.63e+01 angle pdb=" N ARG E 96 " pdb=" CA ARG E 96 " pdb=" C ARG E 96 " ideal model delta sigma weight residual 110.46 119.01 -8.55 1.48e+00 4.57e-01 3.34e+01 angle pdb=" N SER E 97 " pdb=" CA SER E 97 " pdb=" C SER E 97 " ideal model delta sigma weight residual 108.07 116.92 -8.85 1.59e+00 3.96e-01 3.10e+01 angle pdb=" C THR C 64 " pdb=" CA THR C 64 " pdb=" CB THR C 64 " ideal model delta sigma weight residual 111.48 100.92 10.56 1.91e+00 2.74e-01 3.06e+01 angle pdb=" N LYS E 161 " pdb=" CA LYS E 161 " pdb=" C LYS E 161 " ideal model delta sigma weight residual 109.96 101.57 8.39 1.68e+00 3.54e-01 2.49e+01 ... (remaining 7722 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.26: 3115 16.26 - 32.53: 210 32.53 - 48.79: 40 48.79 - 65.05: 22 65.05 - 81.32: 9 Dihedral angle restraints: 3396 sinusoidal: 1349 harmonic: 2047 Sorted by residual: dihedral pdb=" CA PHE B 82 " pdb=" C PHE B 82 " pdb=" N PRO B 83 " pdb=" CA PRO B 83 " ideal model delta harmonic sigma weight residual 0.00 39.35 -39.35 0 5.00e+00 4.00e-02 6.19e+01 dihedral pdb=" C THR C 64 " pdb=" N THR C 64 " pdb=" CA THR C 64 " pdb=" CB THR C 64 " ideal model delta harmonic sigma weight residual -122.00 -110.86 -11.14 0 2.50e+00 1.60e-01 1.99e+01 dihedral pdb=" CA MET A 100 " pdb=" C MET A 100 " pdb=" N VAL A 101 " pdb=" CA VAL A 101 " ideal model delta harmonic sigma weight residual -180.00 -158.00 -22.00 0 5.00e+00 4.00e-02 1.94e+01 ... (remaining 3393 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 668 0.059 - 0.118: 144 0.118 - 0.176: 31 0.176 - 0.235: 7 0.235 - 0.294: 3 Chirality restraints: 853 Sorted by residual: chirality pdb=" CA THR C 64 " pdb=" N THR C 64 " pdb=" C THR C 64 " pdb=" CB THR C 64 " both_signs ideal model delta sigma weight residual False 2.53 2.82 -0.29 2.00e-01 2.50e+01 2.16e+00 chirality pdb=" CB VAL A 101 " pdb=" CA VAL A 101 " pdb=" CG1 VAL A 101 " pdb=" CG2 VAL A 101 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" CA ILE C 70 " pdb=" N ILE C 70 " pdb=" C ILE C 70 " pdb=" CB ILE C 70 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.44e+00 ... (remaining 850 not shown) Planarity restraints: 995 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C3 SPH A 300 " -0.231 2.00e-02 2.50e+03 2.61e-01 6.82e+02 pdb=" C4 SPH A 300 " 0.170 2.00e-02 2.50e+03 pdb=" C5 SPH A 300 " 0.337 2.00e-02 2.50e+03 pdb=" C6 SPH A 300 " -0.277 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO C 54 " 0.018 2.00e-02 2.50e+03 3.60e-02 1.30e+01 pdb=" C PRO C 54 " -0.062 2.00e-02 2.50e+03 pdb=" O PRO C 54 " 0.024 2.00e-02 2.50e+03 pdb=" N VAL C 55 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS E 160 " -0.018 2.00e-02 2.50e+03 3.52e-02 1.24e+01 pdb=" C LYS E 160 " 0.061 2.00e-02 2.50e+03 pdb=" O LYS E 160 " -0.022 2.00e-02 2.50e+03 pdb=" N LYS E 161 " -0.021 2.00e-02 2.50e+03 ... (remaining 992 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 349 2.73 - 3.27: 5311 3.27 - 3.81: 8990 3.81 - 4.36: 11662 4.36 - 4.90: 19253 Nonbonded interactions: 45565 Sorted by model distance: nonbonded pdb=" OG SER E 214 " pdb=" OD1 ASP E 215 " model vdw 2.185 3.040 nonbonded pdb=" OE1 GLU A 108 " pdb=" OH TYR A 258 " model vdw 2.238 3.040 nonbonded pdb=" OD1 ASP C 182 " pdb=" OG1 THR C 185 " model vdw 2.257 3.040 nonbonded pdb=" O GLY E 132 " pdb=" N LYS E 161 " model vdw 2.313 3.120 nonbonded pdb=" OG1 THR B 183 " pdb=" O ASP C 50 " model vdw 2.326 3.040 ... (remaining 45560 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 ========== 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=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: 3.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 16.980 Find NCS groups from input model: 0.050 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: 0.010 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6237 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 : 0.006 0.129 5678 Z= 0.382 Angle : 0.761 10.927 7727 Z= 0.464 Chirality : 0.056 0.294 853 Planarity : 0.010 0.261 995 Dihedral : 13.303 81.316 2058 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.29 % Allowed : 2.43 % Favored : 97.28 % Rotamer: Outliers : 1.45 % Allowed : 5.82 % Favored : 92.73 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 2.13 % 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 (0.29), residues: 699 helix: -1.62 (0.67), residues: 43 sheet: 0.25 (0.38), residues: 174 loop : -1.27 (0.25), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 276 HIS 0.005 0.001 HIS C 109 PHE 0.015 0.002 PHE A 110 TYR 0.011 0.001 TYR A 258 ARG 0.005 0.001 ARG A 254 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 246 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 42 VAL cc_start: -0.0379 (t) cc_final: -0.0752 (t) REVERT: E 71 LYS cc_start: 0.7813 (ptmt) cc_final: 0.7597 (mttm) REVERT: E 105 ASN cc_start: 0.7654 (m-40) cc_final: 0.7217 (m-40) REVERT: E 113 TYR cc_start: 0.7818 (m-80) cc_final: 0.7354 (m-80) REVERT: E 157 PHE cc_start: 0.5165 (p90) cc_final: 0.4901 (p90) REVERT: E 165 ASN cc_start: 0.8326 (t0) cc_final: 0.8056 (t0) REVERT: E 251 TYR cc_start: 0.2438 (m-80) cc_final: 0.2219 (m-80) REVERT: B 74 ASP cc_start: 0.8221 (p0) cc_final: 0.7701 (p0) REVERT: B 95 ASN cc_start: 0.8641 (m-40) cc_final: 0.8313 (m-40) REVERT: B 100 TYR cc_start: 0.7824 (t80) cc_final: 0.6471 (t80) REVERT: B 129 GLU cc_start: 0.6928 (mm-30) cc_final: 0.6640 (mm-30) REVERT: B 132 MET cc_start: 0.9229 (OUTLIER) cc_final: 0.8788 (mmm) REVERT: B 215 ARG cc_start: 0.7235 (ttp-170) cc_final: 0.4934 (mmt180) REVERT: B 219 PHE cc_start: 0.8713 (p90) cc_final: 0.8485 (p90) REVERT: B 256 ARG cc_start: 0.6342 (OUTLIER) cc_final: 0.5594 (ptp-170) REVERT: C 61 LYS cc_start: 0.8364 (mtmt) cc_final: 0.7755 (mttt) REVERT: C 179 VAL cc_start: 0.8318 (t) cc_final: 0.8024 (t) REVERT: A 265 ASN cc_start: 0.8065 (m-40) cc_final: 0.7832 (m-40) outliers start: 9 outliers final: 2 residues processed: 250 average time/residue: 0.1980 time to fit residues: 62.2211 Evaluate side-chains 167 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 163 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 225 CYS Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain A residue 277 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 58 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 17 optimal weight: 9.9990 chunk 35 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 20 optimal weight: 0.0870 chunk 32 optimal weight: 0.8980 chunk 40 optimal weight: 0.6980 chunk 62 optimal weight: 0.5980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 113 ASN B 181 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6481 moved from start: 0.3109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5678 Z= 0.220 Angle : 0.581 5.576 7727 Z= 0.307 Chirality : 0.046 0.225 853 Planarity : 0.005 0.060 995 Dihedral : 6.551 51.584 789 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 4.52 % Allowed : 16.48 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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: -0.75 (0.28), residues: 699 helix: -0.56 (0.79), residues: 45 sheet: 0.32 (0.39), residues: 165 loop : -0.81 (0.24), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 80 HIS 0.006 0.001 HIS B 109 PHE 0.020 0.002 PHE B 226 TYR 0.026 0.002 TYR C 194 ARG 0.006 0.001 ARG A 105 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 176 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 105 ASN cc_start: 0.7775 (m-40) cc_final: 0.7494 (m-40) REVERT: E 113 TYR cc_start: 0.7709 (m-80) cc_final: 0.6743 (m-10) REVERT: E 135 ARG cc_start: 0.5960 (ttt-90) cc_final: 0.4891 (tpp-160) REVERT: E 136 GLU cc_start: 0.6749 (tp30) cc_final: 0.6479 (tp30) REVERT: E 205 LEU cc_start: 0.6371 (mp) cc_final: 0.6100 (mm) REVERT: B 64 TYR cc_start: 0.8667 (m-80) cc_final: 0.8375 (m-80) REVERT: B 70 THR cc_start: 0.9020 (m) cc_final: 0.8680 (p) REVERT: B 72 GLU cc_start: 0.8212 (mp0) cc_final: 0.7855 (mp0) REVERT: B 74 ASP cc_start: 0.8064 (p0) cc_final: 0.7742 (p0) REVERT: B 84 ASP cc_start: 0.7644 (t0) cc_final: 0.7322 (t0) REVERT: B 87 LYS cc_start: 0.8201 (pttt) cc_final: 0.7699 (ptpt) REVERT: B 129 GLU cc_start: 0.6756 (mm-30) cc_final: 0.6365 (mm-30) REVERT: B 132 MET cc_start: 0.9139 (mtt) cc_final: 0.8436 (mtt) REVERT: B 167 GLN cc_start: 0.7182 (tp-100) cc_final: 0.6771 (tp40) REVERT: B 213 MET cc_start: 0.7777 (mmm) cc_final: 0.7407 (mtt) REVERT: B 215 ARG cc_start: 0.6907 (ttp-170) cc_final: 0.4752 (mmt180) REVERT: B 218 ASN cc_start: 0.8471 (m-40) cc_final: 0.7958 (m110) REVERT: B 256 ARG cc_start: 0.7297 (ppt90) cc_final: 0.6148 (mtp-110) REVERT: C 44 MET cc_start: 0.7294 (mmt) cc_final: 0.6704 (tpp) REVERT: C 61 LYS cc_start: 0.8188 (mtmt) cc_final: 0.7839 (mtmt) REVERT: C 95 PHE cc_start: 0.6378 (m-80) cc_final: 0.5639 (m-10) REVERT: C 102 GLU cc_start: 0.7340 (mm-30) cc_final: 0.7057 (mm-30) REVERT: C 134 TYR cc_start: 0.8254 (t80) cc_final: 0.7768 (t80) outliers start: 28 outliers final: 21 residues processed: 194 average time/residue: 0.2082 time to fit residues: 50.5308 Evaluate side-chains 168 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 147 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 119 PHE Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 197 PHE Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 236 ILE Chi-restraints excluded: chain E residue 266 TYR Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 181 ASN Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 164 CYS Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 209 SER Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 231 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 34 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 52 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 62 optimal weight: 0.5980 chunk 67 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 212 GLN E 271 ASN B 95 ASN ** B 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6572 moved from start: 0.3900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5678 Z= 0.255 Angle : 0.577 6.005 7727 Z= 0.305 Chirality : 0.046 0.164 853 Planarity : 0.004 0.031 995 Dihedral : 5.491 52.360 780 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 5.01 % Allowed : 17.77 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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: -0.61 (0.29), residues: 699 helix: -0.49 (0.79), residues: 45 sheet: 0.49 (0.40), residues: 163 loop : -0.73 (0.25), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 276 HIS 0.005 0.001 HIS C 97 PHE 0.030 0.002 PHE B 219 TYR 0.031 0.002 TYR C 194 ARG 0.004 0.000 ARG C 177 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 160 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 82 LEU cc_start: 0.3377 (OUTLIER) cc_final: 0.2562 (tt) REVERT: E 105 ASN cc_start: 0.7984 (m-40) cc_final: 0.7693 (m-40) REVERT: E 113 TYR cc_start: 0.7583 (m-80) cc_final: 0.6626 (m-10) REVERT: E 135 ARG cc_start: 0.5956 (ttt-90) cc_final: 0.5019 (tpp-160) REVERT: E 136 GLU cc_start: 0.6733 (tp30) cc_final: 0.6495 (tp30) REVERT: E 205 LEU cc_start: 0.6297 (mp) cc_final: 0.6037 (mm) REVERT: B 64 TYR cc_start: 0.8639 (m-80) cc_final: 0.8340 (m-80) REVERT: B 70 THR cc_start: 0.9114 (m) cc_final: 0.8582 (p) REVERT: B 72 GLU cc_start: 0.8416 (mp0) cc_final: 0.7872 (mp0) REVERT: B 74 ASP cc_start: 0.8068 (p0) cc_final: 0.7725 (p0) REVERT: B 81 LYS cc_start: 0.8851 (mttm) cc_final: 0.8568 (mttt) REVERT: B 84 ASP cc_start: 0.7704 (t0) cc_final: 0.7361 (t0) REVERT: B 87 LYS cc_start: 0.8318 (pttt) cc_final: 0.7709 (ptpt) REVERT: B 129 GLU cc_start: 0.7108 (mm-30) cc_final: 0.6509 (mm-30) REVERT: B 132 MET cc_start: 0.8903 (mtt) cc_final: 0.8420 (mtt) REVERT: B 175 MET cc_start: 0.8411 (mtp) cc_final: 0.8145 (mtp) REVERT: B 215 ARG cc_start: 0.6593 (ttp-170) cc_final: 0.4645 (mmt180) REVERT: B 218 ASN cc_start: 0.8553 (m-40) cc_final: 0.8225 (m-40) REVERT: B 226 PHE cc_start: 0.8495 (m-80) cc_final: 0.8059 (m-10) REVERT: B 256 ARG cc_start: 0.7417 (ppt90) cc_final: 0.6077 (mtp-110) REVERT: C 44 MET cc_start: 0.7515 (mmt) cc_final: 0.7268 (tpp) REVERT: C 61 LYS cc_start: 0.8309 (mtmt) cc_final: 0.8013 (mtmt) REVERT: C 134 TYR cc_start: 0.8281 (t80) cc_final: 0.7854 (t80) REVERT: C 156 TRP cc_start: 0.7490 (t60) cc_final: 0.6119 (t60) REVERT: C 224 LEU cc_start: 0.6797 (OUTLIER) cc_final: 0.6579 (tt) outliers start: 31 outliers final: 22 residues processed: 176 average time/residue: 0.2006 time to fit residues: 44.4987 Evaluate side-chains 171 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 147 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 35 ASP Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 119 PHE Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 236 ILE Chi-restraints excluded: chain E residue 266 TYR Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 112 CYS Chi-restraints excluded: chain B residue 113 ASN Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 231 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 32 optimal weight: 0.9990 chunk 6 optimal weight: 0.0170 chunk 29 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 17 optimal weight: 7.9990 chunk 55 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 0 optimal weight: 20.0000 overall best weight: 0.6820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 212 GLN B 95 ASN B 218 ASN C 109 HIS C 195 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6576 moved from start: 0.4357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5678 Z= 0.205 Angle : 0.545 6.321 7727 Z= 0.286 Chirality : 0.045 0.158 853 Planarity : 0.004 0.030 995 Dihedral : 4.971 45.277 780 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 5.17 % Allowed : 19.06 % Favored : 75.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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: -0.57 (0.29), residues: 699 helix: -0.39 (0.78), residues: 45 sheet: 0.52 (0.40), residues: 163 loop : -0.71 (0.25), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 80 HIS 0.007 0.001 HIS C 97 PHE 0.032 0.002 PHE B 219 TYR 0.027 0.002 TYR C 194 ARG 0.004 0.001 ARG A 105 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 156 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 82 LEU cc_start: 0.3385 (OUTLIER) cc_final: 0.2697 (tt) REVERT: E 105 ASN cc_start: 0.8035 (m-40) cc_final: 0.7693 (m-40) REVERT: E 113 TYR cc_start: 0.7562 (m-80) cc_final: 0.6712 (m-10) REVERT: E 205 LEU cc_start: 0.6353 (mp) cc_final: 0.6051 (mm) REVERT: B 64 TYR cc_start: 0.8603 (m-80) cc_final: 0.8243 (m-80) REVERT: B 72 GLU cc_start: 0.8473 (mp0) cc_final: 0.8247 (mp0) REVERT: B 74 ASP cc_start: 0.8125 (p0) cc_final: 0.7728 (p0) REVERT: B 84 ASP cc_start: 0.7752 (t0) cc_final: 0.7476 (t0) REVERT: B 87 LYS cc_start: 0.8312 (pttt) cc_final: 0.7677 (ptpt) REVERT: B 96 MET cc_start: 0.8132 (OUTLIER) cc_final: 0.7898 (ttm) REVERT: B 129 GLU cc_start: 0.7362 (mm-30) cc_final: 0.6699 (mm-30) REVERT: B 132 MET cc_start: 0.8828 (mtt) cc_final: 0.8528 (mtt) REVERT: B 154 LYS cc_start: 0.8088 (mtmt) cc_final: 0.7886 (mtmt) REVERT: B 213 MET cc_start: 0.7637 (mtt) cc_final: 0.6742 (mtt) REVERT: B 215 ARG cc_start: 0.6545 (ttp-170) cc_final: 0.4655 (mmt180) REVERT: B 226 PHE cc_start: 0.8598 (m-80) cc_final: 0.8288 (m-10) REVERT: C 44 MET cc_start: 0.7626 (mmt) cc_final: 0.7254 (tpp) REVERT: C 61 LYS cc_start: 0.8265 (mtmt) cc_final: 0.7980 (mtmt) REVERT: C 95 PHE cc_start: 0.7038 (m-80) cc_final: 0.6199 (m-10) REVERT: C 134 TYR cc_start: 0.8261 (t80) cc_final: 0.7847 (t80) outliers start: 32 outliers final: 21 residues processed: 174 average time/residue: 0.1751 time to fit residues: 39.3736 Evaluate side-chains 170 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 147 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 35 ASP Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 119 PHE Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 197 PHE Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 225 CYS Chi-restraints excluded: chain E residue 266 TYR Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 112 CYS Chi-restraints excluded: chain B residue 113 ASN Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 162 SER Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain A residue 113 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 49 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 34 optimal weight: 0.7980 chunk 59 optimal weight: 0.4980 chunk 16 optimal weight: 9.9990 chunk 22 optimal weight: 20.0000 chunk 60 optimal weight: 0.5980 chunk 13 optimal weight: 3.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 95 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6600 moved from start: 0.4706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5678 Z= 0.216 Angle : 0.546 6.798 7727 Z= 0.288 Chirality : 0.045 0.181 853 Planarity : 0.004 0.030 995 Dihedral : 4.646 38.021 780 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.88 % Allowed : 21.81 % Favored : 74.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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: -0.64 (0.29), residues: 699 helix: -0.50 (0.78), residues: 46 sheet: 0.53 (0.42), residues: 151 loop : -0.75 (0.25), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 78 HIS 0.006 0.001 HIS E 242 PHE 0.033 0.002 PHE B 219 TYR 0.027 0.002 TYR C 194 ARG 0.005 0.001 ARG A 105 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 157 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 82 LEU cc_start: 0.3338 (OUTLIER) cc_final: 0.2661 (tt) REVERT: E 105 ASN cc_start: 0.8025 (m-40) cc_final: 0.7674 (m-40) REVERT: E 113 TYR cc_start: 0.7508 (m-80) cc_final: 0.6663 (m-10) REVERT: E 205 LEU cc_start: 0.6331 (mp) cc_final: 0.6059 (mm) REVERT: B 64 TYR cc_start: 0.8618 (m-80) cc_final: 0.8236 (m-80) REVERT: B 72 GLU cc_start: 0.8472 (mp0) cc_final: 0.7930 (mp0) REVERT: B 74 ASP cc_start: 0.8147 (p0) cc_final: 0.7758 (p0) REVERT: B 84 ASP cc_start: 0.7690 (t0) cc_final: 0.7387 (t0) REVERT: B 87 LYS cc_start: 0.8275 (pttt) cc_final: 0.7685 (ptpt) REVERT: B 95 ASN cc_start: 0.8650 (m-40) cc_final: 0.8435 (m-40) REVERT: B 129 GLU cc_start: 0.7402 (mm-30) cc_final: 0.6762 (mm-30) REVERT: B 132 MET cc_start: 0.8757 (mtt) cc_final: 0.8523 (mtt) REVERT: B 213 MET cc_start: 0.7748 (mtt) cc_final: 0.7475 (mpp) REVERT: B 215 ARG cc_start: 0.6523 (ttp-170) cc_final: 0.4550 (mmt180) REVERT: B 226 PHE cc_start: 0.8583 (m-80) cc_final: 0.8250 (m-10) REVERT: C 44 MET cc_start: 0.7783 (mmt) cc_final: 0.7408 (tpp) REVERT: C 134 TYR cc_start: 0.8237 (t80) cc_final: 0.7856 (t80) outliers start: 24 outliers final: 20 residues processed: 168 average time/residue: 0.1832 time to fit residues: 39.6318 Evaluate side-chains 167 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 146 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 35 ASP Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 119 PHE Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 197 PHE Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 112 CYS Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 218 ASN Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 162 SER Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 231 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 39 optimal weight: 0.9990 chunk 16 optimal weight: 10.0000 chunk 66 optimal weight: 0.1980 chunk 55 optimal weight: 0.0020 chunk 30 optimal weight: 0.9990 chunk 5 optimal weight: 0.0980 chunk 22 optimal weight: 10.0000 chunk 35 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 7 optimal weight: 9.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.4592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 271 ASN C 56 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6570 moved from start: 0.4926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5678 Z= 0.178 Angle : 0.533 7.050 7727 Z= 0.280 Chirality : 0.045 0.169 853 Planarity : 0.004 0.030 995 Dihedral : 4.402 30.715 780 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 4.68 % Allowed : 21.49 % Favored : 73.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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: -0.55 (0.29), residues: 699 helix: -0.33 (0.80), residues: 47 sheet: 0.59 (0.42), residues: 150 loop : -0.70 (0.25), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 78 HIS 0.005 0.001 HIS C 97 PHE 0.035 0.002 PHE B 219 TYR 0.026 0.001 TYR B 100 ARG 0.004 0.001 ARG E 246 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 159 time to evaluate : 0.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 82 LEU cc_start: 0.3272 (OUTLIER) cc_final: 0.2657 (tt) REVERT: E 105 ASN cc_start: 0.8054 (m-40) cc_final: 0.7687 (m-40) REVERT: E 113 TYR cc_start: 0.7483 (m-80) cc_final: 0.6658 (m-10) REVERT: E 205 LEU cc_start: 0.6273 (mp) cc_final: 0.5998 (mm) REVERT: E 246 ARG cc_start: 0.7796 (ptp-110) cc_final: 0.7266 (ptp-170) REVERT: B 64 TYR cc_start: 0.8567 (m-80) cc_final: 0.8151 (m-80) REVERT: B 72 GLU cc_start: 0.8503 (mp0) cc_final: 0.8292 (mp0) REVERT: B 74 ASP cc_start: 0.8114 (p0) cc_final: 0.7730 (p0) REVERT: B 84 ASP cc_start: 0.7741 (t0) cc_final: 0.7447 (t0) REVERT: B 87 LYS cc_start: 0.8239 (pttt) cc_final: 0.7658 (ptpt) REVERT: B 95 ASN cc_start: 0.8653 (m-40) cc_final: 0.8429 (m-40) REVERT: B 129 GLU cc_start: 0.7433 (mm-30) cc_final: 0.6816 (mm-30) REVERT: B 213 MET cc_start: 0.7620 (mtt) cc_final: 0.7311 (mpp) REVERT: B 215 ARG cc_start: 0.6884 (ttp-170) cc_final: 0.4625 (mmt180) REVERT: B 226 PHE cc_start: 0.8571 (m-80) cc_final: 0.8139 (m-10) REVERT: C 44 MET cc_start: 0.7788 (mmt) cc_final: 0.7357 (tpp) REVERT: C 134 TYR cc_start: 0.8153 (t80) cc_final: 0.7729 (t80) outliers start: 29 outliers final: 19 residues processed: 174 average time/residue: 0.1712 time to fit residues: 38.5535 Evaluate side-chains 172 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 152 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 35 ASP Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 119 PHE Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 197 PHE Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 271 ASN Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 112 CYS Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain A residue 113 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 48 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 40 optimal weight: 0.0870 chunk 30 optimal weight: 0.9980 chunk 26 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 chunk 20 optimal weight: 20.0000 chunk 13 optimal weight: 5.9990 overall best weight: 0.8160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 218 ASN ** C 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 86 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6627 moved from start: 0.5146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 5678 Z= 0.232 Angle : 0.574 8.749 7727 Z= 0.301 Chirality : 0.045 0.161 853 Planarity : 0.004 0.030 995 Dihedral : 4.485 25.890 780 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 5.01 % Allowed : 22.46 % Favored : 72.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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: -0.59 (0.29), residues: 699 helix: -0.26 (0.79), residues: 47 sheet: 0.55 (0.42), residues: 151 loop : -0.73 (0.25), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 78 HIS 0.004 0.001 HIS C 97 PHE 0.031 0.002 PHE B 219 TYR 0.029 0.002 TYR C 194 ARG 0.004 0.001 ARG B 62 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 156 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 82 LEU cc_start: 0.3297 (OUTLIER) cc_final: 0.2640 (tt) REVERT: E 105 ASN cc_start: 0.8088 (m-40) cc_final: 0.7718 (m-40) REVERT: E 113 TYR cc_start: 0.7504 (m-80) cc_final: 0.7006 (m-10) REVERT: E 157 PHE cc_start: 0.4482 (p90) cc_final: 0.4167 (p90) REVERT: E 205 LEU cc_start: 0.6354 (mp) cc_final: 0.6113 (mm) REVERT: E 247 GLN cc_start: 0.7690 (tt0) cc_final: 0.7489 (tm-30) REVERT: B 64 TYR cc_start: 0.8543 (m-80) cc_final: 0.8190 (m-80) REVERT: B 74 ASP cc_start: 0.8179 (p0) cc_final: 0.7793 (p0) REVERT: B 84 ASP cc_start: 0.7706 (t0) cc_final: 0.7409 (t0) REVERT: B 87 LYS cc_start: 0.8294 (pttt) cc_final: 0.7701 (ptpt) REVERT: B 95 ASN cc_start: 0.8660 (m-40) cc_final: 0.8439 (m-40) REVERT: B 129 GLU cc_start: 0.7461 (mm-30) cc_final: 0.6776 (mm-30) REVERT: B 213 MET cc_start: 0.7572 (mtt) cc_final: 0.7241 (mtt) REVERT: B 215 ARG cc_start: 0.6866 (ttp-170) cc_final: 0.4646 (mmt180) REVERT: B 226 PHE cc_start: 0.8621 (m-80) cc_final: 0.8370 (m-10) REVERT: B 256 ARG cc_start: 0.7793 (ppt90) cc_final: 0.6142 (mtt-85) REVERT: C 44 MET cc_start: 0.7790 (mmt) cc_final: 0.7476 (tpp) REVERT: C 63 ASP cc_start: 0.7114 (t0) cc_final: 0.6874 (t0) REVERT: C 134 TYR cc_start: 0.8167 (t80) cc_final: 0.7805 (t80) REVERT: C 211 MET cc_start: 0.7129 (ttp) cc_final: 0.6768 (ttm) outliers start: 31 outliers final: 25 residues processed: 173 average time/residue: 0.1739 time to fit residues: 38.9033 Evaluate side-chains 171 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 145 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 119 PHE Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 197 PHE Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 112 CYS Chi-restraints excluded: chain B residue 113 ASN Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 175 MET Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 218 ASN Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 149 MET Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain A residue 113 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 12 optimal weight: 0.8980 chunk 42 optimal weight: 0.3980 chunk 45 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 chunk 52 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 61 optimal weight: 0.3980 chunk 37 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6624 moved from start: 0.5360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 5678 Z= 0.232 Angle : 0.593 9.108 7727 Z= 0.310 Chirality : 0.047 0.284 853 Planarity : 0.004 0.031 995 Dihedral : 4.437 21.995 780 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 4.85 % Allowed : 23.10 % Favored : 72.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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: -0.50 (0.30), residues: 699 helix: 0.08 (0.82), residues: 46 sheet: 0.61 (0.43), residues: 151 loop : -0.70 (0.25), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 78 HIS 0.006 0.001 HIS C 97 PHE 0.014 0.001 PHE B 219 TYR 0.025 0.002 TYR C 194 ARG 0.004 0.001 ARG A 104 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 150 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 82 LEU cc_start: 0.3225 (OUTLIER) cc_final: 0.2585 (tt) REVERT: E 105 ASN cc_start: 0.8065 (m-40) cc_final: 0.7724 (m-40) REVERT: E 113 TYR cc_start: 0.7412 (m-80) cc_final: 0.6308 (m-10) REVERT: E 205 LEU cc_start: 0.6335 (mp) cc_final: 0.6079 (mm) REVERT: E 246 ARG cc_start: 0.7614 (ptp-170) cc_final: 0.7027 (ptp-170) REVERT: B 64 TYR cc_start: 0.8525 (m-80) cc_final: 0.8131 (m-80) REVERT: B 72 GLU cc_start: 0.8384 (mp0) cc_final: 0.8150 (mp0) REVERT: B 74 ASP cc_start: 0.8170 (p0) cc_final: 0.7778 (p0) REVERT: B 84 ASP cc_start: 0.7713 (t0) cc_final: 0.7314 (t0) REVERT: B 87 LYS cc_start: 0.8256 (pttt) cc_final: 0.7669 (ptpt) REVERT: B 129 GLU cc_start: 0.7463 (mm-30) cc_final: 0.6829 (mm-30) REVERT: B 154 LYS cc_start: 0.8054 (OUTLIER) cc_final: 0.7697 (mtmt) REVERT: B 213 MET cc_start: 0.7484 (mtt) cc_final: 0.7151 (mtt) REVERT: B 215 ARG cc_start: 0.6872 (ttp-170) cc_final: 0.4677 (mmt180) REVERT: B 226 PHE cc_start: 0.8617 (m-80) cc_final: 0.8337 (m-10) REVERT: C 44 MET cc_start: 0.7862 (mmt) cc_final: 0.7498 (tpp) REVERT: C 134 TYR cc_start: 0.8188 (t80) cc_final: 0.7836 (t80) outliers start: 30 outliers final: 25 residues processed: 164 average time/residue: 0.1741 time to fit residues: 36.8097 Evaluate side-chains 170 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 143 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 119 PHE Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 197 PHE Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 112 CYS Chi-restraints excluded: chain B residue 113 ASN Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 154 LYS Chi-restraints excluded: chain B residue 175 MET Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain A residue 113 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 26 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 56 optimal weight: 0.6980 chunk 58 optimal weight: 0.0970 chunk 61 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6628 moved from start: 0.5510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 5678 Z= 0.236 Angle : 0.614 9.440 7727 Z= 0.322 Chirality : 0.046 0.165 853 Planarity : 0.004 0.031 995 Dihedral : 4.428 19.180 780 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 4.36 % Allowed : 23.91 % Favored : 71.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.30), residues: 699 helix: 0.22 (0.83), residues: 45 sheet: 0.71 (0.43), residues: 151 loop : -0.74 (0.25), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 78 HIS 0.005 0.001 HIS C 97 PHE 0.010 0.001 PHE C 83 TYR 0.025 0.002 TYR C 194 ARG 0.004 0.001 ARG B 62 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 146 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 35 ASP cc_start: 0.4192 (OUTLIER) cc_final: 0.3413 (t70) REVERT: E 82 LEU cc_start: 0.3330 (OUTLIER) cc_final: 0.2662 (tt) REVERT: E 105 ASN cc_start: 0.7999 (m-40) cc_final: 0.7695 (m-40) REVERT: E 113 TYR cc_start: 0.7500 (m-80) cc_final: 0.6417 (m-10) REVERT: E 157 PHE cc_start: 0.4332 (p90) cc_final: 0.3993 (p90) REVERT: E 205 LEU cc_start: 0.6355 (mp) cc_final: 0.6103 (mm) REVERT: B 64 TYR cc_start: 0.8503 (m-80) cc_final: 0.8179 (m-80) REVERT: B 72 GLU cc_start: 0.8397 (mp0) cc_final: 0.8162 (mp0) REVERT: B 74 ASP cc_start: 0.8163 (p0) cc_final: 0.7775 (p0) REVERT: B 84 ASP cc_start: 0.7568 (t0) cc_final: 0.7260 (t0) REVERT: B 87 LYS cc_start: 0.8286 (pttt) cc_final: 0.7684 (ptpt) REVERT: B 129 GLU cc_start: 0.7466 (mm-30) cc_final: 0.6859 (mm-30) REVERT: B 154 LYS cc_start: 0.8077 (OUTLIER) cc_final: 0.7854 (mtmt) REVERT: B 213 MET cc_start: 0.7520 (mtt) cc_final: 0.7211 (mtt) REVERT: B 215 ARG cc_start: 0.6529 (ttp-170) cc_final: 0.4606 (mmt180) REVERT: B 226 PHE cc_start: 0.8580 (m-80) cc_final: 0.8307 (m-10) REVERT: B 256 ARG cc_start: 0.7723 (ppt90) cc_final: 0.6201 (mtt-85) REVERT: C 44 MET cc_start: 0.7881 (mmt) cc_final: 0.7499 (tpp) REVERT: C 134 TYR cc_start: 0.8180 (t80) cc_final: 0.7818 (t80) outliers start: 27 outliers final: 21 residues processed: 160 average time/residue: 0.2004 time to fit residues: 41.1913 Evaluate side-chains 166 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 142 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 35 ASP Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 119 PHE Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 197 PHE Chi-restraints excluded: chain E residue 203 PHE Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 112 CYS Chi-restraints excluded: chain B residue 113 ASN Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 154 LYS Chi-restraints excluded: chain B residue 175 MET Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain A residue 113 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 68 optimal weight: 0.9990 chunk 63 optimal weight: 0.2980 chunk 54 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 42 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 16 optimal weight: 10.0000 chunk 50 optimal weight: 0.2980 chunk 8 optimal weight: 6.9990 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 218 ASN ** C 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6618 moved from start: 0.5671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 5678 Z= 0.234 Angle : 0.639 9.615 7727 Z= 0.337 Chirality : 0.046 0.153 853 Planarity : 0.004 0.031 995 Dihedral : 4.459 20.744 780 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.72 % Allowed : 24.23 % Favored : 72.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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: -0.51 (0.30), residues: 699 helix: 0.30 (0.84), residues: 45 sheet: 0.68 (0.43), residues: 151 loop : -0.75 (0.26), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP B 78 HIS 0.005 0.001 HIS C 97 PHE 0.010 0.001 PHE C 83 TYR 0.024 0.002 TYR B 100 ARG 0.005 0.001 ARG E 246 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 142 time to evaluate : 0.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 113 TYR cc_start: 0.7344 (m-80) cc_final: 0.6577 (m-10) REVERT: E 205 LEU cc_start: 0.6393 (mp) cc_final: 0.6141 (mm) REVERT: B 64 TYR cc_start: 0.8498 (m-80) cc_final: 0.8243 (m-80) REVERT: B 72 GLU cc_start: 0.8424 (mp0) cc_final: 0.8197 (mp0) REVERT: B 74 ASP cc_start: 0.8153 (p0) cc_final: 0.7777 (p0) REVERT: B 84 ASP cc_start: 0.7485 (t0) cc_final: 0.7201 (t0) REVERT: B 87 LYS cc_start: 0.8272 (pttt) cc_final: 0.7652 (ptpt) REVERT: B 96 MET cc_start: 0.8010 (ttp) cc_final: 0.7610 (ttp) REVERT: B 129 GLU cc_start: 0.7440 (mm-30) cc_final: 0.6849 (mm-30) REVERT: B 154 LYS cc_start: 0.8073 (OUTLIER) cc_final: 0.7842 (mtmt) REVERT: B 213 MET cc_start: 0.7478 (mtt) cc_final: 0.6810 (mtt) REVERT: B 215 ARG cc_start: 0.6524 (ttp-170) cc_final: 0.4637 (mmt180) REVERT: B 226 PHE cc_start: 0.8565 (m-80) cc_final: 0.8301 (m-10) REVERT: B 256 ARG cc_start: 0.7708 (ppt90) cc_final: 0.6216 (mtt-85) REVERT: C 44 MET cc_start: 0.7901 (mmt) cc_final: 0.7495 (tpp) REVERT: C 134 TYR cc_start: 0.8144 (t80) cc_final: 0.7795 (t80) outliers start: 23 outliers final: 21 residues processed: 153 average time/residue: 0.1843 time to fit residues: 36.1757 Evaluate side-chains 159 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 137 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 35 ASP Chi-restraints excluded: chain E residue 119 PHE Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 197 PHE Chi-restraints excluded: chain E residue 203 PHE Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 112 CYS Chi-restraints excluded: chain B residue 113 ASN Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 154 LYS Chi-restraints excluded: chain B residue 175 MET Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 218 ASN Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain A residue 113 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 15 optimal weight: 6.9990 chunk 54 optimal weight: 3.9990 chunk 22 optimal weight: 8.9990 chunk 56 optimal weight: 0.9980 chunk 6 optimal weight: 20.0000 chunk 10 optimal weight: 0.5980 chunk 48 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 62 optimal weight: 0.0170 chunk 36 optimal weight: 4.9990 overall best weight: 1.1222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 218 ASN ** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.215227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.145717 restraints weight = 7311.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.150409 restraints weight = 4490.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.153849 restraints weight = 3185.962| |-----------------------------------------------------------------------------| r_work (final): 0.3793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6957 moved from start: 0.5715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.160 5678 Z= 0.356 Angle : 1.144 59.200 7727 Z= 0.692 Chirality : 0.046 0.178 853 Planarity : 0.004 0.031 995 Dihedral : 4.544 25.160 780 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.72 % Allowed : 24.88 % Favored : 71.41 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 4.26 % 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: -0.52 (0.30), residues: 699 helix: 0.30 (0.84), residues: 45 sheet: 0.68 (0.43), residues: 151 loop : -0.77 (0.25), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 78 HIS 0.004 0.001 HIS C 97 PHE 0.010 0.001 PHE C 83 TYR 0.023 0.002 TYR C 194 ARG 0.003 0.001 ARG B 62 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1860.89 seconds wall clock time: 35 minutes 6.35 seconds (2106.35 seconds total)